Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 5 of 168
Found at i:1350100 original size:12 final size:12
Alignment explanation
Indices: 1350085--1350111 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1350075 ATGGTTAAAG
1350085 AAATAATAAATA
1 AAATAATAAATA
1350097 AAATAATAAATA
1 AAATAATAAATA
1350109 AAA
1 AAA
1350112 CAGTTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAATAATAAATA
Found at i:1355646 original size:25 final size:25
Alignment explanation
Indices: 1355609--1355740 Score: 151
Period size: 25 Copynumber: 5.3 Consensus size: 25
1355599 TGGACACACC
*
1355609 ACAGCTCGTATGAGCTTCTCGTTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
* *
1355634 ACAGCTCACATGATCTT-TCCGTTAT
1 ACAGCTCGCATGAGCTTCT-CGTTAT
* *
1355659 ATAGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
1355684 ACAGCT-GCATGAGCTTCTCGTTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
*** *
1355708 TTGGCTCGCATGAGCTTCCCGTTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
*
1355733 TCAGCTCG
1 ACAGCTCG
1355741 GAGGAGTTTC
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
24 21 0.24
25 68 0.76
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCTCGTTAT
Found at i:1355715 original size:49 final size:50
Alignment explanation
Indices: 1355611--1355739 Score: 172
Period size: 49 Copynumber: 2.6 Consensus size: 50
1355601 GACACACCAC
* * *
1355611 AGCTCGTATGAGCTTCTCGTTATACAGCTCACATGATCTTTCCGTTATAT
1 AGCTCGCATGAGCTTCCCGTTATACAGCTCACATGAGCTTTCCGTTATAT
* *
1355661 AGCTCGCATGAGCTTCCCGTTATACAGCT-GCATGAGC-TTCTCGTTATTT
1 AGCTCGCATGAGCTTCCCGTTATACAGCTCACATGAGCTTTC-CGTTATAT
* *
1355710 GGCTCGCATGAGCTTCCCGTTATTCAGCTC
1 AGCTCGCATGAGCTTCCCGTTATACAGCTC
1355740 GGAGGAGTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 3 0.04
49 40 0.57
50 27 0.39
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (50 bp):
AGCTCGCATGAGCTTCCCGTTATACAGCTCACATGAGCTTTCCGTTATAT
Found at i:1359569 original size:17 final size:16
Alignment explanation
Indices: 1359549--1359593 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
1359539 GTCCATTTTT
1359549 TTATTTTCTTTATTTAA
1 TTATTTT-TTTATTTAA
*
1359566 TTATTTTTCATATTTAA
1 TTATTTTT-TTATTTAA
1359583 TTATTTTTTTA
1 TTATTTTTTTA
1359594 ATATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 22 0.88
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTTTTTTATTTAA
Found at i:1359604 original size:15 final size:17
Alignment explanation
Indices: 1359584--1359618 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
1359574 CATATTTAAT
1359584 TATTTTTT-TA-ATATA
1 TATTTTTTATACATATA
1359599 TATTTTTTATACATATA
1 TATTTTTTATACATATA
1359616 TAT
1 TAT
1359619 ATACATACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 2 0.11
17 8 0.44
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTTATACATATA
Found at i:1359661 original size:19 final size:17
Alignment explanation
Indices: 1359632--1359671 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
1359622 CATACGCATA
1359632 TTTTTTAATGTAATTATT
1 TTTTTTAATGTAATT-TT
*
1359650 TTTTTTATATGTAGTTTT
1 TTTTTTA-ATGTAATTTT
1359668 TTTT
1 TTTT
1359672 ATAAACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.72
Consensus pattern (17 bp):
TTTTTTAATGTAATTTT
Found at i:1359703 original size:12 final size:12
Alignment explanation
Indices: 1359678--1359717 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
1359668 TTTTATAAAC
1359678 TATATATATGTA
1 TATATATATGTA
1359690 TATAT-T-TGTA
1 TATATATATGTA
1359700 TATATATATGTA
1 TATATATATGTA
*
1359712 TGTATA
1 TATATA
1359718 CATATTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 9 0.36
11 2 0.08
12 14 0.56
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (12 bp):
TATATATATGTA
Found at i:1360052 original size:13 final size:12
Alignment explanation
Indices: 1360028--1360066 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
1360018 TCATGAATTA
1360028 TTGTTT-TTTAT
1 TTGTTTATTTAT
1360039 TTCGTTTATTTAT
1 TT-GTTTATTTAT
1360052 TTGTTTATATTAT
1 TTGTTTAT-TTAT
1360065 TT
1 TT
1360067 TTATGTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.08
12 10 0.40
13 13 0.52
ACGTcount: A:0.15, C:0.03, G:0.08, T:0.74
Consensus pattern (12 bp):
TTGTTTATTTAT
Found at i:1360503 original size:98 final size:98
Alignment explanation
Indices: 1360382--1360577 Score: 365
Period size: 98 Copynumber: 2.0 Consensus size: 98
1360372 TAAAAAAATC
*
1360382 ATAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTT
1 ATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTT
1360447 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
* *
1360480 ATAAAGGAAATATTCTGAGTTTGGGATTCTAAAGGGATTGTGCCCTAACGTATTGGGTGTGATTT
1 ATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTT
1360545 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 CTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
1360578 GTTTTATTGT
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 95 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (98 bp):
ATAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTT
CTTAAATCTTGGATAAGTGGATGTTCTTTTAAA
Found at i:1361176 original size:25 final size:25
Alignment explanation
Indices: 1361143--1361283 Score: 110
Period size: 25 Copynumber: 5.7 Consensus size: 25
1361133 CGGACACATC
1361143 ACAGCTCGCATGAGCTTCTCGTTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
* *
1361168 ACAACTCGCATGAG-TTTTCTGTTAT
1 ACAGCTCGCATGAGCTTCTC-GTTAT
* * *
1361193 ACAGCTCGTATGAGCTTCCCATTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
** * *
1361218 TTAGCTCGCATGAGCTTCCCGCTAT
1 ACAGCTCGCATGAGCTTCTCGTTAT
* *
1361243 TCAGCTCAG-AGGAGCTTC-CTGTT-T
1 ACAGCTC-GCATGAGCTTCTC-GTTAT
* *
1361267 ACAGCTCGTACGAGCTT
1 ACAGCTCGCATGAGCTT
1361284 ACATAAATAT
Statistics
Matches: 94, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
23 1 0.01
24 19 0.20
25 70 0.74
26 4 0.04
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
ACAGCTCGCATGAGCTTCTCGTTAT
Found at i:1363675 original size:136 final size:136
Alignment explanation
Indices: 1363431--1363694 Score: 438
Period size: 136 Copynumber: 1.9 Consensus size: 136
1363421 AAAATTCCCC
* * *
1363431 TTACTTATAACTTTTAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCATTTG
1 TTACTCATAACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAATCATTTG
1363496 AAAGACTAGTATTCAAGATTGAATACATAGAATATGAGAAAGTATGTAATGTTTTCATGAGGGGG
66 AAAGACTAGTATTCAAGATTGAATACATAGAATATGAGAAAGTATGTAATGTTTTCATGAGGGGG
1363561 AACCCT
131 AACCCT
* * *
1363567 TTACTCATGACTTTCAAAAGAATGGTGATATAAATGCTTAGCAAATACATTTAAATAATCATTTG
1 TTACTCATAACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAATCATTTG
* * * *
1363632 AAAGATTAGTATTCAAGATTGAATACGTAGAATATGAGGAAGTATGTGATGTTTTCATGAGGG
66 AAAGACTAGTATTCAAGATTGAATACATAGAATATGAGAAAGTATGTAATGTTTTCATGAGGG
1363695 AGAGTAAATA
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
136 118 1.00
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.33
Consensus pattern (136 bp):
TTACTCATAACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAATCATTTG
AAAGACTAGTATTCAAGATTGAATACATAGAATATGAGAAAGTATGTAATGTTTTCATGAGGGGG
AACCCT
Found at i:1364376 original size:25 final size:25
Alignment explanation
Indices: 1364348--1364397 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1364338 ATATAGTTTT
1364348 TATATTAT-TTATAAATGTTATAATA
1 TATATTATATTAT-AATGTTATAATA
1364373 TATATTATATTATAATGTTATAATA
1 TATATTATATTATAATGTTATAATA
1364398 AAACAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (25 bp):
TATATTATATTATAATGTTATAATA
Found at i:1365352 original size:43 final size:43
Alignment explanation
Indices: 1365286--1365414 Score: 129
Period size: 43 Copynumber: 3.0 Consensus size: 43
1365276 CATAGGATTC
* *
1365286 CGATATGTGTTTTCGTGTAAGACCACATCTGGGATGTTGGCAT
1 CGATATGTGTTTACGTGTAAGACCACATCTGGGAAGTTGGCAT
*
1365329 CGACT-TGTGTTTACGTGTAAGACC-CTATCTGGGACAG-TGACAT
1 CGA-TATGTGTTTACGTGTAAGACCAC-ATCTGGGA-AGTTGGCAT
* * * * * *
1365372 CGATATGTGATTACATGTAAGACAACGTCCGGGACGTTGGCAT
1 CGATATGTGTTTACGTGTAAGACCACATCTGGGAAGTTGGCAT
1365415 TGTACAAGCC
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
42 3 0.04
43 64 0.91
44 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
CGATATGTGTTTACGTGTAAGACCACATCTGGGAAGTTGGCAT
Found at i:1366464 original size:2 final size:2
Alignment explanation
Indices: 1366452--1366489 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1366442 AATTTGCTTG
*
1366452 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1366490 GTATGTATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1367458 original size:2 final size:2
Alignment explanation
Indices: 1367451--1367486 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1367441 AATGATTTAA
1367451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1367487 GAATTGATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1377717 original size:26 final size:26
Alignment explanation
Indices: 1377681--1377735 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
1377671 TGAGTAGTGC
1377681 CAACTGCTTTAGGGATTGTTAAAGAA
1 CAACTGCTTTAGGGATTGTTAAAGAA
1377707 CAACTGCTTTAGGGATTGTTAAAGAA
1 CAACTGCTTTAGGGATTGTTAAAGAA
1377733 CAA
1 CAA
1377736 AGATGAACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (26 bp):
CAACTGCTTTAGGGATTGTTAAAGAA
Found at i:1377908 original size:11 final size:12
Alignment explanation
Indices: 1377894--1377962 Score: 63
Period size: 11 Copynumber: 5.9 Consensus size: 12
1377884 AAAGTTGTTT
1377894 TTACATATATT-
1 TTACATATATTA
1377905 TTACATATATTA
1 TTACATATATTA
*
1377917 ATACATAT-TTA
1 TTACATATATTA
*
1377928 TTAATATATATTA
1 TT-ACATATATTA
* * *
1377941 ATAAAT-TATTT
1 TTACATATATTA
1377952 TTACATATATT
1 TTACATATATT
1377963 GCAATGATTT
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
11 23 0.50
12 19 0.41
13 4 0.09
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (12 bp):
TTACATATATTA
Found at i:1377939 original size:24 final size:25
Alignment explanation
Indices: 1377909--1377961 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
1377899 TATATTTTAC
*
1377909 ATATATTAATACA-TATTTATTA-AT
1 ATATATTAATAAATTATTT-TTACAT
1377933 ATATATTAATAAATTATTTTTACAT
1 ATATATTAATAAATTATTTTTACAT
1377958 ATAT
1 ATAT
1377962 TGCAATGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
ATATATTAATAAATTATTTTTACAT
Found at i:1379193 original size:35 final size:36
Alignment explanation
Indices: 1379147--1379215 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
1379137 TGTCAATCAT
1379147 TTCAATATCCAACAAGCTTAAAACATAAT-AATAAA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
1379182 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1 TTCAATATCCAACAAGCTTAAAACATAATCAATA
1379216 TCTAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.52, C:0.19, G:0.03, T:0.26
Consensus pattern (36 bp):
TTCAATATCCAACAAGCTTAAAACATAATCAATAAA
Found at i:1379213 original size:27 final size:28
Alignment explanation
Indices: 1379183--1379252 Score: 81
Period size: 27 Copynumber: 2.5 Consensus size: 28
1379173 AATAATAAAT
*
1379183 TCAATATCCAACAAGCTT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
1379210 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
1379238 TCAAAATCCAACAAA
1 TCAATATCCAACAAA
1379253 CTAAAATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.06
27 20 0.56
28 14 0.39
ACGTcount: A:0.53, C:0.21, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:1383376 original size:25 final size:27
Alignment explanation
Indices: 1383321--1383388 Score: 97
Period size: 25 Copynumber: 2.6 Consensus size: 27
1383311 AAGCTTTGAG
1383321 GAATGGAAAATGTCTGCTGCTTAGAAGA
1 GAATGGAAAATGTCT-CTGCTTAGAAGA
1383349 GAATGGAAAATGT-T-TGCTTAG-AGAA
1 GAATGGAAAATGTCTCTGCTTAGAAG-A
1383374 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
1383389 TACCAATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
24 2 0.05
25 21 0.55
26 1 0.03
27 1 0.03
28 13 0.34
ACGTcount: A:0.38, C:0.07, G:0.28, T:0.26
Consensus pattern (27 bp):
GAATGGAAAATGTCTCTGCTTAGAAGA
Found at i:1386510 original size:36 final size:35
Alignment explanation
Indices: 1386462--1386537 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 35
1386452 GTTGCGCCTT
* * *
1386462 ACACTGGTCGGTATAACCGACAGATAGATGTGCCCA
1 ACACTGGCCGGTATAACCAACAAATAGA-GTGCCCA
* *
1386498 GCACTGGCCGGTATAACCAACAAATGGAGTGCCCA
1 ACACTGGCCGGTATAACCAACAAATAGAGTGCCCA
1386533 ACACT
1 ACACT
1386538 CCTCGACACG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 11 0.32
36 23 0.68
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.17
Consensus pattern (35 bp):
ACACTGGCCGGTATAACCAACAAATAGAGTGCCCA
Found at i:1387819 original size:41 final size:41
Alignment explanation
Indices: 1387774--1387930 Score: 233
Period size: 41 Copynumber: 3.8 Consensus size: 41
1387764 TTGTATATAA
* ** * * *
1387774 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
1387815 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1387856 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
1387897 CACCGGCACAAAGCCTGCTAGGTATAAAGCCTGA
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGA
1387931 ACTTACAAAA
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:1389184 original size:42 final size:42
Alignment explanation
Indices: 1389121--1389219 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
1389111 CTCTCGGTAT
* *
1389121 CGCACACTTAGTGCCCGTTATTCAACATCATTATTATAATTC
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
* * *
1389163 CGCACACTTAGTGCCTATTATTCAACATCATCATTTTAATTT
1 CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
**
1389205 TACACACTTAGTGCC
1 CGCACACTTAGTGCC
1389220 ATTCATATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.26, G:0.09, T:0.36
Consensus pattern (42 bp):
CGCACACTTAGTGCCCATTATTCAACATCATCATTATAATTC
Found at i:1392270 original size:2 final size:2
Alignment explanation
Indices: 1392263--1392305 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1392253 NNNNNNNNNN
1392263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA
1392305 T
1 T
1392306 GGAATTGTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1395688 original size:40 final size:39
Alignment explanation
Indices: 1395627--1395802 Score: 199
Period size: 40 Copynumber: 4.4 Consensus size: 39
1395617 TATTAATTCG
* * *
1395627 ACTAGTGATGGACACATATTTGATATTGTAGGTTTATCCA
1 ACTAGTGCTGGGCACACATTTGATATTGTA-GTTTATCCA
* * * *
1395667 AATAGTGCTGGGCACACATTTGATATCGTCGGTTTATCCG
1 ACTAGTGCTGGGCACACATTTGATATTGT-AGTTTATCCA
** *
1395707 ACTAGCACTGGGCACACATTTGATATTGTTAGTTTATCTA
1 ACTAGTGCTGGGCACACATTTGATATTG-TAGTTTATCCA
*
1395747 ACTAGTGCTGGGCACACATTTGATATTGTCAGTTTATCCG
1 ACTAGTGCTGGGCACACATTTGATATTGT-AGTTTATCCA
* *
1395787 GCTAGCGCTGGGCACA
1 ACTAGTGCTGGGCACA
1395803 AAAAATTATC
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 111 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (39 bp):
ACTAGTGCTGGGCACACATTTGATATTGTAGTTTATCCA
Found at i:1395758 original size:80 final size:80
Alignment explanation
Indices: 1395639--1395802 Score: 249
Period size: 80 Copynumber: 2.0 Consensus size: 80
1395629 TAGTGATGGA
* *
1395639 CACATATTTGATATTGTAGGTTTATCCAAATAGTGCTGGGCACACATTTGATATCGTCGGTTTAT
1 CACACATTTGATATTGTAGGTTTATCCAAATAGTGCTGGGCACACATTTGATATCGTCAGTTTAT
1395704 CCGACTAGCACTGGG
66 CCGACTAGCACTGGG
* * *
1395719 CACACATTTGATATTGTTA-GTTTATCTAACTAGTGCTGGGCACACATTTGATATTGTCAGTTTA
1 CACACATTTGATATTG-TAGGTTTATCCAAATAGTGCTGGGCACACATTTGATATCGTCAGTTTA
* *
1395783 TCCGGCTAGCGCTGGG
65 TCCGACTAGCACTGGG
1395799 CACA
1 CACA
1395803 AAAAATTATC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
80 74 0.97
81 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (80 bp):
CACACATTTGATATTGTAGGTTTATCCAAATAGTGCTGGGCACACATTTGATATCGTCAGTTTAT
CCGACTAGCACTGGG
Found at i:1408185 original size:21 final size:21
Alignment explanation
Indices: 1408159--1408198 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1408149 AAATTTAAGA
1408159 GTTTAGAATCTTAG-GTTTTGG
1 GTTTAGAAT-TTAGAGTTTTGG
1408180 GTTTAGAATTTAGAGTTTT
1 GTTTAGAATTTAGAGTTTT
1408199 AGCATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (21 bp):
GTTTAGAATTTAGAGTTTTGG
Found at i:1414315 original size:9 final size:9
Alignment explanation
Indices: 1414301--1414330 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1414291 GTTAAACGAA
1414301 TCGAGTTAT
1 TCGAGTTAT
*
1414310 TCGAGTTAA
1 TCGAGTTAT
1414319 TCGAGTTAT
1 TCGAGTTAT
1414328 TCG
1 TCG
1414331 GATCAACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:1414673 original size:30 final size:31
Alignment explanation
Indices: 1414625--1414684 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
1414615 AAACCTTTTA
* *
1414625 TTTTCCCCCCAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
1414655 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
1414685 TTCCACCTCT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 20 0.80
31 5 0.20
ACGTcount: A:0.18, C:0.42, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:1417336 original size:20 final size:20
Alignment explanation
Indices: 1417313--1417350 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1417303 TTTAAAAATC
1417313 TTTTAAAAAAAAGAAAATTG
1 TTTTAAAAAAAAGAAAATTG
* *
1417333 TTTTCAAATAAAGAAAAT
1 TTTTAAAAAAAAGAAAAT
1417351 CATATATTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.58, C:0.03, G:0.08, T:0.32
Consensus pattern (20 bp):
TTTTAAAAAAAAGAAAATTG
Found at i:1417529 original size:4 final size:4
Alignment explanation
Indices: 1417520--1417546 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1417510 CTCTTTCTCA
1417520 ATCT ATCT ATCT ATCT ATCT ATCT ATC
1 ATCT ATCT ATCT ATCT ATCT ATCT ATC
1417547 AATTCATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (4 bp):
ATCT
Found at i:1418048 original size:2 final size:2
Alignment explanation
Indices: 1418043--1418079 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1418033 TAACCATGTT
1418043 TA TA 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 T
1418080 GTATCATCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1421224 original size:29 final size:30
Alignment explanation
Indices: 1421186--1421247 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
1421176 ATTTTTTATG
*
1421186 CTTTCTTTTTTGAT-AAAAAACTTTTGATA
1 CTTTCGTTTTTGATGAAAAAACTTTTGATA
* *
1421215 CTTTCGTTTTTGATGAATAAGCTTTTGATA
1 CTTTCGTTTTTGATGAAAAAACTTTTGATA
1421245 CTT
1 CTT
1421248 GTTATAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (30 bp):
CTTTCGTTTTTGATGAAAAAACTTTTGATA
Found at i:1426758 original size:58 final size:58
Alignment explanation
Indices: 1426654--1426770 Score: 234
Period size: 58 Copynumber: 2.0 Consensus size: 58
1426644 TATGTTACAC
1426654 TATGAACGTCACAAGTGAATAAATCCATGCACGAATTCAGGATCTATTCTACTTGGGT
1 TATGAACGTCACAAGTGAATAAATCCATGCACGAATTCAGGATCTATTCTACTTGGGT
1426712 TATGAACGTCACAAGTGAATAAATCCATGCACGAATTCAGGATCTATTCTACTTGGGT
1 TATGAACGTCACAAGTGAATAAATCCATGCACGAATTCAGGATCTATTCTACTTGGGT
1426770 T
1 T
1426771 CTGCCCGATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (58 bp):
TATGAACGTCACAAGTGAATAAATCCATGCACGAATTCAGGATCTATTCTACTTGGGT
Found at i:1442430 original size:22 final size:22
Alignment explanation
Indices: 1442405--1442449 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1442395 ATGGCCAAGC
1442405 GTTGGTGCGTTGCGATGGGAGG
1 GTTGGTGCGTTGCGATGGGAGG
1442427 GTTGGTGCGTTGCGATGGGAGG
1 GTTGGTGCGTTGCGATGGGAGG
1442449 G
1 G
1442450 CCGAGTAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.09, G:0.56, T:0.27
Consensus pattern (22 bp):
GTTGGTGCGTTGCGATGGGAGG
Found at i:1443275 original size:10 final size:10
Alignment explanation
Indices: 1443228--1443288 Score: 54
Period size: 10 Copynumber: 6.3 Consensus size: 10
1443218 CACACGCATG
*
1443228 TTTATATACA
1 TTTATATATA
1443238 TTT-TATA-A
1 TTTATATATA
* *
1443246 TCTATACATA
1 TTTATATATA
* *
1443256 TATATCTATA
1 TTTATATATA
1443266 TTTATATATA
1 TTTATATATA
*
1443276 TTTATATACA
1 TTTATATATA
1443286 TTT
1 TTT
1443289 TTACGAATAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
8 3 0.07
9 7 0.17
10 31 0.76
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTATATATA
Found at i:1448033 original size:10 final size:10
Alignment explanation
Indices: 1447995--1448039 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
1447985 GAATATTTTG
1447995 AAAAAGAAG-
1 AAAAAGAAGA
*
1448004 AAGAA-AAGA
1 AAAAAGAAGA
*
1448013 TAAAA-AAGA
1 AAAAAGAAGA
1448022 AAAAAGAAGA
1 AAAAAGAAGA
1448032 AAAAAGAA
1 AAAAAGAA
1448040 AAAGACAAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 3 0.10
9 15 0.50
10 12 0.40
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:1448034 original size:17 final size:16
Alignment explanation
Indices: 1447996--1448042 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1447986 AATATTTTGA
*
1447996 AAAAGAAGAAGAAAAGAT
1 AAAA-AAGAA-AAAAGAG
1448014 AAAAAAGAAAAAAGAAG
1 AAAAAAGAAAAAAG-AG
1448031 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1448043 GACAAAGGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 5 0.19
17 18 0.67
18 4 0.15
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAAAGAG
Found at i:1449377 original size:45 final size:45
Alignment explanation
Indices: 1449260--1449471 Score: 207
Period size: 44 Copynumber: 4.8 Consensus size: 45
1449250 CAGATCAATA
* ** *
1449260 AAGATAGCAGATCATGCCTTCCTGTACTGATGGCAAAGCAGATTG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGACTG
* * * **
1449305 AAGAAACCAG-CCTTGCCTTCCTGTACTGACAGCGGAGCAGACTG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGACTG
* * * *
1449349 AAGATAGCAGATCTTGCTTTCCTGTACTGGCAACAAAGTAGATCT-
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGA-CTG
* * * *
1449394 AAGACACCAG-CCTTGCCTTCCTGTACTGACAGCAGAA-TAGACTG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCA-AAGCAGACTG
* *
1449438 AAGATAGCAGATCTTGCCTTGCTGTACTAACAGC
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGC
1449472 GAAGTAGATC
Statistics
Matches: 133, Mismatches: 29, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
43 2 0.02
44 67 0.50
45 62 0.47
46 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.24
Consensus pattern (45 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGCAGACTG
Found at i:1449477 original size:89 final size:90
Alignment explanation
Indices: 1449260--1449485 Score: 305
Period size: 89 Copynumber: 2.5 Consensus size: 90
1449250 CAGATCAATA
* ** *
1449260 AAGATAGCAGATCATGCCTTCCTGTACTGATGGCAAAGCAGAT-TGAAGAAACCAGCCTTGCCTT
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGTAGATCTGAAGAAACCAGCCTTGCCTT
* *
1449324 CCTGTACTGACAGCGGAGCAGACTG
66 CCTGTACTGACAGCAGAACAGACTG
* * * *
1449349 AAGATAGCAGATCTTGCTTTCCTGTACTGGCAACAAAGTAGATCT-AAGACACCAGCCTTGCCTT
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGTAGATCTGAAGAAACCAGCCTTGCCTT
*
1449413 CCTGTACTGACAGCAGAATAGACTG
66 CCTGTACTGACAGCAGAACAGACTG
* * *
1449438 AAGATAGCAGATCTTGCCTTGCTGTACTAACAGCGAAGTAGATC-GAAG
1 AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGTAGATCTGAAG
1449486 CCATTAGTCA
Statistics
Matches: 118, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
89 117 0.99
90 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (90 bp):
AAGATAGCAGATCTTGCCTTCCTGTACTGACAGCAAAGTAGATCTGAAGAAACCAGCCTTGCCTT
CCTGTACTGACAGCAGAACAGACTG
Found at i:1449679 original size:132 final size:132
Alignment explanation
Indices: 1449472--1449830 Score: 565
Period size: 132 Copynumber: 2.7 Consensus size: 132
1449462 TACTAACAGC
** * *
1449472 GAAGTAGATCGAAGCCATTAGTCACTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGTAG
1 GAAGTAGATTTAAGCCATTAGTC-CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAG
*
1449537 ATTCTATCACCCTAAGCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGT
65 ATTCTATCACCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATCTTATCTTCCCAAGACAGT
1449602 AGA
130 AGA
*
1449605 GAAGTAGATTTAAGCCATTAGACCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGA
1 GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGA
* * * * * * *
1449670 TTCTGTCACCCTAAGCAGTAGTAGAGCATATCAAAGATGGTGAATCTTATCTTCCTAAGATAGTG
66 TTCTATCACCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATCTTATCTTCCCAAGACAGTA
1449735 GA
131 GA
* *
1449737 GAAGCAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGA
1 GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGA
*
1449802 TTCTATCTCCCTAAGCAGTAGTGGAGTAG
66 TTCTATCACCCTAAGCAGTAGTGGAGTAG
1449831 GCTGAAGATT
Statistics
Matches: 205, Mismatches: 21, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
132 185 0.90
133 20 0.10
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
GAAGTAGATTTAAGCCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGA
TTCTATCACCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATCTTATCTTCCCAAGACAGTA
GA
Found at i:1449830 original size:176 final size:176
Alignment explanation
Indices: 1449628--1450003 Score: 653
Period size: 176 Copynumber: 2.1 Consensus size: 176
1449618 GCCATTAGAC
*
1449628 CTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTA
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTA
* * * *
1449693 GAGCATATCAAAGATGGTGAATCTTATCTTCCTAAGATAGTGGAGAAGCAGATTTAAGCCATTAG
66 GAGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCAGATTTAAGCCATTAG
*
1449758 TCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATT
131 TCCTATCTCCCTAAGCAGTAGTGGAGTAAGCTGAAGATTGCAGATT
*
1449804 CTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
1 CTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTA
*
1449869 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCAGATTTAAGCCATTAG
66 GAGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCAGATTTAAGCCATTAG
*
1449934 TCCTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATT
131 TCCTATCTCCCTAAGCAGTAGTGGAGTAAGCTGAAGATTGCAGATT
* *
1449980 CTGTCACCCTAAGCAGTAGTGGAG
1 CTATCTCCCTAAGCAGTAGTGGAG
1450004 CAAATTAAAA
Statistics
Matches: 189, Mismatches: 11, Indels: 0
0.94 0.05 0.00
Matches are distributed among these distances:
176 189 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (176 bp):
CTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTA
GAGCAGATCAAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCAGATTTAAGCCATTAG
TCCTATCTCCCTAAGCAGTAGTGGAGTAAGCTGAAGATTGCAGATT
Found at i:1449897 original size:132 final size:129
Alignment explanation
Indices: 1449487--1450005 Score: 405
Period size: 132 Copynumber: 3.9 Consensus size: 129
1449477 AGATCGAAGC
* *
1449487 CATTAGTCACTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGTAGATTCTATCACCCTAA
1 CATTAATC-CTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGCAGATTCTATCACCCTAA
* ** * * * *
1449552 GCAGTAGTGGAGTAGATCGAAGATGGTGAATCTTATCTTCCC-AAGACAGTAGAGAAGTAGATTT
65 GCAGTAGTGGAGTAGCT-GAAGATGCAGAATCTTATC-ACCCTAAG-CAGTAGTGGAGCAGATTT
1449616 AAG
127 AAG
* *
1449619 CCATTAGA-CCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTA
1 -CATTA-ATCCTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGCAGATTCTATCACCCTA
* * * ** **
1449683 AGCAGTAGTAGAGCATATC-AAAGATGGTGAATCTTATCTTCCTAAG-A-TAGTGGAGAAGCAGA
64 AGCAGTAGTGGAG--TAGCTGAAGATGCAGAATCTTATCACCCTAAGCAGTAGT-G-G-AGCAGA
1449745 TTTAAG
124 TTTAAG
* * * *
1449751 CCATTAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTATCTCCCTAA
1 -CATTAATCCTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGCAGATTCTATCACCCTAA
* * **
1449816 GCAGTAGTGGAGTAGGCTGAAGATTGCAGATTC-TGTCACCCTAAGCAGTAGTGGAGCAGATCGA
65 GCAGTAGTGGAGTA-GCTGAAGA-TGCAGAATCTTATCACCCTAAGCAGTAGTGGAGCAGATTTA
1449880 AG
128 AG
* ** * * * * * *
1449882 -ATGGTGAATCTTATCTTCCC-AAGACAGCGGAGAAGCAGATTTAAGCCATT--AG-TCCTATCT
1 CAT--T-AATCCTATC-TCCCTAAG-CAGTAGTGAAGTAGGTTGAAG--ATTGCAGATTCTATCA
* * *
1449942 CCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTC-TGTCACCCTAAGCAGTAGTGGAGCA
59 CCCTAAGCAGTAGTGGAGT-AGCTGAAGA-TGCAGAATCTTATCACCCTAAGCAGTAGTGGAGCA
1450006 AATTAAAAAT
Statistics
Matches: 326, Mismatches: 39, Indels: 43
0.80 0.10 0.11
Matches are distributed among these distances:
129 5 0.02
130 4 0.01
131 15 0.05
132 259 0.79
133 34 0.10
134 6 0.02
135 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (129 bp):
CATTAATCCTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGCAGATTCTATCACCCTAAG
CAGTAGTGGAGTAGCTGAAGATGCAGAATCTTATCACCCTAAGCAGTAGTGGAGCAGATTTAAG
Found at i:1449946 original size:88 final size:88
Alignment explanation
Indices: 1449678--1449959 Score: 279
Period size: 88 Copynumber: 3.2 Consensus size: 88
1449668 GATTCTGTCA
* * * * *
1449678 CCCTAAGCAGTAGTAGAGCATATCAAAGATGGTGAATCTTATCTTCCTAAGATAGTGGAGAAGCA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCA
1449743 GATTTAAGCCATTAGTCCTATCT
66 GATTTAAGCCATTAGTCCTATCT
* * ** * * * *
1449766 CCCTAAGCAGTAGTGGAGTAG-GCTGAAGATTGCAGATTC-TATC-TCCCTAAG-CAGTAGTGGA
1 CCCTAAGCAGTAGTGGAGCAGATC-GAAGA-TGGTGAATCTTATCTTCCC-AAGACAGTGGAGAA
* ** * * * *
1449827 GTAGGCTGAAG--ATTGCAGATTCTGTCA
63 GCAGATTTAAGCCATT--AG-TCCTATCT
*
1449854 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCA
1 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCA
1449919 GATTTAAGCCATTAGTCCTATCT
66 GATTTAAGCCATTAGTCCTATCT
1449942 CCCTAAGCAGTAGTGGAG
1 CCCTAAGCAGTAGTGGAG
1449960 TAAGTTGAAG
Statistics
Matches: 146, Mismatches: 36, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
85 3 0.02
87 25 0.17
88 89 0.61
89 26 0.18
91 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (88 bp):
CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGCA
GATTTAAGCCATTAGTCCTATCT
Found at i:1450018 original size:132 final size:132
Alignment explanation
Indices: 1449804--1450089 Score: 482
Period size: 132 Copynumber: 2.2 Consensus size: 132
1449794 ATTGCAGATT
*
1449804 CTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
1 CTATCTCCCTAAGCAGTAGTGGAGTAAGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
* * * * *
1449869 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCAGATTTAAGCCATTAG
66 GAGCAAATCAAAAATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGAAAATTTAAGCCATTAG
1449934 TC
131 TC
*
1449936 CTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
1 CTATCTCCCTAAGCAGTAGTGGAGTAAGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
* *
1450001 GAGCAAATTAAAAATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGAAAATTTAAGCCATTAG
66 GAGCAAATCAAAAATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGAAAATTTAAGCCATTAG
1450066 TC
131 TC
*
1450068 CTATCCCCCTAAGCAGTAGTGG
1 CTATCTCCCTAAGCAGTAGTGG
1450090 GATACATCCG
Statistics
Matches: 144, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 144 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (132 bp):
CTATCTCCCTAAGCAGTAGTGGAGTAAGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
GAGCAAATCAAAAATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGAAAATTTAAGCCATTAG
TC
Found at i:1450058 original size:308 final size:308
Alignment explanation
Indices: 1449496--1450089 Score: 1017
Period size: 308 Copynumber: 1.9 Consensus size: 308
1449486 CCATTAGTCA
* *
1449496 CTATCTCCCTAAGCAGTAGTGAAGTAGGTTGAAGATTGTAGATTCTATCACCCTAAGCAGTAGTG
1 CTATCTCCCTAAGCAGTAGTGAAGTAGGCTGAAGATTGCAGATTCTATCACCCTAAGCAGTAGTG
* * *
1449561 GAGTAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGTAGAGAAGTAGATTTAAGCCATTAG
66 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCAGAGAAGCAGATTTAAGCCATTAG
*
1449626 ACCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAG
131 ACCTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAG
* * * * * *
1449691 TAGAGCATATCAAAGATGGTGAATCTTATCTTCCTAAGATAGTGGAGAAGCAGATTTAAGCCATT
196 TAGAGCAAATCAAAAATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGAAAATTTAAGCCATT
*
1449756 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATT
261 AGTCCTATCCCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATT
* *
1449804 CTATCTCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGTG
1 CTATCTCCCTAAGCAGTAGTGAAGTAGGCTGAAGATTGCAGATTCTATCACCCTAAGCAGTAGTG
*
1449869 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCGGAGAAGCAGATTTAAGCCATTAG
66 GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCAGAGAAGCAGATTTAAGCCATTAG
*
1449934 TCCTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAG
131 ACCTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAG
* *
1449999 TGGAGCAAATTAAAAATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGAAAATTTAAGCCATT
196 TAGAGCAAATCAAAAATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGAAAATTTAAGCCATT
1450064 AGTCCTATCCCCCTAAGCAGTAGTGG
261 AGTCCTATCCCCCTAAGCAGTAGTGG
1450090 GATACATCCG
Statistics
Matches: 267, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
308 267 1.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (308 bp):
CTATCTCCCTAAGCAGTAGTGAAGTAGGCTGAAGATTGCAGATTCTATCACCCTAAGCAGTAGTG
GAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGACAGCAGAGAAGCAGATTTAAGCCATTAG
ACCTATCTCCCTAAGCAGTAGTGGAGTAAGTTGAAGATTGCAGATTCTGTCACCCTAAGCAGTAG
TAGAGCAAATCAAAAATGGTGAATCTTATCTTCCCAAGACAGTGGAGAAGAAAATTTAAGCCATT
AGTCCTATCCCCCTAAGCAGTAGTGGAGTAGGCTGAAGATTGCAGATT
Found at i:1453844 original size:27 final size:27
Alignment explanation
Indices: 1453807--1453905 Score: 155
Period size: 27 Copynumber: 3.7 Consensus size: 27
1453797 ACACGCCAGA
*
1453807 AAATGGAAGCCTTTGTGGAAATCTATG
1 AAATGAAAGCCTTTGTGGAAATCTATG
1453834 AAAT-AGAAGCCTTTGTGGAAATCTATG
1 AAATGA-AAGCCTTTGTGGAAATCTATG
*
1453861 AAATGAAAGCCTTTGTGGAAATTTATG
1 AAATGAAAGCCTTTGTGGAAATCTATG
*
1453888 AAACGAAAGCCTTTGTGG
1 AAATGAAAGCCTTTGTGG
1453906 CAATTAATGA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
27 66 0.99
28 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.29
Consensus pattern (27 bp):
AAATGAAAGCCTTTGTGGAAATCTATG
Found at i:1453910 original size:27 final size:27
Alignment explanation
Indices: 1453813--1453989 Score: 144
Period size: 27 Copynumber: 6.5 Consensus size: 27
1453803 CAGAAAATGG
* * *
1453813 AAGCCTTTGTGGAAATCTATGAAA-TA
1 AAGCCTTTGTGGCAATTTATGAAAGGA
* * *
1453839 GAAGCCTTTGTGGAAATCTATGAAATGA
1 -AAGCCTTTGTGGCAATTTATGAAAGGA
* *
1453867 AAGCCTTTGTGGAAATTTATGAAACGA
1 AAGCCTTTGTGGCAATTTATGAAAGGA
* *
1453894 AAGCCTTTGTGGCAATTAATGAGATGG-
1 AAGCCTTTGTGGCAATTTATGA-AAGGA
* * * *
1453921 AAGCTTTTGCGGCGATTTAAGGAAAGGA
1 AAGCCTTTGTGGCAATTT-ATGAAAGGA
* *
1453949 AAGCCTTTGTGGCAAATGATGAAAGGA
1 AAGCCTTTGTGGCAATTTATGAAAGGA
*
1453976 ACA-CCTTCGTGGCA
1 A-AGCCTTTGTGGCA
1453990 CACACAAAAG
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
27 105 0.84
28 20 0.16
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.27
Consensus pattern (27 bp):
AAGCCTTTGTGGCAATTTATGAAAGGA
Found at i:1454077 original size:27 final size:26
Alignment explanation
Indices: 1454019--1454091 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 26
1454009 TGTGGCATCT
* *
1454019 ATCTAAAGGGATAGTATGTTTGTCAGA
1 ATCTAAAGGGATAATATGTTGGT-AGA
*
1454046 ATCTAAAGGGATATTATGTATGGT-GA
1 ATCTAAAGGGATAATATGT-TGGTAGA
*
1454072 ATTCTAAATGGATAATATGT
1 A-TCTAAAGGGATAATATGT
1454092 CTGGCGAACT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.08
27 34 0.85
28 3 0.08
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (26 bp):
ATCTAAAGGGATAATATGTTGGTAGA
Found at i:1454108 original size:27 final size:27
Alignment explanation
Indices: 1454020--1454108 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 27
1454010 GTGGCATCTA
* * * *
1454020 TCTAAAGGGATAGTATGTTTGTCAGAA-
1 TCTAAATGGATAATATGTATGGC-GAAC
* * * *
1454047 TCTAAAGGGATATTATGTATGGTGAAT
1 TCTAAATGGATAATATGTATGGCGAAC
*
1454074 TCTAAATGGATAATATGTCTGGCGAAC
1 TCTAAATGGATAATATGTATGGCGAAC
*
1454101 TCTGAATG
1 TCTAAATG
1454109 AGCGGTAGGC
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.06
27 48 0.94
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.34
Consensus pattern (27 bp):
TCTAAATGGATAATATGTATGGCGAAC
Found at i:1456866 original size:40 final size:40
Alignment explanation
Indices: 1456822--1456955 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 40
1456812 GCACCCAGCG
1456822 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
1 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
* * ** * * **
1456862 CTAGTTAGATAAA-CAAACA-ATC-AGT-TGCGCCCAATG
1 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
* *
1456898 CTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCA
1 CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
1456938 CTAGTC-GAATAAACCGAT
1 CTAGTCAG-ATAAACCGAT
1456956 AATGATTTGC
Statistics
Matches: 71, Mismatches: 18, Indels: 10
0.72 0.18 0.10
Matches are distributed among these distances:
36 19 0.27
37 5 0.07
38 6 0.08
39 6 0.08
40 35 0.49
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (40 bp):
CTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACA
Found at i:1456966 original size:76 final size:76
Alignment explanation
Indices: 1456738--1456990 Score: 275
Period size: 76 Copynumber: 3.4 Consensus size: 76
1456728 GTAACAAAGT
* * * * *
1456738 TTTGCGCCCAGCCCTAGTCGGATAAACCAATG--AT---AGGTGTGCCCTGCACTAGTCGAATAG
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
* *
1456798 ATCAACAATGT
66 ACCAACAATGA
* * * *
1456809 TTTGCACCCAGCGCTAGTCAGATAAACCGATGATATCAAATGTGTGCCCAACACTAGT-TAGATA
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGA-ATA
* *
1456873 AACAAACAATCA
65 AACCAACAATGA
* **
1456885 GTTGCGCCCAATGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
* *
1456950 ACCGATAATGA
66 ACCAACAATGA
* *
1456961 TTTGCGCCCAGCACTAGCCGGATAAACCGA
1 TTTGCGCCCAGCGCTAGTCGGATAAACCGA
1456991 CAAATACATA
Statistics
Matches: 146, Mismatches: 29, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
71 28 0.19
73 2 0.01
75 1 0.01
76 114 0.78
77 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGCGCCCAGCGCTAGTCGGATAAACCGATGATATCAAATGTGTGCCCAGCACTAGTCGAATAA
ACCAACAATGA
Found at i:1466807 original size:15 final size:15
Alignment explanation
Indices: 1466787--1466832 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
1466777 AAAGTTAAAA
1466787 CATGACCAAAATAAG
1 CATGACCAAAATAAG
*
1466802 CATGACCAAAATAAA
1 CATGACCAAAATAAG
1466817 CATGACCAAAATAAG
1 CATGACCAAAATAAG
1466832 C
1 C
1466833 TTGAAAATCC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.54, C:0.22, G:0.11, T:0.13
Consensus pattern (15 bp):
CATGACCAAAATAAG
Found at i:1475326 original size:24 final size:24
Alignment explanation
Indices: 1475288--1475346 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
1475278 GTTGTCTAAG
1475288 GGGAAGCTCAT-AAGAGCCAATAAC
1 GGGAAGCTC-TGAAGAGCCAATAAC
* *
1475312 GGGTAGCTCTGAAGAGCCATTAAC
1 GGGAAGCTCTGAAGAGCCAATAAC
1475336 GGGAAGCTCTG
1 GGGAAGCTCTG
1475347 GATAGCTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.32, C:0.20, G:0.31, T:0.17
Consensus pattern (24 bp):
GGGAAGCTCTGAAGAGCCAATAAC
Found at i:1475438 original size:26 final size:26
Alignment explanation
Indices: 1475381--1475439 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
1475371 AGCGAGCCAT
* *
1475381 ATCGGGAAGCTCACAAAGAGCCTTTA
1 ATCGGGAAGCTCACAAAGAGCATATA
*
1475407 ATCGGGAAGCTTACAAAGAGCAATATA
1 ATCGGGAAGCTCACAAAGAGC-ATATA
1475434 A-CGGGA
1 ATCGGGA
1475440 CACTTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (26 bp):
ATCGGGAAGCTCACAAAGAGCATATA
Found at i:1476475 original size:14 final size:16
Alignment explanation
Indices: 1476445--1476477 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
1476435 TTTTCTTTAT
1476445 TTTATTATTTATCATC
1 TTTATTATTTATCATC
1476461 TTTATT-TTT-TCATC
1 TTTATTATTTATCATC
1476475 TTT
1 TTT
1476478 CCAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTATTTATCATC
Found at i:1478811 original size:47 final size:47
Alignment explanation
Indices: 1478647--1478872 Score: 294
Period size: 47 Copynumber: 4.6 Consensus size: 47
1478637 TAGGACGCCA
* * * *
1478647 ATGCCATATCCCAGATATGGTCTTACA-TGGGA-TCACATCTCGGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT--GACTCTCATCTC-GAGCCG
*
1478695 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCAAAACTAATCTCGAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACT-G-ACT-----CTCATCTCGAGCCG
1478749 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCGAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCGAGCCG
*
1478796 ATGCCATGTCTCAGACATGGTCTTACACTGACTCTCATCTCGAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCGAGCCG
1478843 ATGCCATGTCCCAGACATGGTCTTACACTG
1 ATGCCATGTCCCAGACATGGTCTTACACTG
1478873 GCACACTCAC
Statistics
Matches: 162, Mismatches: 8, Indels: 17
0.87 0.04 0.09
Matches are distributed among these distances:
47 88 0.54
48 27 0.17
49 2 0.01
50 1 0.01
52 3 0.02
53 1 0.01
54 34 0.21
55 6 0.04
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCATCTCGAGCCG
Found at i:1479195 original size:41 final size:41
Alignment explanation
Indices: 1479144--1479280 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
1479134 TTGCCATCGT
* * *
1479144 ATAGCTGAAGCTATCATAATCTCGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATCATAATCTCGCACACTAAGTGCCATAA
** * *
1479185 ATAGCCGAAGCTATC-TCGGTCTCGCACACTAAATGTCATAA
1 ATAGCCGAAGCTATCAT-AATCTCGCACACTAAGTGCCATAA
*
1479226 ATAGCCGAAGCTATTCCA-AA--TCGCACACTACGTGCCATAA
1 ATAGCCGAAGCTA-T-CATAATCTCGCACACTAAGTGCCATAA
1479266 ATAGCCGAAGCTATC
1 ATAGCCGAAGCTATC
1479281 TCGAATTTCA
Statistics
Matches: 80, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 31 0.39
41 45 0.56
42 1 0.01
43 1 0.01
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (41 bp):
ATAGCCGAAGCTATCATAATCTCGCACACTAAGTGCCATAA
Found at i:1479265 original size:40 final size:41
Alignment explanation
Indices: 1479165--1479282 Score: 148
Period size: 40 Copynumber: 2.9 Consensus size: 41
1479155 TATCATAATC
* * ****
1479165 TCGCACACTAAGTGCCTTACATAGCCGAAGCTATCTCGGTC
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCCAAA
* *
1479206 TCGCACACTAAATGTCATAAATAGCCGAAGCTAT-TCCAAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCCAAA
*
1479246 TCGCACACTACGTGCCATAAATAGCCGAAGCTATCTC
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC
1479283 GAATTTCATA
Statistics
Matches: 65, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 33 0.51
41 32 0.49
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCCAAA
Found at i:1485115 original size:54 final size:49
Alignment explanation
Indices: 1484996--1485178 Score: 223
Period size: 47 Copynumber: 3.7 Consensus size: 49
1484986 TAGGACGCCA
* * * *
1484996 ATGCCATATCCCAGATATGGTCTTACA-TGGGA-TC-ACATCTCGGTGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCTA-ATCTC-GAGCCG
1485044 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCAAAACTAATCTCGAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACT-----CTAATCTCGAGCCG
*
1485098 ATGCCATGTCCCAGACATGGTCTTACACT-G-ACTCTCATCTCGAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCTAATCTCGAGCCG
1485145 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCAC
1485179 ACTCACTGCC
Statistics
Matches: 120, Mismatches: 5, Indels: 19
0.83 0.03 0.13
Matches are distributed among these distances:
47 42 0.35
48 26 0.22
49 6 0.05
50 1 0.01
52 3 0.03
53 1 0.01
54 34 0.28
55 6 0.05
56 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCACTCTAATCTCGAGCCG
Found at i:1485172 original size:101 final size:101
Alignment explanation
Indices: 1484996--1485178 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 101
1484986 TAGGACGCCA
* *
1484996 ATGCCATATCCCAGATATGGTCTTACATGGGATCACATCTCGGTGCCGATGCCATGTCCCAGACA
1 ATGCCATATCCCAGACATGGTCTTACAT-GGATCACATCTCGGAGCCGATGCCATGTCCCAGACA
1485061 TGGTCTTACACTGGCACTCAAAACTAATCTCGAGCCG
65 TGGTCTTACACTGGCACTCAAAACTAATCTCGAGCCG
* *
1485098 ATGCCATGTCCCAGACATGGTCTTACACT-GACTCTCATCTC-GAGCCGATGCCATGTCCCAGAC
1 ATGCCATATCCCAGACATGGTCTTACA-TGGA-TCACATCTCGGAGCCGATGCCATGTCCCAGAC
1485161 ATGGTCTTACACTGGCAC
64 ATGGTCTTACACTGGCAC
1485179 ACTCACTGCC
Statistics
Matches: 75, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
101 41 0.55
102 33 0.44
103 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (101 bp):
ATGCCATATCCCAGACATGGTCTTACATGGATCACATCTCGGAGCCGATGCCATGTCCCAGACAT
GGTCTTACACTGGCACTCAAAACTAATCTCGAGCCG
Found at i:1485497 original size:41 final size:41
Alignment explanation
Indices: 1485446--1485582 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
1485436 TTGCCATCGT
* * *
1485446 ATAGCTGAAGCTATCATAATCTCGCACACTAAGTGCCTTAC
1 ATAGCCGAAGCTATCATAATCTCGCACACTAAGTGCCATAA
** * *
1485487 ATAGCCGAAGCTATC-TCGGTCTCGCACACTAAATGTCATAA
1 ATAGCCGAAGCTATCAT-AATCTCGCACACTAAGTGCCATAA
1485528 ATAGCCGAAGCTATTCCA-AA--TCGCACACTAAGTGCCATAA
1 ATAGCCGAAGCTA-T-CATAATCTCGCACACTAAGTGCCATAA
1485568 ATAGCCGAAGCTATC
1 ATAGCCGAAGCTATC
1485583 TCGAATTTCA
Statistics
Matches: 81, Mismatches: 11, Indels: 11
0.79 0.11 0.11
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 32 0.40
41 45 0.56
42 1 0.01
43 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (41 bp):
ATAGCCGAAGCTATCATAATCTCGCACACTAAGTGCCATAA
Found at i:1485567 original size:40 final size:41
Alignment explanation
Indices: 1485467--1485584 Score: 157
Period size: 40 Copynumber: 2.9 Consensus size: 41
1485457 TATCATAATC
* * ****
1485467 TCGCACACTAAGTGCCTTACATAGCCGAAGCTATCTCGGTC
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCCAAA
* *
1485508 TCGCACACTAAATGTCATAAATAGCCGAAGCTAT-TCCAAA
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCCAAA
1485548 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC
1 TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTC
1485585 GAATTTCATA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
40 34 0.52
41 32 0.48
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATAAATAGCCGAAGCTATCTCCAAA
Found at i:1491475 original size:27 final size:26
Alignment explanation
Indices: 1491429--1491484 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
1491419 AACTGAGTTC
* *
1491429 TATTTTTATTTAATATATAATTACTTT
1 TATTTTTATTTAATAAATAAATA-TTT
1491456 TATTTTTATTATAA-AAATAAATATTT
1 TATTTTTATT-TAATAAATAAATATTT
1491482 TAT
1 TAT
1491485 ACTGAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.23
27 17 0.65
28 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
TATTTTTATTTAATAAATAAATATTT
Found at i:1492431 original size:2 final size:2
Alignment explanation
Indices: 1492424--1492450 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1492414 GAATTTACAA
1492424 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1492451 ACAATGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1497332 original size:30 final size:30
Alignment explanation
Indices: 1497288--1497375 Score: 114
Period size: 25 Copynumber: 3.1 Consensus size: 30
1497278 TTTCTTATGT
*
1497288 CAATATCTCGATACCCATATCTTTGACTTTC
1 CAATAT-TTGATACCCATATCTTTGACTTTC
*
1497319 CAATATTTGATACCTATATCTTTGAC-TT-
1 CAATATTTGATACCCATATCTTTGACTTTC
1497347 ---TATTTGATACCCATATCTTTGACTTTC
1 CAATATTTGATACCCATATCTTTGACTTTC
1497374 CA
1 CA
1497376 CAAAAATGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 22 0.44
26 2 0.04
29 2 0.04
30 18 0.36
31 6 0.12
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (30 bp):
CAATATTTGATACCCATATCTTTGACTTTC
Found at i:1499109 original size:12 final size:12
Alignment explanation
Indices: 1499072--1499116 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
1499062 AGAGAATCCA
1499072 ACCATCATCATC
1 ACCATCATCATC
*
1499084 ACCA-C--CACC
1 ACCATCATCATC
1499093 ACCATCATCATC
1 ACCATCATCATC
1499105 ACCATCATCATC
1 ACCATCATCATC
1499117 CTCTCACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 1 0.04
12 19 0.68
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (12 bp):
ACCATCATCATC
Found at i:1500075 original size:15 final size:16
Alignment explanation
Indices: 1500043--1500075 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1500033 AGTGGGAGAA
1500043 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
1500060 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
1500075 T
1 T
1500076 TTCCTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:1503308 original size:3 final size:3
Alignment explanation
Indices: 1503302--1503352 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
1503292 AAAAAATTCC
* *
1503302 TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TTT TAC TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT
1503347 T-T TAT T
1 TAT TAT T
1503353 TTCATTTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1503365 original size:6 final size:6
Alignment explanation
Indices: 1503304--1503367 Score: 58
Period size: 6 Copynumber: 10.3 Consensus size: 6
1503294 AAAATTCCTA
* * *
1503304 TTATTA TTATTA TTATTA TTATTAT TTATTT TTACTATT TTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATT-T TTATTT TTA-T-TT TTATTT TTATTT
*
1503354 TCATTT TTATTT TT
1 TTATTT TTATTT TT
1503368 GCAGGAAAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
5 5 0.10
6 35 0.69
7 6 0.12
8 5 0.10
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (6 bp):
TTATTT
Found at i:1504575 original size:15 final size:16
Alignment explanation
Indices: 1504543--1504575 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1504533 AGTGGGAGAA
1504543 TATTATGGGATTTATTT
1 TATTATGGGA-TTATTT
1504560 TATTATGGGA-TATTT
1 TATTATGGGATTATTT
1504575 T
1 T
1504576 TTCCTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TATTATGGGATTATTT
Found at i:1507546 original size:43 final size:43
Alignment explanation
Indices: 1507499--1507707 Score: 312
Period size: 43 Copynumber: 4.9 Consensus size: 43
1507489 GCTAAAGGTT
* *
1507499 ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCACTAAAGAAA
1 ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAAC
*
1507542 ATGACTTTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGAAC
1 ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAAC
* *
1507585 ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATC
1 ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAAC
* **
1507628 ATGACTTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAGGTC
1 ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAAC
* *
1507671 ATG-TTCTTTAGCAGCGCTTTTCCCACAAACGCCGCTA
1 ATGACT-TTTAGCGGCGCTTTTCCCACAAACGCCGCTA
1507708 TTGTTTGGTG
Statistics
Matches: 153, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 1 0.01
43 152 0.99
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAAC
Found at i:1508102 original size:21 final size:21
Alignment explanation
Indices: 1508054--1508103 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1508044 TTTCTGCTTG
1508054 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* *
1508075 TTTTGCTTCCCTCGCTGTC-GC
1 CTCTGCTTCCCTCGCTG-CAGC
1508096 CTCTGCTT
1 CTCTGCTT
1508104 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.02, C:0.42, G:0.18, T:0.38
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:1513568 original size:9 final size:9
Alignment explanation
Indices: 1513554--1513822 Score: 181
Period size: 9 Copynumber: 31.4 Consensus size: 9
1513544 TTTTTATGTA
1513554 TTATGTAAG
1 TTATGTAAG
1513563 TTATGTACTAAG
1 TTATG---TAAG
1513575 TTATGTATTAAG
1 TTATG---TAAG
1513587 TTATGT-A-
1 TTATGTAAG
1513594 TTATGTAAG
1 TTATGTAAG
*
1513603 TTATGTGAG
1 TTATGTAAG
1513612 -T-TGTATA-
1 TTATGTA-AG
*
1513619 TTATGTGAG
1 TTATGTAAG
1513628 TTATGTAAG
1 TTATGTAAG
*
1513637 TTGTGT-A-
1 TTATGTAAG
1513644 TTATGTAAG
1 TTATGTAAG
1513653 TTATGT-A-
1 TTATGTAAG
*
1513660 TTATGTATG
1 TTATGTAAG
1513669 TTATGTAAG
1 TTATGTAAG
1513678 TTATGTAAG
1 TTATGTAAG
1513687 TTATGTAAG
1 TTATGTAAG
1513696 TTATGT-A-
1 TTATGTAAG
*
1513703 TTATGTATG
1 TTATGTAAG
1513712 TTATGT-A-
1 TTATGTAAG
1513719 TTATGT-A-
1 TTATGTAAG
1513726 TTATGTAAG
1 TTATGTAAG
1513735 -TACTGTAAG
1 TTA-TGTAAG
1513744 TTATGTAAG
1 TTATGTAAG
*
1513753 TTATGAAAG
1 TTATGTAAG
* **
1513762 TAACAT-A-
1 TTATGTAAG
1513769 TTATGTAAG
1 TTATGTAAG
1513778 -T-TGTATA-
1 TTATGTA-AG
*
1513785 TAATGTAAG
1 TTATGTAAG
*
1513794 TTA-GGAAGG
1 TTATGTAA-G
1513803 TTATGT-A-
1 TTATGTAAG
1513810 TTATGTAAG
1 TTATGTAAG
1513819 TTAT
1 TTAT
1513823 TATGTTATTA
Statistics
Matches: 208, Mismatches: 23, Indels: 58
0.72 0.08 0.20
Matches are distributed among these distances:
7 52 0.25
8 22 0.11
9 111 0.53
10 3 0.01
12 20 0.10
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1513568 original size:16 final size:16
Alignment explanation
Indices: 1513547--1513796 Score: 169
Period size: 16 Copynumber: 16.2 Consensus size: 16
1513537 TGATATATTT
1513547 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
1513563 TTATG---TA-CTAAG
1 TTATGTATTATGTAAG
1513575 TTATG---TAT-TAAG
1 TTATGTATTATGTAAG
1513587 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
*
1513603 TTATGTGAGT-TGTATA-
1 TTATGT-ATTATGTA-AG
1513619 TTATGTGAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
1513637 TTGTGTATTATGTAAG
1 TTATGTATTATGTAAG
1513653 TTATGTATTA--T--G
1 TTATGTATTATGTAAG
1513665 -TATG--TTATGTAAG
1 TTATGTATTATGTAAG
1513678 TTATGTAAGTTATGTAAG
1 TTATGT-A-TTATGTAAG
*
1513696 TTATGTATTATGTATG
1 TTATGTATTATGTAAG
1513712 TTATGTATTATGT-A-
1 TTATGTATTATGTAAG
*
1513726 TTATGTAAGTACTGTAAG
1 TTATGT-ATTA-TGTAAG
*
1513744 TTATGTAAGTTATGAAAG
1 TTATGT-A-TTATGTAAG
* **
1513762 TAACATATTATGTAAG
1 TTATGTATTATGTAAG
* * *
1513778 TTGTATATAATGTAAG
1 TTATGTATTATGTAAG
1513794 TTA
1 TTA
1513797 GGAAGGTTAT
Statistics
Matches: 191, Mismatches: 19, Indels: 48
0.74 0.07 0.19
Matches are distributed among these distances:
9 3 0.02
11 5 0.03
12 21 0.11
13 3 0.02
14 11 0.06
15 6 0.03
16 91 0.48
17 9 0.05
18 40 0.21
19 2 0.01
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:1513594 original size:12 final size:12
Alignment explanation
Indices: 1513559--1513596 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1513549 ATGTATTATG
*
1513559 TAAGTTATGTAC
1 TAAGTTATGTAT
1513571 TAAGTTATGTAT
1 TAAGTTATGTAT
1513583 TAAGTTATGTAT
1 TAAGTTATGTAT
1513595 TA
1 TA
1513597 TGTAAGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (12 bp):
TAAGTTATGTAT
Found at i:1513620 original size:25 final size:25
Alignment explanation
Indices: 1513583--1513779 Score: 156
Period size: 25 Copynumber: 7.9 Consensus size: 25
1513573 AGTTATGTAT
* *
1513583 TAAGTTATGTATTATGTAAGTTATG
1 TAAGTTGTATATTATGTAAGTTATG
* *
1513608 TGAGTTGTATATTATGTGAGTTATG
1 TAAGTTGTATATTATGTAAGTTATG
*
1513633 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTGTATATTATGTAAGTTATG
* *
1513658 T-ATTATGTATGTTATGTAAGTTATG
1 TAAGT-TGTATATTATGTAAGTTATG
1513683 TAAGTTATGTA-AGTTATGT-A-TTATG
1 TAAG-T-TGTATA-TTATGTAAGTTATG
* * *
1513708 TATGTTATGTATTATGT-A-TTATG
1 TAAGTTGTATATTATGTAAGTTATG
1513731 TAAGTACTGTA-AGTTATGTAAGTTATG
1 TAAGT--TGTATA-TTATGTAAGTTATG
* ***
1513758 AAAGTAACATATTATGTAAGTT
1 TAAGTTGTATATTATGTAAGTT
1513780 GTATATAATG
Statistics
Matches: 139, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
23 18 0.13
24 5 0.04
25 91 0.65
26 4 0.03
27 21 0.15
ACGTcount: A:0.31, C:0.01, G:0.21, T:0.47
Consensus pattern (25 bp):
TAAGTTGTATATTATGTAAGTTATG
Found at i:1513665 original size:66 final size:64
Alignment explanation
Indices: 1513553--1513830 Score: 222
Period size: 66 Copynumber: 4.4 Consensus size: 64
1513543 ATTTTTATGT
1513553 ATTATGTAAGTTATGTACTAAGTTATG---TAT-TAAGTTATGTATTATGTAAGTTATGTGAGTT
1 ATTATGTAAGTTATG---TAAGTTATGTATTATGTAAGTTATGTATTATGTAAGTTATGT-AGTT
1513614 GTA
62 GTA
* * *
1513617 TATTATGTGAGTTATGTAAGTTGTGTATTATGTAAGTTATGTATTATGTATGTTATGTA-----A
1 -ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAAGTTATGTAGTTGTA
* *
1513677 GTTATGTAAGTTATGTAAGTTATGTATTATGTATGTTATGTATTATGT-A-TTATGTAAGTACTG
1 ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAAGTTATGT-AGT--TG
1513740 TA
63 TA
* * ** * * * * *
1513742 AGTTATGTAAGTTATGAAAGTAACATATTATGTAAGTTGTATATAATGTAAGTTAGGAAGGTTAT
1 A-TTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAAGTTATGTA-G-T-T
1513807 GT-
62 GTA
*
1513809 ATTATGTAAGTTAT-TATGTTAT
1 ATTATGTAAGTTATGTAAGTTAT
1513831 TATATAAGTT
Statistics
Matches: 172, Mismatches: 24, Indels: 34
0.75 0.10 0.15
Matches are distributed among these distances:
57 6 0.03
58 1 0.01
59 44 0.26
60 1 0.01
62 8 0.05
65 23 0.13
66 77 0.45
67 3 0.02
68 8 0.05
69 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.47
Consensus pattern (64 bp):
ATTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTATGTATTATGTAAGTTATGTAGTTGTA
Found at i:1513773 original size:57 final size:58
Alignment explanation
Indices: 1513653--1513775 Score: 153
Period size: 57 Copynumber: 2.1 Consensus size: 58
1513643 ATTATGTAAG
* * ** *
1513653 TTATGTATTATGTATGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTATG
1 TTATGTATTATGTA-GTTATGTAAGTTATGTAAGTTATGTAAGTTATGAAGTATACATA
1513712 TTATGTATTATGTA-TTATGTAAG-TACTGTAAGTTATGTAAGTTATGAAAGTA-ACATA
1 TTATGTATTATGTAGTTATGTAAGTTA-TGTAAGTTATGTAAGTTATG-AAGTATACATA
1513769 TTATGTA
1 TTATGTA
1513776 AGTTGTATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
56 2 0.04
57 38 0.67
58 3 0.05
59 14 0.25
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (58 bp):
TTATGTATTATGTAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGAAGTATACATA
Found at i:1513783 original size:57 final size:56
Alignment explanation
Indices: 1513653--1513794 Score: 135
Period size: 57 Copynumber: 2.4 Consensus size: 56
1513643 ATTATGTAAG
* * * ** *
1513653 TTATGTATTATGTATGTTATGTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTATG
1 TTATGTAGTATGTA--TTATGTAAG-TATGTAAGTTATGTAAGTTATGAAGTATACATA
*
1513712 TTATGTATTATGTATTATGTAAGTACTGTAAGTTATGTAAGTTATGAAAGTA-ACATA
1 TTATGTAGTATGTATTATGTAAGTA-TGTAAGTTATGTAAGTTATG-AAGTATACATA
1513769 TTATGTAAGT-TGTATATAATGTAAGT
1 TTATGT-AGTATGTAT-T-ATGTAAGT
1513795 TAGGAAGGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
56 2 0.03
57 42 0.58
58 6 0.08
59 22 0.31
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (56 bp):
TTATGTAGTATGTATTATGTAAGTATGTAAGTTATGTAAGTTATGAAGTATACATA
Found at i:1513833 original size:20 final size:19
Alignment explanation
Indices: 1513803--1513842 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
1513793 GTTAGGAAGG
*
1513803 TTATGTATTATGTAAGTTA
1 TTATGTATTATATAAGTTA
1513822 TTATGTTATTATATAAGTTA
1 TTATG-TATTATATAAGTTA
1513842 T
1 T
1513843 GCAAGTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (19 bp):
TTATGTATTATATAAGTTA
Found at i:1513892 original size:16 final size:16
Alignment explanation
Indices: 1513868--1513908 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1513858 AGTTTATATA
*
1513868 TTATATATTATTTAAG
1 TTATATATTATGTAAG
*
1513884 TTATGTATTATGTAAG
1 TTATATATTATGTAAG
1513900 TTTATATAT
1 -TTATATAT
1513909 AAGTTATGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (16 bp):
TTATATATTATGTAAG
Found at i:1513920 original size:12 final size:12
Alignment explanation
Indices: 1513845--1513913 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
1513835 TAAGTTATGC
1513845 AAGTTTATATAT
1 AAGTTTATATAT
1513857 AAGTTTATATAT
1 AAGTTTATATAT
* * *
1513869 TA-TATATTATTT
1 AAGTTTA-TATAT
*
1513881 AAGTTATGTATTATGT
1 AAG-T-T-TA-TATAT
1513897 AAGTTTATATAT
1 AAGTTTATATAT
1513909 AAGTT
1 AAGTT
1513914 ATGATATGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
11 3 0.07
12 27 0.60
13 2 0.04
14 2 0.04
15 1 0.02
16 10 0.22
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (12 bp):
AAGTTTATATAT
Found at i:1514009 original size:15 final size:15
Alignment explanation
Indices: 1513976--1514018 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
1513966 TTTGAAAAAA
* * *
1513976 AAAAATATAAATTTT
1 AAAAATATATATATG
1513991 AAAAATATATATATG
1 AAAAATATATATATG
*
1514006 AAAAATGTATATA
1 AAAAATATATATA
1514019 AATATTTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
AAAAATATATATATG
Found at i:1514866 original size:13 final size:13
Alignment explanation
Indices: 1514833--1514870 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1514823 AAAGAACTCG
1514833 CAGCAACATTAAC
1 CAGCAACATTAAC
*
1514846 C-CCTAACATTAAC
1 CAGC-AACATTAAC
1514859 CAGCAACATTAA
1 CAGCAACATTAA
1514871 GCAGAACTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 1 0.05
13 19 0.90
14 1 0.05
ACGTcount: A:0.45, C:0.32, G:0.05, T:0.18
Consensus pattern (13 bp):
CAGCAACATTAAC
Found at i:1516577 original size:47 final size:47
Alignment explanation
Indices: 1516487--1516577 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
1516477 AAATTTGATT
* * *
1516487 TATAGTGCTTGTATTTTTCTTAAAATTTATAGTAGGAACTTAATCCG
1 TATAGTGCTTGTATTTTTCTTAAAATTCAAAGTAGAAACTTAATCCG
* * *
1516534 TATAGTGTTTGTATTTTTC-TAAAACTTCAAATTAGAAATTTAAT
1 TATAGTGCTTGTATTTTTCTTAAAA-TTCAAAGTAGAAACTTAAT
1516578 TCTATGAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
46 5 0.14
47 32 0.86
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.46
Consensus pattern (47 bp):
TATAGTGCTTGTATTTTTCTTAAAATTCAAAGTAGAAACTTAATCCG
Found at i:1516757 original size:14 final size:14
Alignment explanation
Indices: 1516620--1516763 Score: 51
Period size: 14 Copynumber: 10.2 Consensus size: 14
1516610 CTAATTAATA
*
1516620 TAAACCCTAAACCA
1 TAAACCCTAAACCT
* *
1516634 TAACCCCT-ATCCT
1 TAAACCCTAAACCT
* * *
1516647 GAAAACCATAAACCA
1 -TAAACCCTAAACCT
**
1516662 TAAACCCTATTCCT
1 TAAACCCTAAACCT
* * * * *
1516676 TAGACACTAGATCA
1 TAAACCCTAAACCT
* *
1516690 TAGACCCTAACCCT
1 TAAACCCTAAACCT
* *
1516704 TAAACCTTAAACCCA
1 TAAACCCTAAA-CCT
*
1516719 CAAACCCTAAA--T
1 TAAACCCTAAACCT
*
1516731 AATAACCCATAAACCT
1 TA-AACCC-TAAACCT
*
1516747 TAAACCCTAAACTT
1 TAAACCCTAAACCT
1516761 TAA
1 TAA
1516764 GCCCCTCTTA
Statistics
Matches: 89, Mismatches: 34, Indels: 14
0.65 0.25 0.10
Matches are distributed among these distances:
12 1 0.01
13 8 0.09
14 59 0.66
15 19 0.21
16 2 0.02
ACGTcount: A:0.43, C:0.33, G:0.03, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:1517083 original size:39 final size:39
Alignment explanation
Indices: 1517029--1517112 Score: 141
Period size: 39 Copynumber: 2.2 Consensus size: 39
1517019 CCATATTTCT
* *
1517029 TAAACCTTGACTCATAAAACATATATAAACTATAAACCC
1 TAAACCCTGAATCATAAAACATATATAAACTATAAACCC
*
1517068 TAAACCCTGAATCATAAAACATATATAAACTATAAACCT
1 TAAACCCTGAATCATAAAACATATATAAACTATAAACCC
1517107 TAAACC
1 TAAACC
1517113 TCAACCCTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.50, C:0.23, G:0.02, T:0.25
Consensus pattern (39 bp):
TAAACCCTGAATCATAAAACATATATAAACTATAAACCC
Found at i:1517548 original size:114 final size:114
Alignment explanation
Indices: 1517364--1517607 Score: 278
Period size: 114 Copynumber: 2.1 Consensus size: 114
1517354 ATAAAACGTT
* * * * *
1517364 GTCGTTTGCTTAAAAACTTTTGCGGTGCTATTGTGAAAGCACCTCTAATTCTTGCCTTTTGCGGC
1 GTCGTTTGCTT-AAAACTATTGCGATGCTATTGTGAAAGCACCGCTAATGCTTGACTTTTGCGGC
*
1517429 GTTTTTAGGAATGCGCCACTAATATCTCGAAAGCTGAAAAAG-AAAAC-ATC
65 GTTTTTAGGAAAGCGCCACTAATATCTCGAAAGCT-AAAAAGAAAAACGA-C
* * ** *
1517479 GTCGTTTGCTTAAAACTATTGTGATGCTTTTGAT-AAAGCGTCGCTAATGCTTGACTTTTGTGGC
1 GTCGTTTGCTTAAAACTATTGCGATGCTATTG-TGAAAGCACCGCTAATGCTTGACTTTTGCGGC
* * * * *
1517543 GTTTTTAGTAAAGCGCCACTAATGTCTCTAAAGCTCAACAGAAAAACGAC
65 GTTTTTAGGAAAGCGCCACTAATATCTCGAAAGCTAAAAAGAAAAACGAC
*
1517593 GCCGTTTGCTTAAAA
1 GTCGTTTGCTTAAAA
1517608 ATTTTTACGG
Statistics
Matches: 109, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
113 4 0.04
114 92 0.84
115 13 0.12
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (114 bp):
GTCGTTTGCTTAAAACTATTGCGATGCTATTGTGAAAGCACCGCTAATGCTTGACTTTTGCGGCG
TTTTTAGGAAAGCGCCACTAATATCTCGAAAGCTAAAAAGAAAAACGAC
Found at i:1531615 original size:108 final size:108
Alignment explanation
Indices: 1531480--1531699 Score: 422
Period size: 108 Copynumber: 2.0 Consensus size: 108
1531470 ATATATTGCG
*
1531480 TGTAGATATGGCCAACATGACAGATCTCATGTTGTAAACAACTTGGTAGGTCTAGGTTAAAATTT
1 TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGGTAGGTCTAGGTTAAAATTT
*
1531545 TCTATTAGTCCTTGTATTTTTCTAAAGTTATAGATTTAGTCCA
66 TCTATTAGTCCTTGAATTTTTCTAAAGTTATAGATTTAGTCCA
1531588 TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGGTAGGTCTAGGTTAAAATTT
1 TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGGTAGGTCTAGGTTAAAATTT
1531653 TCTATTAGTCCTTGAATTTTTCTAAAGTTATAGATTTAGTCCA
66 TCTATTAGTCCTTGAATTTTTCTAAAGTTATAGATTTAGTCCA
1531696 TGTA
1 TGTA
1531700 CTTTAATTTG
Statistics
Matches: 110, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 110 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (108 bp):
TGTAGATATGACCAACATGACAGATCTCATGTTGTAAACAACTTGGTAGGTCTAGGTTAAAATTT
TCTATTAGTCCTTGAATTTTTCTAAAGTTATAGATTTAGTCCA
Found at i:1537301 original size:38 final size:38
Alignment explanation
Indices: 1537250--1537326 Score: 120
Period size: 38 Copynumber: 2.0 Consensus size: 38
1537240 AATTGTCCCT
* *
1537250 TTCTGTTAAAAATT-ACATTTATTTCTACTATTAAAAAC
1 TTCTGTTAAAAATTCA-ATTCACTTCTACTATTAAAAAC
1537288 TTCTGTTAAAAATTCAATTCACTTCTACTATTAAAAAC
1 TTCTGTTAAAAATTCAATTCACTTCTACTATTAAAAAC
1537326 T
1 T
1537327 GGCATGACTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 35 0.97
39 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.43
Consensus pattern (38 bp):
TTCTGTTAAAAATTCAATTCACTTCTACTATTAAAAAC
Found at i:1556019 original size:25 final size:24
Alignment explanation
Indices: 1555978--1556029 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
1555968 AAAAAATTCA
* *
1555978 AAAATTCAATATTTAATTAATAAT
1 AAAATTAAATATATAATTAATAAT
1556002 AAAATTAAATATGATAATTAATAAT
1 AAAATTAAATAT-ATAATTAATAAT
1556027 AAA
1 AAA
1556030 TATAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
AAAATTAAATATATAATTAATAAT
Found at i:1556044 original size:15 final size:15
Alignment explanation
Indices: 1555997--1556047 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 15
1555987 TATTTAATTA
1555997 ATAATAAAATTAAAT
1 ATAATAAAATTAAAT
*
1556012 ATGATAATTAATAATAAAT
1 ATAATAA--AAT--TAAAT
1556031 ATAATAAAATTAAAT
1 ATAATAAAATTAAAT
1556046 AT
1 AT
1556048 GTTTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 13 0.43
17 6 0.20
19 11 0.37
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (15 bp):
ATAATAAAATTAAAT
Found at i:1556791 original size:17 final size:17
Alignment explanation
Indices: 1556769--1556801 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1556759 ATCTTATTCC
*
1556769 TTGGTATCACGATACCT
1 TTGGTATCACAATACCT
1556786 TTGGTATCACAATACC
1 TTGGTATCACAATACC
1556802 AACATCGTGA
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:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (17 bp):
TTGGTATCACAATACCT
Found at i:1558756 original size:19 final size:20
Alignment explanation
Indices: 1558724--1558761 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1558714 CCCTAATTCA
* *
1558724 AAGATTAATGAACC-CCATC
1 AAGATCAATCAACCACCATC
1558743 AAGATCAATCAACCACCAT
1 AAGATCAATCAACCACCAT
1558762 TTAATAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.45, C:0.29, G:0.08, T:0.18
Consensus pattern (20 bp):
AAGATCAATCAACCACCATC
Found at i:1562302 original size:24 final size:24
Alignment explanation
Indices: 1562274--1562325 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1562264 TTAGTAGGTC
* *
1562274 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
1562298 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
1562322 AAAT
1 AAAT
1562326 CTTTTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:1565314 original size:18 final size:17
Alignment explanation
Indices: 1565268--1565315 Score: 71
Period size: 17 Copynumber: 2.8 Consensus size: 17
1565258 ATAGGTCTCT
1565268 GACGAGCTTCCAACCAA
1 GACGAGCTTCCAACCAA
1565285 GACGAGCTTCCAACCAA
1 GACGAGCTTCCAACCAA
1565302 -ATCGAGCCTTCCAA
1 GA-CGAG-CTTCCAA
1565316 TGATCTACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 1 0.03
17 21 0.72
18 7 0.24
ACGTcount: A:0.33, C:0.35, G:0.17, T:0.15
Consensus pattern (17 bp):
GACGAGCTTCCAACCAA
Found at i:1574040 original size:21 final size:20
Alignment explanation
Indices: 1574011--1574051 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1574001 GGTGACAACA
1574011 TGATCTTATAAGATAATGATG
1 TGATCTTATAAGATAA-GATG
* *
1574032 TGATGTTATAAGTTAAGATG
1 TGATCTTATAAGATAAGATG
1574052 CTGACGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.02, G:0.22, T:0.39
Consensus pattern (20 bp):
TGATCTTATAAGATAAGATG
Found at i:1575306 original size:3 final size:3
Alignment explanation
Indices: 1575298--1575322 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1575288 AGTGGAGCTG
1575298 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
1575323 AGATGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:1575330 original size:3 final size:3
Alignment explanation
Indices: 1575324--1575351 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1575314 TTCTTCTTCA
1575324 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1575352 GTAACAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:1575836 original size:3 final size:3
Alignment explanation
Indices: 1575828--1575880 Score: 72
Period size: 3 Copynumber: 17.7 Consensus size: 3
1575818 TGAGAAGCCA
* *
1575828 AAG AAG AAG ATG AAG AAA AAG AAG AAG AAG AAG AAG AAG AA- AACG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G
1575873 AAG AAG AA
1 AAG AAG AA
1575881 AGTGGAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 2 0.05
3 40 0.91
4 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.28, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1600686 original size:22 final size:22
Alignment explanation
Indices: 1600654--1600704 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
1600644 ATTCTCATAC
* * *
1600654 CACGAATTGCTTCGAGTATGGG
1 CACGAACTGCTTCCAGTATAGG
1600676 CACGAACTGCTTCCAGTATAGG
1 CACGAACTGCTTCCAGTATAGG
*
1600698 CTCGAAC
1 CACGAAC
1600705 AATTTTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.24
Consensus pattern (22 bp):
CACGAACTGCTTCCAGTATAGG
Found at i:1603347 original size:25 final size:27
Alignment explanation
Indices: 1603297--1603348 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1603287 GTTTTAAATG
*
1603297 ATATTTTCATTAAATAATAATTATTTA
1 ATATTTTCATTAAATAATAATAATTTA
*
1603324 ATATTTT-ATTTAA-AATAATAATTTA
1 ATATTTTCATTAAATAATAATAATTTA
1603349 TTAAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 5 0.22
27 7 0.30
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (27 bp):
ATATTTTCATTAAATAATAATAATTTA
Found at i:1611150 original size:19 final size:21
Alignment explanation
Indices: 1611114--1611156 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1611104 AAAGAAATAA
1611114 ATAAAAAAATGAATAAGAT-T
1 ATAAAAAAATGAATAAGATAT
1611134 ATAAAAAAA-GTAA-AAGATAT
1 ATAAAAAAATG-AATAAGATAT
1611154 ATA
1 ATA
1611157 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (21 bp):
ATAAAAAAATGAATAAGATAT
Found at i:1611217 original size:34 final size:38
Alignment explanation
Indices: 1611164--1611256 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 38
1611154 ATATATATAT
* * * *
1611164 ATATGTATATATATGTATATAAATTAGT-AAGATAAAA
1 ATATATATATAGATATATATAAATTAGTGAAAATAAAA
* *
1611201 A-ATATATA-AG-TATATATATATTCGTGAAAATAAAA
1 ATATATATATAGATATATATAAATTAGTGAAAATAAAA
*
1611236 ATATGTATATAGATATATATA
1 ATATATATATAGATATATATA
1611257 TATATATATA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
34 12 0.27
35 10 0.22
36 12 0.27
37 3 0.07
38 8 0.18
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.38
Consensus pattern (38 bp):
ATATATATATAGATATATATAAATTAGTGAAAATAAAA
Found at i:1611252 original size:36 final size:35
Alignment explanation
Indices: 1611164--1611257 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 35
1611154 ATATATATAT
* * *
1611164 ATATGTATATATATGTATATAAATTAGTAAGATAAAA
1 ATATGTATATAGA--TATATATATTAGTAAAATAAAA
* *
1611201 A-ATATATA-AGTATATATATATTCGTGAAAATAAAA
1 ATATGTATATAG-ATATATATATTAGT-AAAATAAAA
1611236 ATATGTATATAGATATATATAT
1 ATATGTATATAGATATATATAT
1611258 ATATATATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
34 11 0.23
35 10 0.21
36 23 0.49
37 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (35 bp):
ATATGTATATAGATATATATATTAGTAAAATAAAA
Found at i:1611281 original size:10 final size:10
Alignment explanation
Indices: 1611242--1611297 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
1611232 AAAAATATGT
* *
1611242 ATATAGATAT
1 ATATATATAG
*
1611252 ATATATATAT
1 ATATATATAG
1611262 ATATATATAG
1 ATATATATAG
*
1611272 GTATATATAG
1 ATATATATAG
*
1611282 AAAT-TATAG
1 ATATATATAG
1611291 ATATATA
1 ATATATA
1611298 AAAATAAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
9 8 0.21
10 31 0.79
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (10 bp):
ATATATATAG
Found at i:1611297 original size:2 final size:2
Alignment explanation
Indices: 1611150--1611280 Score: 58
Period size: 2 Copynumber: 66.5 Consensus size: 2
1611140 AAAGTAAAAG
* * *
1611150 AT AT AT AT AT AT AT AT AT GT AT AT AT AT GT AT AT AA AT -T AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * * *
1611192 A- AG AT A- AA AA AT AT AT A- AGT AT AT AT AT AT -T CGT GA- AA
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT -AT -AT AT
* * * * *
1611230 AT AA AA AT AT GT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1611272 GT AT AT AT A
1 AT AT AT AT A
1611281 GAAATTATAG
Statistics
Matches: 99, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
1 6 0.06
2 89 0.90
3 4 0.04
ACGTcount: A:0.50, C:0.01, G:0.08, T:0.40
Consensus pattern (2 bp):
AT
Found at i:1611297 original size:8 final size:8
Alignment explanation
Indices: 1611241--1611297 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
1611231 TAAAAATATG
1611241 TATATAGA
1 TATATAGA
*
1611249 TATATATA
1 TATATAGA
*
1611257 TATATATA
1 TATATAGA
1611265 TATATAGGTA
1 TATATA-G-A
1611275 TATATAGA
1 TATATAGA
*
1611283 AATTATAGA
1 TA-TATAGA
1611292 TATATA
1 TATATA
1611298 AAAATAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
8 27 0.64
9 8 0.19
10 7 0.17
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (8 bp):
TATATAGA
Found at i:1611674 original size:3 final size:3
Alignment explanation
Indices: 1611668--1611709 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1611658 AACAATACCT
1611668 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1611710 GAAAAGAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1612782 original size:11 final size:11
Alignment explanation
Indices: 1612766--1612791 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1612756 TTTTAATTTT
1612766 TGTTTTGGGTC
1 TGTTTTGGGTC
1612777 TGTTTTGGGTC
1 TGTTTTGGGTC
1612788 TGTT
1 TGTT
1612792 GCTGGGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.35, T:0.58
Consensus pattern (11 bp):
TGTTTTGGGTC
Found at i:1612937 original size:60 final size:60
Alignment explanation
Indices: 1612861--1613123 Score: 258
Period size: 60 Copynumber: 4.3 Consensus size: 60
1612851 GGGCCTTACA
** * *
1612861 TAGAGTTTTGCCACAAAGGCATCCTTTACATTTAGTACTCACCACAAAGGTTTTCCTGTC
1 TAGAGTTTTGCCACAAAGGCATCCTTTACATCCAATACTCACCACAAAGGCTTTCCTGTC
* * **
1612921 TAGAGCTTTGCTACAAAGGCATCCTTTACATCCAATACTTGCCACAAAGGCTTTCCTGTC
1 TAGAGTTTTGCCACAAAGGCATCCTTTACATCCAATACTCACCACAAAGGCTTTCCTGTC
* * * * * * * *
1612981 AAGAGTTTTGCCAGAAAAGTG-GTCCTTTACATCCAATAGTCGCTACATAGGCTTTCTTGTC
1 TAGAGTTTTGCCA-CAAAG-GCATCCTTTACATCCAATACTCACCACAAAGGCTTTCCTGTC
* * * ** * * *
1613042 CAGAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCACAAAGGCTTTCATGTC
1 TAGAGTTTTGCC-ACAAAGG-CATCCTTTACATCCAATACTCACCACAAAGGCTTTCCTGTC
*
1613104 CAGAGTTTTGCCACAAAGGC
1 TAGAGTTTTGCCACAAAGGC
1613124 TTTCCTGTCC
Statistics
Matches: 169, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
60 63 0.37
61 59 0.35
62 47 0.28
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (60 bp):
TAGAGTTTTGCCACAAAGGCATCCTTTACATCCAATACTCACCACAAAGGCTTTCCTGTC
Found at i:1613033 original size:61 final size:62
Alignment explanation
Indices: 1612942--1613116 Score: 235
Period size: 61 Copynumber: 2.8 Consensus size: 62
1612932 TACAAAGGCA
* * * *
1612942 TCCTTTACATCCAATACTTGCCACAAAGGCTTTCCTGTCAAGAGTTTTGCCAGAAAA-GTGG
1 TCCTTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGGTGG
* * * * * *
1613003 TCCTTTACATCCAATAGTCGCTACATAGGCTTTCTTGTCCAGAGTTATGCCAAAAAAGGTTG
1 TCCTTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGGTGG
* *
1613065 TCATTTACATCCAATACTCCCCACAAAGGCTTTCATGTCCAGAGTTTTGCCA
1 TCCTTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCA
1613117 CAAAGGCTTT
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 49 0.51
62 48 0.49
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.31
Consensus pattern (62 bp):
TCCTTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGGTGG
Found at i:1613097 original size:62 final size:61
Alignment explanation
Indices: 1612945--1613116 Score: 227
Period size: 62 Copynumber: 2.8 Consensus size: 61
1612935 AAAGGCATCC
* * * * *
1612945 TTTACATCCAATACTTGCCACAAAGGCTTTCCTGTCAAGAGTTTTGCCAGAAAAGTGGTCC
1 TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGTGGTCA
* * * * * *
1613006 TTTACATCCAATAGTCGCTACATAGGCTTTCTTGTCCAGAGTTATGCCAAAAAAGGTTGTCA
1 TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAA-GTGGTCA
*
1613068 TTTACATCCAATACTCCCCACAAAGGCTTTCATGTCCAGAGTTTTGCCA
1 TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCA
1613117 CAAAGGCTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
61 46 0.49
62 48 0.51
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (61 bp):
TTTACATCCAATACTCGCCACAAAGGCTTTCATGTCCAGAGTTTTGCCAAAAAAGTGGTCA
Found at i:1613118 original size:29 final size:29
Alignment explanation
Indices: 1613085--1613151 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
1613075 CCAATACTCC
* *
1613085 CCACAAAGGCTTTCATGTCCAGAGTTTTG
1 CCACAAAGGCTTTCATGTCCAAAGTTGTG
*
1613114 CCACAAAGGCTTTCCTGTCCAAAGTTGTG
1 CCACAAAGGCTTTCATGTCCAAAGTTGTG
1613143 CCACAAAGG
1 CCACAAAGG
1613152 TTGTCATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (29 bp):
CCACAAAGGCTTTCATGTCCAAAGTTGTG
Found at i:1613183 original size:90 final size:91
Alignment explanation
Indices: 1613029--1613212 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 91
1613019 GTCGCTACAT
* * *
1613029 AGGCTTTCTTGTCCAGAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCACAAAGG
1 AGGCTTTCCTGTCCAAAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCAAAAAGG
* *
1613094 CTTTCATGTCCAGAGTTTTGCCACAA
66 CTTTCATATCCAGAGTTGTGCCACAA
* * *
1613120 AGGCTTTCCTGTCCAAAGTTGTGCC-ACAAAGGTTGTCATTTACATCCAATACTCGCCAAAAAGG
1 AGGCTTTCCTGTCCAAAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCAAAAAGG
* *
1613184 CTTTCCTATTCAGAGTTGTGCCACAA
66 CTTTCATATCCAGAGTTGTGCCACAA
1613210 AGG
1 AGG
1613213 TTGTCATTTA
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 61 0.73
91 22 0.27
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (91 bp):
AGGCTTTCCTGTCCAAAGTTATGCCAAAAAAGGTTGTCATTTACATCCAATACTCCCCAAAAAGG
CTTTCATATCCAGAGTTGTGCCACAA
Found at i:1613187 original size:61 final size:60
Alignment explanation
Indices: 1613113--1613282 Score: 268
Period size: 61 Copynumber: 2.8 Consensus size: 60
1613103 CCAGAGTTTT
* *
1613113 GCCACAAAGGCTTTCCTGTCCAAAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTC
1 GCCACAAAGGCTTTCCTAT-CAGAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTC
* *
1613174 GCCAAAAAGGCTTTCCTATTCAGAGTTGTGCCACAAAGGTTGTCATTTACATCCAGTACTC
1 GCCACAAAGGCTTTCCTA-TCAGAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTC
* *
1613235 ACCACAAAGGCTTTCCTATCAGAGTTGTGCCACAAAGGTTGTCCTTTA
1 GCCACAAAGGCTTTCCTATCAGAGTTGTGCCACAAAGGTTGTCATTTA
1613283 ACTGGTGTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
60 29 0.29
61 71 0.70
62 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (60 bp):
GCCACAAAGGCTTTCCTATCAGAGTTGTGCCACAAAGGTTGTCATTTACATCCAATACTC
Found at i:1613211 original size:29 final size:28
Alignment explanation
Indices: 1613085--1613272 Score: 92
Period size: 29 Copynumber: 6.3 Consensus size: 28
1613075 CCAATACTCC
* *
1613085 CCACAAAGGCTTTCATGTCCAGAGTTTTG
1 CCACAAAGGCTTTCAT-TTCAGAGTTGTG
* * *
1613114 CCACAAAGGCTTTCCTGTCCAAAGTTGTG
1 CCACAAAGGCTTTCAT-TTCAGAGTTGTG
* * **
1613143 CCACAAAGG-TTGTCATTTACATCCAATACTCG
1 CCACAAAGGCTT-TCATTT-CA--GAGTTGT-G
* *
1613175 CCAAAAAGGCTTTCCTATTCAGAGTTGTG
1 CCACAAAGGCTTTCAT-TTCAGAGTTGTG
* ** *
1613204 CCACAAAGG-TTGTCATTTACATCCAGTACTCA
1 CCACAAAGGCTT-TCATTT-CA--GAGTTGT-G
* *
1613236 CCACAAAGGCTTTCCTATCAGAGTTGTG
1 CCACAAAGGCTTTCATTTCAGAGTTGTG
1613264 CCACAAAGG
1 CCACAAAGG
1613273 TTGTCCTTTA
Statistics
Matches: 119, Mismatches: 27, Indels: 27
0.69 0.16 0.16
Matches are distributed among these distances:
28 16 0.13
29 58 0.49
30 3 0.03
31 9 0.08
32 27 0.23
33 6 0.05
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (28 bp):
CCACAAAGGCTTTCATTTCAGAGTTGTG
Found at i:1615644 original size:9 final size:9
Alignment explanation
Indices: 1615630--1615704 Score: 89
Period size: 9 Copynumber: 8.2 Consensus size: 9
1615620 TTTGGTTAAA
1615630 AATTACCCG
1 AATTACCCG
1615639 AATTACCCG
1 AATTACCCG
1615648 AATTACCCG
1 AATTACCCG
* *
1615657 AATTACTCA
1 AATTACCCG
*
1615666 AATTAACCG
1 AATTACCCG
1615675 AATTA-CCG
1 AATTACCCG
*
1615683 AAAAATACCCG
1 --AATTACCCG
1615694 AATTACCCG
1 AATTACCCG
1615703 AA
1 AA
1615705 ATTTTTTTAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
8 3 0.05
9 46 0.82
10 4 0.07
11 3 0.05
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Done.