Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 5 of 228
Found at i:1642686 original size:21 final size:21
Alignment explanation
Indices: 1642660--1642700 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1642650 ATCTGCTCAA
* *
1642660 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1642681 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1642701 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1652497 original size:2 final size:2
Alignment explanation
Indices: 1652490--1652522 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1652480 AATTACATTT
1652490 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1652523 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1655484 original size:22 final size:22
Alignment explanation
Indices: 1655458--1655507 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
1655448 AAGAAAATTG
1655458 TTATTTATTCTCATTATTATTA
1 TTATTTATTCTCATTATTATTA
* * * *
1655480 TTATTAATTTTTATTATTATTT
1 TTATTTATTCTCATTATTATTA
1655502 TTATTT
1 TTATTT
1655508 TTATATTCAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (22 bp):
TTATTTATTCTCATTATTATTA
Found at i:1655493 original size:13 final size:12
Alignment explanation
Indices: 1655470--1655511 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1655460 ATTTATTCTC
*
1655470 ATTATTATTATT
1 ATTATTTTTATT
1655482 ATTAATTTTTATT
1 ATT-ATTTTTATT
1655495 ATTATTTTTATT
1 ATTATTTTTATT
*
1655507 TTTAT
1 ATTAT
1655512 ATTCATGCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
ATTATTTTTATT
Found at i:1655493 original size:19 final size:18
Alignment explanation
Indices: 1655471--1655511 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
1655461 TTTATTCTCA
1655471 TTATTATTATTATTAATTT
1 TTATTATTATT-TTAATTT
*
1655490 TTATTATTATTTTTATTT
1 TTATTATTATTTTAATTT
1655508 TTAT
1 TTAT
1655512 ATTCATGCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTATTATTTTAATTT
Found at i:1656381 original size:98 final size:98
Alignment explanation
Indices: 1656273--1656469 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
1656263 TTAAAAATAA
* * * * *
1656273 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATTGTGTCCTAACATATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGGCCTAACATATTGGGTGTGATTTC
*
1656338 TTAAATTTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
1656371 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGGCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGGCCTAACATATTGGGTGTGATTTC
1656436 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
1656469 T
1 T
1656470 TTTATTGTAC
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGGCCTAACATATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:1660519 original size:12 final size:12
Alignment explanation
Indices: 1660498--1660533 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
1660488 TTCAGATTCA
1660498 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
1660510 AAAAACAAAAAC
1 AAAAAAAAAAAC
1660522 AAAAAAACAAAA
1 AAAAAAA-AAAA
1660534 AATGAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1660519 original size:14 final size:14
Alignment explanation
Indices: 1660496--1660534 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1660486 AGTTCAGATT
1660496 CAAAAAAA-AAAAA
1 CAAAAAAACAAAAA
1660509 C--AAAAACAAAAA
1 CAAAAAAACAAAAA
1660521 CAAAAAAACAAAAA
1 CAAAAAAACAAAAA
1660535 ATGAAAGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 5 0.22
12 6 0.26
13 1 0.04
14 11 0.48
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAACAAAAA
Found at i:1660525 original size:20 final size:19
Alignment explanation
Indices: 1660496--1660534 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1660486 AGTTCAGATT
1660496 CAAAAAAAAAAAACAAAAA
1 CAAAAAAAAAAAACAAAAA
1660515 CAAAAACAAAAAAACAAAAA
1 CAAAAA-AAAAAAACAAAAA
1660535 ATGAAAGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAACAAAAA
Found at i:1660942 original size:54 final size:54
Alignment explanation
Indices: 1660860--1660972 Score: 226
Period size: 54 Copynumber: 2.1 Consensus size: 54
1660850 TTTTTTATTA
1660860 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1660914 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1 AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
1660968 AATTT
1 AATTT
1660973 CTTTGTTATC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.45
Consensus pattern (54 bp):
AATTTGTTATTTTTTGGAATACCTCATTCTTTTCCAAGATATACATTCCCAATC
Found at i:1662250 original size:84 final size:86
Alignment explanation
Indices: 1662038--1662276 Score: 247
Period size: 84 Copynumber: 2.8 Consensus size: 86
1662028 GTCTTTTCCT
* *
1662038 CCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTTATCTC-CCTGAAGTTGCAGAGGAGC
1 CCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTTATCTCTCCTGAAGTTGCAGA-GAGC
*
1662102 AGATTAAAGCCGATAATCCTATCTC
63 AGATT-AAGCAGATAATCCTATCTC
* * * *
1662127 CCTGAAGTTGCAGTGGAGCGGATTAA-AACCTCAGATCTTATCTCTCC-GAAGTTGCAGAGAGCA
1 CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCTTATCTCTCCTGAAGTTGCAGAGAGCA
* ** * *
1662190 GA-T-CGCATCTAGTCTTATCTC
64 GATTAAGCAGATAATCCTATCTC
*
1662211 CCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTGCAGTGAGGCA
1 CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTTATCTCTCCTGAAGTTGCAGAGA-GCA
1662275 GA
64 GA
1662277 CTAAAGATTT
Statistics
Matches: 126, Mismatches: 17, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
83 4 0.03
84 55 0.44
85 7 0.06
86 5 0.04
87 10 0.08
88 22 0.17
89 23 0.18
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.25
Consensus pattern (86 bp):
CCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTTATCTCTCCTGAAGTTGCAGAGAGCAGA
TTAAGCAGATAATCCTATCTC
Found at i:1662259 original size:44 final size:43
Alignment explanation
Indices: 1661988--1662280 Score: 221
Period size: 44 Copynumber: 6.7 Consensus size: 43
1661978 AGCAGATCCC
*
1661988 ATCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATAGCAAGTCTT
1 ATCCTCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTT
* * *
1662033 TTCCTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGGCAAGTCTT
1 ATCCTCCTGAAGTTGCAGTGGAGCAGACT-AAGA-AGCAAGTCTT
* * * *
1662078 AT-CTCCCTGAAGTTGCAGAGGAGCAGA-TTA-AAGCCGATAATCCT
1 ATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A-AGTCTT
* * * *
1662122 AT-CTCCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTCAGATCTT
1 ATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCTT
* * * * *
1662166 ATCTCTCC-GAAGTTGCAG-AGAGCAGA-T-CGCATCTAGTCTT
1 ATC-CTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTT
1662206 AT-CTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTT
1 ATCCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCTT
1662250 ATCCTCCTGAAGTTGCAGT-GAGGCAGACTAA
1 ATCCTCCTGAAGTTGCAGTGGA-GCAGACTAA
1662281 AGATTTCAGA
Statistics
Matches: 203, Mismatches: 28, Indels: 35
0.76 0.11 0.13
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 16 0.08
41 10 0.05
42 6 0.03
43 12 0.06
44 81 0.40
45 72 0.35
46 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (43 bp):
ATCCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCTT
Found at i:1663701 original size:3 final size:3
Alignment explanation
Indices: 1663687--1663748 Score: 88
Period size: 3 Copynumber: 20.3 Consensus size: 3
1663677 AAATTGTTAT
* *
1663687 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA GTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
*
1663733 TTA TTA TTA TTT TTA T
1 TTA TTA TTA TTA TTA T
1663749 ATTCATGCGC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
3 50 0.96
4 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1664021 original size:28 final size:27
Alignment explanation
Indices: 1663967--1664027 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
1663957 TATATATTTT
* *
1663967 TATATTTTTCTTATGTTCATAAGTGTA
1 TATATTTTTCTTATATTCATAAATGTA
*
1663994 T-TATTTTTTTTATATTCATATTAATGTA
1 TATATTTTTCTTATATTCATA--AATGTA
1664022 TATATT
1 TATATT
1664028 ATGTGCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 17 0.61
27 1 0.04
28 6 0.21
29 4 0.14
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.61
Consensus pattern (27 bp):
TATATTTTTCTTATATTCATAAATGTA
Found at i:1664223 original size:15 final size:15
Alignment explanation
Indices: 1664200--1664232 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1664190 GTGATATGTC
1664200 ATTGATGTATTTATT
1 ATTGATGTATTTATT
*
1664215 ATTGTTGTATTTATT
1 ATTGATGTATTTATT
1664230 ATT
1 ATT
1664233 ATAGCATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (15 bp):
ATTGATGTATTTATT
Found at i:1664623 original size:98 final size:98
Alignment explanation
Indices: 1664506--1664699 Score: 334
Period size: 98 Copynumber: 2.0 Consensus size: 98
1664496 TTAAAAATAA
* * * *
1664506 TAAAGGAAATATTCTGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACATATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
1664571 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
* *
1664604 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGGCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
1664669 TTAAATCTTGGATAAGTGGATGTTCTTTTAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAA
1664700 TGTTTTACTG
Statistics
Matches: 90, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGAGATTCTAAAGGAATCGTGCCCTAACATATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:1669733 original size:11 final size:11
Alignment explanation
Indices: 1669717--1669744 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1669707 TGTGTGTTCA
1669717 TCTTCTCAATT
1 TCTTCTCAATT
1669728 TCTTCTCAATT
1 TCTTCTCAATT
1669739 TCTTCT
1 TCTTCT
1669745 GCTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (11 bp):
TCTTCTCAATT
Found at i:1671406 original size:20 final size:21
Alignment explanation
Indices: 1671374--1671412 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1671364 TGGTTTTGGA
1671374 AAATAAATAATTA-GTTTTAT
1 AAATAAATAATTATGTTTTAT
1671394 AAATAGAAT-ATTATGTTTT
1 AAATA-AATAATTATGTTTT
1671413 TAATTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (21 bp):
AAATAAATAATTATGTTTTAT
Found at i:1672683 original size:37 final size:37
Alignment explanation
Indices: 1672642--1672716 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
1672632 AGAAAACATG
*
1672642 AGAAATACAATAAAAAGATTGGAATTATGCAGAATAA
1 AGAAAAACAATAAAAAGATTGGAATTATGCAGAATAA
1672679 AGAAAAACAATAAAAAGATTGGAATTATGCAGAATAA
1 AGAAAAACAATAAAAAGATTGGAATTATGCAGAATAA
1672716 A
1 A
1672717 CTTTGTAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (37 bp):
AGAAAAACAATAAAAAGATTGGAATTATGCAGAATAA
Found at i:1675367 original size:40 final size:40
Alignment explanation
Indices: 1675312--1675391 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
1675302 AAGATTGGAA
1675312 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
1 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
1675352 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
1 TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
1675392 CCTGAGTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (40 bp):
TTATGCACAATAAACTTTGTAACCTTGTTTATTATCTTGT
Found at i:1696237 original size:13 final size:13
Alignment explanation
Indices: 1696219--1696243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1696209 TTATAAACAA
1696219 AGAATACCTCTTT
1 AGAATACCTCTTT
1696232 AGAATACCTCTT
1 AGAATACCTCTT
1696244 AAAGACTAAT
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:0.24, G:0.08, T:0.36
Consensus pattern (13 bp):
AGAATACCTCTTT
Found at i:1696768 original size:18 final size:17
Alignment explanation
Indices: 1696720--1696768 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1696710 GTGTCGTTCG
1696720 TTTCCAAAACATTACTCA
1 TTTCC-AAACATTACTCA
* *
1696738 TTTACAAATCATTATTCAA
1 TTTCCAAA-CATTACTC-A
1696757 TTTCCAAACATT
1 TTTCCAAACATT
1696769 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.12
18 15 0.58
19 8 0.31
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTCCAAACATTACTCA
Found at i:1700548 original size:16 final size:16
Alignment explanation
Indices: 1700529--1700575 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1700519 AATTTAGCCA
1700529 TTTATTTTTATTTCA-T
1 TTTATTTTT-TTTCAGT
1700545 TTTATTTTTCTTTTCAGT
1 TTTA-TTTT-TTTTCAGT
*
1700563 TTAATTTTTTTTC
1 TTTATTTTTTTTC
1700576 TAATTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 9 0.33
17 13 0.48
18 5 0.19
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTTTCAGT
Found at i:1700559 original size:17 final size:16
Alignment explanation
Indices: 1700529--1700575 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1700519 AATTTAGCCA
* *
1700529 TTTATTTTTATTTCAT
1 TTTATTTTTTTTTCAG
1700545 TTTATTTTTCTTTTCAG
1 TTTATTTTT-TTTTCAG
*
1700562 TTTAATTTTTTTTC
1 TTTATTTTTTTTTC
1700576 TAATTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTATTTTTTTTTCAG
Found at i:1706966 original size:12 final size:12
Alignment explanation
Indices: 1706949--1706973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1706939 CGCCAACTTG
1706949 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1706961 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1706973 T
1 T
1706974 GGTTTTGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGTTCTTGCTT
Found at i:1717307 original size:21 final size:21
Alignment explanation
Indices: 1717281--1717321 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1717271 ATCTGCTCAA
* *
1717281 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
1717302 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
1717322 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:1739929 original size:15 final size:14
Alignment explanation
Indices: 1739904--1739936 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1739894 GTGGGTTACA
1739904 TTTTTCCTTTTTTT
1 TTTTTCCTTTTTTT
1739918 TCTTTT-CTTTTTTT
1 T-TTTTCCTTTTTTT
1739932 TTTTT
1 TTTTT
1739937 TAACATGGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.22
14 10 0.56
15 4 0.22
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (14 bp):
TTTTTCCTTTTTTT
Found at i:1742235 original size:22 final size:21
Alignment explanation
Indices: 1742187--1742236 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1742177 CCACAAAAAT
* *
1742187 ACAAATTTATATATATATATA
1 ACAAATTTATAAACATATATA
*
1742208 ATCAAATTTATAAACATTTTATA
1 A-CAAATTTATAAACA-TATATA
1742231 ACAAAT
1 ACAAAT
1742237 AGATTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 17 0.71
23 6 0.25
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (21 bp):
ACAAATTTATAAACATATATA
Found at i:1752532 original size:32 final size:35
Alignment explanation
Indices: 1752493--1752584 Score: 118
Period size: 32 Copynumber: 2.6 Consensus size: 35
1752483 CCTATATAAA
1752493 AAATAGTTTGATACCCTGTGCATTTGG-ATA-TAT
1 AAATAGTTTGATACCCTGTGCATTTGGTATATTAT
*
1752526 -AATAGTTTGATACCTTGTGCAATTTGGTTATATTAT
1 AAATAGTTTGATACCCTGTGC-ATTTGG-TATATTAT
*
1752562 AAACTAGTTCGATACCCTGTGCA
1 AAA-TAGTTTGATACCCTGTGCA
1752585 CTGCTCAGAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
32 19 0.38
33 6 0.12
35 3 0.06
36 3 0.06
37 3 0.06
38 16 0.32
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (35 bp):
AAATAGTTTGATACCCTGTGCATTTGGTATATTAT
Found at i:1753012 original size:22 final size:22
Alignment explanation
Indices: 1752987--1753054 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 22
1752977 TTGACAATAT
*
1752987 AATATGCTTTATTACTGCACAC
1 AATATGCTTTATTAATGCACAC
* *
1753009 AATA--C-TTATAAAATCCACAC
1 AATATGCTTTAT-TAATGCACAC
*
1753029 AATATGCTTTATTATTGCACATC
1 AATATGCTTTATTAATGCACA-C
1753052 AAT
1 AAT
1753055 GGATTTTATT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
19 4 0.11
20 12 0.34
22 11 0.31
23 8 0.23
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (22 bp):
AATATGCTTTATTAATGCACAC
Found at i:1754972 original size:21 final size:21
Alignment explanation
Indices: 1754948--1754991 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1754938 AGTACTCGAT
1754948 TCAAACAACTCATGACCCTAA
1 TCAAACAACTCATGACCCTAA
* ***
1754969 TCAAGCTTTTCATGACCCTAA
1 TCAAACAACTCATGACCCTAA
1754990 TC
1 TC
1754992 TTGAGTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.32, G:0.07, T:0.27
Consensus pattern (21 bp):
TCAAACAACTCATGACCCTAA
Found at i:1756687 original size:23 final size:23
Alignment explanation
Indices: 1756657--1756704 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1756647 CTAAGCCTAT
1756657 TTAAAGGGGTCATTATATCACTG
1 TTAAAGGGGTCATTATATCACTG
1756680 TTAAAGGGGTCATTATATCACTG
1 TTAAAGGGGTCATTATATCACTG
1756703 TT
1 TT
1756705 TAGTTATGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (23 bp):
TTAAAGGGGTCATTATATCACTG
Found at i:1757495 original size:15 final size:15
Alignment explanation
Indices: 1757475--1757509 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1757465 ATGTGCTTAA
1757475 TTCAGTGGAGCTGTT
1 TTCAGTGGAGCTGTT
1757490 TTCAGTGGAGCTGTT
1 TTCAGTGGAGCTGTT
1757505 TTCAG
1 TTCAG
1757510 GATCCACACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (15 bp):
TTCAGTGGAGCTGTT
Found at i:1757977 original size:535 final size:535
Alignment explanation
Indices: 1756962--1758020 Score: 1969
Period size: 535 Copynumber: 2.0 Consensus size: 535
1756952 CGGATAAAAA
1756962 GAGCTATTTTCAGGATCCACACGGCCTGGGGCCAGGGCATTTCCACATGGGCTGGCCACACGCCC
1 GAGCTATTTTCAGGATCCACACGGCCTGGGGCCAGGGCATTTCCACATGGGCTGGCCACACGCCC
*
1757027 ATGTGCCAGCCCATGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
66 ATGTGCCAGCCCATGTCAATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
*
1757092 CTTTTTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGAAGAA
131 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGAAGAA
1757157 GAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
196 GAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
1757222 GAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTAAC
261 GAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTAAC
*
1757287 TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
326 TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACCTA
*
1757352 AGATGAATCTTATTATTTGATTTTTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
391 AGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
1757417 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAGTG
456 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAGTG
1757482 GAGCTGTTTTCAGTG
521 GAGCTGTTTTCAGTG
*
1757497 GAGCTGTTTTCAGGATCCACACGGCCTGGGGCCTA-GGCATTTCCACATGGGCTGGCCACACGCC
1 GAGCTATTTTCAGGATCCACACGGCCTGGGGCC-AGGGCATTTCCACATGGGCTGGCCACACGCC
* *
1757561 CATGTGCCAGCCCGTGTCAATTTCGCACCCTGATTCCCAAACACGTAGAAAAACTCAATTTTTAG
65 CATGTGCCAGCCCATGTCAATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAG
*
1757626 GCTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGC-AGAG
130 GCTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGA-AG
* * *
1757690 AAGAACGAAGAAAATACTCGAAGAACGCCATCGAATTCAACTCAGAAGCGAATCTCCTCCAAGAT
194 AAGAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGAT
*
1757755 TGGAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTA
259 TGGAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTA
1757820 ACTTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACC
324 ACTTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACC
1757885 TAAGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTA
389 TAAGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTA
*
1757950 TGTATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAG
454 TGTATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAG
1758015 TGGAGC
519 TGGAGC
1758021 AAAAGTCCCT
Statistics
Matches: 509, Mismatches: 13, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
534 1 0.00
535 507 1.00
536 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (535 bp):
GAGCTATTTTCAGGATCCACACGGCCTGGGGCCAGGGCATTTCCACATGGGCTGGCCACACGCCC
ATGTGCCAGCCCATGTCAATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACACGAAGAA
GAACAAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
GAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGATGTTATCCTAAC
TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAAGGAAGATGAAACCTA
AGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTAATTCAGTG
GAGCTGTTTTCAGTG
Found at i:1765253 original size:10 final size:11
Alignment explanation
Indices: 1765205--1765252 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
1765195 ATAAATACCA
1765205 AAAAATTATTTT
1 AAAAA-TATTTT
* **
1765217 AAAAA-AATAA
1 AAAAATATTTT
1765227 AAAAATATTTT
1 AAAAATATTTT
1765238 AAAAATATTTT
1 AAAAATATTTT
1765249 AAAA
1 AAAA
1765253 TTTAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
10 7 0.24
11 17 0.59
12 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1777027 original size:13 final size:13
Alignment explanation
Indices: 1776994--1777027 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1776984 AATTATAAAC
*
1776994 ACATGTACTTTTT
1 ACATGTATTTTTT
*
1777007 GCATGTATTTTTT
1 ACATGTATTTTTT
1777020 ACATGTAT
1 ACATGTAT
1777028 ACTTAAACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (13 bp):
ACATGTATTTTTT
Found at i:1778494 original size:31 final size:32
Alignment explanation
Indices: 1778435--1778494 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1778425 TCCGAAATCA
*
1778435 AAATTGAACCAAACCTTAAATAACTTGAATTC
1 AAATTGAACCAAACCTAAAATAACTTGAATTC
*
1778467 AAATTG-ACCATAACC-AAAATGACTTGAA
1 AAATTGAACCA-AACCTAAAATAACTTGAA
1778495 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.25
Consensus pattern (32 bp):
AAATTGAACCAAACCTAAAATAACTTGAATTC
Found at i:1780170 original size:27 final size:30
Alignment explanation
Indices: 1780140--1780212 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
1780130 GCTAGGCTTT
1780140 TTAAA-AAAAA-TTT-AACAGCTCAATGAC
1 TTAAATAAAAACTTTAAACAGCTCAATGAC
* *
1780167 TTAAATAAAAACTTTTAAATAGTTCAATGAC
1 TTAAATAAAAAC-TTTAAACAGCTCAATGAC
**
1780198 TTAAATGGAAACTTT
1 TTAAATAAAAACTTT
1780213 CGAATAGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
27 5 0.13
28 5 0.13
30 6 0.16
31 22 0.58
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (30 bp):
TTAAATAAAAACTTTAAACAGCTCAATGAC
Found at i:1780194 original size:31 final size:31
Alignment explanation
Indices: 1780159--1780221 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1780149 ATTTAACAGC
*
1780159 TCAATGACTTAAATAAAAACTTTTAAATAGT
1 TCAATGACTTAAATAAAAACTTTCAAATAGT
** *
1780190 TCAATGACTTAAATGGAAACTTTCGAATAGT
1 TCAATGACTTAAATAAAAACTTTCAAATAGT
1780221 T
1 T
1780222 TAGTGACCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (31 bp):
TCAATGACTTAAATAAAAACTTTCAAATAGT
Found at i:1781236 original size:40 final size:39
Alignment explanation
Indices: 1781163--1781280 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 39
1781153 ACTGTTCATG
1781163 CCACGTCAGCAAATCGCGTCCTAGA-G-GGA-GCGATTTCCTT
1 CCACGTCAGCAAATCGCG--CT-GACGTGGACGCGATTTCC-T
1781203 CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
1 CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
* * * *
1781242 GCGCGT-ACCCTGACATCGCGCTGACGTGGACGCGATTTC
1 CCACGTCA-GC--AAATCGCGCTGACGTGGACGCGATTTC
1781281 GCGGAAAATG
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
37 2 0.03
38 4 0.06
39 9 0.13
40 27 0.40
41 26 0.38
ACGTcount: A:0.19, C:0.32, G:0.27, T:0.21
Consensus pattern (39 bp):
CCACGTCAGCAAATCGCGCTGACGTGGACGCGATTTCCT
Found at i:1790808 original size:15 final size:15
Alignment explanation
Indices: 1790788--1790819 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1790778 TTTTGGTATT
1790788 TGAGTTTGATTTTAA
1 TGAGTTTGATTTTAA
1790803 TGAGTTTGATTTTAA
1 TGAGTTTGATTTTAA
1790818 TG
1 TG
1790820 TATAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (15 bp):
TGAGTTTGATTTTAA
Found at i:1792420 original size:8 final size:7
Alignment explanation
Indices: 1792393--1792418 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1792383 GAAATTTTCT
1792393 TTAAATC
1 TTAAATC
1792400 TTAAATC
1 TTAAATC
1792407 TTAAATC
1 TTAAATC
1792414 TTAAA
1 TTAAA
1792419 ATTATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAATC
Found at i:1794204 original size:16 final size:17
Alignment explanation
Indices: 1794185--1794227 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1794175 AAGATATATT
* *
1794185 ATTTTAAATTTGACTC-
1 ATTTTAAATTCGAATCA
1794201 ATTTTAAAATTCGAATCA
1 ATTTT-AAATTCGAATCA
1794219 ATTTTAAAT
1 ATTTTAAAT
1794228 ATCAATCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 5 0.22
17 13 0.57
18 5 0.22
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (17 bp):
ATTTTAAATTCGAATCA
Found at i:1814897 original size:23 final size:23
Alignment explanation
Indices: 1814871--1814935 Score: 112
Period size: 23 Copynumber: 2.8 Consensus size: 23
1814861 GATTTTTTCC
*
1814871 AAATATTATCACTAAATAATTTT
1 AAATATTATCACTAAATAATTCT
*
1814894 AAATATTATCACTAAATAGTTCT
1 AAATATTATCACTAAATAATTCT
1814917 AAATATTATCACTAAATAA
1 AAATATTATCACTAAATAA
1814936 CTAAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATATTATCACTAAATAATTCT
Found at i:1814911 original size:13 final size:13
Alignment explanation
Indices: 1814871--1814934 Score: 61
Period size: 13 Copynumber: 5.4 Consensus size: 13
1814861 GATTTTTTCC
1814871 AAATATTATCACT
1 AAATATTATCACT
1814884 AAATAATT-T---T
1 AAAT-ATTATCACT
1814894 AAATATTATCACT
1 AAATATTATCACT
*
1814907 AAATAGT-T--CT
1 AAATATTATCACT
1814917 AAATATTATCACT
1 AAATATTATCACT
1814930 AAATA
1 AAATA
1814935 ACTAAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 16
0.69 0.03 0.27
Matches are distributed among these distances:
9 3 0.07
10 14 0.34
11 1 0.02
12 1 0.02
13 19 0.46
14 3 0.07
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (13 bp):
AAATATTATCACT
Found at i:1822073 original size:17 final size:18
Alignment explanation
Indices: 1822051--1822084 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1822041 TTTTGATATT
1822051 TGAACAA-AAAAAAAATA
1 TGAACAATAAAAAAAATA
*
1822068 TGAACAATAAATAAAAT
1 TGAACAATAAAAAAAAT
1822085 TTTACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (18 bp):
TGAACAATAAAAAAAATA
Found at i:1825419 original size:31 final size:31
Alignment explanation
Indices: 1825376--1825434 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1825366 TAAATTACAT
1825376 TGAACTATTCGAAAGCTTTCATTTAAGTCAC
1 TGAACTATTCGAAAGCTTTCATTTAAGTCAC
* *
1825407 TGAATTATTCGAAAGCTTTTATTTAAGT
1 TGAACTATTCGAAAGCTTTCATTTAAGT
1825435 AATTGAGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (31 bp):
TGAACTATTCGAAAGCTTTCATTTAAGTCAC
Found at i:1829334 original size:15 final size:15
Alignment explanation
Indices: 1829314--1829346 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1829304 TTCACCTAAA
1829314 TTTTTA-ATAAATTAT
1 TTTTTACATAAATT-T
1829329 TTTTTACATAAATTT
1 TTTTTACATAAATTT
1829344 TTT
1 TTT
1829347 CATCTACACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTTACATAAATTT
Found at i:1838648 original size:24 final size:24
Alignment explanation
Indices: 1838614--1838660 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1838604 TTTACAATTA
*
1838614 TTTTTATATTAAGATTTTAATTTT
1 TTTTTAAATTAAGATTTTAATTTT
*
1838638 TTTTTAAATTAAGTTTTTAATTT
1 TTTTTAAATTAAGATTTTAATTT
1838661 GATAATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTTTAAATTAAGATTTTAATTTT
Found at i:1848163 original size:27 final size:26
Alignment explanation
Indices: 1848133--1848185 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1848123 ATATTTTTCA
1848133 ATTTTCAAAAAATAGAAAATAAAAACT
1 ATTTTCAAAAAAT-GAAAATAAAAACT
** *
1848160 ATTTTCTGAAAATGAAAATGAAAACT
1 ATTTTCAAAAAATGAAAATAAAAACT
1848186 GATAACATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.28
Consensus pattern (26 bp):
ATTTTCAAAAAATGAAAATAAAAACT
Found at i:1848249 original size:13 final size:13
Alignment explanation
Indices: 1848231--1848255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1848221 TTTTAAAAAT
1848231 ATTTTCTATTTTA
1 ATTTTCTATTTTA
1848244 ATTTTCTATTTT
1 ATTTTCTATTTT
1848256 TTAAAATTGA
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:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTCTATTTTA
Found at i:1857328 original size:21 final size:20
Alignment explanation
Indices: 1857304--1857343 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1857294 CATTTCAAAC
1857304 TTTAGTCACTTCAAC-TTTAAG
1 TTTAGTC-CTT-AACGTTTAAG
1857325 TTTAGTCCTTAACGTTTAA
1 TTTAGTCCTTAACGTTTAA
1857344 TGAATGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 8 0.44
21 7 0.39
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTAGTCCTTAACGTTTAAG
Found at i:1861437 original size:54 final size:54
Alignment explanation
Indices: 1861377--1861527 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 54
1861367 AAATTGTACA
*
1861377 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGGA-TATGAT-
1 GCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAAATGGACTATG-TG
* ** *
1861431 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCG-ATTGACTATGTAGCACTAAGTGTGCGAAATGGACTATGTG
* *
1861486 GCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCGA
1861528 GTTGATTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 42 0.50
55 42 0.50
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAAATGGACTATGTG
Found at i:1861544 original size:82 final size:82
Alignment explanation
Indices: 1861373--1861555 Score: 210
Period size: 82 Copynumber: 2.2 Consensus size: 82
1861363 GATTAAATTG
* * *
1861373 TACAGCACTAAGTGTGCGA-TTCGACTATGTTGCACTAAGTGTGCGAAATGGATATGATGCACTA
1 TACAGCACTAAGTGTGCGAGATCGACTATGTGGCACTAAGTGTGCGAAATGGATACGATGCACTA
1861437 AGTGTGCGAATTGACCA
66 AGTGTGCGAATTGACCA
* * * * *
1861454 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCG-ATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGAGATCGACTATGTGGCACTAAGTGTGCGAAATGGA-TACGAT-GCAC
* **
1861517 TAAGTGTGCGAGTTGATTA
64 TAAGTGTGCGAATTGACCA
* *
1861536 TATAGCACTGAGTGTGCGAG
1 TACAGCACTAAGTGTGCGAG
1861556 CTCAATAAAT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 22 0.26
82 62 0.74
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (82 bp):
TACAGCACTAAGTGTGCGAGATCGACTATGTGGCACTAAGTGTGCGAAATGGATACGATGCACTA
AGTGTGCGAATTGACCA
Found at i:1861555 original size:27 final size:27
Alignment explanation
Indices: 1861376--1861555 Score: 159
Period size: 27 Copynumber: 6.6 Consensus size: 27
1861366 TAAATTGTAC
*
1861376 AGCACTAAGTGTGCGA-TTCGACTATGT
1 AGCACTAAGTGTGCGAGTT-GATTATGT
* * *
1861403 TGCACTAAGTGTGCGAAATGGA-TATG-
1 AGCACTAAGTGTGCG-AGTTGATTATGT
* ** *
1861429 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
1861457 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
* * *
1861485 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
1861512 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
1861539 AGCACTGAGTGTGCGAG
1 AGCACTAAGTGTGCGAG
1861556 CTCAATAAAT
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
26 5 0.04
27 96 0.75
28 26 0.20
29 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:1869175 original size:54 final size:54
Alignment explanation
Indices: 1869115--1869265 Score: 189
Period size: 54 Copynumber: 2.8 Consensus size: 54
1869105 AAATTGTACA
*
1869115 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGGA-TATGAT-
1 GCACTAAGTGTGCGATT-GACTATGTAGCACTAAGTGTGCGAAATGGACTATG-TG
* ** *
1869169 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCG-ATTGACTATGTAGCACTAAGTGTGCGAAATGGACTATGTG
* *
1869224 GCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA-TTGACTATGTAGCACTAAGTGTGCGA
1869266 GTTGATTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
54 42 0.50
55 42 0.50
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTGACTATGTAGCACTAAGTGTGCGAAATGGACTATGTG
Found at i:1869282 original size:82 final size:82
Alignment explanation
Indices: 1869111--1869293 Score: 210
Period size: 82 Copynumber: 2.2 Consensus size: 82
1869101 GATTAAATTG
* * *
1869111 TACAGCACTAAGTGTGCGA-TTCGACTATGTTGCACTAAGTGTGCGAAATGGATATGATGCACTA
1 TACAGCACTAAGTGTGCGAGATCGACTATGTGGCACTAAGTGTGCGAAATGGATACGATGCACTA
1869175 AGTGTGCGAATTGACCA
66 AGTGTGCGAATTGACCA
* * * * *
1869192 TGCGGCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCG-ATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGAGATCGACTATGTGGCACTAAGTGTGCGAAATGGA-TACGAT-GCAC
* **
1869255 TAAGTGTGCGAGTTGATTA
64 TAAGTGTGCGAATTGACCA
* *
1869274 TATAGCACTGAGTGTGCGAG
1 TACAGCACTAAGTGTGCGAG
1869294 CTCAATAAAT
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
81 22 0.26
82 62 0.74
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (82 bp):
TACAGCACTAAGTGTGCGAGATCGACTATGTGGCACTAAGTGTGCGAAATGGATACGATGCACTA
AGTGTGCGAATTGACCA
Found at i:1869293 original size:27 final size:27
Alignment explanation
Indices: 1869114--1869293 Score: 159
Period size: 27 Copynumber: 6.6 Consensus size: 27
1869104 TAAATTGTAC
*
1869114 AGCACTAAGTGTGCGA-TTCGACTATGT
1 AGCACTAAGTGTGCGAGTT-GATTATGT
* * *
1869141 TGCACTAAGTGTGCGAAATGGA-TATG-
1 AGCACTAAGTGTGCG-AGTTGATTATGT
* ** *
1869167 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGAGTTGATTATGT
* * *
1869195 GGCACTAAGTGTGCGAGATGGACTATGT
1 AGCACTAAGTGTGCGAG-TTGATTATGT
* * *
1869223 GGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
1869250 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGATTATGT
*
1869277 AGCACTGAGTGTGCGAG
1 AGCACTAAGTGTGCGAG
1869294 CTCAATAAAT
Statistics
Matches: 128, Mismatches: 19, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
26 5 0.04
27 96 0.75
28 26 0.20
29 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGATTATGT
Found at i:1874348 original size:22 final size:23
Alignment explanation
Indices: 1874323--1874369 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1874313 AAGAAATTGT
*
1874323 AAAATTTTATAAAAT-CATAAAA
1 AAAATATTATAAAATGCATAAAA
*
1874345 AAAATATTATAAAATGCATCAAA
1 AAAATATTATAAAATGCATAAAA
1874368 AA
1 AA
1874370 GGTGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.64, C:0.06, G:0.02, T:0.28
Consensus pattern (23 bp):
AAAATATTATAAAATGCATAAAA
Found at i:1874566 original size:19 final size:19
Alignment explanation
Indices: 1874521--1874572 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
1874511 AAAAATTATA
1874521 ATTTTTATAAATTTCTTTAC
1 ATTTTT-TAAATTTCTTTAC
** *
1874541 AAATTTTATATTTCTTTAC
1 ATTTTTTAAATTTCTTTAC
*
1874560 ATTTTTTTAATTT
1 ATTTTTTAAATTT
1874573 TCTCACAACT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 21 0.84
20 4 0.16
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTTTAAATTTCTTTAC
Found at i:1876648 original size:15 final size:16
Alignment explanation
Indices: 1876623--1876655 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1876613 TCGATTCCCA
*
1876623 AAGATTTTATTGGTTT
1 AAGATTTTATTAGTTT
1876639 AAGA-TTTATTAGTTT
1 AAGATTTTATTAGTTT
1876654 AA
1 AA
1876656 CATACGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
AAGATTTTATTAGTTT
Found at i:1878369 original size:20 final size:20
Alignment explanation
Indices: 1878344--1878408 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
1878334 AGCTTAAGTT
1878344 AAATTAATGTTGCATTAATC
1 AAATTAATGTTGCATTAATC
**** *
1878364 AAATTAATCAAACAGT--T-
1 AAATTAATGTTGCATTAATC
1878381 AAATTAATGTTGCATTAATC
1 AAATTAATGTTGCATTAATC
1878401 AAATTAAT
1 AAATTAAT
1878409 CAAACGATTA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
17 11 0.34
18 1 0.03
19 1 0.03
20 19 0.59
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (20 bp):
AAATTAATGTTGCATTAATC
Found at i:1878390 original size:37 final size:37
Alignment explanation
Indices: 1878340--1878413 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
1878330 GTTTAGCTTA
1878340 AGTTAAATTAATGTTGCATTAATCAAATTAATCAAAC
1 AGTTAAATTAATGTTGCATTAATCAAATTAATCAAAC
1878377 AGTTAAATTAATGTTGCATTAATCAAATTAATCAAAC
1 AGTTAAATTAATGTTGCATTAATCAAATTAATCAAAC
1878414 GATTAATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (37 bp):
AGTTAAATTAATGTTGCATTAATCAAATTAATCAAAC
Found at i:1879773 original size:23 final size:21
Alignment explanation
Indices: 1879735--1879776 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1879725 TAAATTTTAA
1879735 TTATTATTAAATTAAATATAT
1 TTATTATTAAATTAAATATAT
*
1879756 TTATTAATTTAATGTAAATAT
1 TTATT-ATTAAAT-TAAATAT
1879777 TTTTTGTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATTATTAAATTAAATATAT
Found at i:1879872 original size:19 final size:20
Alignment explanation
Indices: 1879839--1879878 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1879829 TTTATTTTAA
*
1879839 TTTAATATTATAATTTACTT
1 TTTAATATTAAAATTTACTT
*
1879859 TTTAATA-TAAAATTTTCTT
1 TTTAATATTAAAATTTACTT
1879878 T
1 T
1879879 ATTTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAATATTAAAATTTACTT
Found at i:1886217 original size:16 final size:17
Alignment explanation
Indices: 1886191--1886224 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1886181 CATTTCACGA
1886191 ATAATGGGATTCTTTTT
1 ATAATGGGATTCTTTTT
*
1886208 ATAA-GGGATTTTTTTT
1 ATAATGGGATTCTTTTT
1886224 A
1 A
1886225 ACGTTCTACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (17 bp):
ATAATGGGATTCTTTTT
Found at i:1886540 original size:21 final size:21
Alignment explanation
Indices: 1886497--1886571 Score: 62
Period size: 21 Copynumber: 3.4 Consensus size: 21
1886487 TATACTTGAG
*
1886497 TTTTATTAGATTTTTATTATTATA
1 TTTTATTA-A-TTTAATT-TTATA
1886521 TTTTATTAATTTAATTTTATA
1 TTTTATTAATTTAATTTTATA
* * *
1886542 TTGTGATT-ATTCAATTATATA
1 TT-TTATTAATTTAATTTTATA
1886563 TTTTTATTA
1 -TTTTATTA
1886572 TCTCAAGTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
21 22 0.51
22 12 0.28
23 1 0.02
24 8 0.19
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTATTAATTTAATTTTATA
Found at i:1907179 original size:24 final size:24
Alignment explanation
Indices: 1907147--1907195 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1907137 TTAAATCATC
1907147 TTCATCTCCATCCTATTGACTTTG
1 TTCATCTCCATCCTATTGACTTTG
1907171 TTCATCTCCATCCTATTGACTTTG
1 TTCATCTCCATCCTATTGACTTTG
1907195 T
1 T
1907196 CACTTTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.16, C:0.29, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCATCTCCATCCTATTGACTTTG
Found at i:1914028 original size:96 final size:96
Alignment explanation
Indices: 1913864--1914056 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
1913854 ATTAACTTGA
*
1913864 ATTCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACTCAGAACATGGAGGA
1 ATTCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGA
*
1913929 ACTCGAAATGATCCAAACATATAATGATTCG
66 ACTCAAAATGATCCAAACATATAATGATTCG
1913960 ATTCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGA
1 ATTCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGA
1914025 ACTCAAAATGATCCAAACATATAATGATTCG
66 ACTCAAAATGATCCAAACATATAATGATTCG
1914056 A
1 A
1914057 CTTGAATAAT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (96 bp):
ATTCAAAATGATCCGAATATGAAATAATCTTAACAAGTAACTCGAAATACCCAGAACATGGAGGA
ACTCAAAATGATCCAAACATATAATGATTCG
Found at i:1919179 original size:87 final size:88
Alignment explanation
Indices: 1919074--1919248 Score: 235
Period size: 87 Copynumber: 2.0 Consensus size: 88
1919064 ACTAAACAAG
* * * * *
1919074 TTGTTGTTGAACGTTAAAATATTAGCAACAACTTTAAAATGTTG-GTATGTAATTTACTTTCATG
1 TTGTTGTTAAACGTTAAAATATTAACAACAACCTTAAAATGTTGTGTATGTAATCTAATTTCATG
* *
1919138 CTTATTCGTTGCAATGGCACGAT
66 CTTATTCATTGCAATGACACGAT
* * * *
1919161 TTGTTGTTAAATGTTAAAATATTAACAACCACCTTAAAATGTTGTTTATGTAATCTAATTTTATG
1 TTGTTGTTAAACGTTAAAATATTAACAACAACCTTAAAATGTTGTGTATGTAATCTAATTTCATG
*
1919226 CTTGTTCATTGCAATGACACGAT
66 CTTATTCATTGCAATGACACGAT
1919249 CTGCACGTTG
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
87 39 0.52
88 36 0.48
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (88 bp):
TTGTTGTTAAACGTTAAAATATTAACAACAACCTTAAAATGTTGTGTATGTAATCTAATTTCATG
CTTATTCATTGCAATGACACGAT
Found at i:1921122 original size:12 final size:12
Alignment explanation
Indices: 1921105--1921133 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1921095 AACAAATAAT
1921105 ATATATACATAC
1 ATATATACATAC
1921117 ATATATACATAC
1 ATATATACATAC
1921129 ATATA
1 ATATA
1921134 CATGTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATATACATAC
Found at i:1921153 original size:10 final size:10
Alignment explanation
Indices: 1921103--1921153 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
1921093 ATAACAAATA
1921103 ATATATATAC
1 ATATATATAC
1921113 ATACATATATAC
1 AT--ATATATAC
*
1921125 ATACATATAC
1 ATATATATAC
* *
1921135 ATGTTTATAC
1 ATATATATAC
1921145 ATATATATA
1 ATATATATA
1921154 TGGATCTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 23 0.70
12 10 0.30
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (10 bp):
ATATATATAC
Found at i:1932142 original size:3 final size:3
Alignment explanation
Indices: 1932134--1932182 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
1932124 TCGCTTGCTT
1932134 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1932182 A
1 A
1932183 TCTTTGAGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1936434 original size:19 final size:19
Alignment explanation
Indices: 1936410--1936466 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
1936400 ATTTTTTTCC
1936410 TTAAATTTATATTATTGAA
1 TTAAATTTATATTATTGAA
* *
1936429 TTAAATTTCACATT-TTGTA
1 TTAAATTT-ATATTATTGAA
*
1936448 CT--ATTTATATTATTGAA
1 TTAAATTTATATTATTGAA
1936465 TT
1 TT
1936467 GTTTAATCAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
19 13 0.43
20 4 0.13
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
TTAAATTTATATTATTGAA
Found at i:1938335 original size:10 final size:9
Alignment explanation
Indices: 1938312--1938338 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1938302 TTTTATTCTT
1938312 GTTTTTACA
1 GTTTTTACA
1938321 GTTTTTACA
1 GTTTTTACA
1938330 GTTTTTACA
1 GTTTTTACA
1938339 AAATCAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GTTTTTACA
Found at i:1943652 original size:13 final size:13
Alignment explanation
Indices: 1943634--1943658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1943624 TTAATGTTTA
1943634 ATATTTTAAATAT
1 ATATTTTAAATAT
1943647 ATATTTTAAATA
1 ATATTTTAAATA
1943659 AGTTGGTTAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:1944419 original size:20 final size:20
Alignment explanation
Indices: 1944384--1944424 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1944374 GGTCCTAGGT
* *
1944384 TTTTATTTAGATAAAATAAA
1 TTTTATTTAGAAAAAAAAAA
*
1944404 TTTTATTTTGAAAAAAAAAA
1 TTTTATTTAGAAAAAAAAAA
1944424 T
1 T
1944425 CACGAACATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTATTTAGAAAAAAAAAA
Found at i:1966781 original size:18 final size:18
Alignment explanation
Indices: 1966758--1966799 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1966748 CATTAATACA
*
1966758 AGAACCTGAAACAGAACC
1 AGAACCGGAAACAGAACC
* *
1966776 AGAACCGGAAGCCGAACC
1 AGAACCGGAAACAGAACC
1966794 AGAACC
1 AGAACC
1966800 AGAGCATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.31, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAACCGGAAACAGAACC
Found at i:1966896 original size:3 final size:3
Alignment explanation
Indices: 1966888--1966929 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1966878 GTCACCCTTT
1966888 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1966930 AAATCACTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1968884 original size:33 final size:33
Alignment explanation
Indices: 1968837--1968910 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 33
1968827 GGGTTTATGG
* *
1968837 CTAACCCTCTTAAGAACATCATCTCCATAGATA
1 CTAAACCTCTTAAGAACATCATCTCCACAGATA
1968870 CTAAACCTCTTAAGAACATCATCTCCACAGATA
1 CTAAACCTCTTAAGAACATCATCTCCACAGATA
1968903 CTAAACCT
1 CTAAACCT
1968911 TTATCATGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.38, C:0.31, G:0.05, T:0.26
Consensus pattern (33 bp):
CTAAACCTCTTAAGAACATCATCTCCACAGATA
Found at i:1970807 original size:21 final size:21
Alignment explanation
Indices: 1970768--1970807 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1970758 TACTACTTTA
1970768 ATATAAATTTTTAACTTTTTT
1 ATATAAATTTTTAACTTTTTT
*
1970789 ATATATATTCTTTAA-TTTT
1 ATATAAATT-TTTAACTTTT
1970808 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATAAATTTTTAACTTTTTT
Found at i:1972841 original size:26 final size:28
Alignment explanation
Indices: 1972805--1972857 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1972795 TCACAAGTTC
1972805 AGTTCTAATGTATATTTT-TC-TCGAAG
1 AGTTCTAATGTATATTTTCTCTTCGAAG
*
1972831 AGTTTTAATGTATATTTTCTCTTCGAA
1 AGTTCTAATGTATATTTTCTCTTCGAA
1972858 TTTGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.71
27 2 0.08
28 5 0.21
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (28 bp):
AGTTCTAATGTATATTTTCTCTTCGAAG
Found at i:1974068 original size:213 final size:215
Alignment explanation
Indices: 1973687--1974153 Score: 688
Period size: 213 Copynumber: 2.2 Consensus size: 215
1973677 TTGTGCTCTC
* * *
1973687 TTTTTTGTAAATTGGGGTTCTTGAGATGAA-GCTGCTTTCTGATTTGTTTTTGTTGGTTTCTTAT
1 TTTTTTGTGAATTGGGGTTCTTGAGAT-AATGCTGCTTTCTCATTTGTTTTTATTGGTTTCTTAT
* * * ** *
1973751 TGTATATATATTGGGGATGTTTAGTTCTTCTAGGACCTAGGTTAATGCTTATTTCATGTTTATCC
65 TATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTATTTCATGTTTATCC
*
1973816 TGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAGTCCAA
130 TGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAATCCAA
* *
1973881 TTTGTGCTGGTTTTTACTCCA
195 TTTGTGCTGGCTTTTAATCCA
* * *
1973902 -TTTTTGTGAATT-GGGTTCTTGAGATAATGGTGTTTTTTCATTTGTTTTTATTGGTTTCTTATT
1 TTTTTTGTGAATTGGGGTTCTTGAGATAATGCTGCTTTCTCATTTGTTTTTATTGGTTTCTTATT
* * * * *
1973965 ATATATTTGTTGGGTATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTCTTTCATGTTTATTCT
66 ATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTATTTCATGTTTATCCT
* *
1974030 GCATATTTGGTGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGGAGCTATGACCAATCCAAT
131 GCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAATCCAAT
1974095 TTGTGCTGGCTTTTAATCCA
196 TTGTGCTGGCTTTTAATCCA
*
1974115 TTTTTTTGTGAATTGGGGTTCTTGAGATAATTCTGCTTT
1 -TTTTTTGTGAATTGGGGTTCTTGAGATAATGCTGCTTT
1974154 TCCGATAAAA
Statistics
Matches: 223, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
212 2 0.01
213 177 0.79
214 11 0.05
215 12 0.05
216 21 0.09
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.48
Consensus pattern (215 bp):
TTTTTTGTGAATTGGGGTTCTTGAGATAATGCTGCTTTCTCATTTGTTTTTATTGGTTTCTTATT
ATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTATTTCATGTTTATCCT
GCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGCTATGACCAATCCAAT
TTGTGCTGGCTTTTAATCCA
Found at i:1979409 original size:28 final size:28
Alignment explanation
Indices: 1979375--1979431 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1979365 TATAGCACAG
1979375 AAAGGAACTAAAAACCAAATTGGCACGT
1 AAAGGAACTAAAAACCAAATTGGCACGT
1979403 AAAGGAACTAAAAACCAAATTGGCACGT
1 AAAGGAACTAAAAACCAAATTGGCACGT
1979431 A
1 A
1979432 TATGCTAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.51, C:0.18, G:0.18, T:0.14
Consensus pattern (28 bp):
AAAGGAACTAAAAACCAAATTGGCACGT
Found at i:1982518 original size:26 final size:27
Alignment explanation
Indices: 1982470--1982521 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1982460 TCATATAAAT
*
1982470 AAAATAAATTATTATTTTAATATATTA
1 AAAATAAATTATTAGTTTAATATATTA
*
1982497 AAAATAAATTATT-GTTTCATATATT
1 AAAATAAATTATTAGTTTAATATATT
1982522 TACGGTGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTATTAGTTTAATATATTA
Found at i:1982703 original size:25 final size:25
Alignment explanation
Indices: 1982640--1982703 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
1982630 AAATATTTTA
*
1982640 ATATATAATTTATACACATACAAGT
1 ATATATAATATATACACATACAAGT
* * *
1982665 ATATCTTAATTATATACATATA-AATT
1 ATAT-ATAA-TATATACACATACAAGT
1982691 ATATATGAATATA
1 ATATAT-AATATA
1982704 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.29
26 12 0.39
27 10 0.32
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATATATAATATATACACATACAAGT
Found at i:1991546 original size:186 final size:183
Alignment explanation
Indices: 1991220--1991565 Score: 444
Period size: 186 Copynumber: 1.9 Consensus size: 183
1991210 ATCACATGAA
* * *
1991220 CCAACCAACATTATGTAACTAGTTCAAATGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
1 CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
* * * * *
1991285 TTATCAAACATTAGGACAAGTTTATGCTCTAACAACGATTGAAGTTGCAAAACATCATTCACAGT
66 TTATCAAACACTAGGACAAGCTTATACTCTAACAACGATTGAAATTG-AAAACATCATTCACAGC
*
1991350 GACATCAAGAATTGTCAAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
130 AACATCAAGAATTGTCAAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
* ** * * * **
1991404 CCAACCTACATTACGTGGCTAGTGCAAAAGGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTT
1 CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGG-TACGAACATTGGATCATT
*
1991469 CTTATCAAACGCTAGGACAAGCTTATACATCTAACAATC-ATTGAAATCATG-AAACATCATTCA
65 CTTATCAAACACTAGGACAAGCTTATAC-TCTAACAA-CGATTGAAAT--TGAAAACATCATTCA
**
1991532 CAGCAACATCAAGAATTGTCGGAATACTAATAAA
126 CAGCAACATCAAGAATTGTCAAAATACTAATAAA
1991566 CACTGTATGG
Statistics
Matches: 137, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
184 39 0.28
185 38 0.28
186 57 0.42
187 1 0.01
188 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (183 bp):
CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
TTATCAAACACTAGGACAAGCTTATACTCTAACAACGATTGAAATTGAAAACATCATTCACAGCA
ACATCAAGAATTGTCAAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
Found at i:1991715 original size:155 final size:155
Alignment explanation
Indices: 1991433--1991720 Score: 400
Period size: 155 Copynumber: 1.9 Consensus size: 155
1991423 TAGTGCAAAA
** * * *
1991433 GGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTTCTTATCAAACGCTAGGACAAGCTTATACA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACACTAGGACAAGCTTATACA
* *
1991498 TCTAACAATCATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
66 TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
1991563 AAACACTGTATGGAAACGCCGCAAC
131 AAACACTGTATGGAAACGCCGCAAC
*
1991588 GGCAAACCCTTTGCAGGATTCGAAC-TT-CATCTCGATCTTATCAAACATTAGGACAAGCTTATA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCAT-T-GATCTTATCAAACACTAGGACAAGCTTATA
* * ** ** **
1991651 CGTCCAACAATAATTGAAGTTGTGAAACATCATTCACAGTGATGTCAAGAATTGTCGGAATACTA
64 CATCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTA
1991716 ATAAA
129 ATAAA
1991721 GACCGTACAT
Statistics
Matches: 115, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
153 2 0.02
154 3 0.03
155 110 0.96
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.26
Consensus pattern (155 bp):
GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACACTAGGACAAGCTTATACA
TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
AAACACTGTATGGAAACGCCGCAAC
Found at i:1994315 original size:25 final size:27
Alignment explanation
Indices: 1994287--1994337 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1994277 GGTACTACTA
*
1994287 CTTGTT-ATA-AATATTTTTATAAAGG
1 CTTGTTAATAGAATATATTTATAAAGG
1994312 CTTGTTAATAGAATATATTTATAAAG
1 CTTGTTAATAGAATATATTTATAAAG
1994338 TTTATGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.26
26 3 0.13
27 14 0.61
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (27 bp):
CTTGTTAATAGAATATATTTATAAAGG
Found at i:1997054 original size:51 final size:53
Alignment explanation
Indices: 1996971--1997111 Score: 155
Period size: 54 Copynumber: 2.7 Consensus size: 53
1996961 TGCAGTGGAA
* * * *
1996971 GTTGATTCCCTTCTCA-TAATTTGGTTTACAGTAATGCTG-TC-AGAAGCAGAG
1 GTTGATTCTCTTCT-AGAAATTTGGTTTCCAGTAATGCTGCACTAGAAGCAGAG
* *
1997022 GTTGATT-TCATTCTAGAAATTTGATTTCCAGTAATGGTGCCACTAGAAGCAGAG
1 GTTGATTCTC-TTCTAGAAATTTGGTTTCCAGTAATGCTG-CACTAGAAGCAGAG
* *
1997076 TTTGATTCTCTTCTAGAAATTCGGTTTCCAGTAATG
1 GTTGATTCTCTTCTAGAAATTTGGTTTCCAGTAATG
1997112 ATCCTCTCAG
Statistics
Matches: 75, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
50 2 0.03
51 30 0.40
53 1 0.01
54 40 0.53
55 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (53 bp):
GTTGATTCTCTTCTAGAAATTTGGTTTCCAGTAATGCTGCACTAGAAGCAGAG
Found at i:1997199 original size:108 final size:107
Alignment explanation
Indices: 1997130--1997363 Score: 308
Period size: 108 Copynumber: 2.2 Consensus size: 107
1997120 AGGGGTTATG
* * * *
1997130 GTTGATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGACATTAATTCCGC
* * *
1997195 TCTAGGAAGTTGATCCCCAGTAACGATCCCACCGGAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
**
1997238 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGATGTTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGACATTAATTCCGC
* * * * *
1997303 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCA-GAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCA-CAGGAAGTAGGA
1997346 GTTGATTCCCTTCTAGAA
1 GTTGATTCCCTTCTAGAA
1997364 ATCTGAATTC
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
108 114 0.99
109 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (107 bp):
GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGTGGACATTAATTCCGC
TCTAGAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
Found at i:1997327 original size:54 final size:52
Alignment explanation
Indices: 1997157--1997328 Score: 143
Period size: 54 Copynumber: 3.2 Consensus size: 52
1997147 AGTTTGGTTT
* *
1997157 CCAGTAATGACCTTATCAGGATTGGACATTAATTCCGCTCTAGGAAGTTGATCC
1 CCAGTAATGACCTTA-CAGGAGTGGA-GTTAATTCCGCTCTAGGAAGTTGATCC
* * * * * **
1997211 CCAGTAACGATCC-CACCGGAAGTGGGAGTTGATTCC-CTTCTA-GAAGTTTGGTTT
1 CCAGTAATGA-CCTTACAGG-AGT-GGAGTTAATTCCGC-TCTAGGAAG-TTGATCC
* *
1997265 CCAATAATGACCTTAGCAGGAGTGGATGTTAATTCCGCTCTAGGAAGTTGATCG
1 CCAGTAATGACCTTA-CAGGAGTGGA-GTTAATTCCGCTCTAGGAAGTTGATCC
1997319 CCAGTAATGA
1 CCAGTAATGA
1997329 GCCCACCAGA
Statistics
Matches: 90, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
53 13 0.14
54 64 0.71
55 13 0.14
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (52 bp):
CCAGTAATGACCTTACAGGAGTGGAGTTAATTCCGCTCTAGGAAGTTGATCC
Found at i:1997361 original size:54 final size:53
Alignment explanation
Indices: 1997195--1997361 Score: 160
Period size: 54 Copynumber: 3.1 Consensus size: 53
1997185 TTAATTCCGC
* *
1997195 TCTAGGAAGTTGATCCCCAGTAACGATCCCACCGGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGA-CCCACCAGAAGTGGGAGTTGATTCCCT
* ** * * * * *
1997249 TCTA-GAAGTTTGGTTTCCAATAATGACCTTAGCAGGAGT-GGATGTTAATTCCGC-
1 TCTAGGAAG-TTGATCCCCAGTAATGACC-CACCAGAAGTGGGA-GTTGATTCC-CT
*
1997303 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGA-CCCACCAGAAGTGGGAGTTGATTCCCT
1997357 TCTAG
1 TCTAG
1997362 AAATCTGAAT
Statistics
Matches: 87, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
53 10 0.11
54 67 0.77
55 10 0.11
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.28
Consensus pattern (53 bp):
TCTAGGAAGTTGATCCCCAGTAATGACCCACCAGAAGTGGGAGTTGATTCCCT
Found at i:2004749 original size:24 final size:22
Alignment explanation
Indices: 2004704--2004749 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
2004694 ATATAGGTAG
**
2004704 AAAAAATATAAAAGTAATTTTT
1 AAAAAATATAAAAAAAATTTTT
2004726 AAAAAATATATAAAAAAATATTTT
1 AAAAAATATA-AAAAAAAT-TTTT
2004750 CATAATGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 6 0.30
24 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAAATATAAAAAAAATTTTT
Found at i:2013426 original size:276 final size:276
Alignment explanation
Indices: 2012931--2013452 Score: 859
Period size: 276 Copynumber: 1.9 Consensus size: 276
2012921 AAAAAAACCA
* *
2012931 AAGAAACAATCACTAAAAGTTTCATATGACTTTGCTTAAATTAAATTTCTTCAAAAAAAATTTTA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTC--AAAAAATTTTA
* * * *
2012996 AATTGAAATAAAACTTATGCTTCTCATTACATTTGGTTGAATACAATGAGTGTTACAAGCTCAAC
64 AAATGAAATAAAACTTATGCTTCTCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAAC
*
2013061 CTTGCAAATCATGTAAGCTAAAAAAGTTAATAGACTCCATTTTTCTTGTATTTTCTATAACTTTC
129 CTTGCAAATCATGTAAGCTAAAAAAGTTAAGAGACTCCATTTTTCTTGTATTTTCTATAACTTTC
* *
2013126 CTCGAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAATAACTAAATTTCCAAAAAAAA
194 CTCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAA
2013191 GTGACGCAAACATGAGCT
259 GTGACGCAAACATGAGCT
* * *
2013209 AAGAAACAATTACTACAGGTTTAATACGACTTTGCTTAAATTAAATTTCTTC-AAAAATTTTAAA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAATTTTAAA
2013273 ATGAAATAAAACTTATGCTTCTCACTGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACC
66 ATGAAATAAAACTTATGCTTCTCA-TGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACC
* *
2013338 TTGCAAATCATGTAAGCTAAAAATGTTAACGA-ACTCCATTTTTCTTGTATTTTCTATCACTTTC
130 TTGCAAATCATGTAAGCTAAAAAAGTTAA-GAGACTCCATTTTTCTTGTATTTTCTATAACTTTC
*
2013402 CTCAAACTTTCTCGACACCCAAACAGAGCTTCATCATTCAACAAGAACTAA
194 CTCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAA
2013453 GGCCACCCCC
Statistics
Matches: 227, Mismatches: 15, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
275 35 0.15
276 144 0.63
277 1 0.00
278 47 0.21
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (276 bp):
AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAATTTTAAA
ATGAAATAAAACTTATGCTTCTCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACCT
TGCAAATCATGTAAGCTAAAAAAGTTAAGAGACTCCATTTTTCTTGTATTTTCTATAACTTTCCT
CAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAAGT
GACGCAAACATGAGCT
Found at i:2024075 original size:44 final size:43
Alignment explanation
Indices: 2024004--2024386 Score: 208
Period size: 44 Copynumber: 8.8 Consensus size: 43
2023994 ATCTGAAACG
* * * * * *
2024004 ATCTACTCTACTGTAACCTTAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-CTTTACTTTA
* * * * *
2024048 ATCCGTTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-TTA-CTTTA
* * * * **
2024092 ATCTGCTCCGCTGTAATCTCAGGGAGATAGGATAGTGT-CTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-CTTTACTTTA
* ** *
2024135 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTTCGGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTT-TACTTTA
* *
2024179 ATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT-CTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT----TTACTTTA
* * * * * *
2024225 GTCTGTTCCACTGTAATCTCAGGGAGATAAGA-CCTGA-TGTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTACTTTA
* * * * *
2024266 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATAATTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTTTACTTTA
* * *
2024310 ATCTGCTCCACTGTAA-CTTCAGGGAGAT-TGGT-TTATCGACTTCA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTT-T--ACTTTA
* **
2024354 ATTTGCTCCGTTGTAATCTCAGGGAGATAAGAT
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
2024387 TTCTGGCTTT
Statistics
Matches: 265, Mismatches: 54, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.00
41 31 0.12
42 3 0.01
43 42 0.16
44 149 0.56
45 5 0.02
46 33 0.12
48 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (43 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTTTACTTTA
Found at i:2024865 original size:88 final size:88
Alignment explanation
Indices: 2024570--2024998 Score: 480
Period size: 88 Copynumber: 4.9 Consensus size: 88
2024560 TGTAACCTTT
* ** * * *
2024570 AACCAGCTCCAAT-GCAACCGATGGAGGCAAGGCTTTGT-T-TTTGATCTGCTTTGCTGTTAATG
1 AACCAGCTCC-ATCACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* ** *
2024632 CAGGAAGGCAAGATCTGCT-TCTTT
64 CAGAAAGGCAAGATCTTTTGTCTTC
* * * ** * *
2024656 AACTAGCTCCA-CTGCAATCGATGGATGCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATG
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATG
* * ** *
2024718 TAGGAAGGCAAGATCTGCT-TCTTT
64 CAGAAAGGCAAGATCTTTTGTCTTC
* * *
2024742 AACCAGCTCCA-CTACAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGC
1 AACCAGCTCCATC-ACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGC
*
2024806 AGGAAGGCAAGATCTTTTGTCTTC
65 AGAAAGGCAAGATCTTTTGTCTTC
* *
2024830 AACCAGCTCTATCACAACCGAAAGATGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
2024895 GAAAGGCAAGATCTTTTGTCTTC
66 GAAAGGCAAGATCTTTTGTCTTC
* *
2024918 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTTTTTCTTCGATCTGCTTCGCTGTCAATGCA
1 AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
2024983 GAAAGGCAAGATCTTT
66 GAAAGGCAAGATCTTT
2024999 AACTTCATTG
Statistics
Matches: 308, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
85 6 0.02
86 104 0.34
87 36 0.12
88 161 0.52
89 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (88 bp):
AACCAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
GAAAGGCAAGATCTTTTGTCTTC
Found at i:2024990 original size:44 final size:44
Alignment explanation
Indices: 2024766--2024992 Score: 146
Period size: 44 Copynumber: 5.2 Consensus size: 44
2024756 CAACCGAGAG
* * * *
2024766 AGGCAAGGTTTGTGTCTTCGACCTGCTTCACTGTCAATGCAGGA
1 AGGCAAGGTTTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
* * * * * * *
2024810 AGGCAAGATCTTTTGTCTTCAACCAGC-T--CTATCACA-ACCGAA
1 AGGCAAGGT-TTTTGTCTTCGATCTGCTTCGCTGTCA-ATGCAGAA
*
2024852 AGATGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 AG--GCAAGGTTTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
* * * * * * *
2024898 AGGCAAGATCTTTTGTCTTCAACCAGC-TC-C-ATCACA-ACCGAAA
1 AGGCAAGGT-TTTTGTCTTCGATCTGCTTCGCTGTCA-ATGCAG-AA
*
2024941 GAGGCAAGGTTTTTTTCTTCGATCTGCTTCGCTGTCAATGCAGAA
1 -AGGCAAGGTTTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
2024986 AGGCAAG
1 AGGCAAG
2024993 ATCTTTAACT
Statistics
Matches: 135, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
42 15 0.11
43 31 0.23
44 41 0.30
45 32 0.24
46 16 0.12
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.29
Consensus pattern (44 bp):
AGGCAAGGTTTTTGTCTTCGATCTGCTTCGCTGTCAATGCAGAA
Found at i:2026272 original size:21 final size:21
Alignment explanation
Indices: 2026231--2026274 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2026221 TTAGCCTCTC
*
2026231 CATTTTTACTCTTTTCATTTT
1 CATTTTTACTCTTATCATTTT
* *
2026252 CATTTTTATTCTTCATCTTTTT
1 CATTTTTACTCTT-ATCATTTT
2026274 C
1 C
2026275 TCTTTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.14, C:0.20, G:0.00, T:0.66
Consensus pattern (21 bp):
CATTTTTACTCTTATCATTTT
Found at i:2040882 original size:14 final size:13
Alignment explanation
Indices: 2040843--2040884 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
2040833 ATCACTGATA
2040843 ATTTAATTTAATT
1 ATTTAATTTAATT
2040856 -TTTGAACTTTAATT
1 ATTT-AA-TTTAATT
2040870 ATTTAATTATAATT
1 ATTTAATT-TAATT
2040884 A
1 A
2040885 ATCAATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 3 0.12
13 4 0.16
14 15 0.60
15 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (13 bp):
ATTTAATTTAATT
Found at i:2047896 original size:48 final size:48
Alignment explanation
Indices: 2047825--2047924 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
2047815 TAAGTGCTGA
2047825 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
1 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
2047873 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
1 AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
2047921 AATA
1 AATA
2047925 TGGAGGGACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (48 bp):
AATAGCAACCAGTCGGTAACACTTGACATATCACGTGTACCTTATGTT
Found at i:2050603 original size:30 final size:29
Alignment explanation
Indices: 2050567--2050634 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
2050557 ATAGTTGGAC
* *
2050567 CTAAATT-TTGAAAATTGAAAAGTAGAGGGA
1 CTAAATTCCTGAAAA-T-AAAAGTACAGGGA
*
2050597 CTAAATTCCTGGAAATAAAAGTACAGGGA
1 CTAAATTCCTGAAAATAAAAGTACAGGGA
2050626 CTAAATTCC
1 CTAAATTCC
2050635 AAATTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 21 0.62
30 8 0.24
31 5 0.15
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (29 bp):
CTAAATTCCTGAAAATAAAAGTACAGGGA
Found at i:2053318 original size:31 final size:30
Alignment explanation
Indices: 2053263--2053327 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
2053253 AAATCAATTT
2053263 AAAAGTTGGAACTTCTGTACAATTAACCAA
1 AAAAGTTGGAACTTCTGTACAATTAACCAA
* *
2053293 AAAAGTTGAGAACTTTTTGTA-AATTAACCCA
1 AAAAGTTG-GAAC-TTCTGTACAATTAACCAA
2053324 AAAA
1 AAAA
2053328 TAACATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 17 0.55
32 6 0.19
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAAGTTGGAACTTCTGTACAATTAACCAA
Found at i:2061962 original size:13 final size:13
Alignment explanation
Indices: 2061946--2061994 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
2061936 TAAACTAAAT
*
2061946 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
*
2061959 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
2061972 -TTT-AAAAGCAC
1 TTTTCAAAAGCAC
2061983 TTTTCAAAAGCA
1 TTTTCAAAAGCA
2061995 TTGAAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
11 9 0.31
12 3 0.10
13 12 0.41
14 5 0.17
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:2068843 original size:18 final size:18
Alignment explanation
Indices: 2068822--2068865 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2068812 GAAACAGAAT
*
2068822 AAAAAATAATAAGCCCAA
1 AAAAAATAACAAGCCCAA
* *
2068840 AAAAATTTACAAGCCCAA
1 AAAAAATAACAAGCCCAA
2068858 AAGAAAAT
1 AA-AAAAT
2068866 TTATTACAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.64, C:0.16, G:0.07, T:0.14
Consensus pattern (18 bp):
AAAAAATAACAAGCCCAA
Found at i:2072949 original size:15 final size:15
Alignment explanation
Indices: 2072929--2072959 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2072919 CCAACCTTCA
2072929 AATTTTACCTCAATT
1 AATTTTACCTCAATT
2072944 AATTTTACCTCAATT
1 AATTTTACCTCAATT
2072959 A
1 A
2072960 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:2075219 original size:11 final size:11
Alignment explanation
Indices: 2075203--2075229 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2075193 TAGAAATTAG
2075203 TTTGTGAAACT
1 TTTGTGAAACT
2075214 TTTGTGAAACT
1 TTTGTGAAACT
2075225 TTTGT
1 TTTGT
2075230 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:2076757 original size:93 final size:92
Alignment explanation
Indices: 2076625--2076819 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
2076615 TTGATTTTAG
* *
2076625 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
2076689 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
2076717 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
2076782 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
2076810 CAAATTCATA
1 TAAATTCATA
2076820 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:2076877 original size:17 final size:17
Alignment explanation
Indices: 2076852--2076885 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2076842 ATAATTTTAA
*
2076852 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
2076869 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
2076886 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:2076887 original size:15 final size:16
Alignment explanation
Indices: 2076852--2076890 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2076842 ATAATTTTAA
*
2076852 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
2076869 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
2076884 ATTTAAT
1 ATTTAAT
2076891 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:2076894 original size:17 final size:18
Alignment explanation
Indices: 2076856--2076895 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2076846 TTTTAAATTT
*
2076856 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
2076874 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
2076890 TATTAA
1 TATTAA
2076896 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:2077019 original size:120 final size:119
Alignment explanation
Indices: 2076851--2077069 Score: 338
Period size: 120 Copynumber: 1.8 Consensus size: 119
2076841 AATAATTTTA
*
2076851 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTGAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTATGTT--AATTTATATTT
*
2076914 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
*
2076970 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATT-ATTATGTTAATTTATATT
1 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAAT-ATTAATTATGTTAATTTATATT
2077033 TTACAGTATCATATATTATGATTTGAGTAAATTCATA
63 TTACAGTATCATATATTATGATTTGAGTAAATTCATA
2077070 TTAAATTATA
Statistics
Matches: 92, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
119 23 0.25
120 61 0.66
121 8 0.09
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.51
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTATGTTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:2077098 original size:16 final size:16
Alignment explanation
Indices: 2077077--2077118 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
2077067 ATATTAAATT
*
2077077 ATATATTTTAATTATA
1 ATATATTTTAATAATA
2077093 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
2077108 AT-TATGTTTAA
1 ATATAT-TTTAA
2077119 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:2077228 original size:154 final size:156
Alignment explanation
Indices: 2077068--2077365 Score: 546
Period size: 154 Copynumber: 1.9 Consensus size: 156
2077058 AGTAAATTCA
*
2077068 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
2077133 TTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
2077196 AAATTTATGCTAATTATTAAGAATTT
131 AAATTTATGCTAATTATTAAGAATTT
2077222 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
*
2077287 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
2077352 CAAATTTCTGCTAA
130 CAAATTTATGCTAA
2077366 GGGTATTCTA
Statistics
Matches: 138, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
154 76 0.55
155 2 0.01
157 60 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:2077246 original size:18 final size:17
Alignment explanation
Indices: 2077218--2077252 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2077208 ATTATTAAGA
*
2077218 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
2077235 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
2077253 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:2077506 original size:16 final size:16
Alignment explanation
Indices: 2077497--2077570 Score: 112
Period size: 16 Copynumber: 4.6 Consensus size: 16
2077487 TACACAGCTT
2077497 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
2077513 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
2077529 TTCCATTACACCTCTA
1 TTCCATTACACCTCTA
* *
2077545 ATCCAATACACCTCTA
1 TTCCATTACACCTCTA
* *
2077561 ATCCAATACA
1 TTCCATTACA
2077571 GCGAACCAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 56 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.32
Consensus pattern (16 bp):
TTCCATTACACCTCTA
Found at i:2078919 original size:28 final size:29
Alignment explanation
Indices: 2078879--2078935 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
2078869 GCAACCCATT
*
2078879 TTTATTATCATATC-GAACGCTATTCCTA
1 TTTATTATCATATCAAAACGCTATTCCTA
2078907 TTTATTATCATATCAAAACGCTATTCCTA
1 TTTATTATCATATCAAAACGCTATTCCTA
2078936 ATAGAAGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 14 0.52
29 13 0.48
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTATTATCATATCAAAACGCTATTCCTA
Found at i:2080531 original size:15 final size:16
Alignment explanation
Indices: 2080511--2080542 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2080501 ATTATTTAAA
2080511 TTTTAAAA-TTATTAT
1 TTTTAAAATTTATTAT
2080526 TTTTAAAATTTATTAT
1 TTTTAAAATTTATTAT
2080542 T
1 T
2080543 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAAATTTATTAT
Found at i:2080558 original size:21 final size:21
Alignment explanation
Indices: 2080532--2080594 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
2080522 TTATTTTTAA
2080532 AATTTATTATTAAAATAAAAT
1 AATTTATTATTAAAATAAAAT
* *
2080553 AATTTATTA-CAATAATAAATT
1 AATTTATTATTAA-AATAAAAT
*
2080574 ATTTATATTATTAAATATAAA
1 AATT-TATTATTAAA-ATAAA
2080595 TAAATATGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 2 0.06
21 19 0.56
22 6 0.18
23 7 0.21
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTTATTATTAAAATAAAAT
Found at i:2084468 original size:197 final size:196
Alignment explanation
Indices: 2084057--2084639 Score: 737
Period size: 197 Copynumber: 2.9 Consensus size: 196
2084047 ATGTTGTTCG
*
2084057 GACTCTTCATTTTTCTTGAAGCAC-CAGTGTTTGACAGATGGATATTACATGGAAAACCTTTGAA
1 GACTCTTCATTTTTCTTGAAGCACTC-GTGTTTGACACATGGATATTACATGGAAAACCTTTG-A
* * *
2084121 AAATGAAAATTCTTACGATA-T-TCGTGTCAAATGCACACCCATATTTGACACTCACACCCAAGT
64 AAA-G-----TCTAACGATACTCTCGT-T-AAATACAAACCCATATTTGACACTCACACCCAAGT
* * *
2084184 CCGAATAACATAGGGCAAAATTCACTATGCCAACTAACAATTGACAGCTAGGGATCACACAATGA
121 CCGAGTAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGA
2084249 TAAGTTGCTCA
186 TAAGTTGCTCA
** *
2084260 GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAAA
1 GACTCTTCATTTTTCTTGAAGCACTCGTGTTTGACACATGGATATTACATGGAAAACCTTTGAAA
* * * * *
2084325 AGCCTGATGATACTCTCGTTAAATACAAACCCATATTTGACACTTACA-CCAGAGTCAGAGTAAC
66 AGTCTAACGATACTCTCGTTAAATACAAACCCATATTTGACACTCACACCCA-AGTCCGAGTAAC
* * * * *
2084389 GTAAGGGCAAAATTAACTATGTCAACTGACAATTGACAGCAAGCGG-TCACACAATGCTATGTTG
130 AT-AGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAG-GGATCACACAATGATAAGTTG
2084453 CTCA
193 CTCA
* * * *
2084457 TACTCTTCATTTTTCTTGAAGCACTCGTGTTTGATATATGTATATTACATGGAAAACCTTTGAAA
1 GACTCTTCATTTTTCTTGAAGCACTCGTGTTTGACACATGGATATTACATGGAAAACCTTTGAAA
* *
2084522 AGTCTAACGATACTCGT-GTTAAATACATACCCATTTTTGACACTCACACCCAAGTCCGAGTAAC
66 AGTCTAACGATACTC-TCGTTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAAC
*
2084586 ATAGGGCAAAATTCACTATGTCAACTAACAAATCGACAGCAAGGGATCATCACA
130 ATAGGGCAAAATTCACTATGTCAACTAAC-AATTGACAGCAAGGGATCA-CACA
2084640 CAAGATTTTT
Statistics
Matches: 332, Mismatches: 37, Indels: 27
0.84 0.09 0.07
Matches are distributed among these distances:
195 3 0.01
196 70 0.21
197 183 0.55
198 14 0.04
201 1 0.00
202 4 0.01
203 56 0.17
204 1 0.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (196 bp):
GACTCTTCATTTTTCTTGAAGCACTCGTGTTTGACACATGGATATTACATGGAAAACCTTTGAAA
AGTCTAACGATACTCTCGTTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAACA
TAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGATAAGTTGCTC
A
Done.