Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold23
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3125668
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.28
Warning! 362582 characters in sequence are not A, C, G, or T
File 12 of 18
Found at i:1725992 original size:33 final size:32
Alignment explanation
Indices: 1725933--1726022 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
1725923 CAACCTTCAA
* **
1725933 AAGCCCACAAGTCCGTGGCATTTTTTCCCTTTC
1 AAGCCCACAACTCCGTGGCACCTTTT-CCTTTC
* * *
1725966 AAGCCCACAACTCCGTGGCGCCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCACCTTTTCCTTTC
*
1725998 AAGTCCACAACTCCGTGGCACCTTT
1 AAGCCCACAACTCCGTGGCACCTTT
1726023 AAGCCCAATA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 27 0.55
33 22 0.45
ACGTcount: A:0.19, C:0.34, G:0.16, T:0.31
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCACCTTTTCCTTTC
Found at i:1726100 original size:35 final size:34
Alignment explanation
Indices: 1726056--1726170 Score: 135
Period size: 35 Copynumber: 3.4 Consensus size: 34
1726046 GTCAGCATAT
*
1726056 TGGCA-CCTTTTCTTTTTTAAGTCCACAACTCCG
1 TGGCATCCTTTTCTTTTTTAAGCCCACAACTCCG
*
1726089 TGGCATTCCTTTTCTTTTGTAAGCCCACAACTCCG
1 TGGCA-TCCTTTTCTTTTTTAAGCCCACAACTCCG
* * * *
1726124 TGGCACTCTTTTTC-CTTTTAAGCCCACAAGTCAG
1 TGGCA-TCCTTTTCTTTTTTAAGCCCACAACTCCG
*
1726158 TGGCACCCTTTTC
1 TGGCATCCTTTTC
1726171 AAAAGCCCAC
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 11 0.16
34 21 0.30
35 38 0.54
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.37
Consensus pattern (34 bp):
TGGCATCCTTTTCTTTTTTAAGCCCACAACTCCG
Found at i:1726209 original size:28 final size:29
Alignment explanation
Indices: 1726143--1726212 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
1726133 TTTTCCTTTT
*
1726143 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
1726173 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
1726201 AAGCACACAAGT
1 AAGCCCACAAGT
1726213 TGGTGGCGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 16 0.42
30 22 0.58
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.16
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:1726299 original size:49 final size:49
Alignment explanation
Indices: 1726227--1726373 Score: 179
Period size: 49 Copynumber: 3.0 Consensus size: 49
1726217 GGCGTCTTCT
* * *
1726227 TCTAAGTCTAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTTATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * *
1726276 TCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
* * * *
1726325 TTTAAGCCCAATATCACTAGTCC-TGAATCAGCATATTGGCACCTTTATC
1 TCTAAGACCAATATCGCT-GGCCTTGAATCAGCATATTGGCACCTTTATC
1726374 ACTTTTCTCA
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
49 79 0.96
50 3 0.04
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (49 bp):
TCTAAGACCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATC
Found at i:1726444 original size:49 final size:49
Alignment explanation
Indices: 1726390--1726694 Score: 358
Period size: 52 Copynumber: 6.0 Consensus size: 49
1726380 CTCATCCTCA
* *
1726390 TCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCT
* * * * *
1726439 TCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-G-GCATCT
*
1726490 GTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
1 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCT
* * * *
1726540 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTGCCTTT
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-G-GCATCT
*
1726591 GTCATCTTCAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCT
1 -TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-TCT
* * * * *
1726642 TCTTATCTTCAAGTCTAAATGTCGCTGACCGTGAATCAGCACATTGACATCT
1 TC--ATCTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTGGCATCT
1726694 T
1 T
1726695 TTTTCTCATC
Statistics
Matches: 219, Mismatches: 27, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
49 77 0.35
50 9 0.04
51 11 0.05
52 93 0.42
53 29 0.13
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (49 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCT
Found at i:1726489 original size:119 final size:120
Alignment explanation
Indices: 1726273--1726498 Score: 375
Period size: 119 Copynumber: 1.9 Consensus size: 120
1726263 TGGCACCTTT
1726273 ATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGCCCAATA
1 ATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGCCCAATA
1726338 TCACTAGTCCTGAATCAGCATATTGGCACCTTTATCA-CTTTTCTCATCCTCATC
66 TCACTAGTCCTGAATCAGCATATTGGCACCTTTATCATCTTTTCTCATCCTCATC
* * *
1726392 ATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATA
1 ATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGCCCAATA
* * *
1726457 TCGCTAG-CCTTGAATCAGCATATTGGCGCCTTTGTCATCTTT
66 TCACTAGTCC-TGAATCAGCATATTGGCACCTTTATCATCTTT
1726499 AAGTCCAATG
Statistics
Matches: 99, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
118 2 0.02
119 93 0.94
120 4 0.04
ACGTcount: A:0.24, C:0.27, G:0.15, T:0.34
Consensus pattern (120 bp):
ATCTCTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGCCCAATA
TCACTAGTCCTGAATCAGCATATTGGCACCTTTATCATCTTTTCTCATCCTCATC
Found at i:1726568 original size:101 final size:101
Alignment explanation
Indices: 1726390--1726687 Score: 452
Period size: 101 Copynumber: 2.9 Consensus size: 101
1726380 CTCATCCTCA
* *
1726390 TCATCTTTAAGACCAATGTCGTTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAA
*
1726455 TATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTG
66 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTG
*
1726491 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAA
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAA
*
1726556 TATCGCTGGCCTTGAATCAGCATATTGGTGCCTTTG
66 TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTG
* *
1726592 TCATCTTCAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCTTATCTTCAAGTC
1 TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-TCTTC--ATCTTTAAGTC
* * * * *
1726657 TAAATGTCGCTGACCGTGAATCAGCACATTG
63 -CAATATCGCTGGCCTTGAATCAGCATATTG
1726688 ACATCTTTTT
Statistics
Matches: 180, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
101 141 0.78
102 4 0.02
104 10 0.06
105 25 0.14
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.33
Consensus pattern (101 bp):
TCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAA
TATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTG
Found at i:1727407 original size:13 final size:13
Alignment explanation
Indices: 1727389--1727428 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1727379 TTTCAGCGAT
1727389 TTGTATCGATACA
1 TTGTATCGATACA
*
1727402 TTGTATCGCTACA
1 TTGTATCGATACA
*
1727415 ATGTATCGATACA
1 TTGTATCGATACA
1727428 T
1 T
1727429 AAGTATTGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1727443 original size:19 final size:19
Alignment explanation
Indices: 1727419--1727510 Score: 64
Period size: 19 Copynumber: 5.5 Consensus size: 19
1727409 GCTACAATGT
1727419 ATCGATACATAAGTATTGC
1 ATCGATACATAAGTATTGC
*
1727438 ATCGATAC---A--A-TGT
1 ATCGATACATAAGTATTGC
*
1727451 ATCGATACATAAGTTTTGC
1 ATCGATACATAAGTATTGC
*
1727470 ATCGATAC---A--A-TGT
1 ATCGATACATAAGTATTGC
*
1727483 ATCGATACATAAGTTTTGC
1 ATCGATACATAAGTATTGC
1727502 ATCGATACA
1 ATCGATACA
1727511 ATGTATCGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 24
0.64 0.08 0.28
Matches are distributed among these distances:
13 20 0.37
14 1 0.02
16 4 0.07
19 29 0.54
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (19 bp):
ATCGATACATAAGTATTGC
Found at i:1727452 original size:32 final size:32
Alignment explanation
Indices: 1727401--1727518 Score: 200
Period size: 32 Copynumber: 3.7 Consensus size: 32
1727391 GTATCGATAC
* *
1727401 ATTGTATCGCTACAATGTATCGATACATAAGT
1 ATTGCATCGATACAATGTATCGATACATAAGT
1727433 ATTGCATCGATACAATGTATCGATACATAAGT
1 ATTGCATCGATACAATGTATCGATACATAAGT
*
1727465 TTTGCATCGATACAATGTATCGATACATAAGT
1 ATTGCATCGATACAATGTATCGATACATAAGT
*
1727497 TTTGCATCGATACAATGTATCG
1 ATTGCATCGATACAATGTATCG
1727519 CTACGAAGCT
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 83 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
ATTGCATCGATACAATGTATCGATACATAAGT
Found at i:1727581 original size:13 final size:13
Alignment explanation
Indices: 1727563--1727587 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1727553 ATTACTCAAA
1727563 TGTATCGATACAT
1 TGTATCGATACAT
1727576 TGTATCGATACA
1 TGTATCGATACA
1727588 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1732945 original size:19 final size:18
Alignment explanation
Indices: 1732920--1733004 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
1732910 TAGCGATACA
1732920 TTGTATCGATACAATAGT
1 TTGTATCGATACAATAGT
1732938 TATGTATCGATAC---A--
1 T-TGTATCGATACAATAGT
* *
1732952 TTGTAT-GATACAACACT
1 TTGTATCGATACAATAGT
1732969 TATGTATCGATACAATTACTGT
1 T-TGTATCGATACAA-TA--GT
1732991 TTGTATCGATACAA
1 TTGTATCGATACAA
1733005 ATTGTTGAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
12 5 0.09
13 5 0.09
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 6 0.11
19 18 0.33
20 1 0.02
21 13 0.24
22 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (18 bp):
TTGTATCGATACAATAGT
Found at i:1732972 original size:31 final size:32
Alignment explanation
Indices: 1732913--1732982 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
1732903 AGCTTCGTAG
* *
1732913 CGATACATTGTATCGATACAATAGTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1732945 CGATACATTGTAT-GATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1732976 CGATACA
1 CGATACA
1732983 ATTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1737107 original size:20 final size:22
Alignment explanation
Indices: 1737063--1737109 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
1737053 AATTTTCCAC
1737063 AAAT-TTTCACTTTTTCACTTCA
1 AAATCTTTCACTTTTTCAC-TCA
1737085 AAATCTTTCA-TTTTTCA-TCA
1 AAATCTTTCACTTTTTCACTCA
1737105 AAATC
1 AAATC
1737110 ATCAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (22 bp):
AAATCTTTCACTTTTTCACTCA
Found at i:1739409 original size:13 final size:13
Alignment explanation
Indices: 1739391--1739417 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1739381 ACATTATGCT
1739391 TTGTATCGATACA
1 TTGTATCGATACA
1739404 TTGTATCGATACA
1 TTGTATCGATACA
1739417 T
1 T
1739418 GTTAATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1739446 original size:20 final size:20
Alignment explanation
Indices: 1739403--1739477 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
1739393 GTATCGATAC
**
1739403 ATTGTATCGATACAT-GTTA
1 ATTGTATCGATACATGGACA
1739422 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
1739442 ATTGTATCGATACATGGACA
1 ATTGTATCGATACATGGACA
1739462 ATTGTATCGATACATG
1 ATTGTATCGATACATG
1739478 AGATTGGCAG
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
19 15 0.28
20 38 0.72
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (20 bp):
ATTGTATCGATACATGGACA
Found at i:1748375 original size:22 final size:21
Alignment explanation
Indices: 1748330--1748410 Score: 81
Period size: 22 Copynumber: 3.8 Consensus size: 21
1748320 ATTTAAAAAA
* * *
1748330 TATTTTTAAAAACTATTCAGT
1 TATTTTTAAAAATTATTAATT
*
1748351 TATTTTTAAAAAATTTTTAATT
1 TATTTTT-AAAAATTATTAATT
* **
1748373 TATTCTTAAAAATTATTGGTT
1 TATTTTTAAAAATTATTAATT
1748394 TATTTTTGAAAAATTAT
1 TATTTTT-AAAAATTAT
1748411 CATATGTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
21 24 0.49
22 25 0.51
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (21 bp):
TATTTTTAAAAATTATTAATT
Found at i:1749437 original size:19 final size:19
Alignment explanation
Indices: 1749415--1749451 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1749405 AAAGTAATTT
1749415 AAAAAATTCAAAAA-AAATC
1 AAAAAATT-AAAAATAAATC
1749434 AAAAAATTAAAAATAAAT
1 AAAAAATTAAAAATAAAT
1749452 AAGATAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
AAAAAATTAAAAATAAATC
Found at i:1757216 original size:122 final size:122
Alignment explanation
Indices: 1756990--1757219 Score: 352
Period size: 122 Copynumber: 1.9 Consensus size: 122
1756980 TTCTTTATTT
* *
1756990 ATTTTTTTAATAAAGGAAACTTGATAAGGGAATTTAATAATTGCTGATATAAACAAACTACTGCA
1 ATTTTTTTAATAAAGGAAAATCGATAAGGGAATTTAATAATTGCTGATATAAACAAACTACTGCA
* * *
1757055 ATTTGGTAAAACTGTATACTCATTGTCTACATTCTAAAAGATTGGCATCCAAGGTTG
66 ATTTGGTAAAACTGTATACTAATTGTCTACATGCAAAAAGATTGGCATCCAAGGTTG
* * *
1757112 ATTTTTTTGATAAAGGAAAATCGATAAGGGAATTTAATACTTGCTGATGTAAACAAACTACTGCA
1 ATTTTTTTAATAAAGGAAAATCGATAAGGGAATTTAATAATTGCTGATATAAACAAACTACTGCA
* * * *
1757177 ATTTGGTAAAATTGTATATTAATTGTCTACGTGGAAAAAGATT
66 ATTTGGTAAAACTGTATACTAATTGTCTACATGCAAAAAGATT
1757220 AGCCGCTAGG
Statistics
Matches: 96, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
122 96 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (122 bp):
ATTTTTTTAATAAAGGAAAATCGATAAGGGAATTTAATAATTGCTGATATAAACAAACTACTGCA
ATTTGGTAAAACTGTATACTAATTGTCTACATGCAAAAAGATTGGCATCCAAGGTTG
Found at i:1759092 original size:2 final size:2
Alignment explanation
Indices: 1759087--1759113 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1759077 CATGTGTGTG
1759087 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1759114 TAATTATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1760114 original size:18 final size:18
Alignment explanation
Indices: 1760091--1760127 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1760081 AAACCCTCCA
*
1760091 CTGCTCTCCACTGCATCG
1 CTGCTCTCCACTACATCG
1760109 CTGCTCTCCACTACATCG
1 CTGCTCTCCACTACATCG
1760127 C
1 C
1760128 AGGGTGGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.46, G:0.14, T:0.27
Consensus pattern (18 bp):
CTGCTCTCCACTACATCG
Found at i:1760898 original size:8 final size:8
Alignment explanation
Indices: 1760887--1760977 Score: 55
Period size: 8 Copynumber: 11.1 Consensus size: 8
1760877 TTAATATAAA
1760887 TATATTTT
1 TATATTTT
1760895 TATATATTT
1 TATAT-TTT
*
1760904 TTTATTATT
1 TATATT-TT
**
1760913 TA-ATTAAA
1 TATATT-TT
1760921 TATATTTT
1 TATATTTT
1760929 TA-ATTATT
1 TATATT-TT
*
1760937 TATATATT
1 TATATTTT
1760945 TATATATTT
1 TATAT-TTT
1760954 TA-A-TTT
1 TATATTTT
*
1760960 AATATTTT
1 TATATTTT
1760968 TAATATTTT
1 T-ATATTTT
1760977 T
1 T
1760978 TAATATAATT
Statistics
Matches: 64, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
6 4 0.06
7 4 0.06
8 29 0.45
9 27 0.42
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (8 bp):
TATATTTT
Found at i:1760902 original size:25 final size:25
Alignment explanation
Indices: 1760840--1760903 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
1760830 TTCAATTAAT
* *
1760840 TATTATTCAATA-TAAATATAAATA
1 TATTTTTCAATATTTAATATAAATA
*
1760864 TATTTTTCACTATTTAATATAAATA
1 TATTTTTCAATATTTAATATAAATA
1760889 TATTTTT-ATATATTT
1 TATTTTTCA-ATATTT
1760904 TTTATTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 11 0.32
25 23 0.68
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTTTTCAATATTTAATATAAATA
Found at i:1760937 original size:34 final size:35
Alignment explanation
Indices: 1760861--1760930 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
1760851 ATAAATATAA
1760861 ATATATTTTTCACTATTTAATATAAATATATTTTT
1 ATATATTTTTCACTATTTAATATAAATATATTTTT
* *
1760896 ATATATTTTTTATTATTTAAT-TAAATATATTTTT
1 ATATATTTTTCACTATTTAATATAAATATATTTTT
1760930 A
1 A
1760931 ATTATTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
34 14 0.42
35 19 0.58
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (35 bp):
ATATATTTTTCACTATTTAATATAAATATATTTTT
Found at i:1760973 original size:22 final size:22
Alignment explanation
Indices: 1760934--1760976 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1760924 ATTTTTAATT
1760934 ATTTATATATTTATATATTTTA
1 ATTTATATATTTATATATTTTA
*
1760956 ATTTA-ATATTTTTAATATTTT
1 ATTTATATATTTAT-ATATTTT
1760977 TTAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTATATATTTATATATTTTA
Found at i:1760978 original size:24 final size:24
Alignment explanation
Indices: 1760919--1760986 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
1760909 TATTTAATTA
*
1760919 AATATATTTTTAATTATTTATATATTT
1 AATAT-TTTTTAA-T-TTAATATATTT
* *
1760946 -ATATATTTTAATTTAATATTTTT
1 AATATTTTTTAATTTAATATATTT
*
1760969 AATATTTTTTAATATAAT
1 AATATTTTTTAATTTAAT
1760987 TTATCTTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 9 0.26
24 16 0.46
25 6 0.17
26 4 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
AATATTTTTTAATTTAATATATTT
Found at i:1761086 original size:17 final size:17
Alignment explanation
Indices: 1761021--1761087 Score: 55
Period size: 18 Copynumber: 3.6 Consensus size: 17
1761011 TAAAATTAAA
*
1761021 TATATATTTTATTATTAAT
1 TATA-ATTTTATTACT-AT
1761040 TATAATCTAATTATTACTA-
1 TATAAT-T--TTATTACTAT
1761059 TACTCAATTTTATTACTAT
1 TA-T-AATTTTATTACTAT
1761078 TATAATTTTA
1 TATAATTTTA
1761088 ATTTTACTGG
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
17 7 0.17
18 12 0.29
19 9 0.22
20 3 0.07
21 10 0.24
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAATTTTATTACTAT
Found at i:1761324 original size:23 final size:23
Alignment explanation
Indices: 1761298--1761341 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1761288 TATAATTATT
1761298 TTTAAAAATT-AATATCTAATAAA
1 TTTAAAAATTAAATAT-TAATAAA
*
1761321 TTTAAAATTTAAATATTAATA
1 TTTAAAAATTAAATATTAATA
1761342 TTTATAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAAAAATTAAATATTAATAAA
Found at i:1761585 original size:16 final size:16
Alignment explanation
Indices: 1761540--1761585 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1761530 TTATCATATT
1761540 TTATATATAATTTTATA
1 TTATATA-AATTTTATA
*
1761557 -TAT-TAATAATTTATA
1 TTATATAA-ATTTTATA
1761572 TTATATAAATTTTA
1 TTATATAAATTTTA
1761586 ATATATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 11 0.46
17 3 0.12
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTATATAAATTTTATA
Found at i:1764232 original size:19 final size:19
Alignment explanation
Indices: 1764210--1764266 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 19
1764200 TTTTATATCA
1764210 AACATATAAATA-TAAATAT
1 AACATA-AAATATTAAATAT
*
1764229 AACATAAATTATTAAATAT
1 AACATAAAATATTAAATAT
* *
1764248 -A-TTAAAATTTTAAATAT
1 AACATAAAATATTAAATAT
1764265 AA
1 AA
1764267 ATATGATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 13 0.41
18 6 0.19
19 13 0.41
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AACATAAAATATTAAATAT
Found at i:1764875 original size:24 final size:25
Alignment explanation
Indices: 1764838--1764884 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1764828 TAATCAAAAT
*
1764838 TATAATTATTAAAAATATGATATGA
1 TATAAATATTAAAAATATGATATGA
1764863 TATAAATA-TAAAAATATGATAT
1 TATAAATATTAAAAATATGATAT
1764885 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.38
Consensus pattern (25 bp):
TATAAATATTAAAAATATGATATGA
Found at i:1771617 original size:68 final size:68
Alignment explanation
Indices: 1771536--1771662 Score: 218
Period size: 68 Copynumber: 1.9 Consensus size: 68
1771526 TAAATTAGAA
*
1771536 AAGTCAAATATCTTCTAATAAAAGAAAACATCCCTCATAATCAGCCAACTAATAATCTCCAACAT
1 AAGTCAAAGATCTTCTAATAAAAGAAAACATCCCTCATAATCAGCCAACTAATAATCTCCAACAT
1771601 TCT
66 TCT
* * *
1771604 AAGTCAAAGATCTTCTAATAAAGGAAAACATCCCTTATAATTAGCCAACTAATAATCTC
1 AAGTCAAAGATCTTCTAATAAAAGAAAACATCCCTCATAATCAGCCAACTAATAATCTC
1771663 TAACGCTCAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.44, C:0.23, G:0.06, T:0.27
Consensus pattern (68 bp):
AAGTCAAAGATCTTCTAATAAAAGAAAACATCCCTCATAATCAGCCAACTAATAATCTCCAACAT
TCT
Found at i:1775144 original size:52 final size:52
Alignment explanation
Indices: 1775038--1775153 Score: 162
Period size: 52 Copynumber: 2.2 Consensus size: 52
1775028 TTTGCCTGCA
* * ***
1775038 TGTATCGATACATTTGGGCAAATTTGCCTGCATGTATCGATAGATTTTATAG
1 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATAG
*
1775090 TGTATTGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAGATCAG
1 TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-AG
1775142 TGTATCGATACA
1 TGTATCGATACA
1775154 ATGTATCGAT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
51 2 0.04
52 54 0.96
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (52 bp):
TGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATAG
Found at i:1775246 original size:13 final size:13
Alignment explanation
Indices: 1775228--1775252 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1775218 ACAAAACTTA
1775228 TGTATCGATACAT
1 TGTATCGATACAT
1775241 TGTATCGATACA
1 TGTATCGATACA
1775253 ATACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1775248 original size:32 final size:33
Alignment explanation
Indices: 1775207--1775272 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1775197 AGTAGCTTAA
1775207 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1775239 ATTGTATCGATACAATACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1775272 A
1 A
1775273 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1775850 original size:55 final size:51
Alignment explanation
Indices: 1775774--1776198 Score: 299
Period size: 49 Copynumber: 8.8 Consensus size: 51
1775764 GATAAAAGGA
* * * * * *
1775774 CCAATACGTTGATTCACGGCCAACGATATTGGGTTCAAAGATGAGAAAAAGGATG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGGCTT-AAAGATG-G-AAAAGG-TG
* * * *
1775829 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTG-GCTTAAAGATGGAAAAGGTG
*
1775881 CCAATATGCTGATTCAAGGCCAGCTATATTGGATT-----T---AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGGCTTAAAGATGGAAAAGGTG
* * *
1775924 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAAAGATGGAAAAGGTG
1775973 CCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAAAGATGGAAAAGGTG
* *
1776016 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAAAGATGGAAAAGGTG
* *
1776065 CCAATATGCTGACTCAATGCCAGCTATATTGGAC-T-----T---AAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAAAGATGGAAAAGGTG
* * *
1776108 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTG
1 CCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTAAAGATGGAAAAGGTG
*
1776157 CCAATATGCTGACTCAAGGCCAGCTATATTGGACTTAGAAGA
1 CCAATATGCTGATTCAAGGCCAGCTATATTGG-CTTA-AAGA
1776199 AGATGCCACC
Statistics
Matches: 309, Mismatches: 36, Indels: 55
0.77 0.09 0.14
Matches are distributed among these distances:
43 112 0.36
44 4 0.01
46 1 0.00
48 2 0.01
49 115 0.37
50 4 0.01
51 2 0.01
52 30 0.10
53 6 0.02
54 1 0.00
55 30 0.10
56 2 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (51 bp):
CCAATATGCTGATTCAAGGCCAGCTATATTGGCTTAAAGATGGAAAAGGTG
Found at i:1775935 original size:43 final size:45
Alignment explanation
Indices: 1775874--1776193 Score: 382
Period size: 49 Copynumber: 7.0 Consensus size: 45
1775864 TAAAGATGGA
1775874 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA-TT-T
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAT
* * *
1775917 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-T
1775965 AGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-T
1 A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAT
* *
1776009 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----AT
* * *
1776058 GAAGGTGCCAATATGCTGACTCAATGCCAGCTATATTGGAC-T-T
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAT
* * *
1776101 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-T
*
1776149 AGAAGGTGCCAATATGCTGACTCAAGGCCAGCTATATTGGACTTA
1 A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1776194 GAAGAAGATG
Statistics
Matches: 237, Mismatches: 22, Indels: 32
0.81 0.08 0.11
Matches are distributed among these distances:
43 113 0.48
44 5 0.02
47 1 0.00
48 4 0.02
49 114 0.48
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (45 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAT
Found at i:1776005 original size:92 final size:92
Alignment explanation
Indices: 1775821--1776193 Score: 638
Period size: 92 Copynumber: 4.0 Consensus size: 92
1775811 AAGATGAGAA
* * *
1775821 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
* *
1775886 ATGCTGATTCAAGGCCAGCTATATTGGATTT
62 ATGCTGACTCAAGGCCAGCTATATTGGACTT
1775917 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
1775982 TGATTCAAGGCCAGCTATATTGGACTT
66 TGACTCAAGGCCAGCTATATTGGACTT
*
1776009 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
1776074 TGACTCAATGCCAGCTATATTGGACTT
66 TGACTCAAGGCCAGCTATATTGGACTT
1776101 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1776166 TGACTCAAGGCCAGCTATATTGGACTT
66 TGACTCAAGGCCAGCTATATTGGACTT
1776193 A
1 A
1776194 GAAGAAGATG
Statistics
Matches: 268, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
92 222 0.83
95 41 0.15
96 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGACTCAAGGCCAGCTATATTGGACTT
Found at i:1776303 original size:29 final size:29
Alignment explanation
Indices: 1776215--1776550 Score: 381
Period size: 29 Copynumber: 11.5 Consensus size: 29
1776205 CACCAACTTG
* * **
1776215 TGTGGGCTTTCGAAAGGATTG-CACCAACT
1 TGTGGGCTTTTGAAAAGA-TGCCACTGACT
* * *
1776244 TGTGTGCTTCTGAAAA-TTGCCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* * *
1776272 TGTGGGCTTTTGAAGAGATACCATTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1776301 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
*
1776331 TGTGGGC-TTTGAAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG-AAAA-GATGCCACTGACT
*
1776361 TGTGGGCTTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* * *
1776390 TGTGGGCTTTGGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
*
1776420 TGTGGGCTTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
* *
1776449 TGTGGGCTTTGGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTGAAAA-GATGCCACTGACT
* *
1776479 TGTGGGCTTTGGAAAAGATGCCACTAACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
*
1776508 TGTGGGCTTTTGAAAAGATACCACTGACT
1 TGTGGGCTTTTGAAAAGATGCCACTGACT
*
1776537 TGTGGGTTTTTGAA
1 TGTGGGCTTTTGAA
1776551 GGGTGAGGAA
Statistics
Matches: 262, Mismatches: 38, Indels: 14
0.83 0.12 0.04
Matches are distributed among these distances:
27 2 0.01
28 19 0.07
29 139 0.53
30 98 0.37
31 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAAGATGCCACTGACT
Found at i:1776331 original size:59 final size:59
Alignment explanation
Indices: 1776261--1776542 Score: 390
Period size: 59 Copynumber: 4.8 Consensus size: 59
1776251 TTCTGAAAAT
* * * * *
1776261 TGCCACTGACTTGTGGGCTTTTGAAGA-GATACCATTGACTTGTGGGCTTTGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAA-GA
*
1776320 TGCCACTGACTTGTGGGC-TTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTG-AAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
* * * *
1776379 TACCACTGACTTGTGGGCTTTGGAAAAGGGTGCCATTGACTTGTGGGCTTTTGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
* *
1776438 TACCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
* * *
1776497 TGCCACTAACTTGTGGGCTTTTGAAAA-GATACCACTGACTTGTGGG
1 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGG
1776543 TTTTTGAAGG
Statistics
Matches: 204, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
58 21 0.10
59 155 0.76
60 28 0.14
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.29
Consensus pattern (59 bp):
TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTGGAAAAGA
Found at i:1776365 original size:89 final size:88
Alignment explanation
Indices: 1776241--1776550 Score: 437
Period size: 89 Copynumber: 3.5 Consensus size: 88
1776231 GATTGCACCA
* * * * * *
1776241 ACTTGTGTGCTTCTGAAAA-TTGCCACTGACTTGTGGGCTTTTGAAGAGATACCATTGACTTGTG
1 ACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTG
1776305 GGCTTTGGAAAAGGGTGCCACTG
66 GGCTTTGGAAAAGGGTGCCACTG
* *
1776328 ACTTGTGGGC-TTTGAAAAAGGGTGCCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
1 ACTTGTGGGCTTTTG-AAAA-GATACCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTG
*
1776392 TGGGCTTTGGAAAAGGGTGCCATTG
64 TGGGCTTTGGAAAAGGGTGCCACTG
* * *
1776417 ACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTGGAAAAGGGTGCCACTGACTTGT
1 ACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTTGAAAA-GATACCACTGACTTGT
* *
1776482 GGGCTTTGGAAAA-GATGCCACTA
65 GGGCTTTGGAAAAGGGTGCCACTG
*
1776505 ACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGTTTTTGAA
1 ACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTTGAA
1776551 GGGTGAGGAA
Statistics
Matches: 202, Mismatches: 16, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
86 3 0.01
87 13 0.06
88 77 0.38
89 105 0.52
90 4 0.02
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (88 bp):
ACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTGGGCTTTTGAAAAGATACCACTGACTTGTG
GGCTTTGGAAAAGGGTGCCACTG
Found at i:1777995 original size:1 final size:1
Alignment explanation
Indices: 1777985--1778082 Score: 52
Period size: 1 Copynumber: 98.0 Consensus size: 1
1777975 ATCTGGACCC
* * * * * ** * * *
1777985 TTTTTGTTTTTGTTGTTTTTGTTTGTTTTTTTTTTGGTTTTTTGTTTTTTGTTTTTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * **
1778050 TCTTCTTTTTTTTTGTTTATTTGGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1778083 GGGGAGGACG
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.01, C:0.02, G:0.13, T:0.84
Consensus pattern (1 bp):
T
Found at i:1778002 original size:9 final size:8
Alignment explanation
Indices: 1777991--1778080 Score: 82
Period size: 7 Copynumber: 11.6 Consensus size: 8
1777981 ACCCTTTTTG
1777991 TTTTTGTT
1 TTTTTGTT
1777999 GTTTTTGTT
1 -TTTTTGTT
*
1778008 TGTTT-TT
1 TTTTTGTT
*
1778015 TTTTTGGT
1 TTTTTGTT
1778023 TTTTTG-T
1 TTTTTGTT
1778030 TTTTTGTT
1 TTTTTGTT
1778038 TTTTTG-T
1 TTTTTGTT
*
1778045 TTTTT-TC
1 TTTTTGTT
*
1778052 TTCTT-TT
1 TTTTTGTT
1778059 TTTTTGTT
1 TTTTTGTT
*
1778067 TATTTGGTT
1 T-TTTTGTT
1778076 TTTTT
1 TTTTT
1778081 TTGGGGAGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
7 28 0.42
8 24 0.36
9 15 0.22
ACGTcount: A:0.01, C:0.02, G:0.13, T:0.83
Consensus pattern (8 bp):
TTTTTGTT
Found at i:1778003 original size:15 final size:14
Alignment explanation
Indices: 1777985--1778082 Score: 92
Period size: 15 Copynumber: 6.7 Consensus size: 14
1777975 ATCTGGACCC
1777985 TTTTTGTTTTTGTTG
1 TTTTTGTTTTT-TTG
*
1778000 TTTTTGTTTGTTTTT
1 TTTTTGTTT-TTTTG
*
1778015 TTTTTGGTTTTTTG
1 TTTTTGTTTTTTTG
1778029 TTTTTTGTTTTTTTG
1 -TTTTTGTTTTTTTG
*
1778044 TTTTT-TTCTTCTTTT
1 TTTTTGTT-TT-TTTG
*
1778059 TTTTTGTTTATTTGG
1 TTTTTGTTT-TTTTG
1778074 TTTTT-TTTT
1 TTTTTGTTTT
1778083 GGGGAGGACG
Statistics
Matches: 70, Mismatches: 7, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
13 3 0.04
14 14 0.20
15 48 0.69
16 5 0.07
ACGTcount: A:0.01, C:0.02, G:0.13, T:0.84
Consensus pattern (14 bp):
TTTTTGTTTTTTTG
Found at i:1778011 original size:13 final size:12
Alignment explanation
Indices: 1777993--1778067 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 12
1777983 CCTTTTTGTT
1777993 TTTGTTGTTTTTG
1 TTTGTT-TTTTTG
1778006 TTTGTTTTTTT-
1 TTTGTTTTTTTG
*
1778017 TTTGGTTTTTTG
1 TTTGTTTTTTTG
1778029 TTT-TTTGTTTT-
1 TTTGTTT-TTTTG
*
1778040 TTTGTTTTTTTC
1 TTTGTTTTTTTG
*
1778052 TTCTTTTTTTTTG
1 TT-TGTTTTTTTG
1778065 TTT
1 TTT
1778068 ATTTGGTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
11 19 0.36
12 18 0.34
13 16 0.30
ACGTcount: A:0.00, C:0.03, G:0.13, T:0.84
Consensus pattern (12 bp):
TTTGTTTTTTTG
Found at i:1778027 original size:8 final size:7
Alignment explanation
Indices: 1777985--1778079 Score: 79
Period size: 8 Copynumber: 12.7 Consensus size: 7
1777975 ATCTGGACCC
1777985 TTTTTG-
1 TTTTTGT
1777991 TTTTTGTT
1 TTTTTG-T
1777999 GTTTTTGT
1 -TTTTTGT
*
1778007 TTGTTTTT
1 TT-TTTGT
1778015 TTTTTGGT
1 TTTTT-GT
1778023 TTTTTGT
1 TTTTTGT
1778030 TTTTTGTT
1 TTTTTG-T
1778038 TTTTTGT
1 TTTTTGT
1778045 TTTTT-T
1 TTTTTGT
1778051 CTTCTTT-T
1 -TT-TTTGT
1778059 TTTTTGT
1 TTTTTGT
1778066 TTATTTGGT
1 TT-TTT-GT
1778075 TTTTT
1 TTTTT
1778080 TTTGGGGAGG
Statistics
Matches: 76, Mismatches: 2, Indels: 20
0.78 0.02 0.20
Matches are distributed among these distances:
6 10 0.13
7 26 0.34
8 30 0.39
9 10 0.13
ACGTcount: A:0.01, C:0.02, G:0.14, T:0.83
Consensus pattern (7 bp):
TTTTTGT
Found at i:1791906 original size:52 final size:52
Alignment explanation
Indices: 1791841--1791969 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1791831 CGAAATATGA
*
1791841 AAATTTGCATGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1791893 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
* *
1791945 AAATTTTCCGGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1791970 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
Found at i:1791980 original size:52 final size:52
Alignment explanation
Indices: 1791841--1791989 Score: 192
Period size: 52 Copynumber: 2.9 Consensus size: 52
1791831 CGAAATATGA
** ***
1791841 AAATTTGCATGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCGGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
* ***
1791893 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCGGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
*
1791945 AAATTTTCCGGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCGGCATGTATCGATACATAAGAT-AGTGTATCGATACA
1791990 ATGCATCAAT
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCGGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGC
Found at i:1792069 original size:19 final size:18
Alignment explanation
Indices: 1792045--1792142 Score: 90
Period size: 13 Copynumber: 5.8 Consensus size: 18
1792035 TAGCTTAAAT
1792045 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1792064 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1792077 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1792096 TGTATCGATAC--A---A
1 TGTATCGATACAAACTTA
1792109 TGTATCGATACAATACTTTA
1 TGTATCGATACAA-AC-TTA
1792129 TGTATCGATACAAA
1 TGTATCGATACAAA
1792143 TCGTTGAATT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 23 0.35
14 1 0.02
16 4 0.06
18 1 0.02
19 23 0.35
20 14 0.21
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1792084 original size:32 final size:32
Alignment explanation
Indices: 1792043--1792140 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
1792033 AATAGCTTAA
1792043 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
*
1792075 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTATGTATCGATAC
* *
1792107 AATGTATCGATACAATACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1792140 A
1 A
1792141 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 47 0.76
33 15 0.24
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAAAACTTATGTATCGATAC
Found at i:1792751 original size:52 final size:52
Alignment explanation
Indices: 1792673--1792801 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1792663 CGAAATATGG
*
1792673 AAATTTGCCTGCATGTATCGATACATTTAACAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAACAATGTATCGATACATCTGGGC
* *
1792725 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAACAATGTATCGATACATCTGGGC
1792777 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1792802 AAGATTAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAACAATGTATCGATACATCTGGGC
Found at i:1792814 original size:52 final size:52
Alignment explanation
Indices: 1792673--1792819 Score: 215
Period size: 52 Copynumber: 2.8 Consensus size: 52
1792663 CGAAATATGG
* **
1792673 AAATTTGCCTGCATGTATCGATACATTTAACAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGGGC
* *
1792725 AAATTTGCCTGCATGTATCGATAC-ATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACAATTAT-TAGTGTATCGATACATCTGGGC
**
1792777 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATA
1 AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATCGATA
1792820 TAATGTATCG
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.95
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACAATTATTAGTGTATCGATACATCTGGGC
Found at i:1792831 original size:33 final size:34
Alignment explanation
Indices: 1792789--1792853 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1792779 ATTTGCCTGC
* *
1792789 ATGTATCGATACA-AAGATTAGTGTATCGATATA
1 ATGTATCGATACATAAGAGTAATGTATCGATATA
*
1792822 ATGTATCGATACATTAGAGTAATGTATCGATA
1 ATGTATCGATACATAAGAGTAATGTATCGATA
1792854 CATTAGAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.46
34 15 0.54
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.34
Consensus pattern (34 bp):
ATGTATCGATACATAAGAGTAATGTATCGATATA
Found at i:1792846 original size:21 final size:21
Alignment explanation
Indices: 1792820--1792878 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
1792810 TGTATCGATA
1792820 TAATGTATCGATACATTAGAG
1 TAATGTATCGATACATTAGAG
1792841 TAATGTATCGATACATTAGAG
1 TAATGTATCGATACATTAGAG
1792862 TAATGTATCGATACATT
1 TAATGTATCGATACATT
1792879 TTTTGGCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (21 bp):
TAATGTATCGATACATTAGAG
Found at i:1792923 original size:20 final size:20
Alignment explanation
Indices: 1792894--1792951 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1792884 GCAGTAGCTT
1792894 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1792913 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1792933 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1792952 TCGTTGCAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1793561 original size:52 final size:52
Alignment explanation
Indices: 1793483--1793611 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 52
1793473 CGAAATATGG
* * *
1793483 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
* *
1793535 AAATTTGCCTACATGTATCGATACATTTTATAATGTATTGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1793587 AAATTTGCC-AGCATGTATCGATACA
1 AAATTTGCCTA-CATGTATCGATACA
1793612 AAGATCAGTG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
51 1 0.01
52 70 0.99
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1793624 original size:52 final size:51
Alignment explanation
Indices: 1793483--1793631 Score: 185
Period size: 52 Copynumber: 2.9 Consensus size: 51
1793473 CGAAATATGG
* *
1793483 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCAGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* * *
1793535 AAATTTGCCTA-CATGTATCGATACATTTTATAATGTATTGATACATCTGGGC
1 AAATTTGCC-AGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1793587 AAATTTGCCAGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCAGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1793632 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
51 3 0.04
52 81 0.96
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCAGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1793638 original size:13 final size:13
Alignment explanation
Indices: 1793620--1793644 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1793610 CAAAGATCAG
1793620 TGTATCGATACAA
1 TGTATCGATACAA
1793633 TGTATCGATACA
1 TGTATCGATACA
1793645 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1794362 original size:52 final size:52
Alignment explanation
Indices: 1794284--1794412 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 52
1794274 CGAAATATAG
*
1794284 AAATTTGCCTGCATGTATCGATACA-TTTAGTAGTGTATCAATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTTA-TAATGTATCAATACATCTAGGC
* * * *
1794336 AAATTTGCCTGCATATATCGATACATTTTATAATTTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTAGGC
1794388 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1794413 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
52 66 0.94
53 4 0.06
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCAATACATCTAGGC
Found at i:1794427 original size:52 final size:52
Alignment explanation
Indices: 1794284--1794432 Score: 194
Period size: 52 Copynumber: 2.9 Consensus size: 52
1794274 CGAAATATAG
*
1794284 AAATTTGCCTGCATGTATCGATACATTTAG-TAGTGTATCAATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAGATAGTGTATCGATACATCTAGGC
* ** * * *
1794336 AAATTTGCCTGCATATATCGATACATTTTATAATTTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAGATAGTGTATCGATACATCTAGGC
*
1794388 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTAGAT-AGTGTATCGATACA
1794433 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 4 0.05
52 78 0.95
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTAGATAGTGTATCGATACATCTAGGC
Found at i:1794439 original size:13 final size:13
Alignment explanation
Indices: 1794421--1794445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1794411 CAAAGATCAG
1794421 TGTATCGATACAA
1 TGTATCGATACAA
1794434 TGTATCGATACA
1 TGTATCGATACA
1794446 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1794523 original size:33 final size:33
Alignment explanation
Indices: 1794486--1794552 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1794476 AGTAGCTTAA
*
1794486 ATTGTATGGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1794519 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1794552 A
1 A
1794553 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1794526 original size:13 final size:13
Alignment explanation
Indices: 1794508--1794532 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1794498 CAAAAAAATA
1794508 TGTATCGATACAT
1 TGTATCGATACAT
1794521 TGTATCGATACA
1 TGTATCGATACA
1794533 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1794667 original size:801 final size:799
Alignment explanation
Indices: 1791496--1795910 Score: 7328
Period size: 801 Copynumber: 5.5 Consensus size: 799
1791486 AAATCCAACC
*
1791496 TTTTATAGGCAAGAATTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1791561 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
66 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
* * * * * *
1791626 AAGATAGGGTGGCTGGAATTAATGTTTGGCAGCCTTAGCATCCATGGTAGCCAATGAATTTGGAC
131 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
1791691 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
196 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
* * *
1791756 TGGCAATTGAGATTTGACATGAATCCTGATCATTTATGATGCAAAAAACTTGTTTGGCAAAGGAA
261 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
* *
1791821 GAAAAAGTCCCGAAATATGAAAATTTGCATGCATGTATCGATACATTTTATAGTGTATCGATACA
326 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACA-TTTATAGTGTATCGATACA
*
1791886 TCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGCAAATTT
390 TCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTT
* * * *
1791951 TCCGGCATGTATCGATACAAAGATCAGTGTATCGATACAATGCATCAATACATTTGAGTAATGTA
455 GCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTA
* *
1792016 TCGATACATTTTTTGGCAATAGCTTAAATTGTATCGATACAAAACTTATGTATCGATACATTGTA
520 TCGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAA---A---A---AT--A-TGTA
1792081 TCGATACAACACTTATGTATCGATACAATGTATCGATACAATACTTTATGTATCGATACAAATCG
573 TCGAT---ACA--T-TGTATCG-----A--TA-C-A-AC---ACTTTATGTATCGATACAAATCG
* *
1792146 TTGAATTTCAAAATTTTTAACCGTTGGGACCTTGTATCGATACATTCTAACAATGTATCGATACA
619 TTGAAATTC-AAATTTTTGACCGTTGGGACCTTGTATCGATACATTCTAACAATGTATCGATACA
* * * * *
1792211 TTTGGACCAAAATGTAATTTTTTCATCCTTTTTGCCTTCGAAACACCTTATCTCGACTAGGGACG
683 TTTGGACCAAAATGTGATTTTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACTAGGGACG
*
1792276 ATGGGAAATGGATTCGGGCATAACAAAAAGTTATAAAAATCTAAAAAACCAT
748 ATGGGAAATGGATTCGGGCTTAACAAAAAGTTATAAAAATCTAAAAAACCAT
*
1792328 TTTTATAGGCAAGATTTGTGGTGAAAAAATAAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
*
1792393 ATGGGAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
66 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
* *
1792458 AAGATAGGGTGGCTGGAATTAATGTTTGGTAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
131 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
1792523 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
196 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
1792588 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
261 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
*
1792653 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTTAACAGTGTATCGATACA
326 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTT-ATAGTGTATCGATACA
1792718 TCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTT
390 TCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTT
* * *
1792783 GCCTGCATGTATCGATACAAAGATTAGTGTATCGATATAATGTATCGATACATTAGAGTAATGTA
455 GCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTA
*** ** * * * * * **
1792848 TCGATACA-TTAGAGTAATGTATCGATACATTTTTTGGCAGTAGC--TTAAAT-TGTATCGATAC
520 TCGATACATTTTTTGGCA-GTAGC-TTAAATTGTATGG-A-TA-CAAAAAAATATGTATCGATAC
*
1792909 AAAAAAATATGTATCGATACAACACTTTATGTATCGATACAAATCGTTGCAATTCAAAATTTTTG
580 ------AT-TGTATCGATACAACACTTTATGTATCGATACAAATCGTTGAAATTC-AAATTTTTG
*
1792974 ACCGTTGGGACCTTGTATCGATACATTCTAACAATGTATCAATACATTTGGACCAAAATGTGATT
637 ACCGTTGGGACCTTGTATCGATACATTCTAACAATGTATCGATACATTTGGACCAAAATGTGATT
1793039 TTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGC
702 TTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGC
*
1793104 ATAACAAAAAGTTATAAAAATCTAAAAAACCAT
767 TTAACAAAAAGTTATAAAAATCTAAAAAACCAT
* * *
1793137 TTTTGTAGGCTAGATTTGTGGTGAAAAAAAGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1793202 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
66 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
1793267 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
131 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
1793332 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
196 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
*
1793397 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGCTGGAAAAAAACTTATTTGGCAAAGGA
261 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGG-AAAAAACTTATTTGGCAAAGGA
*
1793462 AGAAAAAGTCCCGAAATATGGAAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATAC
325 AGAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTT-ATAGTGTATCGATAC
* *
1793527 ATCTGGGCAAATTTGCCTACATGTATCGATACATTTTATAATGTATTGATACATCTGGGCAAATT
389 ATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATT
*
1793592 TGCCAGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGT
454 TGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGT
*
1793657 ATCGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAAAAATATGTATCGAAACATTG
519 ATCGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAAAAATATGTATCGATACATTG
1793722 TATCGATACAACACTTTATGTATCGATACAAATCGTTGAAATTCAAATGTTTTGACCGTTGGGAC
584 TATCGATACAACACTTTATGTATCGATACAAATCGTTGAAATTCAAAT-TTTTGACCGTTGGGAC
* *
1793787 CTTGTATCGATACATTCCAAGAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATT
648 CTTGTATCGATACATTCTAACAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATT
*
1793852 TTTGCCTTCCAAACGCCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAG
713 TTTGCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAG
1793917 TTATAAAAATCTAAAAAACCAT
778 TTATAAAAATCTAAAAAACCAT
1793939 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
*
1794004 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTAGCTGGCAGAACTCAGGGAG
66 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
*
1794069 AAGATAGGGGGGCTGGAACTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
131 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
1794134 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
196 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
1794199 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
261 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
* * * *
1794264 AAAAAAGTCTCGAAATATAGAAATTTGCCTGCATGTATCGATACATTTAGTAGTGTATCAATACA
326 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTTA-TAGTGTATCGATACA
* * *
1794329 TCTAGGCAAATTTGCCTGCATATATCGATACATTTTATAATTTATCGATACATCTGGGCAAATTT
390 TCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTT
1794394 GCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTA
455 GCCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTA
1794459 TCGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAAAAATATGTATCGATACATTGT
520 TCGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAAAAATATGTATCGATACATTGT
1794524 ATCGATACAACACTTTATGTATCGATACAAATCGTTGAAATTCAAATGTTTTGACCGTTGGGACC
585 ATCGATACAACACTTTATGTATCGATACAAATCGTTGAAATTCAAAT-TTTTGACCGTTGGGACC
* *
1794589 TTGTATCGATACATTCCAAGAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATTT
649 TTGTATCGATACATTCTAACAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATTT
*
1794654 TTGCCTTCCAAACGCCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAGT
714 TTGCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAGT
1794719 TATAAAAATCTAAAAAACCAT
779 TATAAAAATCTAAAAAACCAT
1794740 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
* *
1794805 ATGGAAAGCTTGCTGGCTGAGATAGATGATATCATTGCCTATGGTAGCTGGCAGAACTCAGGGAG
66 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
* *
1794870 AAGATAGGGGGGCTGGAACTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTAGAC
131 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
1794935 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
196 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
1795000 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
261 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
* *
1795065 AAAAAAGTCCCGAAATATAGAAATTTG-C--C-----T-G---C------A-TGTATCGATACAT
326 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTTATAGTGTATCGATACAT
*
1795111 CTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATTTATCGATACATCTGGGCAAATTTG
391 CTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
1795176 CCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTAT
456 CCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTAT
**
1795241 CGATACATTTTTTGGCAGTAGCTTAAATTGTATCAATACAAAAAAATATGTATCGATACATTGTA
521 CGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAAAAATATGTATCGATACATTGTA
* * *
1795306 TCGATACAACACTTTATGTATCAATACAAATAGTTGAAATTTAAAATTTTTGACCGTTGGGACCT
586 TCGATACAACACTTTATGTATCGATACAAATCGTTGAAA-TTCAAATTTTTGACCGTTGGGACCT
1795371 TGTATCGATACATTCTAACAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATTTT
650 TGTATCGATACATTCTAACAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATTTT
1795436 TGCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAGTT
715 TGCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAGTT
1795501 ATAAAAATCTAAAAAACCAT
780 ATAAAAATCTAAAAAACCAT
1795521 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
1 TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
* *
1795586 ATGGAAAGCTTGCTGGCTAAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTTAGGGAG
66 ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
*
1795651 AAGATAGGGTGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
131 AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
* * *
1795716 CACATGGTTTTGGTATTCAATGCCATACTTTATCTTCAAAAGTGATCAAAATGTGTTGTGACATG
196 CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
1795781 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
261 TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
***
1795846 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
326 GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTTAT-AGTGTATCGATACA
1795911 ATGTATCGAT
Statistics
Matches: 3418, Mismatches: 125, Indels: 111
0.94 0.03 0.03
Matches are distributed among these distances:
781 745 0.22
782 8 0.00
784 1 0.00
789 2 0.00
790 1 0.00
792 1 0.00
793 2 0.00
798 1 0.00
800 3 0.00
801 850 0.25
802 504 0.15
803 2 0.00
806 1 0.00
807 2 0.00
808 5 0.00
809 509 0.15
810 222 0.06
811 4 0.00
812 2 0.00
813 1 0.00
814 1 0.00
815 2 0.00
817 1 0.00
818 2 0.00
821 9 0.00
822 9 0.00
824 1 0.00
825 2 0.00
828 1 0.00
831 8 0.00
832 504 0.15
833 8 0.00
834 1 0.00
835 2 0.00
836 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (799 bp):
TTTTATAGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAA
ATGGAAAGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAG
AAGATAGGGGGGCTGGAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGAC
CACATGGTTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATG
TGGCAATTGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAA
GAAAAAGTCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTTATAGTGTATCGATACAT
CTGGGCAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTG
CCTGCATGTATCGATACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGTAATGTAT
CGATACATTTTTTGGCAGTAGCTTAAATTGTATGGATACAAAAAAATATGTATCGATACATTGTA
TCGATACAACACTTTATGTATCGATACAAATCGTTGAAATTCAAATTTTTGACCGTTGGGACCTT
GTATCGATACATTCTAACAATGTATCGATACATTTGGACCAAAATGTGATTTTTTCATCATTTTT
GCCTTCCAAACACCCTATGTCGACTAGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAGTTA
TAAAAATCTAAAAAACCAT
Found at i:1795208 original size:52 final size:52
Alignment explanation
Indices: 1795097--1795213 Score: 173
Period size: 52 Copynumber: 2.2 Consensus size: 52
1795087 ATTTGCCTGC
***
1795097 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTTATA
1 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
*
1795149 ATTTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA-AAGATCA
1 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-A
*
1795201 GTGTATCGATACA
1 ATGTATCGATACA
1795214 ATGTATCGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 2 0.03
52 56 0.97
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
Found at i:1795220 original size:13 final size:13
Alignment explanation
Indices: 1795202--1795226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1795192 CAAAGATCAG
1795202 TGTATCGATACAA
1 TGTATCGATACAA
1795215 TGTATCGATACA
1 TGTATCGATACA
1795227 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1795307 original size:13 final size:13
Alignment explanation
Indices: 1795289--1795313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1795279 CAAAAAAATA
1795289 TGTATCGATACAT
1 TGTATCGATACAT
1795302 TGTATCGATACA
1 TGTATCGATACA
1795314 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1795917 original size:13 final size:13
Alignment explanation
Indices: 1795899--1795923 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1795889 CAAAGATCAG
1795899 TGTATCGATACAA
1 TGTATCGATACAA
1795912 TGTATCGATACA
1 TGTATCGATACA
1795924 TTTGAGCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1796004 original size:13 final size:13
Alignment explanation
Indices: 1795986--1796010 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1795976 CAAAAAAATA
1795986 TGTATCGATACAT
1 TGTATCGATACAT
1795999 TGTATCGATACA
1 TGTATCGATACA
1796011 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1796021 original size:33 final size:33
Alignment explanation
Indices: 1795964--1796030 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1795954 AGTAGCTTAA
*
1795964 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
* ***
1795997 ATTGTATCGATACAACACTTTATGTATCAATAC
1 ATTGTATCGATACAAAAAAATATGTATCAATAC
1796030 A
1 A
1796031 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCAATAC
Found at i:1796632 original size:52 final size:52
Alignment explanation
Indices: 1796554--1796682 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1796544 CGAAATATAG
*
1796554 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1796606 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1796658 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1796683 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1796695 original size:52 final size:51
Alignment explanation
Indices: 1796554--1796702 Score: 228
Period size: 52 Copynumber: 2.9 Consensus size: 51
1796544 CGAAATATAG
1796554 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
1796606 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1796658 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1796703 ATGTATCGAT
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1796709 original size:13 final size:13
Alignment explanation
Indices: 1796691--1796715 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1796681 CAAAGATCAG
1796691 TGTATCGATACAA
1 TGTATCGATACAA
1796704 TGTATCGATACA
1 TGTATCGATACA
1796716 TTTGAGCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1796793 original size:33 final size:33
Alignment explanation
Indices: 1796756--1796855 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1796746 AGTAGCTTAA
* ***
1796756 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
1796789 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
1796822 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACACTTTATGTATCGATAC
1796855 A
1 A
1796856 AATCGTTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAACACTTTATGTATCGATAC
Found at i:1796796 original size:13 final size:13
Alignment explanation
Indices: 1796778--1796835 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
1796768 CAAAAAAATA
1796778 TGTATCGATACAT
1 TGTATCGATACAT
1796791 TGTATCGATACAACACTTT
1 TGTATCGAT---ACA---T
1796810 ATGTATCGATACAT
1 -TGTATCGATACAT
1796824 TGTATCGATACA
1 TGTATCGATACA
1796836 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 9 0.24
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1796816 original size:20 final size:20
Alignment explanation
Indices: 1796791--1796856 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1796781 ATCGATACAT
1796791 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
1796811 TGTATCGAT---ACA---T-
1 TGTATCGATACAACACTTTA
1796824 TGTATCGATACAACACTTTA
1 TGTATCGATACAACACTTTA
1796844 TGTATCGATACAA
1 TGTATCGATACAA
1796857 ATCGTTGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 3 0.08
17 3 0.08
19 1 0.03
20 22 0.56
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (20 bp):
TGTATCGATACAACACTTTA
Found at i:1797464 original size:52 final size:52
Alignment explanation
Indices: 1797386--1797514 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1797376 CGAAATATGG
*
1797386 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
1797438 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
1797490 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1797515 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:1797487 original size:832 final size:824
Alignment explanation
Indices: 1795964--1797621 Score: 3012
Period size: 832 Copynumber: 2.0 Consensus size: 824
1795954 AGTAGCTTAA
1795964 ATTGTATCGATACAAAAAAATATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATA
1 ATTGTATCGATACAAAAAAATATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATA
1796029 CAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCTAACAATGTAT
66 CAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCTAACAATGTAT
* *
1796094 CGATACATTTGGACCAAAATATGATTTTTTCATCATTTTTGCCTTCCATACACCCTGTGTCGACT
131 CGATACATTTGGACCAAAATATGATTTTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACT
*
1796159 AGGGACGATGGGAAATGGATTCGGGCATAACAAAAAGTTATAAAAATCTAAAAAACCATTTTTAT
196 AGGGACGATGGGAAATGGATTCGGGCATAACAAAAAATTATAAAAATCTAAAAAACCA-TTTTAT
1796224 AGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAAATGGAA
260 AGGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAAATGGAA
*
1796289 AGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTAGCTGGCAGAACTCCGGGAGAAGATA
325 AGCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTAGCTGGCAGAACTCAGGGAGAAGATA
*
1796354 GGGGGGCTGGAATTAATGTTTGGCAGCCTTGGCAGCCAATGAACTTGGACCACATGGTTTTGGCA
390 GGGGGGCTGAAATTAATGTTTGGCAGCCTTGGCAGCCAATGAACTTGGACCACATGGTTTTGGCA
1796419 TTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGTGGCAATTGAGATTT
455 TTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGTGGCAATTGAGATTT
1796484 GACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAAGAAAAAGTCCCGAAA
520 GACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAAGAAAAAGTCCCGAAA
1796549 TATAGAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
585 TATAGAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1796614 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGA
650 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGA
* *
1796679 TACAAAGATCAGTGTATCGATACAATGTATCGATACATTTGAGCAATGTATCGATACATTTTTTG
715 TACAAAGATCAGTGTATCGATAAAATGTATCGATACATTCGAGCAATGTATCGATACATTTTTTG
*
1796744 GTAGTAGCTTAAATTGTATCGATACAAAAAAATATGTATCGATAC
780 GCAGTAGCTTAAATTGTATCGATACAAAAAAATATGTATCGATAC
* *** *
1796789 ATTGTATCGATACAACACTTTATGTATCGATACATTGTATCGATACAACACTTTATGTATCGATA
1 ATTGTATCGATACAAAAAAATATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATA
1796854 CAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCTAACAATGTAT
66 CAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCTAACAATGTAT
*
1796919 CGATACATTTGGACCAAAATGTGATTTTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACT
131 CGATACATTTGGACCAAAATATGATTTTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACT
*
1796984 AGGGACGATGGGAAATGGATTCGGGCTTAACAAAAAATTATAAAAATCTAAAAAACCA-TTTATA
196 AGGGACGATGGGAAATGGATTCGGGCATAACAAAAAATTATAAAAATCTAAAAAACCATTTTATA
*
1797048 GGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAAATGGGAA
261 GGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAAATGGAAA
* *
1797113 GCTTGCTTGCTGAGGTAGATGATATCATTGCCTATGGTGGCTGGCAGAACTCAGGGAGAAGATAG
326 GCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTAGCTGGCAGAACTCAGGGAGAAGATAG
*
1797178 GGTGGCTGAAATTAATGTTTGGCAGCCTTGGAAGCCATGGCAGCCAATGAACTTGGACCACATGG
391 GGGGGCTGAAATTAATGTTTGGCAGCC-T--------TGGCAGCCAATGAACTTGGACCACATGG
1797243 TTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGTGGCAAT
447 TTTTGGCATTCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGTGGCAAT
* *
1797308 TGAGATTTGACATGAATCCTGATCACTTATTATGGAAAAAACTTATTTGGTAAAGGAAGAAAAAG
512 TGAGATTTGACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAAGAAAAAG
*
1797373 TCCCGAAATATGGAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
577 TCCCGAAATATAGAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1797438 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCA
642 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCA
1797503 TGTATCGATACAAAGATCAGTGTATCGATAAAATGTATCGATACATTCGAGCAATGTATCGATAC
707 TGTATCGATACAAAGATCAGTGTATCGATAAAATGTATCGATACATTCGAGCAATGTATCGATAC
*
1797568 ATTTTTTGGCAGTAGCTTAAATTGTATCGATACAAAAAAATATGTATTGATAC
772 ATTTTTTGGCAGTAGCTTAAATTGTATCGATACAAAAAAATATGTATCGATAC
1797621 A
1 A
1797622 ACACTTTATG
Statistics
Matches: 801, Mismatches: 23, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
823 157 0.20
824 1 0.00
825 243 0.30
832 400 0.50
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (824 bp):
ATTGTATCGATACAAAAAAATATGTATCGATACATTGTATCGATACAACACTTTATGTATCAATA
CAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTCTAACAATGTAT
CGATACATTTGGACCAAAATATGATTTTTTCATCATTTTTGCCTTCCAAACACCCTATGTCGACT
AGGGACGATGGGAAATGGATTCGGGCATAACAAAAAATTATAAAAATCTAAAAAACCATTTTATA
GGCAAGATTTGTGGTGAAAAAATGAGGGCACTTGAGACATTTCATACTCAAGCATTAAATGGAAA
GCTTGCTGGCTGAGGTAGATGATATCATTGCCTATGGTAGCTGGCAGAACTCAGGGAGAAGATAG
GGGGGCTGAAATTAATGTTTGGCAGCCTTGGCAGCCAATGAACTTGGACCACATGGTTTTGGCAT
TCAATGCCATTCTTTATCTTCAAAAGTGATCAAAATGTGTTTTGACATGTGGCAATTGAGATTTG
ACATGAATCCTGATCACTTATGATGGAAAAAACTTATTTGGCAAAGGAAGAAAAAGTCCCGAAAT
ATAGAAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGAT
ACAAAGATCAGTGTATCGATAAAATGTATCGATACATTCGAGCAATGTATCGATACATTTTTTGG
CAGTAGCTTAAATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1797527 original size:52 final size:51
Alignment explanation
Indices: 1797386--1797532 Score: 224
Period size: 52 Copynumber: 2.8 Consensus size: 51
1797376 CGAAATATGG
1797386 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
1797438 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
*
1797490 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATA
1797533 AAATGTATCG
Statistics
Matches: 88, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:1798349 original size:33 final size:33
Alignment explanation
Indices: 1798312--1798378 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1798302 AGTAGCTTAA
1798312 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1798345 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1798378 A
1 A
1798379 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1798352 original size:13 final size:13
Alignment explanation
Indices: 1798334--1798358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1798324 CAAAAAAATA
1798334 TGTATCGATACAT
1 TGTATCGATACAT
1798347 TGTATCGATACA
1 TGTATCGATACA
1798359 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1799450 original size:48 final size:48
Alignment explanation
Indices: 1799223--1799709 Score: 514
Period size: 48 Copynumber: 10.2 Consensus size: 48
1799213 CTTAGGAATG
* *
1799223 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGAC
1 TTAAAGA-GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
1799272 TTAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGA-G---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
1799324 TT----A-AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC
1 TTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * *
1799367 TTAAAGAAGAAAGTGCCAATATGCTGATTCAAGGCCGGCGACACTGGTC
1 TTAAAG-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
1799416 TTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGC
1 TTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
1799464 TTAAAG-GTGAGGTACCAATGTGCTGATTTAAGGCCAGCTACATTGGAC
1 TTAAAGAG-AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * *
1799512 TTAAAGATGAAGGTGCCAATATGCTGATTCATGGCCAGCGATATTAGAC
1 TTAAAGA-GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* *
1799561 TT----A-AAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGAC
1 TTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* ** *
1799604 TTAAAGATGAA-GTGCCAATGTGCTGATTCAAGGATAGCTACATTGGAC
1 TTAAAGA-GAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
* * * * *
1799652 TTAAAGACAAGGTGCCAATACGCTGATTCAAGGCCAGCTATATTGGGC
1 TTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
1799700 TTAAA-AGAAG
1 TTAAAGAGAAG
1799710 ACGCCACCAA
Statistics
Matches: 367, Mismatches: 52, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
43 77 0.21
45 1 0.00
47 7 0.02
48 157 0.43
49 86 0.23
50 1 0.00
52 38 0.10
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (48 bp):
TTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC
Found at i:1799573 original size:188 final size:189
Alignment explanation
Indices: 1799223--1799705 Score: 559
Period size: 188 Copynumber: 2.5 Consensus size: 189
1799213 CTTAGGAATG
*
1799223 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGG
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG----AGG
* * *
1799288 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT---AAAGGTGCCAATGTGCTGATTCAA
62 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAAAGGTGCCAATATGCTGATTCAA
* * * *
1799350 GGCCAGCGACATTGGGCTTAAAGAAGAAAGTGCCAATATGCTGATTCAAGGCCGGCGACACTGGT
127 GGCCAGCGACATTAGACTT-AAGAAG--AGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGA
1799415 C
189 C
* * * * * *
1799416 TTAAAGA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAGGTACC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* * * *
1799480 AATGTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCATG
66 AATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA-A--AAGGTGCCAATATGCTGATTCAAG
* * * *
1799545 GCCAGCGATATTAGACTT-A-AAG-GTGCCAATATGCTGATTTAAGGCCAGCGATATTGGAC
128 GCCAGCGACATTAGACTTAAGAAGAGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGAC
** * **
1799604 TTAAAGATGAA-GTGCCAATGTGCTGATTCAAGGATAGCTACATTGGACTTAAAGACAAGGTGCC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
* *
1799668 AATACGCTGATTCAAGGCCAGCTATATTGGGCTTAAAA
66 AATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAA
1799706 GAAGACGCCA
Statistics
Matches: 245, Mismatches: 38, Indels: 20
0.81 0.13 0.07
Matches are distributed among these distances:
187 1 0.00
188 149 0.61
189 2 0.01
191 3 0.01
192 46 0.19
193 7 0.03
194 37 0.15
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (189 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAGGTGCC
AATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAAAAGGTGCCAATATGCTGATTCAAGGCC
AGCGACATTAGACTTAAGAAGAGTGCCAATATGCTGATTCAAGGCCAGCGACACTGGAC
Found at i:1799579 original size:140 final size:137
Alignment explanation
Indices: 1799283--1799704 Score: 544
Period size: 140 Copynumber: 3.0 Consensus size: 137
1799273 TAAAGATGAC
*
1799283 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGT--G-CCAATGTGCTGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAGTCCAATGTGCTGA
* * * * *
1799345 TTCAAGGCCAGCGACATTGGGCTTAAAGAAGAAAGTGCCAATATGCTGATTCAAGGCCGGCGACA
66 TTCAAGGCCAGCTACATTGGACTTAAAG-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
* *
1799410 CTGGTCTT
130 TTGGACTT
*
1799418 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAAGGTGAGGTACCAAT
1 ----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGA-GT-CCAAT
* *
1799483 GTGCTGATTTAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCATGGCC
59 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-GAAGGTGCCAATATGCTGATTCAAGGCC
*
1799548 AGCGATATTAGACTT
123 AGCGATATTGGACTT
* *
1799563 AAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTAAAGATGAAGTGCCAATGTGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTG-AGT-CCAATGTGCT
** * * *
1799628 GATTCAAGGATAGCTACATTGGACTTAAAGACAAGGTGCCAATACGCTGATTCAAGGCCAGCTAT
64 GATTCAAGGCCAGCTACATTGGACTTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGAT
*
1799693 ATTGGGCTT
129 ATTGGACTT
1799702 AAA
1 AAA
1799705 AGAAGACGCC
Statistics
Matches: 250, Mismatches: 25, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
139 41 0.16
140 132 0.53
141 2 0.01
143 1 0.00
144 1 0.00
145 73 0.29
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.24
Consensus pattern (137 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAGTCCAATGTGCTGA
TTCAAGGCCAGCTACATTGGACTTAAAGAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
TGGACTT
Found at i:1799781 original size:28 final size:28
Alignment explanation
Indices: 1799724--1800480 Score: 270
Period size: 28 Copynumber: 25.3 Consensus size: 28
1799714 CACCAACTTG
*
1799724 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTT-AAAGG-TTGCCACT-GACT
* * *
1799753 TATGTGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1799781 TGTGGGCTTTTAAAGATTGCTACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
*
1799809 TGTGGGCTTTTAAAGGTTTCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1799837 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
* * * * *
1799867 TGTGGGC-TTAAAAGGAAAAAGAGTGCTACGGAGT
1 TGTGGGCTTTTAAA-G-----G-TTGCCACTGACT
* ** * * *
1799901 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT-TTAAAG-----G-TTGCCACTGACT
* * * *
1799936 TGTGGACTTTGGAAA-ATATGCCACCGACT
1 TGTGGGCTTT-TAAAGGT-TGCCACTGACT
** * *
1799965 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTT--TTAAAGGTTGCCACTGACT
* *
1799995 TGTGGGC-TTTGAAGGTTGCCACTGATT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * * *
1800022 TGTGGACTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
* *
1800051 TATGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1800079 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
* * *
1800109 TGTGGGC-TTAAAAGGAAAAATAGTGCCACGGAGT
1 TGTGGGCTTTTAAAGG-----T--TGCCACTGACT
* * * *
1800143 TGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT-TTAAAG-----G-TTGCCACTGACT
* * * *
1800178 TGTGGACTTTGGAAA-ATATGCCACCGACT
1 TGTGGGCTTT-TAAAGGT-TGCCACTGACT
** * *
1800207 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTT--TTAAAGGTTGCCACTGACT
* *
1800237 TGTGGGC-TTTGAAGGTTGCCACTGATT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * * *
1800264 TGTGGACTTTGAAAAAGATGCCACTGACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
*
1800293 TGTGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* *
1800321 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
* ** * * *
1800351 TCTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGT
1 TGTGGGCTT------TTAAAGGTTGCCACTGACT
* * * *
1800385 TGTGGGCTTTGAAAAAGATGCCACTAACT
1 TGTGGGCTTT-TAAAGGTTGCCACTGACT
*
1800414 TGTGGGCTTTGAAAGGTTGCCACTGACT
1 TGTGGGCTTTTAAAGGTTGCCACTGACT
* * *
1800442 TGTGGGCTTTTGAAAAGGGTGCCATTAACT
1 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1800472 TGTGGGCTT
1 TGTGGGCTT
1800481 AAAAGGAAAA
Statistics
Matches: 560, Mismatches: 114, Indels: 107
0.72 0.15 0.14
Matches are distributed among these distances:
27 53 0.09
28 146 0.26
29 116 0.21
30 127 0.23
33 1 0.00
34 52 0.09
35 53 0.09
36 10 0.02
37 1 0.00
41 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTTAAAGGTTGCCACTGACT
Found at i:1799826 original size:56 final size:57
Alignment explanation
Indices: 1799749--1800480 Score: 368
Period size: 57 Copynumber: 12.2 Consensus size: 57
1799739 GGTTTGCATC
* * * * *
1799749 AACTTATGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTT-AAAGATTGCTACT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTAAAAGAGTGCCACT
* * *
1799805 GACTTGTGGGCTTTTAAAGGTTTCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTT-AAAAGAGTGCCACT
* * * * * * **
1799863 AACTTGTGGGC-TTAAAAGGAAAAAGAGTGCTACGGAGTTGTGAGCTTACAAAAGAAAAAGAGTG
1 AACTTGTGGGCTTTTAAA-G-----G-TTGCCACTGACTTGTGGGCTT------TTAAAAGAGTG
*
1799927 CCACG
53 CCACT
* * * * * * ** *
1799932 GAGTTGTGGACTTTGGAAA-ATATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACT
1 AACTTGTGGGCTTT-TAAAGGT-TGCCACTGACTTGTGGGCTT-TTAAAAGAGTGCCACT
* * * * * *
1799991 GATTTGTGGGC-TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAA-AGATGCCACT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTAAAAGAG-TGCCACT
* * * *
1800047 GACTTATGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTT-AAAAGAGTGCCACT
* * * *
1800105 AACTTGTGGGC-TTAAAAGGAAAAATAGTGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTG
1 AACTTGTGGGCTTTTAAAGG-----T--TGCCACTGACTTGTGGGCTT-T-----TAAAAGAGTG
*
1800169 CCACG
53 CCACT
* * * * * * ** *
1800174 GAGTTGTGGACTTTGGAAA-ATATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACT
1 AACTTGTGGGCTTT-TAAAGGT-TGCCACTGACTTGTGGGCTT-TTAAAAGAGTGCCACT
* * * * * *
1800233 GATTTGTGGGC-TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAA-AGATGCCACT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTAAAAGAG-TGCCACT
* * *
1800289 GACTTGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTT-AAAAGAGTGCCACT
* ** * * * *
1800347 AACTTCTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAA-AGATGCCACT
1 AACTTGTGGGCTT------TTAAAGGTTGCCACTGACTTGTGGGCTTTTAAAAGAG-TGCCACT
* * *
1800410 AACTTGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCATT
1 AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTT-AAAAGAGTGCCACT
1800468 AACTTGTGGGCTT
1 AACTTGTGGGCTT
1800481 AAAAGGAAAA
Statistics
Matches: 516, Mismatches: 108, Indels: 102
0.71 0.15 0.14
Matches are distributed among these distances:
55 2 0.00
56 81 0.16
57 126 0.24
58 92 0.18
59 46 0.09
62 2 0.00
63 24 0.05
64 91 0.18
65 2 0.00
69 40 0.08
70 4 0.01
71 6 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (57 bp):
AACTTGTGGGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTAAAAGAGTGCCACT
Found at i:1799904 original size:34 final size:35
Alignment explanation
Indices: 1799866--1799940 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1799856 TGCCACTAAC
* *
1799866 TTGTGGGCTTA-AAAGGAAAAAGAGTGCTACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
*
1799900 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
1799935 TTGTGG
1 TTGTGG
1799941 ACTTTGGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
34 10 0.28
35 26 0.72
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (35 bp):
TTGTGGGCTTACAAAAGAAAAAGAGTGCCACGGAG
Found at i:1799967 original size:29 final size:29
Alignment explanation
Indices: 1799925--1800544 Score: 326
Period size: 29 Copynumber: 20.7 Consensus size: 29
1799915 AGAAAAAGAG
* * *
1799925 TGCCACGGAGTTGTGGACTTTGGAAAATA
1 TGCCACTGACTTGTGGGCTTTGGAAAATA
* * **
1799954 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-TA
* **
1799984 TGCCACTGATTTGTGGGCTTT-GAAGGT-
1 TGCCACTGACTTGTGGGCTTTGGAAAATA
* * * *
1800011 TGCCACTGATTTGTGGACTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAATA
* *
1800040 TGCCACTGACTTATGGGCTTT-GAAAGGT-
1 TGCCACTGACTTGTGGGCTTTGGAAA-ATA
* **
1800068 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-TA
* *
1800098 TGCCACTAACTTGTGGGCTTAAAAGGAAAAATA
1 TGCCACTGACTTGTGGGCTT---TGG-AAAATA
* * * *
1800131 GTGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGA
1 -TGCCACTGACTTGTGGGCTT-T----GGAAAATA
* * *
1800166 GTGCCACGGAGTTGTGGACTTTGGAAAATA
1 -TGCCACTGACTTGTGGGCTTTGGAAAATA
* * **
1800196 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-TA
* **
1800226 TGCCACTGATTTGTGGGCTTT-GAAGGT-
1 TGCCACTGACTTGTGGGCTTTGGAAAATA
* * * *
1800253 TGCCACTGATTTGTGGACTTTGAAAAAGA
1 TGCCACTGACTTGTGGGCTTTGGAAAATA
*
1800282 TGCCACTGACTTGTGGGCTTT-GAAAGGT-
1 TGCCACTGACTTGTGGGCTTTGGAAA-ATA
* **
1800310 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-TA
* * *
1800340 TGCCACTAACTTCTGGGCTTAAAAGGAAAA-A
1 TGCCACTGACTTGTGGGCTT---TGGAAAATA
* * * *
1800371 GGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA
1 ---TGCCACTGACTTGTGGGCTTTGGAAAATA
* *
1800403 TGCCACTAACTTGTGGGCTTT-GAAAGGT-
1 TGCCACTGACTTGTGGGCTTTGGAAA-ATA
* **
1800431 TGCCACTGACTTGTGGGCTTTTGAAAAGGG
1 TGCCACTGACTTGTGGGCTTTGGAAAA-TA
* * * *
1800461 TGCCATTAACTTGTGGGCTTAAAAGGAAAAAGA
1 TGCCACTGACTTGTGGGCTT---TGG-AAAATA
* * * *
1800494 GTGCCACGGAGTTGTGGGCTTTGAAAAAGA
1 -TGCCACTGACTTGTGGGCTTTGGAAAATA
1800524 TGCCACTGACTTGTGGGCTTT
1 TGCCACTGACTTGTGGGCTTT
1800545 TGAAGGGTGA
Statistics
Matches: 455, Mismatches: 97, Indels: 78
0.72 0.15 0.12
Matches are distributed among these distances:
27 40 0.09
28 74 0.16
29 138 0.30
30 103 0.23
31 6 0.01
32 2 0.00
33 8 0.02
34 58 0.13
35 25 0.05
36 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.31, T:0.28
Consensus pattern (29 bp):
TGCCACTGACTTGTGGGCTTTGGAAAATA
Found at i:1800135 original size:34 final size:35
Alignment explanation
Indices: 1800091--1800182 Score: 105
Period size: 35 Copynumber: 2.7 Consensus size: 35
1800081 TGGGCTTTTG
* * *
1800091 AAAAGGGTGCCACTAACTTGTGGGCTTA-AAAGGA
1 AAAAGAGTGCCACGAACTTGTGGGCTTATAAAAGA
* * *
1800125 AAAATAGTGCCACGGAGTTGTGGGCTTATAAAAGA
1 AAAAGAGTGCCACGAACTTGTGGGCTTATAAAAGA
* *
1800160 AAAAGAGTGCCACGGAGTTGTGG
1 AAAAGAGTGCCACGAACTTGTGG
1800183 ACTTTGGAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 23 0.46
35 27 0.54
ACGTcount: A:0.35, C:0.13, G:0.32, T:0.21
Consensus pattern (35 bp):
AAAAGAGTGCCACGAACTTGTGGGCTTATAAAAGA
Found at i:1800160 original size:242 final size:242
Alignment explanation
Indices: 1799761--1800544 Score: 1149
Period size: 242 Copynumber: 3.2 Consensus size: 242
1799751 CTTATGTGCT
* * * * *
1799761 TTTGAAGGTTGCCACTGACTTGTGGGCTTT--TAAAGATTGCTACTGACTTGTGGGCTTTTAAAG
1 TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAGA-TGCCACTGACTTGTGGGCTTTGAAAG
*
1799824 GTTTCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGA
65 GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGA
* * *
1799889 GTGCTACGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATA
130 GTGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATA
1799954 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC
195 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC
*
1800002 TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTATGGGCTTTGAAAGG
1 TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGG
*
1800067 TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAATAG
66 TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAG
1800132 TGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATAT
131 TGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATAT
1800197 GCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC
196 GCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC
1800244 TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGG
1 TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGG
* *
1800309 TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTCTGGGCTTAAAAGGAAAAAGGG
66 TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAG
** * * *
1800374 TGCCACGGAGTTGTGGGCTT-T----GAAAAAGA-TGCCACTAACTTGTGGGCTTT-GAAAGGT-
131 TGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAA-ATA
* ** * * *
1800431 TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCATTAACTTGTGGGC
195 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC
* * * *
1800479 TTAAAAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCT
1 TT----TG---AAG-GTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCT
1800543 TT
58 TT
1800545 TGAAGGGTGA
Statistics
Matches: 502, Mismatches: 30, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
235 48 0.10
236 18 0.04
237 8 0.02
239 1 0.00
241 29 0.06
242 392 0.78
243 6 0.01
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (242 bp):
TTTGAAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGG
TTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAGAG
TGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAATAT
GCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGC
Found at i:1800169 original size:35 final size:34
Alignment explanation
Indices: 1800108--1800182 Score: 123
Period size: 35 Copynumber: 2.2 Consensus size: 34
1800098 TGCCACTAAC
* *
1800108 TTGTGGGCTTAAAAGGAAAAATAGTGCCACGGAG
1 TTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAG
1800142 TTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTTA-AAAAGAAAAAGAGTGCCACGGAG
1800177 TTGTGG
1 TTGTGG
1800183 ACTTTGGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 11 0.29
35 27 0.71
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.23
Consensus pattern (34 bp):
TTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAG
Found at i:1800420 original size:121 final size:121
Alignment explanation
Indices: 1799765--1800544 Score: 867
Period size: 121 Copynumber: 6.5 Consensus size: 121
1799755 TGTGCTTTTG
* * * * * * *
1799765 AAGGTTGCCACTGACTTGTGGGCTTT--TAAAGATTGCTACTGACTTGTGGGCTTTTAAAGGTTT
1 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGA-TGCCACTGACTTGTGGGCTTTGAAAGGTTG
1799828 CCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
65 CCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
* * * * * * *
1799885 AAGAGTGCTACGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAA
1 AAGGGTGCCACGGAGTTGTGGGCTT-----TGAAAAAGA-TGCCACTGACTTGTGGGCTTT-GAA
* * ** * * *
1799950 A-ATATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTT----TG---
59 AGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
* * * * *
1800006 AAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTATGGGCTTTGAAAGGTTGC
1 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGC
1800071 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
66 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
** * * *
1800127 AATAGTGCCACGGAGTTGTGGGCTTATAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAA
1 AAGGGTGCCACGGAGTTGTGGGCTT-T----GAAAAAGA-TGCCACTGACTTGTGGGCTTT-GAA
* * ** * * *
1800192 A-ATATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTT----TG---
59 AGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
* * * *
1800248 AAGGTTGCCACTGATTTGTGGACTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGC
1 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGC
*
1800313 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTCTGGGCTTAAAAGGAAA
66 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
*
1800369 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTAACTTGTGGGCTTTGAAAGGTTGC
1 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGC
*
1800434 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCATTAACTTGTGGGCTTAAAAGGAAA
66 CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
*
1800490 AAGAGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTT
1 AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTT
1800545 TGAAGGGTGA
Statistics
Matches: 543, Mismatches: 84, Indels: 65
0.78 0.12 0.09
Matches are distributed among these distances:
114 97 0.18
115 37 0.07
116 16 0.03
118 2 0.00
120 20 0.04
121 223 0.41
122 1 0.00
124 2 0.00
126 8 0.01
127 41 0.08
128 96 0.18
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (121 bp):
AAGGGTGCCACGGAGTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTTTGAAAGGTTGC
CACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAA
Found at i:1801989 original size:15 final size:14
Alignment explanation
Indices: 1801971--1802050 Score: 85
Period size: 14 Copynumber: 5.8 Consensus size: 14
1801961 TCCGGACCCT
1801971 TTTTGTTGTTGTTTG
1 TTTTGTT-TTGTTTG
*
1801986 TTTTGTTTT-TTGTT
1 TTTTGTTTTGTT-TG
1802000 TTTTGTTTT-TTTG
1 TTTTGTTTTGTTTG
* *
1802013 TTTTTTTTTGTTTT
1 TTTTGTTTTGTTTG
1802027 TTTTGTTTTGTTT-
1 TTTTGTTTTGTTTG
*
1802040 TTTTTTTTTGT
1 TTTTGTTTTGT
1802051 GGAGGACGCC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
13 21 0.37
14 29 0.51
15 7 0.12
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (14 bp):
TTTTGTTTTGTTTG
Found at i:1802001 original size:27 final size:26
Alignment explanation
Indices: 1801971--1802047 Score: 97
Period size: 25 Copynumber: 3.0 Consensus size: 26
1801961 TCCGGACCCT
*
1801971 TTTTGTTGTTGTTTGTTTTGTTTTTTG
1 TTTT-TTGTTGTTTGTTTTTTTTTTTG
1801998 TTTTTTGTT-TTT-TTGTTTTTTTTTG
1 TTTTTTGTTGTTTGTT-TTTTTTTTTG
1802023 TTTTTT-TTGTTTTGTTTTTTTTTTT
1 TTTTTTGTTG-TTTGTTTTTTTTTTT
1802048 TGTGGAGGAC
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
24 4 0.09
25 18 0.40
26 17 0.38
27 6 0.13
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (26 bp):
TTTTTTGTTGTTTGTTTTTTTTTTTG
Found at i:1802002 original size:1 final size:1
Alignment explanation
Indices: 1801986--1802048 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
1801976 TTGTTGTTTG
* * * * * * *
1801986 TTTTGTTTTTTGTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTTGTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1802049 GTGGAGGACG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:1802004 original size:19 final size:19
Alignment explanation
Indices: 1801976--1802050 Score: 84
Period size: 19 Copynumber: 3.9 Consensus size: 19
1801966 ACCCTTTTTG
*
1801976 TTGTTGTTTGTTTTGTT-TT
1 TTGTTTTTTGTTTT-TTGTT
1801995 TTGTTTTTTGTTTTTTTGTT
1 TTGTTTTTTG-TTTTTTGTT
*
1802015 TT-TTTTTGTTTTTTTTGTT
1 TTGTTTTT-TGTTTTTTGTT
1802034 TTGTTTTTT-TTTTTTGT
1 TTGTTTTTTGTTTTTTGT
1802051 GGAGGACGCC
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
18 8 0.16
19 28 0.56
20 14 0.28
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (19 bp):
TTGTTTTTTGTTTTTTGTT
Found at i:1802005 original size:14 final size:13
Alignment explanation
Indices: 1801982--1802050 Score: 88
Period size: 13 Copynumber: 5.4 Consensus size: 13
1801972 TTTGTTGTTG
*
1801982 TTTG-TTTTGTTT
1 TTTGTTTTTTTTT
*
1801994 TTTGTTTTTTGTT
1 TTTGTTTTTTTTT
*
1802007 TTT-TTGTTTTTT
1 TTTGTTTTTTTTT
1802019 TTTGTTTTTTTTGT
1 TTTGTTTTTTTT-T
1802033 TTTGTTTTTTTTT
1 TTTGTTTTTTTTT
1802046 TTTGT
1 TTTGT
1802051 GGAGGACGCC
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
12 14 0.29
13 22 0.45
14 13 0.27
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (13 bp):
TTTGTTTTTTTTT
Found at i:1802048 original size:27 final size:27
Alignment explanation
Indices: 1801970--1802051 Score: 105
Period size: 27 Copynumber: 3.0 Consensus size: 27
1801960 ATCCGGACCC
1801970 TTTTTGTTGTTGTTTGTTTTGTTTTT-TGT
1 TTTTTGTT-TTGTTT-TTTT-TTTTTGTGT
*
1801999 TTTTTGTTTT-TTTGTTTTTTTTTGTTT
1 TTTTTGTTTTGTTT-TTTTTTTTTGTGT
1802026 TTTTTGTTTTGTTTTTTTTTTTTGTG
1 TTTTTGTTTTGTTTTTTTTTTTTGTG
1802052 GAGGACGCCT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.10
27 31 0.63
28 5 0.10
29 8 0.16
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (27 bp):
TTTTTGTTTTGTTTTTTTTTTTTGTGT
Found at i:1802050 original size:37 final size:37
Alignment explanation
Indices: 1801971--1802048 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
1801961 TCCGGACCCT
1801971 TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTTT
1 TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTTT
* * *
1802008 TTTTGTTTTTTTTTGTTTTTTTTGTTTTGTTTTTT-TTT
1 TTTTGTTGTTGTTTG-TTTTGTT-TTTTGTTTTTTGTTT
1802046 TTT
1 TTT
1802049 GTGGAGGACG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 13 0.36
38 12 0.33
39 11 0.31
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (37 bp):
TTTTGTTGTTGTTTGTTTTGTTTTTTGTTTTTTGTTT
Found at i:1803978 original size:19 final size:19
Alignment explanation
Indices: 1803954--1804021 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
1803944 AATTCAACAA
1803954 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1803973 TTTGTATCGATGC--AA--
1 TTTGTATCGATACATAAGT
1803988 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1804005 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1804022 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1804079 original size:13 final size:13
Alignment explanation
Indices: 1804061--1804086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1804051 CATTTTTCTG
1804061 TGTATCGATACAT
1 TGTATCGATACAT
1804074 TGTATCGATACAT
1 TGTATCGATACAT
1804087 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1804083 original size:33 final size:33
Alignment explanation
Indices: 1804041--1804107 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1804031 GCCAAGAAAA
***
1804041 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1804074 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1804107 T
1 T
1804108 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1806523 original size:51 final size:48
Alignment explanation
Indices: 1806455--1806571 Score: 130
Period size: 51 Copynumber: 2.4 Consensus size: 48
1806445 AATTCTCCGC
* * *
1806455 AATCGGGGATA-TCCCAACTCCGATTTCATTT-TCAAAACACTGATTTTCTAT
1 AATCAGGGATACT-CCAACTCCGATTTCATTTCT-AAAACA-TCAATTT-T-T
*
1806506 AATCAGGGATACTCCAACTCCGATTTTATTTCTAAAACATCAATTTTT
1 AATCAGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTT
*
1806554 CATCAGGGATACTCCAAC
1 AATCAGGGATACTCCAAC
1806572 CCCGTTAATC
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
48 18 0.31
49 1 0.02
50 5 0.08
51 33 0.56
52 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (48 bp):
AATCAGGGATACTCCAACTCCGATTTCATTTCTAAAACATCAATTTTT
Found at i:1806590 original size:27 final size:27
Alignment explanation
Indices: 1806553--1806629 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
1806543 CATCAATTTT
1806553 TCATCAGGGATACTCCAACCCCGTTAA
1 TCATCAGGGATACTCCAACCCCGTTAA
*
1806580 TCATTAGGGATACTCCAACCCCGTT-A
1 TCATCAGGGATACTCCAACCCCGTTAA
**
1806606 TTTTCGAGAGGATACTCCAACCCC
1 TCATC-AG-GGATACTCCAACCCC
1806630 CGGCTTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
26 3 0.07
27 26 0.59
28 15 0.34
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.25
Consensus pattern (27 bp):
TCATCAGGGATACTCCAACCCCGTTAA
Found at i:1806782 original size:79 final size:78
Alignment explanation
Indices: 1806586--1806819 Score: 283
Period size: 79 Copynumber: 2.9 Consensus size: 78
1806576 TTAATCATTA
* *
1806586 GGGATACTCCAACCCCGTTATTTTCGAGAGGATACTCCAACCCCCGGCTTTATTTCTAAAATATT
1 GGGATACTCCAACCCCGTTATTTTCGAG-GGATACTCCAA-CCCCGGCTTTATTCCCAAAATATT
1806651 AATTTCTCATAATCG
64 AATTTCTCATAATCG
* * * *
1806666 GGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCTCGGCTTTATTCCCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTTCGA-GGGATACTCCAACCCCGGCTTTATTCCCAAAATATTA
*
1806731 ATTTCTCATAATTG
65 ATTTCTCATAATCG
* * * * *
1806745 GGGATACTCCAGCCCCGTTATTTTCAAGGGAACACTCCAA-CCCTGTTATTA-TCTCCAAAATAT
1 GGGATACTCCAACCCCGTTATTTTCGAGGG-ATACTCCAACCCCGGCT-TTATTC-CCAAAATAT
1806808 TAAATTTCTCAT
63 T-AATTTCTCAT
1806820 TGGGAAATAT
Statistics
Matches: 133, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
78 9 0.07
79 78 0.59
80 45 0.34
81 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTTCGAGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTAA
TTTCTCATAATCG
Found at i:1816788 original size:13 final size:13
Alignment explanation
Indices: 1816770--1816795 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1816760 ACAGCAAGTC
1816770 ATGTATCGATACA
1 ATGTATCGATACA
1816783 ATGTATCGATACA
1 ATGTATCGATACA
1816796 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2072413 original size:20 final size:20
Alignment explanation
Indices: 2072390--2072462 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
2072380 ACAATTCAAA
2072390 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2072410 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
*
2072431 GTACCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2072451 GTATCGATACAT
1 GTATCGATACAT
2072463 AAAAAAGATG
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2072438 original size:21 final size:21
Alignment explanation
Indices: 2072408--2072483 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2072398 ACATGTTGCA
2072408 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
* ****
2072429 ATGTACCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2072449 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
2072470 ATGTATCGATACAT
1 ATGTATCGATACAT
2072484 TTCTTGGCAG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2072445 original size:41 final size:41
Alignment explanation
Indices: 2072394--2072483 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
2072384 TTCAAAGTAT
*
2072394 CGATACATGTTGCAATGTATCGATACATGAAAAAGATGTAC
1 CGATACATGTTGCAATGTATCGATACATAAAAAAGATGTAC
*
2072435 CGATACATGTTGCAATGTATCGATACATAAAAAAGATGTAT
1 CGATACATGTTGCAATGTATCGATACATAAAAAAGATGTAC
2072476 CGATACAT
1 CGATACAT
2072484 TTCTTGGCAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (41 bp):
CGATACATGTTGCAATGTATCGATACATAAAAAAGATGTAC
Found at i:2072540 original size:13 final size:13
Alignment explanation
Indices: 2072522--2072547 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2072512 TACAGCAAGT
2072522 ATGTATCGATACA
1 ATGTATCGATACA
2072535 ATGTATCGATACA
1 ATGTATCGATACA
2072548 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2076613 original size:13 final size:13
Alignment explanation
Indices: 2076595--2076620 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2076585 ACATTTTGGG
2076595 ATGTATCGATACA
1 ATGTATCGATACA
2076608 ATGTATCGATACA
1 ATGTATCGATACA
2076621 TAATGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2076615 original size:33 final size:32
Alignment explanation
Indices: 2076573--2076640 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
2076563 CGTTACAAGC
**
2076573 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATAATGGG-TGTATCGATA
*
2076606 CAATGTATCGATACATAATGTGTGTATCGATA
1 CAATGTATCGATACATAATGGGTGTATCGATA
2076638 CAA
1 CAA
2076641 ACAGTTAAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (32 bp):
CAATGTATCGATACATAATGGGTGTATCGATA
Found at i:2076739 original size:13 final size:13
Alignment explanation
Indices: 2076721--2076745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2076711 ACATTTGGTC
2076721 ATGTATCGATACA
1 ATGTATCGATACA
2076734 ATGTATCGATAC
1 ATGTATCGATAC
2076746 TGTGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2082505 original size:13 final size:13
Alignment explanation
Indices: 2082487--2082511 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2082477 ACATTTGGTC
2082487 ATGTATCGATACA
1 ATGTATCGATACA
2082500 ATGTATCGATAC
1 ATGTATCGATAC
2082512 TATGCAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2084650 original size:12 final size:12
Alignment explanation
Indices: 2084633--2084663 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
2084623 TCCTTTGTAC
2084633 AAAAAAAAACAA
1 AAAAAAAAACAA
2084645 AAAAAAAAACAA
1 AAAAAAAAACAA
2084657 AAAAAAA
1 AAAAAAA
2084664 GGGTCCAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:2085979 original size:28 final size:28
Alignment explanation
Indices: 2085944--2086382 Score: 404
Period size: 28 Copynumber: 15.5 Consensus size: 28
2085934 CGACCTTTTC
* *
2085944 CAAAGCCCACATGTTAGTGGCATCCTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
* *
2085972 CAAAGCCCACATGTCAATGGCATCCTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
*
2086000 CAAAGCCCACATGTCTA-TGGCATCCTTT
1 CAAAGCCCACAAGTC-AGTGGCATCCTTT
* *
2086028 CAAAGCCTACATGTCTA-TGGCATCCTTT
1 CAAAGCCCACAAGTC-AGTGGCATCCTTT
*
2086056 CAAAGCCCACATGTCAGTGGCA-CCTTTT
1 CAAAGCCCACAAGTCAGTGGCATCC-TTT
* *
2086084 CAAAGTCCACAAGTCAGTGGAATCCTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
** * *
2086112 CTTAGCCCACAAGTCAATGGAATCCTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
* * * *
2086140 CAAAGCCAACATGTTAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
*
2086168 CAAAGCCCACAAGTCAGTGGCACCCTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
* *
2086196 -TAAGCCCACACAAGTCAGTGGCACCCTTT
1 CAAAG-CC-CACAAGTCAGTGGCATCCTTT
* *
2086225 CGAAGCCCACAAG-CTAGTGGCACCCTTT
1 CAAAGCCCACAAGTC-AGTGGCATCCTTT
* **
2086253 CGAAGCCCACAAGTCAGTGGCATAATTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
** * * *
2086281 TGAAGCCTACAAGTTAGTGGCACCCTTT
1 CAAAGCCCACAAGTCAGTGGCATCCTTT
* *
2086309 CGAAA-CCTACAAATCAGTGGCATCCTTT
1 C-AAAGCCCACAAGTCAGTGGCATCCTTT
* * * *
2086337 TAAAGCCCACAAGTTAGTAGCAACCTTCT
1 CAAAGCCCACAAGTCAGTGGCATCCTT-T
2086366 CTAAAGCTCACACAAGT
1 C-AAAGC-C-CACAAGT
2086383 TGGTGGCAAC
Statistics
Matches: 349, Mismatches: 47, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
27 10 0.03
28 293 0.84
29 30 0.09
30 8 0.02
31 1 0.00
32 7 0.02
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCATCCTTT
Found at i:2086381 original size:32 final size:31
Alignment explanation
Indices: 2086337--2086398 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2086327 GGCATCCTTT
2086337 TAAAGCCCACAAGTTAGTAGCAA-CCTTCTC
1 TAAAGCCCACAAGTTAGTAGCAACCCTTCTC
* *
2086367 TAAAGCTCACACAAGTTGGTGGCAACCCTTCT
1 TAAAGC-C-CACAAGTTAGTAGCAACCCTTCT
2086399 AAACCCAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 6 0.22
31 1 0.04
32 14 0.52
33 6 0.22
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (31 bp):
TAAAGCCCACAAGTTAGTAGCAACCCTTCTC
Found at i:2087112 original size:20 final size:20
Alignment explanation
Indices: 2087087--2087202 Score: 85
Period size: 20 Copynumber: 5.9 Consensus size: 20
2087077 TTTTTCTCCA
2087087 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
*
2087107 AATGTATCGATACATTATGTC
1 AATGTATCGATACATT-TTTC
* * ** *
2087128 -TTTTA-C-CCAGATTTTTC
1 AATGTATCGATACATTTTTC
* *** *
2087145 AATGTATCAATACATGAATG
1 AATGTATCGATACATTTTTC
* *
2087165 AATGTATCGATACAATCTTC
1 AATGTATCGATACATTTTTC
2087185 AATGTATCGATACATTTT
1 AATGTATCGATACATTTT
2087203 GTCTTTTTAC
Statistics
Matches: 68, Mismatches: 24, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
17 3 0.04
18 7 0.10
19 2 0.03
20 53 0.78
21 3 0.04
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:2092605 original size:22 final size:22
Alignment explanation
Indices: 2092579--2092623 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2092569 CGAAATTGTT
2092579 AAATTATTTGATTAAGGGGGAG
1 AAATTATTTGATTAAGGGGGAG
*
2092601 AAATTTTTTGATTAAGGGGGAG
1 AAATTATTTGATTAAGGGGGAG
2092623 A
1 A
2092624 GAAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (22 bp):
AAATTATTTGATTAAGGGGGAG
Found at i:2093321 original size:13 final size:13
Alignment explanation
Indices: 2093303--2093328 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2093293 ACACCCAATA
2093303 TGTATCGATACAT
1 TGTATCGATACAT
2093316 TGTATCGATACAT
1 TGTATCGATACAT
2093329 CCAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.