Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008423.1 Hibiscus syriacus cultivar Beakdansim tig00111206_pilon, whole genome shotgun sequence
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: 1633377
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 8
Found at i:1292850 original size:23 final size:23
Alignment explanation
Indices: 1292707--1292903 Score: 113
Period size: 23 Copynumber: 8.4 Consensus size: 23
1292697 ATTATAAACT
1292707 TATATATATAAAGTATAA-T-TA
1 TATATATATAAAGTATAAGTATA
* * * *
1292728 TAAAGACA-AAAATATAAGTATAA
1 TATATATATAAAGTATAAGTAT-A
*
1292751 TATAAAGTATATAAGTATATAAGTATA
1 TATATA-TATA-AAG--TATAAGTATA
* *
1292778 TA-AGAATATAAAGTAAAAGTATA
1 TATA-TATATAAAGTATAAGTATA
*
1292801 TATATCTATAAAGTATAAGTATATATA
1 TATATATATAAAGTATAAG----TATA
*
1292828 TATATATATAAACTATAAGTATA
1 TATATATATAAAGTATAAGTATA
* *
1292851 TATATATAAAAAATTATAA-T-TA
1 TATATAT-ATAAAGTATAAGTATA
* * *
1292873 TAAAGAT-TAAAGTAT-ATTATA
1 TATATATATAAAGTATAAGTATA
1292894 TATATATATA
1 TATATATATA
1292904 TACTTTATTC
Statistics
Matches: 136, Mismatches: 22, Indels: 35
0.70 0.11 0.18
Matches are distributed among these distances:
19 1 0.01
20 15 0.11
21 13 0.10
22 10 0.07
23 40 0.29
24 11 0.08
25 4 0.03
26 7 0.05
27 26 0.19
28 9 0.07
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.37
Consensus pattern (23 bp):
TATATATATAAAGTATAAGTATA
Found at i:1292857 original size:27 final size:27
Alignment explanation
Indices: 1292797--1292858 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
1292787 AAAGTAAAAG
* *
1292797 TATATATATCTATAAAGTATAAGTATA
1 TATATATATATATAAACTATAAGTATA
1292824 TATATATATATATAAACTATAAGTATA
1 TATATATATATATAAACTATAAGTATA
1292851 TATATATA
1 TATATATA
1292859 AAAAATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (27 bp):
TATATATATATATAAACTATAAGTATA
Found at i:1292975 original size:20 final size:20
Alignment explanation
Indices: 1292889--1293179 Score: 133
Period size: 20 Copynumber: 13.9 Consensus size: 20
1292879 TTAAAGTATA
1292889 TTATA-TATATATATATACT
1 TTATATTATATATATATACT
* *
1292908 TTATTCTTTATAATTATACTCTA-T
1 TTA-T-ATTAT-A-TATA-TATACT
1292932 TTATATGTATAATATACTTATACT
1 TTATAT-TAT-ATATA--TATACT
* * *
1292956 ATATATTATGTGTATATACT
1 TTATATTATATATATATACT
*
1292976 TTATAGTATATATATATACT
1 TTATATTATATATATATACT
*
1292996 TTATA-T-TCT-TATATACT
1 TTATATTATATATATATACT
1293013 TGTATATGTA-ATACTTATATA-T
1 T-TATAT-TATATA--TATATACT
*
1293035 TTATATTATACT-TAGATACT
1 TTATATTATA-TATATATACT
1293055 TTATATTATATGAT-TATACT
1 TTATATTATAT-ATATATACT
*
1293075 TTAATCTTTATAATTACTATATA-T
1 TT-AT-ATTAT-A-TA-TATATACT
*
1293099 ATATATATATATATATTTATACT
1 -T-TATAT-TATATATATATACT
*
1293122 TTATATTATTATATATGTA-T
1 TTATATTA-TATATATATACT
* *
1293142 ATATACTT-TATACTA-AAACT
1 TTATA-TTATATA-TATATACT
1293162 TTATA-TATATATATATAC
1 TTATATTATATATATATAC
1293180 ATACTTTTAC
Statistics
Matches: 209, Mismatches: 26, Indels: 74
0.68 0.08 0.24
Matches are distributed among these distances:
17 9 0.04
18 9 0.04
19 22 0.11
20 64 0.31
21 24 0.11
22 24 0.11
23 24 0.11
24 19 0.09
25 13 0.06
26 1 0.00
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.52
Consensus pattern (20 bp):
TTATATTATATATATATACT
Found at i:1293070 original size:28 final size:27
Alignment explanation
Indices: 1293023--1293075 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 27
1293013 TGTATATGTA
1293023 ATACTTATATATTTATATTATACTTAG
1 ATACTTATATATTTATATTATACTTAG
1293050 ATACTT-TATATTATATGATTATACTT
1 ATACTTATATATT-TAT-ATTATACTT
1293076 TAATCTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 6 0.25
27 9 0.38
28 9 0.38
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.53
Consensus pattern (27 bp):
ATACTTATATATTTATATTATACTTAG
Found at i:1293090 original size:28 final size:28
Alignment explanation
Indices: 1293023--1293101 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 28
1293013 TGTATATGTA
1293023 ATAC-TTATATATT-TATATTATACTTAG
1 ATACTTTATA-ATTATATATTATACTTAG
1293050 ATACTTTAT-ATTATATGATTATACTTTA-
1 ATACTTTATAATTATAT-ATTATAC-TTAG
1293078 AT-CTTTATAATTACTATATATATA
1 ATACTTTATAATTA-TATAT-TATA
1293102 TATATATATA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
26 3 0.07
27 13 0.29
28 19 0.42
29 10 0.22
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (28 bp):
ATACTTTATAATTATATATTATACTTAG
Found at i:1293099 original size:2 final size:2
Alignment explanation
Indices: 1293092--1293178 Score: 63
Period size: 2 Copynumber: 43.0 Consensus size: 2
1293082 TTATAATTAC
* *
1293092 TA TA TA TA TA TA TA TA TA TA TA TT TA TA CTT TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * *
1293133 TA TA TG TA TA TA TA CTT TA TA CTA -A AA CTT TA 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
1293175 TA TA
1 TA TA
1293179 CATACTTTTA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
1 3 0.04
2 60 0.90
3 4 0.06
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1293239 original size:13 final size:15
Alignment explanation
Indices: 1293210--1293242 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1293200 ACATACACAC
1293210 ATATATTGTATACTT
1 ATATATTGTATACTT
1293225 ATATATT-TATA-TT
1 ATATATTGTATACTT
1293238 ATATA
1 ATATA
1293243 CTTTTGTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 4 0.22
15 7 0.39
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (15 bp):
ATATATTGTATACTT
Found at i:1293325 original size:17 final size:17
Alignment explanation
Indices: 1293303--1293341 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1293293 TATGTATATA
* *
1293303 TATATATATTTATAGTT
1 TATATATATATATACTT
1293320 TATATATATATATACTT
1 TATATATATATATACTT
1293337 TATAT
1 TATAT
1293342 TTAAACTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TATATATATATATACTT
Found at i:1293480 original size:2 final size:2
Alignment explanation
Indices: 1293473--1293635 Score: 85
Period size: 2 Copynumber: 83.0 Consensus size: 2
1293463 TAGTTCATGG
* * *
1293473 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA TA TA GTT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
1293516 -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TT TA TA T- 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
* *
1293557 TA TA TA -A TA TA -A TA TA -A TA TA TA CTT TA TA TA TA CA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
* * *
1293596 TA TA -A TT TA TA TG TA GTT TA TA TA TA GTA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
1293636 ATTGTTTAAA
Statistics
Matches: 120, Mismatches: 24, Indels: 34
0.67 0.13 0.19
Matches are distributed among these distances:
1 10 0.08
2 102 0.85
3 8 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1293487 original size:23 final size:20
Alignment explanation
Indices: 1293429--1293487 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 20
1293419 CTATATAATT
1293429 TATATATAGTTTAATAGTTCA
1 TATATATAGTTT-ATAGTTCA
* * *
1293450 TATATAAACTCTATAGTTCA
1 TATATATAGTTTATAGTTCA
1293470 TGGTATATATAGTTTATA
1 ---TATATATAGTTTATA
1293488 CATAATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
23 12 0.41
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (20 bp):
TATATATAGTTTATAGTTCA
Found at i:1293515 original size:11 final size:10
Alignment explanation
Indices: 1293492--1293632 Score: 69
Period size: 11 Copynumber: 13.9 Consensus size: 10
1293482 TTTATACATA
*
1293492 ATATATATAT
1 ATATATATTT
1293502 ATATATAGTTT
1 ATATATA-TTT
*
1293513 ATA-ATA-AT
1 ATATATATTT
* **
1293521 ATAAATATAA
1 ATATATATTT
1293531 ACTATATAGTTT
1 A-TATATA-TTT
*
1293543 ATTTATA-TT
1 ATATATATTT
*
1293552 ATATATATAT
1 ATATATATTT
*
1293562 A-ATATAATATA
1 ATATAT-AT-TT
1293573 ATATATACTTT
1 ATATATA-TTT
*
1293584 ATATATACATT
1 ATATATA-TTT
1293595 ATATA-ATTT
1 ATATATATTT
*
1293604 ATATGTAGTTT
1 ATATATA-TTT
*
1293615 ATATATA-GT
1 ATATATATTT
1293624 ATATATATT
1 ATATATATT
1293633 ATAATTGTTT
Statistics
Matches: 100, Mismatches: 18, Indels: 26
0.69 0.12 0.18
Matches are distributed among these distances:
8 4 0.04
9 29 0.29
10 18 0.18
11 42 0.42
12 7 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (10 bp):
ATATATATTT
Found at i:1293537 original size:30 final size:28
Alignment explanation
Indices: 1293474--1293567 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
1293464 AGTTCATGGT
*
1293474 ATATATAGTTTATACATAATATATATAT
1 ATATATAGTTTATACATAATATATATAA
1293502 ATATATAGTTTATA-ATAATATAAATATAA
1 ATATATAGTTTATACATAATAT--ATATAA
** * *
1293531 ACTATATAGTTTATTTATATTATATATAT
1 A-TATATAGTTTATACATAATATATATAA
1293560 ATAATATA
1 AT-ATATA
1293568 ATATAATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 7 0.12
28 15 0.26
29 17 0.30
30 12 0.21
31 6 0.11
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
ATATATAGTTTATACATAATATATATAA
Found at i:1293553 original size:9 final size:9
Alignment explanation
Indices: 1293541--1293635 Score: 58
Period size: 9 Copynumber: 10.6 Consensus size: 9
1293531 ACTATATAGT
*
1293541 TTATTTATA
1 TTATATATA
1293550 TTATATATA
1 TTATATATA
1293559 -TATA-ATA
1 TTATATATA
1293566 -TA-ATATA
1 TTATATATA
*
1293573 ATATATACT-
1 TTATATA-TA
1293582 TTATATATACA
1 TTATATAT--A
1293593 TTATATA-A
1 TTATATATA
*
1293601 TTTATATGTA
1 -TTATATATA
1293611 GTTTATATATA
1 --TTATATATA
*
1293622 GTATATATA
1 TTATATATA
1293631 TTATA
1 TTATA
1293636 ATTGTTTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
6 1 0.01
7 8 0.11
8 8 0.11
9 35 0.50
10 2 0.03
11 16 0.23
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (9 bp):
TTATATATA
Found at i:1295303 original size:80 final size:80
Alignment explanation
Indices: 1295177--1295464 Score: 434
Period size: 80 Copynumber: 3.6 Consensus size: 80
1295167 AGGGGAGCGG
* * * * *
1295177 ACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAGCGC
1 ACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACCTTATGCAC
*
1295241 ACAGCTAAGGGAACCA
65 ACAGCAAAGGGAACCA
*
1295257 ACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACA
1 ACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACA
* *
1295322 CAACAAAGGGATCCA
66 CAGCAAAGGGAACCA
* * *
1295337 ACCTAAGGATATACATTGGTACCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCTTATGCACA
1 ACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACA
1295402 CAGCAAAGGGAACCA
66 CAGCAAAGGGAACCA
* *
1295417 ACCTAAGGATATGCCTTGGGACCTACCTAAGATATCCTTAGGTCCGTA
1 ACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
1295465 ATGACTTACA
Statistics
Matches: 187, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
80 177 0.95
81 10 0.05
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (80 bp):
ACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGCACA
CAGCAAAGGGAACCA
Found at i:1299664 original size:21 final size:22
Alignment explanation
Indices: 1299638--1299678 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1299628 AATAGCGATC
1299638 AATGACATAAACTAT-AAATCA
1 AATGACATAAACTATGAAATCA
* *
1299659 AATGACTTAATCTATGAAAT
1 AATGACATAAACTATGAAAT
1299679 TTACTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
AATGACATAAACTATGAAATCA
Found at i:1303472 original size:23 final size:23
Alignment explanation
Indices: 1303446--1303521 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
1303436 ATTTATTATT
1303446 TTATTAATTAGGATTCTAGTTTG
1 TTATTAATTAGGATTCTAGTTTG
*
1303469 TTATTAATTAGGATTCTAATTTG
1 TTATTAATTAGGATTCTAGTTTG
*
1303492 CTATT-ATGTAGGATTCTAGTTT-
1 TTATTAAT-TAGGATTCTAGTTTG
1303514 TCTATTAA
1 T-TATTAA
1303522 ATACGATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 2 0.04
23 43 0.93
24 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.51
Consensus pattern (23 bp):
TTATTAATTAGGATTCTAGTTTG
Found at i:1303832 original size:16 final size:16
Alignment explanation
Indices: 1303813--1303849 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1303803 TTTATCTTTT
*
1303813 TTTTATTTTAAATAGG
1 TTTTATTTTAAATAAG
*
1303829 TTTTATTTTAATTAAG
1 TTTTATTTTAAATAAG
1303845 TTTTA
1 TTTTA
1303850 GAATATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (16 bp):
TTTTATTTTAAATAAG
Found at i:1310098 original size:5 final size:5
Alignment explanation
Indices: 1310081--1310165 Score: 64
Period size: 5 Copynumber: 17.0 Consensus size: 5
1310071 TCGTTCTATT
* ** * *
1310081 TTTTA TTTCA TTTTA TTTCG TTCTA TTTCA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*** * *
1310131 TAAAA CTTTA TTTTCA TTCTA -TTTA TTTTA TTTTA
1 TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA
1310166 ATTATTTTTT
Statistics
Matches: 58, Mismatches: 20, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
4 3 0.05
5 51 0.88
6 4 0.07
ACGTcount: A:0.22, C:0.08, G:0.01, T:0.68
Consensus pattern (5 bp):
TTTTA
Found at i:1310155 original size:15 final size:14
Alignment explanation
Indices: 1310101--1310178 Score: 57
Period size: 15 Copynumber: 5.3 Consensus size: 14
1310091 TTTTATTTCG
1310101 TTCTATTTCATTTTA
1 TTCTATTT-ATTTTA
*
1310116 TTTTATTTTATTTTA
1 TTCTA-TTTATTTTA
***
1310131 TAAAACTTTATTTTCA
1 TTCTA-TTTATTTT-A
1310147 TTCTATTTATTTTA
1 TTCTATTTATTTTA
* * *
1310161 TTTTAATTATTTTT
1 TTCTATTTATTTTA
1310175 TTCT
1 TTCT
1310179 CTGGACAGAT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
14 15 0.31
15 28 0.57
16 6 0.12
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (14 bp):
TTCTATTTATTTTA
Found at i:1311323 original size:34 final size:33
Alignment explanation
Indices: 1311243--1311336 Score: 131
Period size: 34 Copynumber: 2.9 Consensus size: 33
1311233 TGACAAGTTG
1311243 GAAAATTCATCTTGG-TGGTGGCCAA-TTATTT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
*
1311274 GAAATTTCATCTTGGTTGGTGGCCAACTTA-TT
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
*
1311306 GAAAAATTCATCTTTGGTAGGTGGCCAACTT
1 G-AAAATTCATC-TTGGTTGGTGGCCAACTT
1311337 TGCACATGGT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
31 14 0.25
32 13 0.23
33 12 0.21
34 17 0.30
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTT
Found at i:1313292 original size:25 final size:25
Alignment explanation
Indices: 1313263--1313314 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1313253 ATTTCTAGCT
*
1313263 TTGATTTCCAGCCTCCAA-ATTTGAC
1 TTGATTTACAGCC-CCAACATTTGAC
*
1313288 TTGATTTACAGCCCCAACTTTTGAC
1 TTGATTTACAGCCCCAACATTTGAC
1313313 TT
1 TT
1313315 CCAACAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (25 bp):
TTGATTTACAGCCCCAACATTTGAC
Found at i:1320425 original size:16 final size:17
Alignment explanation
Indices: 1320399--1320435 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1320389 AGGATATTAT
*
1320399 TAATAAAACAATAATAA
1 TAATAAAACAACAATAA
1320416 TAAT-AAACAACAATAA
1 TAATAAAACAACAATAA
1320432 TAAT
1 TAAT
1320436 TAATATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (17 bp):
TAATAAAACAACAATAA
Found at i:1326806 original size:17 final size:17
Alignment explanation
Indices: 1326784--1326816 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1326774 GTCGGCTAAA
*
1326784 AGAAATGGTTATGGTAT
1 AGAAATGGATATGGTAT
1326801 AGAAATGGATATGGTA
1 AGAAATGGATATGGTA
1326817 AAGGTAAGAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.30, T:0.30
Consensus pattern (17 bp):
AGAAATGGATATGGTAT
Found at i:1328863 original size:22 final size:22
Alignment explanation
Indices: 1328833--1328883 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1328823 CATGGGCCTA
*
1328833 ATGGGCCTAGTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACCTT
*
1328855 ATGGACCTATTTGTAAGACCTT
1 ATGGACCTAGTTGTAAGACCTT
1328877 ATGGACC
1 ATGGACC
1328884 CTAAGGTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (22 bp):
ATGGACCTAGTTGTAAGACCTT
Found at i:1331575 original size:17 final size:18
Alignment explanation
Indices: 1331530--1331576 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1331520 AAAATTAATT
1331530 ATGATAATTAAATTAATAA
1 ATGATAATT-AATTAATAA
* *
1331549 AT-ATACTTAATT-ATTA
1 ATGATAATTAATTAATAA
1331565 ATGATAATTAAT
1 ATGATAATTAAT
1331577 ATACTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 5 0.21
17 12 0.50
18 5 0.21
19 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (18 bp):
ATGATAATTAATTAATAA
Found at i:1331596 original size:14 final size:15
Alignment explanation
Indices: 1331575--1331666 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 15
1331565 ATGATAATTA
1331575 ATATACTTTATATTT
1 ATATACTTTATATTT
1331590 A-ATAC-TTATATTT
1 ATATACTTTATATTT
*
1331603 ATATACTTTAATACTT
1 ATATACTTT-ATATTT
*** *
1331619 ATAT-CCAAACACTTT
1 ATATACTTTATA-TTT
*
1331634 AT-TACTTTACA-TT
1 ATATACTTTATATTT
*
1331647 ATATACTTTATATAT
1 ATATACTTTATATTT
1331662 ATATA
1 ATATA
1331667 TATAGATTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
13 13 0.22
14 19 0.32
15 18 0.31
16 9 0.15
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATACTTTATATTT
Found at i:1331632 original size:22 final size:22
Alignment explanation
Indices: 1331587--1331640 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1331577 ATACTTTATA
** * *
1331587 TTTAATACTTATATTTATATAC
1 TTTAATACTTATATCCAAACAC
1331609 TTTAATACTTATATCCAAACAC
1 TTTAATACTTATATCCAAACAC
*
1331631 TTTATTACTT
1 TTTAATACTT
1331641 TACATTATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTAATACTTATATCCAAACAC
Found at i:1331670 original size:19 final size:19
Alignment explanation
Indices: 1331646--1331685 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1331636 TACTTTACAT
*
1331646 TATATACTTTATATATATA
1 TATATACATTATATATATA
* *
1331665 TATATAGATTATATATGTA
1 TATATACATTATATATATA
1331684 TA
1 TA
1331686 CAAATTGAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TATATACATTATATATATA
Found at i:1332665 original size:2 final size:2
Alignment explanation
Indices: 1332654--1332691 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1332644 TTGAAACAAT
1332654 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1332692 GAATGTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1332775 original size:14 final size:14
Alignment explanation
Indices: 1332752--1332785 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1332742 TACTTTATGT
*
1332752 ATATATATATATAC
1 ATATACATATATAC
1332766 ATATACATATATAC
1 ATATACATATATAC
*
1332780 TTATAC
1 ATATAC
1332786 TTTATAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
ATATACATATATAC
Found at i:1333270 original size:20 final size:20
Alignment explanation
Indices: 1333238--1333288 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1333228 ATAATATATA
1333238 TATATATATATATAATGAATG
1 TATATATA-ATATAATGAATG
* *
1333259 T-TATAATAATATGATGCATG
1 TATAT-ATAATATAATGAATG
1333279 TATATATAAT
1 TATATATAAT
1333289 GTAAAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (20 bp):
TATATATAATATAATGAATG
Found at i:1333335 original size:11 final size:11
Alignment explanation
Indices: 1333316--1333427 Score: 69
Period size: 11 Copynumber: 10.2 Consensus size: 11
1333306 ATATAAAGTG
*
1333316 TAAACTATATA
1 TAAAGTATATA
1333327 TAAAGTATATA
1 TAAAGTATATA
1333338 TATAAGTATATATA
1 TA-AAG--TATATA
*
1333352 TAAAGTGTATA
1 TAAAGTATATA
1333363 T--A-TATATA
1 TAAAGTATATA
*
1333371 T-AAGCTATAAA
1 TAAAG-TATATA
1333382 GTATAAGTATAT-
1 -TA-AAGTATATA
1333394 TATAAGTATATA
1 TA-AAGTATATA
1333406 TATAA--AT-TA
1 TA-AAGTATATA
1333415 TAAAGTATATA
1 TAAAGTATATA
1333426 TA
1 TA
1333428 CTTTCTACTA
Statistics
Matches: 83, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
8 8 0.10
9 6 0.07
10 4 0.05
11 38 0.46
12 9 0.11
13 7 0.08
14 11 0.13
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.39
Consensus pattern (11 bp):
TAAAGTATATA
Found at i:1333338 original size:577 final size:576
Alignment explanation
Indices: 1331686--1333341 Score: 1928
Period size: 577 Copynumber: 2.9 Consensus size: 576
1331676 TATATGTATA
* * *
1331686 CAAATTGAACAAACATGGAATTGAAAATAAAAAATTGAATAAATTAAACAACACACATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
* * ** *
1331751 GGATGAAATTGAATTAATTATAAAATGTGAAG-TTCATATTAATATAAAAATGGACGAAATTGAA
66 GGATGAAATTGAATTAATTATAAAATGTGAAGAAT-ATATTAAAATAAAAATGGAATAAATTGCA
* * * * *
1331815 TAGATTTAAAAAGTTGGTGAACATAATTTGAAAATAAATTTATTATGTGATTTACATTTTATA-G
130 TACACTTAAAAAGTTGATGAACATAATTTGAAAAGAAATTTATTATGTGATTCACATTTTATAGG
* * *
1331879 G---GTTTTAAGTAAATTACAAAAATATAACTAAGTATGGGTCAATTTCAGATACAAATATACTT
195 GTTTGTTTTAAGTAAATTACAAAAATATAAATAAGGATGGGTCAATTTCAGATACAAATATAATT
* * * *
1331941 TGAAGGACTAAATTGAACAAATATGAAATTACAAATTAAAA-TTTAAATACAATAAACAACATAA
260 TGAAGGAATAAATTGAACAAATATGAAATTA-AAAATAAAATTTTAAATAAAATAAACAACACAA
* * * *
1332005 AAGGATCAAATAAAAAAAAAGTGTAAAATGTGAGGAAAATTGTA-AAAA-GAACTGAATTGCATT
324 AAGAATCAAAT-CAAAAAAA-TGTAAAATGTGAAGAAAA-TGTATAAAATGAACTAAATTGCATT
* * * *
1332068 AATTTCAAAAGTT--GTAGAAAATTAAAAAAATTATAATATATAT-T-TAGT-T-TA-AT-GA-A
386 AATTTCAAAAATTAAG-AAAAAATTAAAACAATTATAATATATATATATA-TATATATATATATA
* * ** * * * *
1332124 TGT-TATG-AT-A-A--TATGATGCTG-T---ATATC-----TA-ATGTACATTATACTTTATAT
449 TATATATGAATGACATGTATAATAATGATAAAATATCAAGTATATATATAAATTAAACTATATAT
* * * * *
1332173 ATATAGATATACACATATGCATATATACTTATACTTTATAGTTCATATATGTATATAAAGTAC
514 AAATATATATATACATATACATATATACTTATACTTTATAGTTCATATATGCATATAAAGTAC
*
1332236 CAAATTGAGCAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
*
1332301 GGATGAAATTGAATTAATTATAAAATGTGAAGAATATATTAAAATAAAAATGGACTAAATTGCAT
66 GGATGAAATTGAATTAATTATAAAATGTGAAGAATATATTAAAATAAAAATGGAATAAATTGCAT
1332366 ACACTTAAAAAGTTGATGAACATAATTTGAAAAGAAATTTATTATGTGATTCACATTTTATAGGG
131 ACACTTAAAAAGTTGATGAACATAATTTGAAAAGAAATTTATTATGTGATTCACATTTTATAGGG
* *
1332431 TTTGTTTTAAGTAAATTACAAAAATATAAATAAGTATGGGTCAATTTCGGATACAAATATAATTT
196 TTTGTTTTAAGTAAATTACAAAAATATAAATAAGGATGGGTCAATTTCAGATACAAATATAATTT
* *
1332496 GAAGGAATAAATTGAACAAATATGAAATTAAAAATAAAATTTTAAATAAATTAAACAACACAAAT
261 GAAGGAATAAATTGAACAAATATGAAATTAAAAATAAAATTTTAAATAAAATAAACAACACAAAA
* * * * *
1332561 GAATTAAATCGAAATAATTGTAAAATGTGAAGAAAATGTGTAAAATTAACTAAATTGCATTAATT
326 GAATCAAATC-AAAAAAATGTAAAATGTGAAGAAAATGTATAAAATGAACTAAATTGCATTAATT
* *
1332626 TCAAAAGTTAAGAAAAAATTGAAACAATTATAATATATATATATATATATATATATATATATATA
390 TCAAAAATTAAGAAAAAATTAAAACAATTATAATATATATATATATATATATATATATATATATA
* * * ** * * * * * * *
1332691 TGAATGTATATGTATAATGATGATGATGTATGCATGTATATATGTACATTATACTTTATGTATAT
455 TGAATG-ACATGTATAATAATGATAAAATAT-CAAGTATATATATAAATTAAACTATATATAAAT
*
1332756 ATATATATACATATACATATATACTTATACTTTATAGTTTATATATGCATATAAAGTAC
518 ATATATATACATATACATATATACTTATACTTTATAGTTCATATATGCATATAAAGTAC
*
1332815 CAAATTGAACAAACATGAAATTGG-AA-AAAAAATTGAATAAATTAAGCAACACGCATTGATGAG
1 CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
* * *
1332878 GGATGAAATTGAATTAATTATAAAATGTGAA-ACTAATATTAATATAAAAATGGAATAAATTGGA
66 GGATGAAATTGAATTAATTATAAAATGTGAAGAAT-ATATTAAAATAAAAATGGAATAAATTGCA
* * * *
1332942 TACATTTAAAAAGTTGGTGAACATAATTTGAAAAGAAATTTATTATGTGATTTATATTTTATAGG
130 TACACTTAAAAAGTTGATGAACATAATTTGAAAAGAAATTTATTATGTGATTCACATTTTATAGG
* **
1333007 GTTTGTTTTAAGTAAATTACTAAAATATAAATAAGGATGGGTCAATTTCAGATATGAATATAATT
195 GTTTGTTTTAAGTAAATTACAAAAATATAAATAAGGATGGGTCAATTTCAGATACAAATATAATT
* * * * *
1333072 TGAA-GAACTAAATTGAACAAATCTGAAATTACAAATTTAAA-TTTAAA-AAAATAAATAACATA
260 TGAAGGAA-TAAATTGAACAAATATGAAATTA-AAAATAAAATTTTAAATAAAATAAACAACACA
** * * * * *
1333134 AAAGGGTCAAAT-AAAAAAATGTGAAATGTGAGGAAAAAT-TATAAAATGGATTGAATTGCATTA
323 AAAGAATCAAATCAAAAAAATGTAAAATGTGAAG-AAAATGTATAAAATGAACTAAATTGCATTA
* ** *
1333197 ATTTCAAAAATT-GGGGAAAATTAAAACAATTATAATATATATATATATATATATAATGAATGTT
387 ATTTCAAAAATTAAGAAAAAATTAAAACAATTATAATATATATATATATATATAT-AT--AT-AT
1333261 ATAATAATATG-ATG-CATGTATATATAATG-TAAAATAT-AAGTATATATATAAAGTGTAAACT
448 AT-AT-ATATGAATGACATGTATA-ATAATGATAAAATATCAAGTATATATATAAA-T-TAAACT
1333322 ATATATAAAGTATATATATA
508 ATATATAAA-TATATATATA
1333342 AGTATATATA
Statistics
Matches: 959, Mismatches: 97, Indels: 73
0.85 0.09 0.06
Matches are distributed among these distances:
550 177 0.18
551 3 0.00
552 3 0.00
553 29 0.03
554 147 0.15
555 25 0.03
556 3 0.00
557 3 0.00
558 2 0.00
559 2 0.00
560 1 0.00
561 3 0.00
562 4 0.00
563 2 0.00
565 1 0.00
566 1 0.00
568 8 0.01
569 1 0.00
572 3 0.00
573 39 0.04
574 61 0.06
575 6 0.01
576 50 0.05
577 264 0.28
578 16 0.02
579 105 0.11
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (576 bp):
CAAATTGAACAAACATGAAATTGGAAATAAAAAATTGAATAAATTAAGCAACACACATTGATGAG
GGATGAAATTGAATTAATTATAAAATGTGAAGAATATATTAAAATAAAAATGGAATAAATTGCAT
ACACTTAAAAAGTTGATGAACATAATTTGAAAAGAAATTTATTATGTGATTCACATTTTATAGGG
TTTGTTTTAAGTAAATTACAAAAATATAAATAAGGATGGGTCAATTTCAGATACAAATATAATTT
GAAGGAATAAATTGAACAAATATGAAATTAAAAATAAAATTTTAAATAAAATAAACAACACAAAA
GAATCAAATCAAAAAAATGTAAAATGTGAAGAAAATGTATAAAATGAACTAAATTGCATTAATTT
CAAAAATTAAGAAAAAATTAAAACAATTATAATATATATATATATATATATATATATATATATAT
GAATGACATGTATAATAATGATAAAATATCAAGTATATATATAAATTAAACTATATATAAATATA
TATATACATATACATATATACTTATACTTTATAGTTCATATATGCATATAAAGTAC
Found at i:1333346 original size:43 final size:42
Alignment explanation
Indices: 1333279--1333698 Score: 164
Period size: 44 Copynumber: 9.8 Consensus size: 42
1333269 ATGATGCATG
*
1333279 TATATATAATGTA-AAATATAAGTATATATATAAAGTGTAAA
1 TATATATAAAGTATAAATATAAGTATATATATAAAGTGTAAA
* *
1333320 CTATATATAAAGTATATATATAAGTATATATATAAAGTGTATA
1 -TATATATAAAGTATAAATATAAGTATATATATAAAGTGTAAA
1333363 TATATATATAAGCTATAAAGTATAAGTATAT-TAT-AA--GT--A
1 TATATATA-AAG-TATAAA-TATAAGTATATATATAAAGTGTAAA
* * * * * *
1333402 TATATATAAATTATAAAGTATATA-TACTTTCTACTAAAACTTTATA
1 TATATATAAAGTATAAA-TATA-AGTA-TATATA-T-AAAGTGTAAA
* * **
1333448 TATATTATAAACTTATATATATAAAGTATA-ATTATAAAG-ACAAA
1 TATA-TATAAA-GTATAAATAT-AAGTATATA-TATAAAGTGTAAA
* *
1333492 AATATAT-AAGTATAGAATATAAAGTATATAAGTATATAAGTATATAA
1 TATATATAAAGTATA-AATAT-AAGTATAT-A-TATA-AAGTGTA-AA
* * *
1333539 GA-ATATAAAGTA-AAAGTATATA-TATAAACTATAAAGTATAAGTA
1 TATATATAAAGTATAAA-TATA-AGTATATA-TATAAAGTGTAA--A
* * * *
1333583 TATATATATA-TATATATATATA-TATATATATATA-TATAAA
1 TATATATAAAGTATAAATATA-AGTATATATATAAAGTGTAAA
* * *
1333623 -ATATATAATA-TATAATATATATAAGTATTATATATATA-TATATA
1 TATATATAA-AGTAT-A-A-ATATAAGTA-TATATATAAAGTGTAAA
* *
1333667 TATATATATA-TATATATATATA-TATATATATA
1 TATATATAAAGTATAAATATA-AGTATATATATA
1333699 CTCTATTTTT
Statistics
Matches: 306, Mismatches: 32, Indels: 82
0.73 0.08 0.20
Matches are distributed among these distances:
37 13 0.04
38 5 0.02
39 18 0.06
40 14 0.05
41 14 0.05
42 44 0.14
43 54 0.18
44 58 0.19
45 39 0.13
46 17 0.06
47 21 0.07
48 9 0.03
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (42 bp):
TATATATAAAGTATAAATATAAGTATATATATAAAGTGTAAA
Found at i:1333392 original size:26 final size:24
Alignment explanation
Indices: 1333325--1333403 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 24
1333315 GTAAACTATA
*
1333325 TATAAAGTATATATATAAGTATATA-
1 TATAAAGTATATATAT-ATTATA-AG
*
1333350 TATAAAGTGTATATATATATATAAG
1 TATAAAGTATATATATAT-TATAAG
1333375 CTATAAAGTATA-AGTATATTATAAG
1 -TATAAAGTATATA-TATATTATAAG
1333400 TATA
1 TATA
1333404 TATATAAATT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
24 6 0.13
25 26 0.55
26 15 0.32
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (24 bp):
TATAAAGTATATATATATTATAAG
Found at i:1333519 original size:22 final size:24
Alignment explanation
Indices: 1333494--1333586 Score: 80
Period size: 22 Copynumber: 4.2 Consensus size: 24
1333484 AAGACAAAAA
1333494 TATATAAGTATAGAA-TATA-AAG
1 TATATAAGTATAGAAGTATATAAG
*
1333516 TATATAAGTATATAAGTATATAAG
1 TATATAAGTATAGAAGTATATAAG
*
1333540 AATATAAAGTA-A-AAGTATAT-A-
1 TATAT-AAGTATAGAAGTATATAAG
*
1333561 TATA-AACTATA-AAG--TATAAG
1 TATATAAGTATAGAAGTATATAAG
1333581 TATATA
1 TATATA
1333587 TATATATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.05
19 5 0.08
20 8 0.13
21 4 0.07
22 15 0.25
23 12 0.20
24 8 0.13
25 5 0.08
ACGTcount: A:0.55, C:0.01, G:0.11, T:0.33
Consensus pattern (24 bp):
TATATAAGTATAGAAGTATATAAG
Found at i:1333537 original size:10 final size:8
Alignment explanation
Indices: 1333494--1333650 Score: 91
Period size: 8 Copynumber: 21.4 Consensus size: 8
1333484 AAGACAAAAA
1333494 TATATAAG
1 TATATAAG
*
1333502 TATAGAA-
1 TATATAAG
1333509 TATA-AAG
1 TATATAAG
1333516 TATATAAG
1 TATATAAG
1333524 TATATAAG
1 TATATAAG
1333532 TATATAAG
1 TATATAAG
*
1333540 AATATAAAG
1 TATAT-AAG
1333549 TA-A-AAG
1 TATATAAG
1333555 TATAT-A-
1 TATATAAG
*
1333561 TATA-AAC
1 TATATAAG
1333568 TATA-AAG
1 TATATAAG
1333575 --TATAAG
1 TATATAAG
1333581 TATAT-A-
1 TATATAAG
1333587 TATAT-A-
1 TATATAAG
1333593 TATAT-A-
1 TATATAAG
1333599 TATATATA-
1 TATATA-AG
1333607 TATATATA-
1 TATATA-AG
*
1333615 TATATAAAA
1 TATAT-AAG
1333624 TATATAA-
1 TATATAAG
*
1333631 TATATAATA
1 TATATAA-G
1333640 TATATAAG
1 TATATAAG
1333648 TAT
1 TAT
1333651 TATATATATA
Statistics
Matches: 128, Mismatches: 5, Indels: 32
0.78 0.03 0.19
Matches are distributed among these distances:
5 2 0.02
6 32 0.25
7 24 0.19
8 53 0.41
9 17 0.13
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.38
Consensus pattern (8 bp):
TATATAAG
Found at i:1333588 original size:2 final size:2
Alignment explanation
Indices: 1333581--1333956 Score: 244
Period size: 2 Copynumber: 192.0 Consensus size: 2
1333571 AAAGTATAAG
1333581 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1333622 AA TA TA TA -A TA TA TA -A TA TA TA TA -A GTA T- 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
*
1333661 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * * *
1333704 TT TT TA TA TA TA CTT TA CTT TA TA -A TA TA CTA T- TA TA TG TA
1 TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA
*
1333745 TA TA TA TA CT- TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TC T-
1 TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1333787 TA TA TA CT- TG TA TA TG TA -A TA CT- TA TA TA T- TT TA TA T- TA
1 TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * *
1333826 TA TA CT- TA GA TA CTT TA TA T- TA TA TGA T- TA TA TA CTT TA -A
1 TA TA -TA TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA
* *
1333866 TC TT TA TA -A T- TA TA CTA TA TA TA TA TA T- TA TA T- 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
* * * *
1333905 T- TA T- TA TA TA TG TA TA TA TA CTT TA TA CTA -A AA CTT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA
1333945 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1333957 CATACTTTTA
Statistics
Matches: 300, Mismatches: 32, Indels: 84
0.72 0.08 0.20
Matches are distributed among these distances:
1 25 0.08
2 254 0.85
3 21 0.07
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1333747 original size:33 final size:33
Alignment explanation
Indices: 1333555--1333963 Score: 201
Period size: 31 Copynumber: 12.5 Consensus size: 33
1333545 AAAGTAAAAG
*
1333555 TATATATATAAAC-TATA-AAGTATA-AGTATATA
1 TATATATATATACTTATATAA-TATATA-TATATA
1333587 TATATATATATA--TATAT-ATATATATATATA
1 TATATATATATACTTATATAATATATATATATA
* *
1333617 TATAAAATATATA-ATATATAATATATATAAGTATTA
1 TAT-ATATATATACTTATATAATATATAT-A-TA-TA
1333653 TATATATATATA-TATATATATATATATATATATA
1 TATATATATATACT-TATATA-ATATATATATATA
** *
1333687 TATATATATATACTCTAT-TTTTATATATACTTTA
1 TATATATATATACT-TATATAATATATATA-TATA
* *
1333721 CTTTATA-ATATAC-TAT-T-ATATGTATATATA
1 -TATATATATATACTTATATAATATATATATATA
1333751 TACT-TATATAGTA--TATAT-ATATATATATATA
1 TA-TATATATA-TACTTATATAATATATATATATA
*
1333782 TATCT-TATATACTTGTATATGTAATACT-TATATAT-
1 TATATATATATAC-T-TATA--TAATA-TATATATATA
* * *
1333817 TTTATATTATATACTTAGATACT-T-TATAT-TA
1 TATATA-TATATACTTATATAATATATATATATA
* *
1333848 TATGAT-TATATAC-T-T-TAATCTTTATAATTATA
1 TAT-ATATATATACTTATATAATATATAT-A-TATA
*
1333880 CTATATATATATA-TTATATTATATAT-TATTATA
1 -TATATATATATACTTATATAATATATATA-TATA
* * *
1333913 TATGTATATATACTTTATACTAAAACTTTATATATA
1 TATATATATATAC-TTATA-TAATA-TATATATATA
*
1333949 TATATATACATACTT
1 TATATATATATACTT
1333964 TTACTTTATA
Statistics
Matches: 302, Mismatches: 30, Indels: 87
0.72 0.07 0.21
Matches are distributed among these distances:
27 3 0.01
28 1 0.00
29 9 0.03
30 37 0.12
31 48 0.16
32 37 0.12
33 39 0.13
34 32 0.11
35 38 0.13
36 40 0.13
37 18 0.06
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.49
Consensus pattern (33 bp):
TATATATATATACTTATATAATATATATATATA
Found at i:1333830 original size:22 final size:22
Alignment explanation
Indices: 1333749--1334028 Score: 111
Period size: 22 Copynumber: 12.6 Consensus size: 22
1333739 TATGTATATA
* *
1333749 TATACTTATATA-GTATATATATA
1 TATA-TTATATACTTATATAT-TT
*
1333772 TATATATATATATCTTATATACTTG
1 TATAT-TATATA-CTTATATA-TTT
1333797 TATATGTA-ATACTTATATATTT
1 TATAT-TATATACTTATATATTT
* *
1333819 TATATTATATACTTAGATACTT
1 TATATTATATACTTATATATTT
*
1333841 TATATTATATGA-TTATATACTT
1 TATATTATAT-ACTTATATATTT
* * *
1333863 TA-ATCTTTATAATTATACTA-TA
1 TATAT-TATATACTTATA-TATTT
1333885 TATATATATTATA-TTATATATTAT
1 TATAT-TA-TATACTTATATATT-T
* *
1333909 TATA-TATGTA--TATATACTT
1 TATATTATATACTTATATATTT
* * *
1333928 TATACTA-AAACTT-TATATATA
1 TATATTATATACTTATATAT-TT
* *
1333949 TATATATACATACTT-T-TACTT
1 TATAT-TATATACTTATATATTT
* ** * * *
1333970 TATAGTTTACATACACACACA-TA
1 TATA--TTATATACTTATATATTT
*
1333993 TATATTGTATACTTATATATTT
1 TATATTATATACTTATATATTT
1334015 TATATTATATACTT
1 TATATTATATACTT
1334029 TTGTCTCTAT
Statistics
Matches: 198, Mismatches: 35, Indels: 49
0.70 0.12 0.17
Matches are distributed among these distances:
19 6 0.03
20 13 0.07
21 28 0.14
22 82 0.41
23 42 0.21
24 12 0.06
25 14 0.07
26 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.03, T:0.51
Consensus pattern (22 bp):
TATATTATATACTTATATATTT
Found at i:1334030 original size:15 final size:15
Alignment explanation
Indices: 1333991--1334030 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1333981 TACACACACA
*
1333991 TATATATTGTATACT
1 TATATATTTTATACT
1334006 TATATATTTTATA-T
1 TATATATTTTATACT
1334020 TATATACTTTT
1 TATATA-TTTT
1334031 GTCTCTATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (15 bp):
TATATATTTTATACT
Found at i:1334124 original size:28 final size:25
Alignment explanation
Indices: 1334082--1334226 Score: 78
Period size: 26 Copynumber: 6.0 Consensus size: 25
1334072 TAAAAGTATG
1334082 TATATATATATATATAATTTATAGTT
1 TATATATATATATATAATTTATA-TT
*
1334108 TATATATATACTCATATACTTTATA-T
1 TATATATATA-T-ATATAATTTATATT
* *
1334134 T-TA-A-A-CTATATAATTTATAAT
1 TATATATATATATATAATTTATATT
* *
1334155 TATACATA-ATATATAA-ATATAAGTT
1 TATATATATATATATAATTTAT-A-TT
* * *
1334180 GTATATATTTAAATATAATTCATA-T
1 -TATATATATATATATAATTTATATT
1334205 TA-ATA-A-ACTATATAATTTATAT
1 TATATATATA-TATATAATTTATAT
1334227 ATAGTTTAAT
Statistics
Matches: 92, Mismatches: 14, Indels: 29
0.68 0.10 0.21
Matches are distributed among these distances:
20 11 0.12
21 4 0.04
22 13 0.14
23 8 0.09
24 12 0.13
25 4 0.04
26 18 0.20
27 9 0.10
28 13 0.14
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATATATATATATAATTTATATT
Found at i:1334273 original size:2 final size:2
Alignment explanation
Indices: 1334266--1334428 Score: 78
Period size: 2 Copynumber: 83.0 Consensus size: 2
1334256 TAGTTCATGG
* * *
1334266 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA TA TA TA TA GTT TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
1334309 -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA TT TA TA T- 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
*
1334350 TA TA TA -A TA TA -A TA TA -A TA TA TA CT- TGA TA TA TA CA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA
* * *
1334389 TA TA -A TT TA TA TG TA GTT TA TA TA TA GTA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA
1334429 ATTGTTTAAA
Statistics
Matches: 120, Mismatches: 22, Indels: 38
0.67 0.12 0.21
Matches are distributed among these distances:
1 11 0.09
2 100 0.83
3 9 0.08
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1334280 original size:23 final size:20
Alignment explanation
Indices: 1334222--1334280 Score: 55
Period size: 23 Copynumber: 2.8 Consensus size: 20
1334212 CTATATAATT
1334222 TATATATAGTTTAATAGTTCA
1 TATATATAGTTT-ATAGTTCA
* * *
1334243 TATATAAACTCTATAGTTCA
1 TATATATAGTTTATAGTTCA
1334263 TGGTATATATAGTTTATA
1 ---TATATATAGTTTATA
1334281 CATAATATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 8 0.28
21 9 0.31
23 12 0.41
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.46
Consensus pattern (20 bp):
TATATATAGTTTATAGTTCA
Found at i:1334308 original size:11 final size:10
Alignment explanation
Indices: 1334285--1334425 Score: 60
Period size: 11 Copynumber: 13.9 Consensus size: 10
1334275 TTTATACATA
*
1334285 ATATATATAT
1 ATATATATTT
1334295 ATATATAGTTT
1 ATATATA-TTT
*
1334306 ATA-ATA-AT
1 ATATATATTT
* **
1334314 ATAAATATAA
1 ATATATATTT
1334324 ACTATATAGTTT
1 A-TATATA-TTT
*
1334336 ATTTATA-TT
1 ATATATATTT
*
1334345 ATATATATAT
1 ATATATATTT
*
1334355 A-ATATAATATA
1 ATATAT-AT-TT
*
1334366 ATATATACTTG
1 ATATATA-TTT
*
1334377 ATATATACATT
1 ATATATA-TTT
1334388 ATATA-ATTT
1 ATATATATTT
*
1334397 ATATGTAGTTT
1 ATATATA-TTT
*
1334408 ATATATA-GT
1 ATATATATTT
1334417 ATATATATT
1 ATATATATT
1334426 ATAATTGTTT
Statistics
Matches: 99, Mismatches: 19, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
8 4 0.04
9 29 0.29
10 18 0.18
11 41 0.41
12 7 0.07
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.48
Consensus pattern (10 bp):
ATATATATTT
Found at i:1334330 original size:30 final size:28
Alignment explanation
Indices: 1334267--1334360 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
1334257 AGTTCATGGT
*
1334267 ATATATAGTTTATACATAATATATATAT
1 ATATATAGTTTATACATAATATATATAA
1334295 ATATATAGTTTATA-ATAATATAAATATAA
1 ATATATAGTTTATACATAATAT--ATATAA
** * *
1334324 ACTATATAGTTTATTTATATTATATATAT
1 A-TATATAGTTTATACATAATATATATAA
1334353 ATAATATA
1 AT-ATATA
1334361 ATATAATATA
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
27 7 0.12
28 15 0.26
29 17 0.30
30 12 0.21
31 6 0.11
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
ATATATAGTTTATACATAATATATATAA
Found at i:1334346 original size:9 final size:9
Alignment explanation
Indices: 1334334--1334428 Score: 57
Period size: 9 Copynumber: 9.6 Consensus size: 9
1334324 ACTATATAGT
*
1334334 TTATTTATA
1 TTATATATA
1334343 TTATATATA
1 TTATATATA
1334352 TATAATATAATA
1 T-T-ATAT-ATA
*
1334364 TAATATATA
1 TTATATATA
1334373 CTTGATATATACA
1 -TT-ATATAT--A
1334386 TTATATA-A
1 TTATATATA
*
1334394 TTTATATGTA
1 -TTATATATA
1334404 GTTTATATATA
1 --TTATATATA
*
1334415 GTATATATA
1 TTATATATA
1334424 TTATA
1 TTATA
1334429 ATTGTTTAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
8 1 0.01
9 30 0.43
10 7 0.10
11 24 0.35
12 6 0.09
13 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (9 bp):
TTATATATA
Found at i:1336085 original size:80 final size:80
Alignment explanation
Indices: 1335947--1336238 Score: 442
Period size: 80 Copynumber: 3.6 Consensus size: 80
1335937 CAATAAAAAT
* * * * *
1335947 GGGAGCCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCATTAGATCCGTAGGGTTACC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
* *
1336011 TTAAGCACACAGCTAA
65 TTATGCACACAGCAAA
*
1336027 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
* *
1336092 TATGCACATAACAAA
66 TATGCACACAGCAAA
*
1336107 GGGAACCAACCTAAGGATATACCTTGGTACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1336172 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
1336187 GGGAACCAACCTAAGGATATGCCTTGGGGCCTACCTAAGATATCCTTAGGTC
1 GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTC
1336239 TGTAATGACT
Statistics
Matches: 193, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
80 183 0.95
81 10 0.05
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (80 bp):
GGGAACCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:1336216 original size:160 final size:160
Alignment explanation
Indices: 1335939--1336238 Score: 487
Period size: 160 Copynumber: 1.9 Consensus size: 160
1335929 TCAGCACACA
* *
1335939 ATAAAAATGGGAGCCAACCTAAGGATATACCTTGGATCTACCCAAGGACATCATTAGATCCGTAG
1 ATAAAAATGGGAACCAACCTAAGGATATACCTTGGACCTACCCAAGGACATCATTAGATCCGTAG
*
1336004 GGTTACCTTAAGCACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATA
66 GGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATA
1336069 TCCTTAGGTCCGTAGGGTTACCTTATGCAC
131 TCCTTAGGTCCGTAGGGTTACCTTATGCAC
* * *
1336099 ATAACAAA-GGGAACCAACCTAAGGATATACCTTGGTACCTACCCAA-GATATCCTTAGGTCCGT
1 ATAA-AAATGGGAACCAACCTAAGGATATACCTTGG-ACCTACCCAAGGACATCATTAGATCCGT
* * *
1336162 AGGGTTACCTTATGCACACAGCAAAGGGAACCAACCTAAGGATATGCCTTGGGGCCTACCTAAGA
64 AGGGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGA
1336227 TATCCTTAGGTC
129 TATCCTTAGGTC
1336239 TGTAATGACT
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
160 117 0.91
161 12 0.09
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (160 bp):
ATAAAAATGGGAACCAACCTAAGGATATACCTTGGACCTACCCAAGGACATCATTAGATCCGTAG
GGTTACCTTAAGCACACAGCAAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATA
TCCTTAGGTCCGTAGGGTTACCTTATGCAC
Found at i:1344226 original size:23 final size:23
Alignment explanation
Indices: 1344144--1344218 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
1344134 TTTATTATTT
*
1344144 TATTAATTAGGATTCTAGTTTGT
1 TATTAATTAGGATTCTAGTTTGC
*
1344167 TATTAATTAGGATTCTAATTTGC
1 TATTAATTAGGATTCTAGTTTGC
1344190 TATT-ATGTAGGATTCTAGTTTGC
1 TATTAAT-TAGGATTCTAGTTTGC
1344213 TATTAA
1 TATTAA
1344219 ATACGATTTA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
22 2 0.04
23 44 0.94
24 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.16, T:0.49
Consensus pattern (23 bp):
TATTAATTAGGATTCTAGTTTGC
Found at i:1344562 original size:43 final size:42
Alignment explanation
Indices: 1344515--1344646 Score: 104
Period size: 43 Copynumber: 3.3 Consensus size: 42
1344505 TCTTTGTATT
1344515 TTATTTTAAATATGTTTTAGTATTTTAATTAAGTTTTAGAATA
1 TTATTTTAAATATGTTTTAGTATTTTAATT-AGTTTTAGAATA
* * * *
1344558 TTATTTT---TATATTTTA-TA---T--TT-GTCTTAGGTATT
1 TTATTTTAAATATGTTTTAGTATTTTAATTAGTTTTA-GAATA
* * *
1344591 TTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATA
1 TTATTTTAAATATGTTTTAGTATTTTAATTA-GTTTTAGAATA
1344634 TTATTTTAAATAT
1 TTATTTTAAATAT
1344647 TATTTTTTAG
Statistics
Matches: 64, Mismatches: 13, Indels: 24
0.63 0.13 0.24
Matches are distributed among these distances:
32 5 0.08
33 9 0.14
34 2 0.03
36 8 0.12
37 2 0.03
39 2 0.03
40 9 0.14
42 2 0.03
43 21 0.33
44 4 0.06
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.57
Consensus pattern (42 bp):
TTATTTTAAATATGTTTTAGTATTTTAATTAGTTTTAGAATA
Found at i:1344623 original size:19 final size:19
Alignment explanation
Indices: 1344516--1344629 Score: 58
Period size: 19 Copynumber: 6.0 Consensus size: 19
1344506 CTTTGTATTT
* *
1344516 TATTTTAAATATGTTTTAG
1 TATTTTAATTAGGTTTTAG
*
1344535 TATTTTAATTAAGTTTTAG
1 TATTTTAATTAGGTTTTAG
* **
1344554 AATATTATT-TTTATATTTTA-
1 --TATT-TTAATTAGGTTTTAG
*
1344574 TATTTGT-CTTAGGTATTT--
1 TATTT-TAATTAGGT-TTTAG
* *
1344592 TAGTTTAAATAGGTTTTAG
1 TATTTTAATTAGGTTTTAG
*
1344611 TATTTTAATTAGGATTTAG
1 TATTTTAATTAGGTTTTAG
1344630 AATATTATTT
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
17 5 0.07
18 18 0.25
19 36 0.49
21 12 0.16
22 2 0.03
ACGTcount: A:0.30, C:0.01, G:0.12, T:0.57
Consensus pattern (19 bp):
TATTTTAATTAGGTTTTAG
Found at i:1344699 original size:71 final size:76
Alignment explanation
Indices: 1344510--1344699 Score: 250
Period size: 76 Copynumber: 2.6 Consensus size: 76
1344500 TTTTATCTTT
* * * * *
1344510 GTATTTTATTTTAAATATGTTTTAGTATTTTAATTA-AGTTTTAGAATATTATTTTTATATTTTA
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGA-ATTTAGAATATTATTTTTATAATATA
1344574 TATTTGTCTTAG
65 TATTTGTCTTAG
*
1344586 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTA-TTTTA-AATAT-T
1 GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTTAGAATATTATTTTTATAATATAT
1344648 ATTT-T-TTAG
66 ATTTGTCTTAG
*
1344657 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGAATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGAATTTA
1344700 AGATGTTTTA
Statistics
Matches: 104, Mismatches: 8, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
70 5 0.05
71 39 0.38
72 1 0.01
73 5 0.05
74 3 0.03
75 5 0.05
76 46 0.44
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.57
Consensus pattern (76 bp):
GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGAATTTAGAATATTATTTTTATAATATAT
ATTTGTCTTAG
Found at i:1350901 original size:21 final size:21
Alignment explanation
Indices: 1350853--1350902 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1350843 CGTTCTATTT
*
1350853 TTTTATTTCATTTTATTTTCG
1 TTTTATTTCATTTTATTTTCA
* *
1350874 TTCTATTTCATTTTATTTTTA
1 TTTTATTTCATTTTATTTTCA
1350895 TTTTATTT
1 TTTTATTT
1350903 TTAGAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTATTTCATTTTATTTTCA
Found at i:1350905 original size:11 final size:11
Alignment explanation
Indices: 1350853--1350903 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
1350843 CGTTCTATTT
1350853 TTTTA-TTTCA
1 TTTTATTTTCA
*
1350863 TTTTATTTTCG
1 TTTTATTTTCA
*
1350874 TTCTA-TTTCA
1 TTTTATTTTCA
*
1350884 TTTTATTTTTA
1 TTTTATTTTCA
1350895 TTTTATTTT
1 TTTTATTTT
1350904 TAGAAAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 13 0.38
11 21 0.62
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:1352607 original size:19 final size:19
Alignment explanation
Indices: 1352583--1352620 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1352573 CTTTGTATTT
*
1352583 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAAGTTTTAG
*
1352602 TATTTTAATTAAGTTTTAG
1 TATTTTAAATAAGTTTTAG
1352621 GATATTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
TATTTTAAATAAGTTTTAG
Found at i:1352630 original size:43 final size:42
Alignment explanation
Indices: 1352582--1352712 Score: 102
Period size: 43 Copynumber: 3.3 Consensus size: 42
1352572 TCTTTGTATT
1352582 TTATTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATT-AGTTTTAGGATA
* * *
1352625 TTATTTT-TATA---TTT--TA-TCT--TT-GTTTTAGGTATT
1 TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGG-ATA
* * **
1352658 TTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTATAATA
1 TTATTTTAAATAGGTTTTAGTATTTTAATTA-GTTTTAGGATA
1352701 TTATTTTAAATA
1 TTATTTTAAATA
1352713 TTATTTTTTA
Statistics
Matches: 65, Mismatches: 11, Indels: 24
0.65 0.11 0.24
Matches are distributed among these distances:
32 8 0.12
33 8 0.12
34 5 0.08
36 2 0.03
37 5 0.08
39 5 0.08
40 2 0.03
42 5 0.08
43 20 0.31
44 5 0.08
ACGTcount: A:0.31, C:0.01, G:0.11, T:0.57
Consensus pattern (42 bp):
TTATTTTAAATAGGTTTTAGTATTTTAATTAGTTTTAGGATA
Found at i:1353462 original size:19 final size:19
Alignment explanation
Indices: 1353431--1353478 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 19
1353421 CTATTAATAT
1353431 TTAT-TATTTTA-TTATT-
1 TTATCTATTTTATTTATTA
1353447 TT-TCT-TTTTATTTATTA
1 TTATCTATTTTATTTATTA
1353464 TTATCTATTTTATTT
1 TTATCTATTTTATTT
1353479 TACTAAATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 6 0.22
16 8 0.30
17 2 0.07
18 3 0.11
19 8 0.30
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATCTATTTTATTTATTA
Found at i:1359497 original size:17 final size:17
Alignment explanation
Indices: 1359475--1359507 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1359465 ATTATTTATT
*
1359475 TAATAATTTAATATAAC
1 TAATAATCTAATATAAC
1359492 TAATAATCTAATATAA
1 TAATAATCTAATATAA
1359508 TTTATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATAATCTAATATAAC
Found at i:1360587 original size:2 final size:2
Alignment explanation
Indices: 1360580--1360604 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1360570 TCTCATGTAT
1360580 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1360605 GGTGACCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1366304 original size:21 final size:21
Alignment explanation
Indices: 1366263--1366325 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1366253 TAGTAAGTTT
* *
1366263 GGGATCAATC-CTTTTCAAAA
1 GGGATCAATCATTTTTCGAAA
**
1366283 GGGATGGATCATTTTTCGAAA
1 GGGATCAATCATTTTTCGAAA
1366304 GGGATCAATCATTTTTCTGAAA
1 GGGATCAATCATTTTTC-GAAA
1366326 AATACACAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 8 0.23
21 23 0.66
22 4 0.11
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (21 bp):
GGGATCAATCATTTTTCGAAA
Found at i:1368186 original size:24 final size:24
Alignment explanation
Indices: 1368159--1368210 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
1368149 GTGTTTGGTG
*
1368159 TGTTTAGTGGACTGATTGGTGGGC
1 TGTTTAGTGGACTGATTGGTGGAC
*
1368183 TGTTTAGTGGACTTATTGGTGGAC
1 TGTTTAGTGGACTGATTGGTGGAC
1368207 TGTT
1 TGTT
1368211 CGCTAAGCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.08, G:0.37, T:0.42
Consensus pattern (24 bp):
TGTTTAGTGGACTGATTGGTGGAC
Found at i:1368192 original size:12 final size:12
Alignment explanation
Indices: 1368159--1368210 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
1368149 GTGTTTGGTG
1368159 TGTTTAGTGGAC
1 TGTTTAGTGGAC
* * *
1368171 TGATTGGTGGGC
1 TGTTTAGTGGAC
1368183 TGTTTAGTGGAC
1 TGTTTAGTGGAC
*
1368195 T-TATTGGTGGAC
1 TGT-TTAGTGGAC
1368207 TGTT
1 TGTT
1368211 CGCTAAGCCA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.37, T:0.42
Consensus pattern (12 bp):
TGTTTAGTGGAC
Found at i:1370053 original size:13 final size:13
Alignment explanation
Indices: 1370035--1370059 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1370025 GTTACAACCT
1370035 GACCCGTTGACCC
1 GACCCGTTGACCC
1370048 GACCCGTTGACC
1 GACCCGTTGACC
1370060 GTGTGCTATT
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:0.16, C:0.44, G:0.24, T:0.16
Consensus pattern (13 bp):
GACCCGTTGACCC
Found at i:1370104 original size:29 final size:29
Alignment explanation
Indices: 1370062--1370122 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
1370052 CGTTGACCGT
* *
1370062 GTGCTATTCTGGTAATTATTTGGAAAAGG
1 GTGCCATTCTGGTAATTATTTGGAAAAAG
*
1370091 GTGCCATTCTGGTAATTATTTTGAAAAAG
1 GTGCCATTCTGGTAATTATTTGGAAAAAG
1370120 GTG
1 GTG
1370123 TTATTTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (29 bp):
GTGCCATTCTGGTAATTATTTGGAAAAAG
Found at i:1370197 original size:29 final size:29
Alignment explanation
Indices: 1370164--1370232 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
1370154 TTTTAAAAGT
* *
1370164 TATTTTAGTAATTATTTTGAAAATGGTGA
1 TATTTTAGTAATTATTTTAAAAATGATGA
* * *
1370193 TATTTTGGTAATTGTTTTAAAAATGATGC
1 TATTTTAGTAATTATTTTAAAAATGATGA
*
1370222 TATTTTCGTAA
1 TATTTTAGTAA
1370233 AATGGTTGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (29 bp):
TATTTTAGTAATTATTTTAAAAATGATGA
Found at i:1385020 original size:24 final size:25
Alignment explanation
Indices: 1384986--1385046 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 25
1384976 AGCATATTTG
1384986 AAAAT-AAAACTT-AAAA-ATAAAGA
1 AAAATGAAAACTTGAAAAGA-AAAGA
1385009 AAAATGAAAACTTGAAAAGAAAAGA
1 AAAATGAAAACTTGAAAAGAAAAGA
1385034 AAAGA-GAAAACTT
1 AAA-ATGAAAACTT
1385047 TATAAAACTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.15
24 7 0.21
25 20 0.59
26 2 0.06
ACGTcount: A:0.69, C:0.05, G:0.11, T:0.15
Consensus pattern (25 bp):
AAAATGAAAACTTGAAAAGAAAAGA
Found at i:1385347 original size:22 final size:22
Alignment explanation
Indices: 1385319--1385370 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1385309 TCCATTCGTT
1385319 CTTCTAGAAGCGCTGGCTGGAC
1 CTTCTAGAAGCGCTGGCTGGAC
1385341 CTTCTAGAAGCGCTGGCTGGAC
1 CTTCTAGAAGCGCTGGCTGGAC
1385363 CTTCTAGA
1 CTTCTAGA
1385371 GGGTTCTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (22 bp):
CTTCTAGAAGCGCTGGCTGGAC
Found at i:1386990 original size:3 final size:3
Alignment explanation
Indices: 1386984--1387015 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1386974 AATAATAATA
1386984 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1387016 CTACATTGCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1387813 original size:21 final size:22
Alignment explanation
Indices: 1387787--1387827 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1387777 AATAGCGATC
1387787 AATGACATAAACTAT-AAATCA
1 AATGACATAAACTATGAAATCA
* *
1387808 AATGACTTAATCTATGAAAT
1 AATGACATAAACTATGAAAT
1387828 TTATTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
AATGACATAAACTATGAAATCA
Found at i:1388097 original size:13 final size:13
Alignment explanation
Indices: 1388079--1388104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1388069 CGATTTTCCC
1388079 TCACAGTTATGGG
1 TCACAGTTATGGG
1388092 TCACAGTTATGGG
1 TCACAGTTATGGG
1388105 GTAAGGAAGT
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:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (13 bp):
TCACAGTTATGGG
Found at i:1390124 original size:21 final size:21
Alignment explanation
Indices: 1390100--1390146 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1390090 GCTTTGGAAT
* *
1390100 TTTTCCTGTGATACAACTAGC
1 TTTTCCTGAGATACAACCAGC
**
1390121 TTTTCCTGAGATGTAACCAGC
1 TTTTCCTGAGATACAACCAGC
1390142 TTTTC
1 TTTTC
1390147 TAATGAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTTCCTGAGATACAACCAGC
Found at i:1391985 original size:21 final size:19
Alignment explanation
Indices: 1391955--1392002 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1391945 AGCATATTTG
1391955 AAAAT-AAAACTTAAAATAAA
1 AAAATGAAAACTT--AATAAA
*
1391975 AAAATGAAAACTTGATAAA
1 AAAATGAAAACTTAATAAA
1391994 AAAA-GAAAA
1 AAAATGAAAA
1392003 GAGAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 5 0.19
19 9 0.35
20 5 0.19
21 7 0.27
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (19 bp):
AAAATGAAAACTTAATAAA
Found at i:1392002 original size:25 final size:24
Alignment explanation
Indices: 1391966--1392019 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
1391956 AAATAAAACT
*
1391966 TAAAATAAAAAAA-TGAAAACTTGA
1 TAAAA-AAAAAAAGAGAAAACTTGA
*
1391990 TAAAAAAAGAAAAGAGAAAACTTTA
1 TAAAAAAA-AAAAGAGAAAACTTGA
1392015 TAAAA
1 TAAAA
1392020 CTAGAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 3 0.12
24 9 0.35
25 14 0.54
ACGTcount: A:0.69, C:0.04, G:0.09, T:0.19
Consensus pattern (24 bp):
TAAAAAAAAAAAGAGAAAACTTGA
Found at i:1392153 original size:20 final size:22
Alignment explanation
Indices: 1392103--1392155 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 22
1392093 ATAGCCTTCA
1392103 AAATCCTAAAAACAAGGTAAAT
1 AAATCCTAAAAACAAGGTAAAT
1392125 ATAATTCCTAAAATA-AA-G-AAAT
1 A-AA-TCCTAAAA-ACAAGGTAAAT
1392147 AAATCCTAA
1 AAATCCTAA
1392156 TGAAAATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 6 0.21
23 3 0.11
24 10 0.36
25 1 0.04
ACGTcount: A:0.58, C:0.13, G:0.06, T:0.23
Consensus pattern (22 bp):
AAATCCTAAAAACAAGGTAAAT
Found at i:1395841 original size:3 final size:3
Alignment explanation
Indices: 1395833--1395871 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1395823 AATTAAAGGC
*
1395833 AAT AAT AAT AAT TAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1395872 TATTATTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:1396676 original size:21 final size:22
Alignment explanation
Indices: 1396650--1396690 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1396640 AATAGCGATC
1396650 AATGACATAAACTAT-AAATCA
1 AATGACATAAACTATGAAATCA
* *
1396671 AATGACTTAATCTATGAAAT
1 AATGACATAAACTATGAAAT
1396691 TTACTATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.29
Consensus pattern (22 bp):
AATGACATAAACTATGAAATCA
Found at i:1401360 original size:20 final size:20
Alignment explanation
Indices: 1401335--1401374 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1401325 TTCTATTTGC
*
1401335 GAAATTTGCGTTGCGAAAAT
1 GAAATTCGCGTTGCGAAAAT
1401355 GAAATTCGCGTTGCGAAAAT
1 GAAATTCGCGTTGCGAAAAT
1401375 TTTCATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (20 bp):
GAAATTCGCGTTGCGAAAAT
Found at i:1413222 original size:23 final size:23
Alignment explanation
Indices: 1413196--1413259 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1413186 AACCATAAAC
1413196 AGAACCCGACCCAGAGCCCAAAA
1 AGAACCCGACCCAGAGCCCAAAA
* * *
1413219 AGAACCCAACAC-GAAGCCCAAAC
1 AGAACCCGACCCAG-AGCCCAAAA
*
1413242 TGAACCCGACCCAGAGCC
1 AGAACCCGACCCAGAGCC
1413260 TACCCTAACC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.41, C:0.41, G:0.17, T:0.02
Consensus pattern (23 bp):
AGAACCCGACCCAGAGCCCAAAA
Found at i:1416971 original size:106 final size:106
Alignment explanation
Indices: 1416689--1416995 Score: 368
Period size: 106 Copynumber: 2.9 Consensus size: 106
1416679 TTGATGTTTG
* * * * * *
1416689 ATTCGACCTTGTGGTGA-CCGATCCGAGGTACGATCCATATTATTATTGTCCAGATTCTATTAAC
1 ATTCGAACTTGTGGTGACCCGATCCGGGGTACGATCCACATTATTATGGTCCGGACTCTATTAAC
* *
1416753 TTCTAATTGTTAATTCTTTTTATTAATTTGTTTGAATTATT
66 TACTAATTGTTAATTCTTTTTATTAATTTGTTTGAATTAAT
* * * ** * *
1416794 ATTCGACCTTATGGTAACCCGATCAAGGCTACGATCCACATTATTATGGTCCGAACTCTATTAAC
1 ATTCGAACTTGTGGTGACCCGATCCGGGGTACGATCCACATTATTATGGTCCGGACTCTATTAAC
*
1416859 TCCTAATTGTTAATTCTTTTTATTAATTTGTTTGAATTAAT
66 TACTAATTGTTAATTCTTTTTATTAATTTGTTTGAATTAAT
*
1416900 ATAT-GAACTTGCGGTGACCCGATCCGGGGTACGACTCC-CATTATTATGGTCCGGACTCTATTA
1 AT-TCGAACTTGTGGTGACCCGATCCGGGGTACGA-TCCACATTATTATGGTCCGGACTCTATTA
* * * *
1416963 ACAACTAATTTTTATTTATCTTTTTATTTATTT
64 ACTACTAATTGTTA-AT-TCTTTTTATTAATTT
1416996 ATTTTATGTT
Statistics
Matches: 171, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
105 15 0.09
106 137 0.80
107 5 0.03
108 14 0.08
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (106 bp):
ATTCGAACTTGTGGTGACCCGATCCGGGGTACGATCCACATTATTATGGTCCGGACTCTATTAAC
TACTAATTGTTAATTCTTTTTATTAATTTGTTTGAATTAAT
Found at i:1419881 original size:27 final size:27
Alignment explanation
Indices: 1419793--1419886 Score: 116
Period size: 27 Copynumber: 3.5 Consensus size: 27
1419783 CTTTAGGTAG
* *
1419793 TTTGATCATTTTGGAGTTCAAAGATAA
1 TTTGGTCATTTTGGAGTTCAAGGATAA
* *
1419820 TTTGGTCATTTTGGTGTTTAAGGATAA
1 TTTGGTCATTTTGGAGTTCAAGGATAA
* * *
1419847 TTTGGTCATTTTGGAGTTCAGGGGTAT
1 TTTGGTCATTTTGGAGTTCAAGGATAA
*
1419874 TTTAGTCATTTTG
1 TTTGGTCATTTTG
1419887 TTCAATTCAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.22, C:0.06, G:0.24, T:0.47
Consensus pattern (27 bp):
TTTGGTCATTTTGGAGTTCAAGGATAA
Found at i:1420693 original size:19 final size:19
Alignment explanation
Indices: 1420666--1420702 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1420656 GCATCACTCG
* *
1420666 GTTCGACTCAAGTGGCTCC
1 GTTCAACTCAAATGGCTCC
1420685 GTTCAACTCAAATGGCTC
1 GTTCAACTCAAATGGCTC
1420703 AGTTTGGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (19 bp):
GTTCAACTCAAATGGCTCC
Found at i:1422847 original size:26 final size:25
Alignment explanation
Indices: 1422799--1422847 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
1422789 ATACAAAAGC
* *
1422799 CCAAATCCATCTTCTCCACAACCTA
1 CCAAATCCAGCTTCTCCAAAACCTA
*
1422824 CCAAATCCTAGCTTTTCCAAAACC
1 CCAAATCC-AGCTTCTCCAAAACC
1422848 ATCATCAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 8 0.40
26 12 0.60
ACGTcount: A:0.33, C:0.41, G:0.02, T:0.24
Consensus pattern (25 bp):
CCAAATCCAGCTTCTCCAAAACCTA
Found at i:1429363 original size:29 final size:29
Alignment explanation
Indices: 1429331--1429437 Score: 151
Period size: 29 Copynumber: 3.7 Consensus size: 29
1429321 GCACCCATTT
* *
1429331 CGAATTAATTACCAGAATAGTACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
* * *
1429360 CGAATTATTTACTAGAATAGCAGCAAAAT
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1429389 AGAATTATTTACCAGAATAGCACCAAAAC
1 CGAATTATTTACCAGAATAGCACCAAAAC
*
1429418 CGAATTATTTACCAAAATAG
1 CGAATTATTTACCAGAATAG
1429438 AACCGGTCAA
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.24
Consensus pattern (29 bp):
CGAATTATTTACCAGAATAGCACCAAAAC
Found at i:1436853 original size:29 final size:30
Alignment explanation
Indices: 1436821--1436928 Score: 125
Period size: 29 Copynumber: 3.7 Consensus size: 30
1436811 TACCCATTTC
* *
1436821 GAATTAATTACCAGAATAACACCAAAA-CA
1 GAATTAATTACCAAAATAGCACCAAAACCA
* *
1436850 GAATTATTTACCAGAATAGCACCAAAACCA
1 GAATTAATTACCAAAATAGCACCAAAACCA
*
1436880 -AATT-ATGTACCAAAATAGCACCAAAATC-
1 GAATTAAT-TACCAAAATAGCACCAAAACCA
*
1436908 GAATTATTTACCAAAATAGCA
1 GAATTAATTACCAAAATAGCA
1436929 TCGGTCAAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
28 1 0.01
29 65 0.94
30 3 0.04
ACGTcount: A:0.50, C:0.20, G:0.08, T:0.21
Consensus pattern (30 bp):
GAATTAATTACCAAAATAGCACCAAAACCA
Found at i:1436960 original size:17 final size:17
Alignment explanation
Indices: 1436938--1437002 Score: 57
Period size: 17 Copynumber: 4.0 Consensus size: 17
1436928 ATCGGTCAAG
1436938 GGTCAACGGTCGGGTCA
1 GGTCAACGGTCGGGTCA
**
1436955 GGTCAA----CGGGTTG
1 GGTCAACGGTCGGGTCA
*
1436968 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCA
*
1436985 GGTCAAAGGGTCGGGTCA
1 GGTC-AACGGTCGGGTCA
1437003 ACGGGTCAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
13 11 0.29
17 16 0.42
18 11 0.29
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCA
Found at i:1436971 original size:13 final size:13
Alignment explanation
Indices: 1436948--1437014 Score: 62
Period size: 13 Copynumber: 4.8 Consensus size: 13
1436938 GGTCAACGGT
*
1436948 CGGGTCAGGTCAA
1 CGGGTCGGGTCAA
*
1436961 CGGGTTGGGTCAA
1 CGGGTCGGGTCAA
1436974 CGGTCGGGTCGGGTCAA
1 ----CGGGTCGGGTCAA
*
1436991 AGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
1437004 CGGGTCAGGTC
1 CGGGTCGGGTC
1437015 GTGACCGGTC
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
13 32 0.73
17 12 0.27
ACGTcount: A:0.16, C:0.21, G:0.45, T:0.18
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:1436973 original size:30 final size:30
Alignment explanation
Indices: 1436937--1437006 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
1436927 CATCGGTCAA
* *
1436937 GGGTCAACGGTCGGGTCAGGTCAACGGGTT
1 GGGTCAACGGTCGGGTCAGGTCAAAGGGTC
*
1436967 GGGTCAACGGTCGGGTCGGGTCAAAGGGTC
1 GGGTCAACGGTCGGGTCAGGTCAAAGGGTC
1436997 GGGTCAACGG
1 GGGTCAACGG
1437007 GTCAGGTCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.17, C:0.20, G:0.46, T:0.17
Consensus pattern (30 bp):
GGGTCAACGGTCGGGTCAGGTCAAAGGGTC
Found at i:1447725 original size:18 final size:17
Alignment explanation
Indices: 1447702--1447737 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
1447692 GAACAGTCAC
1447702 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
1447720 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1447737 G
1 G
1447738 GCCGTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.17, C:0.47, G:0.25, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1447790 original size:29 final size:29
Alignment explanation
Indices: 1447748--1447858 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
1447738 GCCGTTGACC
*
1447748 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTATGGTAAATAATTCGGTTTT
*
1447777 GGTGCTATTATGGTAAATAATTCAGTTTT
1 GGTGCTATTATGGTAAATAATTCGGTTTT
1447806 GGTGCTATTATGGTAAATAATTCGGTTTT
1 GGTGCTATTATGGTAAATAATTCGGTTTT
* *
1447835 GGTGCTATTCTGGTAATTAATTCG
1 GGTGCTATTATGGTAAATAATTCG
1447859 AAATGGGTTC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (29 bp):
GGTGCTATTATGGTAAATAATTCGGTTTT
Found at i:1447872 original size:58 final size:58
Alignment explanation
Indices: 1447748--1447879 Score: 185
Period size: 58 Copynumber: 2.3 Consensus size: 58
1447738 GCCGTTGACC
** *
1447748 GGTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCAGTTTT
1 GGTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCAGAATG
* * *
1447806 GGTGCTATTATGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAATTAATTC-GAAATG
1 GGTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCAG-AATG
*
1447864 GGTTCTATTTTGGTAA
1 GGTGCTATTTTGGTAA
1447880 TTATTTAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
57 1 0.02
58 64 0.98
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (58 bp):
GGTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTATTATGGTAAATAATTCAGAATG
Found at i:1449931 original size:12 final size:12
Alignment explanation
Indices: 1449910--1449951 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
1449900 TTAAATAGGT
*
1449910 TTTG-TTTGTAT
1 TTTGATTTGTAA
1449921 TTTGATTTGTAA
1 TTTGATTTGTAA
1449933 TTTGATTTGTAA
1 TTTGATTTGTAA
1449945 TTTGATT
1 TTTGATT
1449952 AACCATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
11 4 0.14
12 25 0.86
ACGTcount: A:0.19, C:0.00, G:0.17, T:0.64
Consensus pattern (12 bp):
TTTGATTTGTAA
Found at i:1451614 original size:21 final size:21
Alignment explanation
Indices: 1451588--1451630 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1451578 TTGGAGTAAG
1451588 AATTAATTATCACAAGTTATA
1 AATTAATTATCACAAGTTATA
1451609 AATTAATTATCACAAGTTATA
1 AATTAATTATCACAAGTTATA
1451630 A
1 A
1451631 GAAATTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (21 bp):
AATTAATTATCACAAGTTATA
Found at i:1460088 original size:21 final size:20
Alignment explanation
Indices: 1460050--1460088 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1460040 ATCCCAGTTA
* *
1460050 TCCCCTAACGATTCAAAAGT
1 TCCCCTAAAGATGCAAAAGT
1460070 TCCCCATAAAGATGCAAAA
1 TCCCC-TAAAGATGCAAAA
1460089 TTCTTGAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.28, G:0.10, T:0.21
Consensus pattern (20 bp):
TCCCCTAAAGATGCAAAAGT
Found at i:1462835 original size:20 final size:20
Alignment explanation
Indices: 1462804--1463248 Score: 138
Period size: 20 Copynumber: 19.6 Consensus size: 20
1462794 AAATTAAAAT
*
1462804 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1462824 GCATTAAAGGATGCTATAACTAAAAT
1 GCATGAAAGGATGC-AT---T--AAG
*
1462850 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1462870 GCATGAAAGGATGCTATAACTAAAT
1 GCATGAAAGGATGC-AT---T-AAG
* *
1462895 GCATGAACA-TACT-CAATAAG
1 GCATGAA-AGGA-TGCATTAAG
*
1462915 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1462941 GCATGTAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1462961 GCATGAAAGGATACCATAACTAAAAT
1 GCATGAAAGGAT-GCAT---T--AAG
1462987 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1463007 GCATGAAAAGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1463033 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1463053 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* * *
1463079 GCTTGAAAGAATGAATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1463099 GCATGAAAAGATGACATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1463125 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1463145 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
1463171 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
1463191 GCATGAAAAGACGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1463217 GCATGAAAGGAAGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1463237 GCATTAAAGGAT
1 GCATGAAAGGAT
1463249 TCCATAATTA
Statistics
Matches: 317, Mismatches: 51, Indels: 114
0.66 0.11 0.24
Matches are distributed among these distances:
19 2 0.01
20 129 0.41
21 19 0.06
22 14 0.04
24 15 0.05
25 27 0.09
26 111 0.35
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1463361 original size:46 final size:46
Alignment explanation
Indices: 1462745--1463354 Score: 760
Period size: 46 Copynumber: 13.3 Consensus size: 46
1462735 TAAACTGAAT
** * *
1462745 CCATAACTAAAATGCATGAAAATATGCATTAATGCATGAAAGGATT
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
1462791 CCAAAATTAAAATGCATGAACGGATGCATTAAGGCATTAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1462837 CTATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1462883 CTATAACT-AAATGCATGAACA-TACT-CAATAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAA-AGGA-TGCATTAAGGCATGAAAGGATG
* * *
1462928 CCATAATTAAAATGCATGTAAGGATGCATTAAGGCATGAAAGGATA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1462974 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1463020 CCATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
1463066 TCATAACTAAAATGCTTGAAAGAATGAATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1463112 ACATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1463158 CCATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGACG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1463204 CCATAACTAAAATGCATGAAAGGAAGCATTAAGGCATTAAAGGATT
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
1463250 CCATAATTAAAATACATGAGAA-GATACATTAAGGAATGAAAGGATG
1 CCATAACTAAAATGCATGA-AAGGATGCATTAAGGCATGAAAGGATG
* * * * * ** *
1463296 CCATGATTAAAATGCATGAACGGATGTATTAATGCATGAAAATATA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1463342 CCATAACTGAAAT
1 CCATAACTAAAAT
1463355 TAATGAATAA
Statistics
Matches: 485, Mismatches: 72, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
45 40 0.08
46 443 0.91
47 2 0.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1465068 original size:21 final size:21
Alignment explanation
Indices: 1465044--1465083 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1465034 CAAACATGTG
1465044 GCAAA-TTGCACAGTGGAGCAT
1 GCAAACTT-CACAGTGGAGCAT
*
1465065 GCAAACTTCTCAGTGGAGC
1 GCAAACTTCACAGTGGAGC
1465084 TTGTTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.20
Consensus pattern (21 bp):
GCAAACTTCACAGTGGAGCAT
Found at i:1465313 original size:20 final size:20
Alignment explanation
Indices: 1465244--1465726 Score: 124
Period size: 20 Copynumber: 21.2 Consensus size: 20
1465234 TAAGAGACTC
1465244 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* * *
1465264 TGATGCCATAACTAAAATGCATGAAC
1 GGATG-CAT---T--AAGGCATGAAA
*
1465290 GGATGCATTAAGGCATTAAA
1 GGATGCATTAAGGCATGAAA
* *
1465310 GGATGCCATAACTAAAATGCATGAAC
1 GGATG-CAT---T--AAGGCATGAAA
1465336 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
*
1465356 GGATGCTATAACTAAATGCATGAACA
1 GGATGC-AT---T-AAGGCATGAA-A
* *
1465382 -TACT-CAATAAGGCATGAAA
1 GGA-TGCATTAAGGCATGAAA
* * *
1465401 AGATGCCATAATTAAAATGCATGTAA
1 GGATG-C---ATT--AAGGCATGAAA
1465427 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* *
1465447 GGATACCATAACTAAAATGCATGAAA
1 GGAT-GCAT---T--AAGGCATGAAA
1465473 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* * *
1465493 AGATGCCATAATTAAAATGCATGAAC
1 GGATG-C---ATT--AAGGCATGAAA
1465519 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* *
1465539 GGATGTCATAACTAAAATGCTTGAAA
1 GGATG-CAT---T--AAGGCATGAAA
* *
1465565 GAATGAATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* * *
1465585 AGATGACATAACTAAAATGCATGAAC
1 GGATG-CAT---T--AAGGCATGAAA
1465611 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* *
1465631 GGATGCCATAATTAAAATGCATGATA
1 GGATG-C---ATT--AAGGCATGAAA
1465657 GGATGCATTAAGGCATGAAA
1 GGATGCATTAAGGCATGAAA
* * *
1465677 AGACGCCATAACTAAAATGCATGAAA
1 GGATG-CAT---T--AAGGCATGAAA
* *
1465703 GGAAGCATTAAGGCATTAAA
1 GGATGCATTAAGGCATGAAA
1465723 GGAT
1 GGAT
1465727 TCCATAATTA
Statistics
Matches: 341, Mismatches: 59, Indels: 126
0.65 0.11 0.24
Matches are distributed among these distances:
19 2 0.01
20 133 0.39
21 23 0.07
22 15 0.04
24 16 0.05
25 31 0.09
26 121 0.35
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.22
Consensus pattern (20 bp):
GGATGCATTAAGGCATGAAA
Found at i:1465839 original size:46 final size:46
Alignment explanation
Indices: 1465243--1465832 Score: 758
Period size: 46 Copynumber: 12.8 Consensus size: 46
1465233 ATAAGAGACT
*
1465243 CGGATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
*
1465289 CGGATGCATTAAGGCATTAAAGGATGCCATAACTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
*
1465335 CGGATGCATTAAGGCATGAAAGGATGCTATAACT-AAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
** * * *
1465380 CATACT-CAATAAGGCATGAAAAGATGCCATAATTAAAATGCATGTAA
1 CGGA-TGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATG-AA
*
1465427 -GGATGCATTAAGGCATGAAAGGATACCATAACTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* * *
1465472 AGGATGCATTAAGGCATGAAAAGATGCCATAATTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* *
1465518 CGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCTTGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* * * * *
1465564 AGAATGAATTAAGGCATGAAAAGATGACATAACTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
*
1465610 CGGATGCATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGATA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA-A
* *
1465657 -GGATGCATTAAGGCATGAAAAGACGCCATAACTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* * * * * *
1465702 AGGAAGCATTAAGGCATTAAAGGATTCCATAATTAAAATACATGAGA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGA-A
* * * * *
1465749 -AGATACATTAAGGAATGAAAGGATGCCATGATTAAAATGCATGAA
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
* * ** * *
1465794 CGGATGTATTAATGCATGAAAATATACCATAACTGAAAT
1 CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAT
1465833 TAATGAATAA
Statistics
Matches: 470, Mismatches: 65, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
45 42 0.09
46 424 0.90
47 4 0.01
ACGTcount: A:0.44, C:0.13, G:0.21, T:0.22
Consensus pattern (46 bp):
CGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA
Found at i:1468225 original size:46 final size:46
Alignment explanation
Indices: 1467721--1468218 Score: 712
Period size: 46 Copynumber: 10.8 Consensus size: 46
1467711 TAAGAGACTC
* *
1467721 GGATGCATTAAGGCATGAAATGATGCCATAACTAAAATGCATGAAC
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
*
1467767 GGATGCATTAAGGCATTAAAGGATGCCATAACTAAAATGCATGAAA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * * *
1467813 TGATGCATTAAGGTATGAAAGGATTCCATAATTAAAATGCATGAACA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAA-A
1467860 -GATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
1467905 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * *
1467951 GGATGAATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAT
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * * **
1467997 GGATGCATTAAGGCATGAAATGATACCATAATTAATTTGCATGAAA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
*
1468043 GGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * * * *
1468089 GGATGCATCAGGGCATGAAAGGATTCCATAATTAAAATGCGTGAAA
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * * *
1468135 GGATGCATTAAGGGATGAAAGGATGCCATGATTAAAATGCATGAAC
1 GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
* * *
1468181 GGATGTATTAATGCATGAAAAGA-GACCATAACTAAAAT
1 GGATGCATTAAGGCATGAAAGGATG-CCATAACTAAAAT
1468219 TAATGAATAA
Statistics
Matches: 402, Mismatches: 47, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
45 2 0.00
46 399 0.99
47 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.23
Consensus pattern (46 bp):
GGATGCATTAAGGCATGAAAGGATGCCATAACTAAAATGCATGAAA
Found at i:1472633 original size:12 final size:12
Alignment explanation
Indices: 1472616--1472646 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
1472606 TGTCAGATAC
1472616 GTCATGCACAAA
1 GTCATGCACAAA
1472628 GTCATGCACAAA
1 GTCATGCACAAA
1472640 GTCATGC
1 GTCATGC
1472647 CCACTAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (12 bp):
GTCATGCACAAA
Found at i:1475257 original size:13 final size:13
Alignment explanation
Indices: 1475239--1475263 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1475229 CTTAGCATGT
1475239 TTAAAAATAAAAC
1 TTAAAAATAAAAC
1475252 TTAAAAATAAAA
1 TTAAAAATAAAA
1475264 TAAAAACAAC
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TTAAAAATAAAAC
Found at i:1476401 original size:13 final size:13
Alignment explanation
Indices: 1476357--1476402 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1476347 CATGTATTTT
*
1476357 TCTTCTTTCTTT-
1 TCTTTTTTCTTTG
*
1476369 TCTTTTTTTTTTG
1 TCTTTTTTCTTTG
1476382 T-TGTTTTTCTTTG
1 TCT-TTTTTCTTTG
1476395 TCTTTTTT
1 TCTTTTTT
1476403 GTCCAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 11 0.39
13 16 0.57
14 1 0.04
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (13 bp):
TCTTTTTTCTTTG
Found at i:1495836 original size:19 final size:18
Alignment explanation
Indices: 1495785--1495833 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
1495775 AATCTCTTTA
1495785 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
1495804 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
1495823 ATTTTTTATTT
1 ATTTTTTATTT
1495834 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:1501374 original size:15 final size:15
Alignment explanation
Indices: 1501312--1501376 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
1501302 ACCCATTTCG
1501312 TTTTATTTTCATTTTA
1 TTTTA-TTTCATTTTA
*
1501328 -TTTATTTCATTTCA
1 TTTTATTTCATTTTA
** *
1501342 TTCCATTACA-TTTA
1 TTTTATTTCATTTTA
*
1501356 TTTTATTTTATTTTA
1 TTTTATTTCATTTTA
1501371 TTTTAT
1 TTTTAT
1501377 CAGATTCTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
14 18 0.47
15 20 0.53
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTATTTCATTTTA
Found at i:1501395 original size:5 final size:5
Alignment explanation
Indices: 1501312--1501376 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
1501302 ACCCATTTCG
* * ** **
1501312 TTTTA TTTTCA TTTTA -TTTA TTTCA TTTCA TTCCA TTACA -TTTA TTTTA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1501361 TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA T
1501377 CAGATTCTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
4 6 0.12
5 41 0.79
6 5 0.10
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (5 bp):
TTTTA
Found at i:1503804 original size:19 final size:19
Alignment explanation
Indices: 1503759--1503801 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1503749 TTTAATTTGC
*
1503759 TTATTTAATTATTTTTCTT
1 TTATTTAATTATTATTCTT
*
1503778 TTATTTAATTCTTATT-TT
1 TTATTTAATTATTATTCTT
1503796 TTATTT
1 TTATTT
1503802 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTTAATTATTATTCTT
Found at i:1504401 original size:14 final size:15
Alignment explanation
Indices: 1504377--1504405 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1504367 ATATACGTGT
1504377 TGGTCATATAAATGG
1 TGGTCATATAAATGG
1504392 TGGT-ATATAAATGG
1 TGGTCATATAAATGG
1504406 GTATTTCGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.34
Consensus pattern (15 bp):
TGGTCATATAAATGG
Found at i:1509872 original size:34 final size:34
Alignment explanation
Indices: 1509824--1509892 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
1509814 GTTAAGGAAC
1509824 ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
1 ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
*
1509858 ACCTGTTATAGTCAATTTCACACGAGCACTCAAA
1 ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
1509892 A
1 A
1509893 ATTTCATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (34 bp):
ACCTCTTATAGTCAATTTCACACGAGCACTCAAA
Found at i:1512075 original size:136 final size:135
Alignment explanation
Indices: 1511909--1512181 Score: 377
Period size: 135 Copynumber: 2.0 Consensus size: 135
1511899 AAACAAATTA
* *
1511909 TTATCGAGTCTGACCTCCCCTAAAGAGTAGCGGAGCATA-TTATTCTCCTTTCAGATTTGGTCTT
1 TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCA-AGTTATTCTCCTTTCAGATTTGGTCTT
** * * * * * *
1511973 CCCTGAAGAGGAGCAAAGCAAATCAAGTTTGATTCAATCTTCCCTGAAGAGTAGTGAAGTGGATC
65 -CCTGAAGAGGAGCAAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATC
1512038 AAAAGTT
129 AAAAGTT
* *
1512045 TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCAAGTTCTTCTTCTTTCAGATTTGGTCTTC
1 TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCAAGTTATTCTCCTTTCAGATTTGGTCTTC
* **
1512110 CTGAAGAGTAGTGAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATCAA
66 CTGAAGAGGAGCAAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATCAA
*
1512175 AATTT
131 AAGTT
1512180 TT
1 TT
1512182 GAGATCTAAT
Statistics
Matches: 120, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
135 62 0.52
136 58 0.48
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (135 bp):
TTATCGAGTCTAACCTCCCCTAAAGAGTAGCAGAGCAAGTTATTCTCCTTTCAGATTTGGTCTTC
CTGAAGAGGAGCAAAGCAAATCAAGTTCAATTCAACCTTCCCTCAAAAGCAGCGAAGTGAATCAA
AAGTT
Found at i:1515183 original size:15 final size:15
Alignment explanation
Indices: 1515163--1515196 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1515153 CACATAAATA
1515163 TCTTTAAAGAAATTG
1 TCTTTAAAGAAATTG
1515178 TCTTTAAAGAAATTG
1 TCTTTAAAGAAATTG
1515193 TCTT
1 TCTT
1515197 GAATTTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (15 bp):
TCTTTAAAGAAATTG
Found at i:1525297 original size:46 final size:45
Alignment explanation
Indices: 1525173--1525298 Score: 121
Period size: 46 Copynumber: 2.8 Consensus size: 45
1525163 GTAACCATGC
* * *
1525173 AAATAAGCTTATGAGCTTATCGAATAATGGCAAGTATATTGAAAA
1 AAATAAGCTTATGAGCTTATGGAATAAAGGTAAGTATATTGAAAA
* * * **
1525218 AAATAA--TAATAAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--TAAA-GGTAAGTATATTGAAAA
*
1525264 AAATAAGCTTATGAGCTTATGGGATGAAAGGTAAG
1 AAATAAGCTTATGAGCTTATGGAAT-AAAGGTAAG
1525299 AAATTTTATA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 13 0.20
45 9 0.14
46 26 0.41
47 3 0.05
48 13 0.20
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAAAGGTAAGTATATTGAAAA
Found at i:1534770 original size:46 final size:46
Alignment explanation
Indices: 1534696--1535305 Score: 765
Period size: 46 Copynumber: 13.3 Consensus size: 46
1534686 TAAACCGAAT
* *
1534696 CCATAACTAAAATGCATGAAAAGATGCATTAATGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
1534742 CCAAAATTAAAATGCATGAATGGTTGCATTAAGGTATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1534788 CCATAACTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
1534834 CTATAACT-AAATGCATGAACA-TATTCAATAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAA-AGGATGCATTAAGGCATGAAAGGATG
* * *
1534879 CCATAATTAAAATGCATGTAAGGATGCATTAAGGCATGAAAGGATA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1534925 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1534971 TCATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
1535017 TCATAACTAAAATGCATGAAAGAATGAATTAAGGCATGAAAAGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* ** *
1535063 ACATAACTAAAATGCATGATCGGATGCACTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* ** * *
1535109 CCATAATTAAAATGTGTGAAAGGATGCATTAAGGCATGAAGGGACG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1535155 CCATAACTAAAATGCATGAAAGGAAGCATTAAGGCATTAAAGGATT
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
1535201 CCATAATTAAAATACATGAGAGGATACATTAAGGAATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * ** *
1535247 CCATGATTAAAATGCATGAACGGATGCATTAATGCATGAAACTATA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1535293 CCATAACTGAAAT
1 CCATAACTAAAAT
1535306 TAATGAATAA
Statistics
Matches: 479, Mismatches: 82, Indels: 6
0.84 0.14 0.01
Matches are distributed among these distances:
45 39 0.08
46 440 0.92
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1534826 original size:20 final size:20
Alignment explanation
Indices: 1534709--1535109 Score: 120
Period size: 20 Copynumber: 17.7 Consensus size: 20
1534699 TAACTAAAAT
* *
1534709 GCATGAAAAGATGCATTAAT
1 GCATGAAAGGATGCATTAAG
*
1534729 GCATGAAAGGATGCCAAAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
* *
1534755 GCATGAATGGTTGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1534775 GTATGAAAGGATGCCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
*
1534801 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1534821 GCATGAAAGGATGCTATAACTAAAT
1 GCATGAAAGGATGC-AT---T-AAG
* * *
1534846 GCATGAACA-TATTCAATAAG
1 GCATGAA-AGGATGCATTAAG
*
1534866 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1534892 GCATGTAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1534912 GCATGAAAGGATACCATAACTAAAAT
1 GCATGAAAGGAT-GCAT---T--AAG
1534938 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1534958 GCATGAAAAGATGTCATAATTAAAAT
1 GCATGAAAGGATG-C---ATT--AAG
*
1534984 GCATGAACGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
1535004 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
* *
1535030 GCATGAAAGAATGAATTAAG
1 GCATGAAAGGATGCATTAAG
* *
1535050 GCATGAAAAGATGACATAACTAAAAT
1 GCATGAAAGGATG-CAT---T--AAG
** *
1535076 GCATGATCGGATGCACTAAG
1 GCATGAAAGGATGCATTAAG
1535096 GCATGAAAGGATGC
1 GCATGAAAGGATGC
1535110 CATAATTAAA
Statistics
Matches: 283, Mismatches: 49, Indels: 98
0.66 0.11 0.23
Matches are distributed among these distances:
19 1 0.00
20 118 0.42
21 17 0.06
22 13 0.05
24 14 0.05
25 25 0.09
26 95 0.34
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:1535079 original size:26 final size:25
Alignment explanation
Indices: 1534866--1535178 Score: 130
Period size: 26 Copynumber: 13.4 Consensus size: 25
1534856 ATTCAATAAG
*
1534866 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGACATAA-TAAAAT
* *
1534892 GCATGTAAGGATG-CAT--T--AAG
1 GCATGAAAGGATGACATAATAAAAT
1534912 GCATGAAAGGAT-ACCATAACTAAAAT
1 GCATGAAAGGATGA-CATAA-TAAAAT
*
1534938 GCATGAAAGGATG-CAT--T--AAG
1 GCATGAAAGGATGACATAATAAAAT
* *
1534958 GCATGAAAAGATGTCATAATTAAAAT
1 GCATGAAAGGATGACATAA-TAAAAT
* *
1534984 GCATGAACGGATG-CAT--T--AAG
1 GCATGAAAGGATGACATAATAAAAT
*
1535004 GCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATGACATAA-TAAAAT
* *
1535030 GCATGAAAGAATGA-AT--T--AAG
1 GCATGAAAGGATGACATAATAAAAT
*
1535050 GCATGAAAAGATGACATAACTAAAAT
1 GCATGAAAGGATGACATAA-TAAAAT
** * *
1535076 GCATGATCGGATG-C--ACT--AAG
1 GCATGAAAGGATGACATAATAAAAT
*
1535096 GCATGAAAGGATGCCATAATTAAAAT
1 GCATGAAAGGATGACATAA-TAAAAT
** *
1535122 GTGTGAAAGGATG-CAT--T--AAG
1 GCATGAAAGGATGACATAATAAAAT
* * *
1535142 GCATGAAGGGACGCCATAACTAAAAT
1 GCATGAAAGGATGACATAA-TAAAAT
1535168 GCATGAAAGGA
1 GCATGAAAGGA
1535179 AGCATTAAGG
Statistics
Matches: 213, Mismatches: 36, Indels: 76
0.66 0.11 0.23
Matches are distributed among these distances:
20 79 0.37
21 15 0.07
22 6 0.03
23 2 0.01
24 6 0.03
25 15 0.07
26 90 0.42
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.21
Consensus pattern (25 bp):
GCATGAAAGGATGACATAATAAAAT
Found at i:1537004 original size:21 final size:21
Alignment explanation
Indices: 1536980--1537020 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1536970 TCAAACATGT
1536980 TGCAAA-TTGCACAGTGGAGCA
1 TGCAAACTT-CACAGTGGAGCA
*
1537001 TGCAAACTTCTCAGTGGAGC
1 TGCAAACTTCACAGTGGAGC
1537021 TTGTTTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
TGCAAACTTCACAGTGGAGCA
Found at i:1542053 original size:46 final size:46
Alignment explanation
Indices: 1542003--1542457 Score: 680
Period size: 46 Copynumber: 9.9 Consensus size: 46
1541993 TAAATAGAAT
*
1542003 CCATAACTAAAATGAATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * * *
1542049 CCATAATTAAAATGCATGAATGGATGCATTACGGTAAGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1542095 CCATAACTAAAATGCATGAACGGATGCATTAAGGTATGAAAGGATT
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * * *
1542141 CCATAACTAAAATACATGAAATGATGCATTAAGGTACGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1542187 CCATAATTAAAATGCATGAACA-GATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAA-AGGATGCATTAAGGCATGAAAGGATG
1542233 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1542279 CCATAACTAAAATGCATGAAAGGATG-AGTTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCA-TTAAGGCATGAAAGGATG
* * *
1542325 ACGTAACTAAAATGCATGAATGGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* * *
1542371 CCATAATTAAATTGCATGAAATGATGCATTAAGGCATGAAAGGATG
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
* *
1542417 TCATAACTAAAATGCATGAAAGGATGCATCAAGGCATGAAA
1 CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAA
1542458 AATATCTTTA
Statistics
Matches: 370, Mismatches: 35, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
45 2 0.01
46 366 0.99
47 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.23, T:0.22
Consensus pattern (46 bp):
CCATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1548511 original size:16 final size:19
Alignment explanation
Indices: 1548490--1548525 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1548480 GGGGTTTTGG
1548490 TAAAAAT-GA-TTAAATAA
1 TAAAAATCGATTTAAATAA
1548507 TAAAAATCGATTTAAATAA
1 TAAAAATCGATTTAAATAA
1548526 AAATAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (19 bp):
TAAAAATCGATTTAAATAA
Found at i:1550252 original size:19 final size:19
Alignment explanation
Indices: 1550217--1550267 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
1550207 TTCTCATGTA
* *
1550217 TTTTTCTTCTTT-CTTTTC
1 TTTTTCTTTTTTGTTTTTC
1550235 TTTTT-TTTTGTTGTTTTTC
1 TTTTTCTTTT-TTGTTTTTC
1550254 TTTTTCTTTTTTGT
1 TTTTTCTTTTTTGT
1550268 CCAAAAATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 3 0.11
18 7 0.25
19 14 0.50
20 4 0.14
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTTTGTTTTTC
Found at i:1570179 original size:34 final size:33
Alignment explanation
Indices: 1570094--1570192 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
1570084 AATTGGAAAG
1570094 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
* *
1570127 TTTGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
*
1570160 TTGGAAAATTCATCTTTGGTAGGTGGCCAACTT
1 TTGGAAAATTCATC-TTGGTTGGTGGCCAACTT
1570193 TGTATATGGG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 43 0.72
34 17 0.28
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (33 bp):
TTGGAAAATTCATCTTGGTTGGTGGCCAACTTA
Done.