Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold123
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: 1422801
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 1358 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:1322925 original size:34 final size:35
Alignment explanation
Indices: 1322862--1322928 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1322852 CTAAGTAATT
1322862 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1322898 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1322929 TCTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1323297 original size:52 final size:52
Alignment explanation
Indices: 1323187--1323304 Score: 184
Period size: 52 Copynumber: 2.3 Consensus size: 52
1323177 CACATTTAAT
**
1323187 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTATAA
1 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAGATAA
* *
1323239 AATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAAGAT-C
1 AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATAC-AAGATAA
1323291 AGTGTATCGATACA
1 AGTGTATCGATACA
1323305 ATGTATCGAT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 57 0.95
53 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (52 bp):
AGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACAAGATAA
Found at i:1323311 original size:13 final size:13
Alignment explanation
Indices: 1323293--1323317 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1323283 CAAAGATCAG
1323293 TGTATCGATACAA
1 TGTATCGATACAA
1323306 TGTATCGATACA
1 TGTATCGATACA
1323318 TGTGAGTAAT
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:1323402 original size:13 final size:13
Alignment explanation
Indices: 1323384--1323408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1323374 CAAAAAAATA
1323384 TGTATCGATACAT
1 TGTATCGATACAT
1323397 TGTATCGATACA
1 TGTATCGATACA
1323409 ACATTTTATG
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:1323404 original size:33 final size:33
Alignment explanation
Indices: 1323362--1323428 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1323352 AGTAGCTTAA
1323362 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1323395 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1323428 A
1 A
1323429 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:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1323863 original size:13 final size:13
Alignment explanation
Indices: 1323845--1323869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1323835 ACAAACAGTA
1323845 AATGTATCGATAC
1 AATGTATCGATAC
1323858 AATGTATCGATA
1 AATGTATCGATA
1323870 TAAAACCACC
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1323964 original size:20 final size:22
Alignment explanation
Indices: 1323921--1323975 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
1323911 TAAGTAAATG
1323921 TATCAATACA-TTTACTATTTA
1 TATCAATACATTTTACTATTTA
*
1323942 TATCAATACATTTTTC-A-TTA
1 TATCAATACATTTTACTATTTA
*
1323962 TATCCATACATTTT
1 TATCAATACATTTT
1323976 GGGCTTTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 16 0.52
21 11 0.35
22 4 0.13
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (22 bp):
TATCAATACATTTTACTATTTA
Found at i:1324108 original size:111 final size:112
Alignment explanation
Indices: 1323897--1324134 Score: 309
Period size: 111 Copynumber: 2.1 Consensus size: 112
1323887 CTGCCAAGGA
*
1323897 AATGTATCAATACATAAGTAAATGTATCAATACATTTACTATTTATATCAATACATTTTTCATTA
1 AATGTATCAATACATAAGTAAATGTATCAATACATTTACTAGTTATATCAATACATTTTTCATTA
* ** *
1323962 TATCCATACATTTTGGGCTTTAACCCAAATATATCGATACATTTCTC
66 CATCCATACATTACGGGCTTTAACCCAAATATATCGACACATTTCTC
* *
1324009 AATGTATCCATACATAAGTAAATGTATCGATACATTTACT-GTTATAT-AGATACATTTTTCATT
1 AATGTATCAATACATAAGTAAATGTATCAATACATTTACTAGTTATATCA-ATACATTTTTCATT
** * * * *
1324072 ACATTGATACATTACGGGTTTTAACCCAGATGTATCGACACATTTTTC
65 ACATCCATACATTACGGGCTTTAACCCAAATATATCGACACATTTCTC
* * *
1324120 ATTATATCGATACAT
1 AATGTATCAATACAT
1324135 TTTGGGCTTT
Statistics
Matches: 109, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
110 1 0.01
111 70 0.64
112 38 0.35
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (112 bp):
AATGTATCAATACATAAGTAAATGTATCAATACATTTACTAGTTATATCAATACATTTTTCATTA
CATCCATACATTACGGGCTTTAACCCAAATATATCGACACATTTCTC
Found at i:1324120 original size:51 final size:51
Alignment explanation
Indices: 1324060--1324186 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 51
1324050 TTATATAGAT
* *
1324060 ACATTTTTCATTACATTGATACATTACGGGTTTTAACCCAGATGTATCGAC
1 ACATTTTTCATTACATCGATACATTACGGGCTTTAACCCAGATGTATCGAC
* ** *
1324111 ACATTTTTCATTATATCGATACATTTTGGGCTTTAACCCAGATGTATCGAT
1 ACATTTTTCATTACATCGATACATTACGGGCTTTAACCCAGATGTATCGAC
* * *
1324162 ACATTTTTCAATATATCCATACATT
1 ACATTTTTCATTACATCGATACATT
1324187 CCTCAATGTA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 68 1.00
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (51 bp):
ACATTTTTCATTACATCGATACATTACGGGCTTTAACCCAGATGTATCGAC
Found at i:1324183 original size:20 final size:20
Alignment explanation
Indices: 1324155--1324207 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1324145 AACCCAGATG
* **
1324155 TATCGATACATTTTTCAATA
1 TATCCATACATTCCTCAATA
*
1324175 TATCCATACATTCCTCAATG
1 TATCCATACATTCCTCAATA
1324195 TATCCATACATTC
1 TATCCATACATTC
1324208 AGGCATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.40
Consensus pattern (20 bp):
TATCCATACATTCCTCAATA
Found at i:1326647 original size:79 final size:78
Alignment explanation
Indices: 1326551--1326861 Score: 388
Period size: 79 Copynumber: 3.9 Consensus size: 78
1326541 TCATTGATGT
* * * *
1326551 TTTTCCACCATCAGGGATACTCCAACCCTGTTATTTCCAAGGGGATACTCAAATCCCGATTTTAT
1 TTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAA-CCCGATTTTAT
1326616 TTCTAAAACATTGA
65 TTCTAAAACATTGA
* *
1326630 TTTTTCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGAGATACTCTAACCTCGATTTTAT
1 TTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAACC-CGATTTTAT
*
1326695 TTCTAAAACATCGA
65 TTCTAAAACATTGA
* * *
1326709 TTTTCCACCATCGTGGATACTCCAACCTTGTTATTTTCGAGGGGATACTCTAACCCTAGTTTTAT
1 TTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAACCCGA-TTTTAT
* *
1326774 TTCTAAAACACTAA
65 TTCTAAAACATTGA
* * * ** * * *
1326788 TTTTCCATCACCGGGGATACTCTAACCCCATTATTTTTTGAGGGGATACTCCAACCCCATTTTTA
1 TTTTCCACCATCGGGGATACTCCAACCCTGTTA-TTTTCGAGGGGATACTCTAACCCGA-TTTTA
*
1326853 TCTCTAAAA
64 TTTCTAAAA
1326862 TATTAAAGTT
Statistics
Matches: 202, Mismatches: 27, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
78 4 0.02
79 163 0.81
80 35 0.17
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (78 bp):
TTTTCCACCATCGGGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCTAACCCGATTTTATT
TCTAAAACATTGA
Found at i:1330289 original size:20 final size:20
Alignment explanation
Indices: 1330264--1330357 Score: 154
Period size: 20 Copynumber: 4.7 Consensus size: 20
1330254 GAAAACCCAA
1330264 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
1330284 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
1330304 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
*
1330324 AATGTATCGATACATCCACT-
1 AATGTATCGATACAT-TACTC
*
1330344 TATGTATCGATACA
1 AATGTATCGATACA
1330358 ATTTTTTCAA
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
20 68 0.96
21 3 0.04
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTACTC
Found at i:1330514 original size:21 final size:21
Alignment explanation
Indices: 1330488--1330541 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
1330478 TGGGACCTTG
1330488 TATCGATACATGAAAGGCATT
1 TATCGATACATGAAAGGCATT
1330509 TATCGATACATGAAAGGCATT
1 TATCGATACATGAAAGGCATT
1330530 TATCGATACATG
1 TATCGATACATG
1330542 TAGACAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (21 bp):
TATCGATACATGAAAGGCATT
Found at i:1332070 original size:2 final size:2
Alignment explanation
Indices: 1332065--1332111 Score: 67
Period size: 2 Copynumber: 22.5 Consensus size: 2
1332055 TTATAGTGTG
*
1332065 TA TA TA TA TA TA TA TA TA TA TA TA CA CTA TA GTA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
1332109 TA T
1 TA T
1332112 TTTTTTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 38 0.93
3 3 0.07
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1333226 original size:17 final size:17
Alignment explanation
Indices: 1333206--1333240 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1333196 TTGAGATGGT
1333206 GAATAATTTTAATAGGA
1 GAATAATTTTAATAGGA
1333223 GAATAATTTTAATAGGA
1 GAATAATTTTAATAGGA
1333240 G
1 G
1333241 TACATCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (17 bp):
GAATAATTTTAATAGGA
Found at i:1339437 original size:24 final size:25
Alignment explanation
Indices: 1339387--1339445 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 25
1339377 GACATGATTT
1339387 TTTTTAATATTATTAAACATAAATA
1 TTTTTAATATTATTAAACATAAATA
1339412 TTTTT-ATATT-TTAATA-AT-AA-A
1 TTTTTAATATTATTAA-ACATAAATA
*
1339433 TTATTAATATTAT
1 TTTTTAATATTAT
1339446 CAAAAAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 5 0.17
22 7 0.23
23 7 0.23
24 6 0.20
25 5 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTAATATTATTAAACATAAATA
Found at i:1340887 original size:20 final size:21
Alignment explanation
Indices: 1340842--1340897 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1340832 ACCCTTTGAA
**
1340842 TGTATCGATACATGTTTAAAT
1 TGTATCGATACATGTAAAAAT
*
1340863 CGTATCGATACAT-TAAAAAT
1 TGTATCGATACATGTAAAAAT
*
1340883 TGTATCAATACATGT
1 TGTATCGATACATGT
1340898 GGCGCAATGG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATGTAAAAAT
Found at i:1343833 original size:20 final size:19
Alignment explanation
Indices: 1343808--1343863 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1343798 TATTGCCAGT
*
1343808 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACA-ATG
1343828 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
**
1343847 AACATGTATCGATACAA
1 TTCATGTATCGATACAA
1343864 AGCATAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:1344811 original size:33 final size:33
Alignment explanation
Indices: 1344774--1344840 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1344764 AAGAGAACTA
* *
1344774 AAGTGCTCATCCATGCACTGCGAGAGTGAAGTG
1 AAGTGCTCATCCATGCACTACGAAAGTGAAGTG
* **
1344807 AAGTGCTCATTCATGTGCTACGAAAGTGAAGTG
1 AAGTGCTCATCCATGCACTACGAAAGTGAAGTG
1344840 A
1 A
1344841 TCAACTCTCG
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:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (33 bp):
AAGTGCTCATCCATGCACTACGAAAGTGAAGTG
Found at i:1346323 original size:13 final size:13
Alignment explanation
Indices: 1346305--1346342 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1346295 AGTAACCCAC
*
1346305 GTATCGATACATT
1 GTATCGATACAAT
1346318 GTATCGATACAAT
1 GTATCGATACAAT
1346331 GTATCGATACAA
1 GTATCGATACAA
1346343 AGAACATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
GTATCGATACAAT
Found at i:1356778 original size:26 final size:26
Alignment explanation
Indices: 1356634--1356778 Score: 64
Period size: 26 Copynumber: 5.3 Consensus size: 26
1356624 AAGTTGGTGG
*
1356634 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
* * **
1356660 CACCTTTCAAAGCCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCACA-AAG-AGCAGGA
* *
1356689 CA-TTTTCCAGTCCTCAAAGAGCAGGA
1 CACCTTT-CAGTCCACAAAGAGCAGGA
* *
1356715 CACCTTTCAAAGCCCACACAAGTTAG-TGG-
1 CACCTTTC--AGTCCACA-AAG--AGCAGGA
** *
1356744 CATTTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCACAAAGAGCAGGA
1356770 CACCTTTCA
1 CACCTTTCA
1356779 AAGCCCACAC
Statistics
Matches: 83, Mismatches: 22, Indels: 28
0.62 0.17 0.21
Matches are distributed among these distances:
24 2 0.02
25 5 0.06
26 24 0.29
27 15 0.18
28 15 0.18
29 15 0.18
30 5 0.06
31 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.22
Consensus pattern (26 bp):
CACCTTTCAGTCCACAAAGAGCAGGA
Found at i:1356947 original size:59 final size:57
Alignment explanation
Indices: 1356558--1357226 Score: 723
Period size: 55 Copynumber: 11.8 Consensus size: 57
1356548 GGACGAATTC
** *
1356558 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC--TC-TT
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTCTTT
* *
1356613 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACACCTTTC---
1 AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
** *
1356668 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACCTTTC---
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTCTTT
* ** *
1356723 AAAGCCCACACAAGTTAGTGGCATTTTTCAGTCCTCAAAGAGCAGGACACCTTTC---
1 AAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
** *
1356778 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACACC--T-TTT
1 AAAGCCCACACAAGTTGGTGGCACCTT-CAGTCCTCAAAGAGCAGGACGCCTTTCTTT
* * * * *
1356833 AAAGCCCACACAGGTTGGTGGCATTCTCCAGTCCTCAAAGAGCGGGATGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCA-CCTTCAGTCCTCAAAGAGCAGGACGCC-TTTC-TTT
*
1356893 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCC-TTTC-TTT
* * * *
1356952 AAAGCCCACACAAATTGGTGGCACTTTGAGTCCTCAAAGAGCGGGACGCCTTTTCTTTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCC-TTTC-TTT
* * * *
1357011 AAAGCCCACCCGAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGATGCTTTTTCTCTT
1 AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGC-CTTTCT-TT
1357070 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC--T-TTT
1 AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
*
1357125 AAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCCCAAAGAGCAGGACGCCTTTC---
1 AAAGCCCACACAAGTTGGTGGCACC-TTCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
* * * * *
1357180 AAAGCCCACACGAGTTGGTGGCACTTTTTACTCCTCAATGAGCAGGA
1 AAAGCCCACACAAGTTGGTGGCAC-CTTCAGTCCTCAAAGAGCAGGA
1357227 TACACTTTAT
Statistics
Matches: 552, Mismatches: 40, Indels: 44
0.87 0.06 0.07
Matches are distributed among these distances:
53 1 0.00
54 6 0.01
55 322 0.58
56 9 0.02
57 4 0.01
58 2 0.00
59 160 0.29
60 48 0.09
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (57 bp):
AAAGCCCACACAAGTTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTTCTTT
Found at i:1358055 original size:13 final size:13
Alignment explanation
Indices: 1358037--1358063 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1358027 CATAAAATGT
1358037 TGTATCGATACAA
1 TGTATCGATACAA
1358050 TGTATCGATACAA
1 TGTATCGATACAA
1358063 T
1 T
1358064 TTAAGCTACT
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:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1358122 original size:13 final size:13
Alignment explanation
Indices: 1358104--1358128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1358094 ATTACTCAAA
1358104 TGTATCGATACAT
1 TGTATCGATACAT
1358117 TGTATCGATACA
1 TGTATCGATACA
1358129 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:1358230 original size:52 final size:52
Alignment explanation
Indices: 1358137--1358264 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
1358127 CACTGATCTT
* *
1358137 TGTATCGATACATGCAGGC-AGTTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
*
1358188 TGTATCGATACATGCAGGCAAATTTGCCCATATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1358240 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1358265 TCATATTTCG
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 19 0.26
52 50 0.69
53 3 0.04
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:1364556 original size:16 final size:15
Alignment explanation
Indices: 1364534--1364595 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 15
1364524 CCTTCTCTTC
1364534 AAAAAAAAAAGCAAA
1 AAAAAAAAAAGCAAA
* **
1364549 AGAAAAAAAA-C-GG
1 AAAAAAAAAAGCAAA
1364562 AAAAAAAAAA-CAAA
1 AAAAAAAAAAGCAAA
*
1364576 AAAAACAAAA-CAAA
1 AAAAAAAAAAGCAAA
1364590 GAAAAA
1 -AAAAA
1364596 GAGAGAAAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
13 10 0.26
14 14 0.37
15 14 0.37
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGCAAA
Found at i:1364565 original size:27 final size:25
Alignment explanation
Indices: 1364535--1364612 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 25
1364525 CTTCTCTTCA
1364535 AAAAAAAAAGCAAAAGAAAAAAAAC
1 AAAAAAAAAGCAAAAGAAAAAAAAC
*
1364560 GGAAAAAAAAAACAAAA-AAAACAAAAC
1 --AAAAAAAAAGCAAAAGAAAA-AAAAC
*
1364587 AAAGAAAAAGAGAGAAAAGAAAAAAA
1 AAA-AAAAA-AG-CAAAAGAAAAAAA
1364613 CCTACTTAAG
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
25 3 0.07
26 9 0.21
27 20 0.47
28 7 0.16
29 4 0.09
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAGCAAAAGAAAAAAAAC
Found at i:1365768 original size:27 final size:27
Alignment explanation
Indices: 1365738--1365877 Score: 74
Period size: 27 Copynumber: 5.1 Consensus size: 27
1365728 TTGGTGGCAT
1365738 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * *
1365765 TTTCAAAGCCCACACAAGTTAG-TGG-CA-T
1 TTTC-CAGTCCTCA-AAG--AGCAGGACACC
1365793 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
* * * * ** *
1365820 TTTCAAAGCCCACACAAGTTGGTGG-CA-T
1 TTTC-CAGTCCTCA-AAG-AGCAGGACACC
1365848 TTTCCAGTCCTCAAAGAGCAGGACACC
1 TTTCCAGTCCTCAAAGAGCAGGACACC
1365875 TTT
1 TTT
1365878 TAAAGCCCAC
Statistics
Matches: 77, Mismatches: 24, Indels: 24
0.62 0.19 0.19
Matches are distributed among these distances:
24 2 0.03
25 5 0.06
26 10 0.13
27 23 0.30
28 20 0.26
29 10 0.13
30 5 0.06
31 2 0.03
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (27 bp):
TTTCCAGTCCTCAAAGAGCAGGACACC
Found at i:1365992 original size:59 final size:58
Alignment explanation
Indices: 1365578--1366252 Score: 775
Period size: 55 Copynumber: 12.0 Consensus size: 58
1365568 TCCGCTTTTT
* *
1365578 AGTCCTCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-C
* *
1365633 AGTCCTCAAAGAGCAGGACACC--TC--TTAAAGCCCACACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
* * * *
1365688 AGTCCCCAAAGAGCAGAACACCTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-C
* * *
1365743 AGTCCTCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTAGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-C
* *
1365798 AGTCCTCAAAGAGCAGGACACCTTTC----AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-C
* * *
1365853 AGTCCTCAAAGAGCAGGAC-AC---CTTTTAAAGCCCACACAGGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT-C
* *
1365908 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC
*
1365967 AGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC
* * *
1366026 AGTCCTCAAAGAGCAGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCACCTTC
1 AGTCCTCAAAGAGCAGGACGCC-TTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC
* * *
1366085 AGTCCTCAAAGAGCAGGATGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGC-CTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
1366145 AGTCCTCAAAGAGCAGGACG-C---CTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTC
**
1366200 AGTCCTCAAAGAGCAGGACGCCTTTC----AAAGCCCACATGAGTTGGTGGCACTTT
1 AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTT
1366253 TTACTCCTCA
Statistics
Matches: 566, Mismatches: 33, Indels: 43
0.88 0.05 0.07
Matches are distributed among these distances:
51 1 0.00
53 2 0.00
54 8 0.01
55 333 0.59
56 5 0.01
57 2 0.00
59 163 0.29
60 52 0.09
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (58 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTTTC
Found at i:1366224 original size:26 final size:26
Alignment explanation
Indices: 1366139--1366226 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
1366129 GTTGGTGGCA
1366139 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
* * * * ** *
1366165 CCTTTTAAAGCCCACACAAGTTGGTGG-CA
1 CC-TTT-CAGTCCTCA-AAG-AGCAGGACG
1366194 CCTTTCAGTCCTCAAAGAGCAGGACG
1 CCTTTCAGTCCTCAAAGAGCAGGACG
1366220 CCTTTCA
1 CCTTTCA
1366227 AAGCCCACAT
Statistics
Matches: 43, Mismatches: 14, Indels: 10
0.64 0.21 0.15
Matches are distributed among these distances:
25 3 0.07
26 13 0.30
27 9 0.21
28 9 0.21
29 6 0.14
30 3 0.07
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (26 bp):
CCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:1369993 original size:15 final size:14
Alignment explanation
Indices: 1369969--1370050 Score: 64
Period size: 15 Copynumber: 5.9 Consensus size: 14
1369959 ACCTTCTCTT
*
1369969 CAAAAAAAAAAAAA
1 CAAAAGAAAAAAAA
1369983 GCAAAAGAAAAAAAA
1 -CAAAAGAAAAAAAA
**
1369998 C-GGA-AAAAAAAA
1 CAAAAGAAAAAAAA
1370010 CAAAA-AAAACAAAA
1 CAAAAGAAAA-AAAA
*
1370024 C-AAAGAAAAAGAGA
1 CAAAAGAAAAA-AAA
*
1370038 GAAAAGAAAAAAA
1 CAAAAGAAAAAAA
1370051 CCTACTTAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
12 9 0.17
13 10 0.19
14 13 0.24
15 22 0.41
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (14 bp):
CAAAAGAAAAAAAA
Found at i:1371101 original size:55 final size:54
Alignment explanation
Indices: 1371011--1371596 Score: 663
Period size: 55 Copynumber: 10.4 Consensus size: 54
1371001 CTCCTTCCGC
* *
1371011 TTTTTAGTCCTCAAAGAGCAGGATACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1371065 TTTTCCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * *
1371120 CCTTTCAGTCCCCAAAGAGCAGAACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1371175 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTCAAAACCCACACAAGTTAGTGGCA
1 TTTTC-AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1371230 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTC-AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
1371285 TTTTCTAGTCCTCAAAGAGCGGGACGCCTTTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTC-AGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCA
* ** * * *
1371345 CTTTCAGTCCTCAAAGAGTGGGACGCCTTTTCTTTTAAAGCCCACCCGAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACACC-TTTC----AAAGCCCACACAAGTTGGTGGCA
** * ***
1371404 CCTTCAGTCGTCAAAGAGCAGGATGCTTTTTCTCTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGA--CACCTT-TC--AAAGCCCACACAAGTTGGTGGCA
* * *
1371463 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1371518 CCTTTT-AGACCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 --TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
1371573 CTTTTTACTCCTCAATGAGCAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
1371597 TACACTTTAT
Statistics
Matches: 476, Mismatches: 40, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
54 15 0.03
55 298 0.63
56 13 0.03
57 1 0.00
58 3 0.01
59 93 0.20
60 50 0.11
61 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:1372491 original size:21 final size:21
Alignment explanation
Indices: 1372465--1372521 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1372455 AAATTATCCA
1372465 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1372486 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1372507 AATGTATCGATACAT
1 AATGTATCGATACAT
1372522 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1372601 original size:19 final size:19
Alignment explanation
Indices: 1372577--1372659 Score: 78
Period size: 19 Copynumber: 4.9 Consensus size: 19
1372567 AATTCAACAA
1372577 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1372596 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1372611 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1372628 TTTG--T--ATAGATAAGT
1 TTTGTATCGATACATAAGT
*
1372643 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1372660 TTAGCTACTG
Statistics
Matches: 51, Mismatches: 3, Indels: 20
0.69 0.04 0.27
Matches are distributed among these distances:
13 11 0.22
15 14 0.27
17 4 0.08
19 22 0.43
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1372616 original size:13 final size:13
Alignment explanation
Indices: 1372598--1372622 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1372588 ACATAAGTTT
1372598 TGTATCGATACAA
1 TGTATCGATACAA
1372611 TGTATCGATACA
1 TGTATCGATACA
1372623 TAAGTTTTGT
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:1372620 original size:32 final size:33
Alignment explanation
Indices: 1372578--1372659 Score: 123
Period size: 32 Copynumber: 2.5 Consensus size: 33
1372568 ATTCAACAAT
*
1372578 TTGTATCGATACATAAGTTTTGTATCGATACA-A
1 TTGTATCGATACATAAGTTTTGTATAGATA-AGA
1372611 -TGTATCGATACATAAGTTTTGTATAGATAAGTA
1 TTGTATCGATACATAAGTTTTGTATAGATAAG-A
1372644 TTGTATCGATACATAA
1 TTGTATCGATACATAA
1372660 TTAGCTACTG
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
31 1 0.02
32 28 0.62
33 1 0.02
34 15 0.33
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.39
Consensus pattern (33 bp):
TTGTATCGATACATAAGTTTTGTATAGATAAGA
Found at i:1372717 original size:13 final size:13
Alignment explanation
Indices: 1372699--1372724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1372689 CATTTTTCTG
1372699 TGTATCGATACAT
1 TGTATCGATACAT
1372712 TGTATCGATACAT
1 TGTATCGATACAT
1372725 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:1372721 original size:33 final size:33
Alignment explanation
Indices: 1372679--1372745 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1372669 GCCAAGGAAA
***
1372679 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1372712 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1372745 T
1 T
1372746 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:1375151 original size:51 final size:53
Alignment explanation
Indices: 1375076--1375468 Score: 183
Period size: 52 Copynumber: 7.5 Consensus size: 53
1375066 AGTTTCTCAA
* * * * *
1375076 TTCTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1375127 TT-TTCTATAATTGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAAT
* * * *** * *
1375181 TTCTTCACAATCGGGGATACTCCAACCCCG--TTGATCATCGGGGATACTCCAACCCCGT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAA-----T
* * * * ***
1375239 TAT-TTC-CGA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGAT
1 T-TCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* * * * * *
1375288 TT-TTCATAATCGGGGATATTCCAA-TCCCAGTTTTA-TTGCTAAAACACTAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGA-TTTTATTTCCAAAAACACCAAT
* * * * *
1375339 TT-TTCCACAATCGGGGATACTTCAACCCCGGTTTTATTTTC-GAAACACCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAA-T
* * * *
1375392 TTCCTT--TAATCGGGGATACTCCAACTCTGATTTCATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
* *
1375444 TT-TTCACAGTCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
1375469 CTTGTTATTT
Statistics
Matches: 254, Mismatches: 59, Indels: 57
0.69 0.16 0.15
Matches are distributed among these distances:
48 4 0.02
49 3 0.01
50 10 0.04
51 60 0.24
52 80 0.31
53 34 0.13
54 26 0.10
55 23 0.09
56 2 0.01
57 6 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (53 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
Found at i:1375260 original size:28 final size:27
Alignment explanation
Indices: 1375190--1375265 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 27
1375180 TTTCTTCACA
1375190 ATCGGGGATACTCCAACCCCGTTGATC
1 ATCGGGGATACTCCAACCCCGTTGATC
1375217 ATCGGGGATACTCCAACCCCGTT-AT-
1 ATCGGGGATACTCCAACCCCGTTGATC
*
1375242 TTCCGAGGGGATACTCCAACCCCG
1 AT-C--GGGGATACTCCAACCCCG
1375266 ACTTTATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 1 0.02
26 3 0.07
27 23 0.51
28 18 0.40
ACGTcount: A:0.22, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTGATC
Found at i:1375503 original size:28 final size:28
Alignment explanation
Indices: 1375457--1375528 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 28
1375447 TCACAGTCGA
** * **
1375457 GGATACTCCAACCTTGTTATTTCATCGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1375485 GGATACTCCAACCCCGTTACTTCCGAGG
1 GGATACTCCAACCCCGTTACTTCAGAGG
*
1375513 GGATACTCTAACCCCG
1 GGATACTCCAACCCCG
1375529 GCTTTATTCC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.26
Consensus pattern (28 bp):
GGATACTCCAACCCCGTTACTTCAGAGG
Found at i:1375546 original size:263 final size:263
Alignment explanation
Indices: 1375079--1375574 Score: 739
Period size: 263 Copynumber: 1.9 Consensus size: 263
1375069 TTCTCAATTC
* * *
1375079 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATTGGGGA
1 TCCACAATCGAGGATATTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
1375144 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTCATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
*
1375209 CGTTGATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATT
131 CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
* * *
1375274 TCCAAAATATTGATTTTTCATAATCGGGGATATTCCAATCCCAGTTTTATTGCTAAAACACTAAT
196 CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAATCCCAGTTTTATTGCTAAAACACTAAT
1375339 TTT
261 TTT
* * * *
1375342 TCCACAATCGGGGATACTT-CAACCCCGGTTTTATTTTCGAAACACCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATA-TTCCAACCCCGATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* * *
1375406 GATACTCCAACTCTGATTTCATTTCC-AAAAATACCAATTT-TTCACAGTCGAGGATACTCCAAC
64 GATACTCCAACTCCGATTTCATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
** * *
1375469 CTTGTT-ATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCCCGGCTT
129 CCCGTTGA--TCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTT
*
1375533 TATTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAA
192 TATTCCCAAAATATTGATTTCTCATAATCGGGGATACTCCAA
1375575 CCTCGTTATT
Statistics
Matches: 208, Mismatches: 21, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
261 1 0.00
262 25 0.12
263 147 0.71
264 35 0.17
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (263 bp):
TCCACAATCGAGGATATTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCCAACTCCGATTTCATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTGATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGACTTTATT
CCCAAAATATTGATTTCTCATAATCGGGGATACTCCAATCCCAGTTTTATTGCTAAAACACTAAT
TTT
Found at i:1375659 original size:77 final size:79
Alignment explanation
Indices: 1375482--1375684 Score: 214
Period size: 77 Copynumber: 2.6 Consensus size: 79
1375472 GTTATTTCAT
* * * *
1375482 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCTAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
* * *
1375547 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * ** *
1375561 TGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAATCCC-GATTT-TTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAAT-A
1375623 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* * * * *
1375638 CGGGGATACTCCAGCCCCGTTATTTTCAAGGGAACATTCCAACCCCG
1 CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
1375685 TTATTATCTC
Statistics
Matches: 101, Mismatches: 21, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
76 3 0.03
77 54 0.53
78 4 0.04
79 40 0.40
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:1377954 original size:20 final size:20
Alignment explanation
Indices: 1377928--1377982 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1377918 AAAAAGATAG
*
1377928 AATGTATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* *
1377948 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
1377968 AATGTATCGATACAT
1 AATGTATCGATACAT
1377983 CTGGGTAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:1381984 original size:20 final size:20
Alignment explanation
Indices: 1381959--1382014 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1381949 TATTGCCAGT
1381959 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
1381979 TTCATGTATCGATACATTTG
1 TTCATGTATCGATACATTTG
1381999 TTCATGTATCGATACA
1 TTCATGTATCGATACA
1382015 ATGAACAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (20 bp):
TTCATGTATCGATACATTTG
Found at i:1382913 original size:19 final size:20
Alignment explanation
Indices: 1382889--1382946 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
1382879 TGTATCGATA
**
1382889 CATTGTATCAATACATG-CT
1 CATTGTATCAATACATGAAG
* *
1382908 CATTGTCTCGATACATGAAG
1 CATTGTATCAATACATGAAG
*
1382928 AATTGTATCAATACATGAA
1 CATTGTATCAATACATGAA
1382947 ACTAACAATA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (20 bp):
CATTGTATCAATACATGAAG
Found at i:1385094 original size:15 final size:15
Alignment explanation
Indices: 1385074--1385111 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1385064 AAAATAATCA
*
1385074 AAAATTATTGAAAAT
1 AAAATTATTGAAAAG
*
1385089 AAAATTCTTGAAAAG
1 AAAATTATTGAAAAG
1385104 AAAATTAT
1 AAAATTAT
1385112 CGAACTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (15 bp):
AAAATTATTGAAAAG
Found at i:1389178 original size:13 final size:13
Alignment explanation
Indices: 1389160--1389184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1389150 AAAACCCAGA
1389160 TGTATCGATACAC
1 TGTATCGATACAC
1389173 TGTATCGATACA
1 TGTATCGATACA
1389185 GGAGCACTAT
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:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1391634 original size:19 final size:20
Alignment explanation
Indices: 1391590--1391642 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1391580 CTGCCAGTTT
**
1391590 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1391610 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1391629 CATGTATCGATACA
1 CATGTATCGATACA
1391643 TTATATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1391687 original size:20 final size:20
Alignment explanation
Indices: 1391664--1391716 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
1391654 CAAAGCATAA
* *
1391664 TGTATTGATACATCTGGGTG
1 TGTATCGATACATCTAGGTG
1391684 TGTATCGATACATCTAGGTG
1 TGTATCGATACATCTAGGTG
*
1391704 TGTATCAATACAT
1 TGTATCGATACAT
1391717 TCAAGGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATCTAGGTG
Found at i:1396334 original size:19 final size:19
Alignment explanation
Indices: 1396290--1396345 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1396280 CTGCTAGTTT
**
1396290 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1396310 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1396329 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1396346 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1396348 original size:13 final size:13
Alignment explanation
Indices: 1396330--1396356 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1396320 TACAATGAAC
1396330 ATGTATCGATACA
1 ATGTATCGATACA
1396343 ATGTATCGATACA
1 ATGTATCGATACA
1396356 A
1 A
1396357 AGCATAATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1397473 original size:31 final size:31
Alignment explanation
Indices: 1397438--1397499 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1397428 AATACGTTTG
1397438 GAAAATTATAATAAGTCTTATTCACTTAAAA
1 GAAAATTATAATAAGTCTTATTCACTTAAAA
*
1397469 GAAAATTGTAATAAGTCTTATTCACTTAAAA
1 GAAAATTATAATAAGTCTTATTCACTTAAAA
1397500 ATACTCTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (31 bp):
GAAAATTATAATAAGTCTTATTCACTTAAAA
Found at i:1397707 original size:20 final size:19
Alignment explanation
Indices: 1397684--1397730 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1397674 AAGTCCAGAA
*
1397684 GTATCGATACATATTGCCTT
1 GTATCGATACATATT-CATT
*
1397704 GTATCGATACATGTTCATT
1 GTATCGATACATATTCATT
1397723 GTATCGAT
1 GTATCGAT
1397731 CCATGAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (19 bp):
GTATCGATACATATTCATT
Found at i:1397726 original size:19 final size:20
Alignment explanation
Indices: 1397684--1397735 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1397674 AAGTCCAGAA
* *
1397684 GTATCGATACATATTGCCTT
1 GTATCGATACATGTTGCATT
1397704 GTATCGATACATGTT-CATT
1 GTATCGATACATGTTGCATT
*
1397723 GTATCGATCCATG
1 GTATCGATACATG
1397736 AAGAATTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
GTATCGATACATGTTGCATT
Found at i:1397796 original size:13 final size:13
Alignment explanation
Indices: 1397778--1397802 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1397768 CATGGGACAT
1397778 TGTATCGATACAA
1 TGTATCGATACAA
1397791 TGTATCGATACA
1 TGTATCGATACA
1397803 TAGTAAAATG
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:1402350 original size:32 final size:33
Alignment explanation
Indices: 1402285--1402352 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
1402275 GGTTTTACAG
* * *
1402285 ATTGTATCGATACAATGAAATTTGTATCGATAC
1 ATTGTATCAATACAATGAAAATTGTATCAATAC
*
1402318 ATTGTATCAATAC-ATTAAAATTGTATCAATAC
1 ATTGTATCAATACAATGAAAATTGTATCAATAC
1402350 ATT
1 ATT
1402353 TCAACTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (33 bp):
ATTGTATCAATACAATGAAAATTGTATCAATAC
Found at i:1403826 original size:32 final size:32
Alignment explanation
Indices: 1403776--1403838 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1403766 CACCCAGATG
* *
1403776 TATCGATACATTATGCTTTGTATCGATACATT
1 TATCAATAAATTATGCTTTGTATCGATACATT
1403808 TATCAATAAATTATGCTTTGTATCGATACAT
1 TATCAATAAATTATGCTTTGTATCGATACAT
1403839 GAAACTGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (32 bp):
TATCAATAAATTATGCTTTGTATCGATACATT
Found at i:1403906 original size:33 final size:32
Alignment explanation
Indices: 1403869--1403933 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
1403859 TACCACTATT
1403869 TGTATCGACACATG-GCACATTGTATTGATACAA
1 TGTATCGACACATGAG-A-ATTGTATTGATACAA
*
1403902 TGTATCGATACATGATGAATTGTATTGATACA
1 TGTATCGACACATGA-GAATTGTATTGATACA
1403934 TTACTTCAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 27 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGACACATGAGAATTGTATTGATACAA
Found at i:1410255 original size:21 final size:22
Alignment explanation
Indices: 1410231--1410280 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
1410221 ATCAAATCTT
* *
1410231 CTTCAAATTTCTT-ATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1410252 CTTCAAAATACTTCATTTTTCA
1 CTTCAAAATACTTCATTTTTCA
1410274 --TCAAAAT
1 CTTCAAAAT
1410281 TATCAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 8 0.31
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (22 bp):
CTTCAAAATACTTCATTTTTCA
Found at i:1413232 original size:23 final size:23
Alignment explanation
Indices: 1413205--1413253 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1413195 AAGGTTATAC
1413205 CTTTGCCTTAAAGGTAATCAATT
1 CTTTGCCTTAAAGGTAATCAATT
1413228 CTTTGCCTTAAAGGTAATCAATT
1 CTTTGCCTTAAAGGTAATCAATT
1413251 CTT
1 CTT
1413254 GTAGTGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (23 bp):
CTTTGCCTTAAAGGTAATCAATT
Found at i:1413882 original size:13 final size:13
Alignment explanation
Indices: 1413864--1413889 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1413854 TACACAAAGT
1413864 ATGTATCGATACA
1 ATGTATCGATACA
1413877 ATGTATCGATACA
1 ATGTATCGATACA
1413890 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:1413887 original size:32 final size:33
Alignment explanation
Indices: 1413846--1413909 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1413836 TAGCCAACCT
**
1413846 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1413878 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1413910 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1417972 original size:15 final size:15
Alignment explanation
Indices: 1417952--1417982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1417942 TAAAAATATC
*
1417952 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1417967 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1417982 C
1 C
1417983 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1420083 original size:13 final size:13
Alignment explanation
Indices: 1420065--1420102 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1420055 CATTTTTCTT
1420065 TGTATCGATACAA
1 TGTATCGATACAA
*
1420078 TGTATCGATACAC
1 TGTATCGATACAA
*
1420091 TATATCGATACA
1 TGTATCGATACA
1420103 GGGGGGATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1422655 original size:19 final size:17
Alignment explanation
Indices: 1422626--1422695 Score: 65
Period size: 19 Copynumber: 4.0 Consensus size: 17
1422616 TTGCAGTAGC
*
1422626 CAAATTGTATCGATACA
1 CAAAATGTATCGATACA
1422643 CAAAGTATGTATCGAT--A
1 CAAA--ATGTATCGATACA
1422660 C-AAATGTATCGATACA
1 CAAAATGTATCGATACA
1422676 CAAAAAATTGTATCGATACA
1 C--AAAA-TGTATCGATACA
1422696 TTGGCTTGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
14 10 0.23
16 4 0.09
17 6 0.14
19 12 0.27
20 12 0.27
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (17 bp):
CAAAATGTATCGATACA
Found at i:1422668 original size:14 final size:14
Alignment explanation
Indices: 1422649--1422675 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1422639 TACACAAAGT
1422649 ATGTATCGATACAA
1 ATGTATCGATACAA
1422663 ATGTATCGATACA
1 ATGTATCGATACA
1422676 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (14 bp):
ATGTATCGATACAA
Found at i:1422669 original size:33 final size:35
Alignment explanation
Indices: 1422626--1422695 Score: 108
Period size: 33 Copynumber: 2.1 Consensus size: 35
1422616 TTGCAGTAGC
**
1422626 CAAATTGTATCGATACACAAAGTA-TGTATCGATA
1 CAAATTGTATCGATACACAAAAAATTGTATCGATA
1422660 CAAA-TGTATCGATACACAAAAAATTGTATCGATA
1 CAAATTGTATCGATACACAAAAAATTGTATCGATA
1422694 CA
1 CA
1422696 TTGGCTTGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 17 0.52
34 16 0.48
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (35 bp):
CAAATTGTATCGATACACAAAAAATTGTATCGATA
Done.