Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 82 of 202
Found at i:24128642 original size:38 final size:38
Alignment explanation
Indices: 24128591--24128667 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
24128581 ACCCCTGGAG
*
24128591 TATGAATTTTTCTATCTTCTGCCATGAAGTTCTAACTA
1 TATGAATTTTTCTATCTTCTACCATGAAGTTCTAACTA
24128629 TATGAATTTTTCTATCTTCTACCATGAAGTTCTAACTA
1 TATGAATTTTTCTATCTTCTACCATGAAGTTCTAACTA
24128667 T
1 T
24128668 TTTCAATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (38 bp):
TATGAATTTTTCTATCTTCTACCATGAAGTTCTAACTA
Found at i:24134532 original size:16 final size:17
Alignment explanation
Indices: 24134511--24134543 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24134501 AAAATACATT
*
24134511 AAATAAAGCTT-TTAAA
1 AAATAAACCTTATTAAA
24134527 AAATAAACCTTATTAAA
1 AAATAAACCTTATTAAA
24134544 TACGAAACAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.58, C:0.09, G:0.03, T:0.30
Consensus pattern (17 bp):
AAATAAACCTTATTAAA
Found at i:24135914 original size:43 final size:43
Alignment explanation
Indices: 24135866--24136172 Score: 359
Period size: 43 Copynumber: 7.2 Consensus size: 43
24135856 AGAAATAAAT
*
24135866 GCCGCTATAGACCATAACCTTTAGCGGCGCTTTTCCCACAAAC
1 GCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
*
24135909 GCCGCTATAGACCATGACCTTTAGCGGCTC-TTTCCCACAAAC
1 GCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
* **
24135951 GCCGCTATAGACCATTACCTTTAGCGGCGCTTTTATCACAAAC
1 GCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
* * **
24135994 GCCGCTATAGATCATTACCTTTAGCGGCGCTTTTATCACAAAC
1 GCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
* * * * *
24136037 GCCGCTAAAGACCATTACCTTTAGTGCCGCTTCTCCCACAAAC
1 GCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
* ** * * **
24136080 GCCGTTATAGGTCATGACTTTTAGCGACGCTTTTTCGTACAAAC
1 GCCGCTATAGACCATGACCTTTAGCGGCGC-TTTTCCCACAAAC
* * *
24136124 ACCGCTATAGA--ATTGGCCTTTAGCGGCGCTTTTCACACAAAC
1 GCCGCTATAGACCA-TGACCTTTAGCGGCGCTTTTCCCACAAAC
24136166 GCCGCTA
1 GCCGCTA
24136173 AAAACATATC
Statistics
Matches: 227, Mismatches: 34, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
42 58 0.26
43 151 0.67
44 18 0.08
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (43 bp):
GCCGCTATAGACCATGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:24136293 original size:17 final size:14
Alignment explanation
Indices: 24136258--24136286 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
24136248 GGATAAATAC
24136258 AAATTATTATTTAA
1 AAATTATTATTTAA
24136272 AAATTATTATTTAA
1 AAATTATTATTTAA
24136286 A
1 A
24136287 TTAAATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATTATTATTTAA
Found at i:24136511 original size:43 final size:43
Alignment explanation
Indices: 24136463--24136553 Score: 112
Period size: 43 Copynumber: 2.1 Consensus size: 43
24136453 ACATATGCAA
** * ** *
24136463 GGTAATAAATTATACAATGCATTTTGTTAATCAAGTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
24136506 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
24136549 -GTAAT
1 GGTAAT
24136554 GAACTCAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 5 0.12
43 36 0.88
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:24141251 original size:83 final size:81
Alignment explanation
Indices: 24141105--24141347 Score: 279
Period size: 83 Copynumber: 2.9 Consensus size: 81
24141095 CTTTATTTAG
** * * * * *
24141105 TCAATGAAACAACGCCGTTTTGTGAAATTTTTAATTTATTTTTTGTGGCGTTTTTATAGAAAACG
1 TCAATGAAACGGCGCCGTTTTGTTAAA-TTTTAATATATTTTTTGCGGC-ATTTTATACAAAACG
24141170 CCACTAATATTTAATTCA
64 CCACTAATATTTAATTCA
* *
24141188 TCAATGAAATGGCGCCGTTTTATTAAATTCTTAATATATTTTTTGCGGCATTTGTATACAAAACG
1 TCAATGAAACGGCGCCGTTTTGTTAAATT-TTAATATATTTTTTGCGGCATTT-TATACAAAACG
*
24141253 CCACTAATATTTAATTCG
64 CCACTAATATTTAATTCA
** * * * *
24141271 TCAATGAAACGGTACCGTTTGGTTAAATTTTAAATGTATTTTTTGCGGCATTTTTTACCAAACGC
1 TCAATGAAACGGCGCCGTTTTGTTAAATTTT-AATATATTTTTTGCGGCATTTTATACAAAACGC
*
24141336 CGCTAATGATTT
65 CACTAAT-ATTT
24141348 CACTTTTAAA
Statistics
Matches: 137, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
82 23 0.17
83 114 0.83
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (81 bp):
TCAATGAAACGGCGCCGTTTTGTTAAATTTTAATATATTTTTTGCGGCATTTTATACAAAACGCC
ACTAATATTTAATTCA
Found at i:24143471 original size:21 final size:21
Alignment explanation
Indices: 24143446--24143487 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
24143436 AGTGTAAGGG
24143446 CTACTATGCGTCTCTCTCAGA
1 CTACTATGCGTCTCTCTCAGA
24143467 CTACTATGCGTCTCTCTCAGA
1 CTACTATGCGTCTCTCTCAGA
24143488 ATAGACTGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.14, T:0.33
Consensus pattern (21 bp):
CTACTATGCGTCTCTCTCAGA
Found at i:24150525 original size:54 final size:54
Alignment explanation
Indices: 24150458--24150586 Score: 145
Period size: 54 Copynumber: 2.4 Consensus size: 54
24150448 TATAATATTA
*
24150458 TATATTATGATTTTTTTTAATT-CATATAATAATTATATTAAGAATATTG-TTAAAT
1 TATA-TATTATTTTTTTTAATTGCATATAATAATTATATTAA-AATA-TGATTAAAT
* * * * *
24150513 TATATATTATTTTATTAAATTGTATTTAATAATTATGTTAAAATATGATTAAAT
1 TATATATTATTTTTTTTAATTGCATATAATAATTATATTAAAATATGATTAAAT
* *
24150567 TATTTATTATTATTTTTAAT
1 TATATATTATTTTTTTTAAT
24150587 AAAATATATT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
53 2 0.03
54 40 0.65
55 20 0.32
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.55
Consensus pattern (54 bp):
TATATATTATTTTTTTTAATTGCATATAATAATTATATTAAAATATGATTAAAT
Found at i:24150598 original size:26 final size:25
Alignment explanation
Indices: 24150563--24150618 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
24150553 AAATATGATT
** *
24150563 AAATTATTTATTATTATTTTTAATA
1 AAATTATTTAACAATATTTTTAATA
*
24150588 AAATATATTTAACAATATTTTTATTA
1 AAAT-TATTTAACAATATTTTTAATA
24150614 AAATT
1 AAATT
24150619 TAATAACAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
AAATTATTTAACAATATTTTTAATA
Found at i:24150625 original size:25 final size:26
Alignment explanation
Indices: 24150577--24150629 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
24150567 TATTTATTAT
*
24150577 TATTTTTAATAAAATATATTTAACAA
1 TATTTTTAATAAAATATATATAACAA
* *
24150603 TATTTTTATTAAAATTTA-ATAACAA
1 TATTTTTAATAAAATATATATAACAA
24150628 TA
1 TA
24150630 ACAGATCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TATTTTTAATAAAATATATATAACAA
Found at i:24154837 original size:2 final size:2
Alignment explanation
Indices: 24154832--24154867 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
24154822 AAAAAAGTAG
24154832 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
24154868 AAGTTGAAGA
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):
TA
Found at i:24157156 original size:31 final size:30
Alignment explanation
Indices: 24157121--24157180 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
24157111 AGAGGTGGGA
*
24157121 TGGGAAAGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAA-GAATAAAAATTTTAGGGGAAAAG
* * *
24157152 TGGGAGAGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAAGAATAAAAATTTTAGGGGAAAA
24157181 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAAAGAATAAAAATTTTAGGGGAAAAG
Found at i:24159523 original size:24 final size:25
Alignment explanation
Indices: 24159467--24159529 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
24159457 AATGTTCATT
* *
24159467 TTGGTACCTAAGTTTTTTTTCCCAA
1 TTGGTACCTATGTTTTTTTTCACAA
*
24159492 TTAAGTACCTATGTTTTTTTTCACAA
1 TT-GGTACCTATGTTTTTTTTCACAA
*
24159518 -TGGTACATATGT
1 TTGGTACCTATGT
24159530 CAAACATTCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
24 9 0.28
25 3 0.09
26 20 0.62
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.48
Consensus pattern (25 bp):
TTGGTACCTATGTTTTTTTTCACAA
Found at i:24160662 original size:14 final size:17
Alignment explanation
Indices: 24160639--24160674 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
24160629 AAGACTTATT
24160639 TTTTTCTCAAG-CTA-A
1 TTTTTCTCAAGCCTATA
24160654 TTTTT-TCAAGCCTATA
1 TTTTTCTCAAGCCTATA
24160670 TTTTT
1 TTTTT
24160675 GCCCAAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 5 0.26
15 8 0.42
16 6 0.32
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTTTCTCAAGCCTATA
Found at i:24161557 original size:7 final size:8
Alignment explanation
Indices: 24161538--24161564 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
24161528 TGTTTTGTAA
24161538 AAAAAATT
1 AAAAAATT
24161546 AAAAAATT
1 AAAAAATT
24161554 AAAAAATT
1 AAAAAATT
24161562 AAA
1 AAA
24161565 TATTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATT
Found at i:24163216 original size:68 final size:68
Alignment explanation
Indices: 24163138--24163311 Score: 303
Period size: 68 Copynumber: 2.6 Consensus size: 68
24163128 TAAAAAATGT
* *
24163138 TAAATCTCAAGTTTTAACATAATATAGGGACTAAAATTTTGGACTAAAATGTATAAGGATTATAA
1 TAAATCTCAAGTTTTAATATAGTATAGGGACTAAAATTTTGGACTAAAATGTATAAGGATTATAA
24163203 AAG
66 AAG
* * *
24163206 TAAATCTCAAGTTTTAATATAGTATAGGGATTAAAATTTTGGACTAAAATGTTTAGGGATTATAA
1 TAAATCTCAAGTTTTAATATAGTATAGGGACTAAAATTTTGGACTAAAATGTATAAGGATTATAA
24163271 AAG
66 AAG
24163274 TAAATCTCAAGTTTTAATATAGTATAGGGACTAAAATT
1 TAAATCTCAAGTTTTAATATAGTATAGGGACTAAAATT
24163312 AGATTGTTAA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 100 1.00
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (68 bp):
TAAATCTCAAGTTTTAATATAGTATAGGGACTAAAATTTTGGACTAAAATGTATAAGGATTATAA
AAG
Found at i:24166391 original size:22 final size:21
Alignment explanation
Indices: 24166340--24166401 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
24166330 CAGTAACCAG
* *
24166340 AATGGCTAAGAGCTGTAAACAG
1 AATGGCTAA-AGCTATAAACAA
* *
24166362 GATAGCTATAAGCTATAAACAA
1 AATGGCTA-AAGCTATAAACAA
*
24166384 AATGGCTACAAGCCATAA
1 AATGGCTA-AAGCTATAA
24166402 GTACATTAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.19
Consensus pattern (21 bp):
AATGGCTAAAGCTATAAACAA
Found at i:24166446 original size:32 final size:32
Alignment explanation
Indices: 24166393--24166500 Score: 128
Period size: 32 Copynumber: 3.4 Consensus size: 32
24166383 AAATGGCTAC
* * *
24166393 AAGCCATAAGTA-CATTAATATGATTGGTACA
1 AAGCCATCAGTAGCAGTAATATGATTGGCACA
*
24166424 AAGCCATCAGTAGTAGTAATATGATTGGCACA
1 AAGCCATCAGTAGCAGTAATATGATTGGCACA
* * * * *
24166456 CAGCCATCAGTAACGGTAACATGATCGGCACA
1 AAGCCATCAGTAGCAGTAATATGATTGGCACA
24166488 AAGCCATCAGTAG
1 AAGCCATCAGTAG
24166501 ATCGCAGCAA
Statistics
Matches: 64, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
31 11 0.17
32 53 0.83
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAGCAGTAATATGATTGGCACA
Found at i:24166550 original size:26 final size:26
Alignment explanation
Indices: 24166501--24166554 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
24166491 CCATCAGTAG
* *
24166501 ATCGCAGCAAAGCTGTCAACAACAGT
1 ATCGCAACAAAGCTGCCAACAACAGT
**
24166527 ATCGCAACAAAGCTGCCAGTAACAGT
1 ATCGCAACAAAGCTGCCAACAACAGT
24166553 AT
1 AT
24166555 ATGTGGCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (26 bp):
ATCGCAACAAAGCTGCCAACAACAGT
Found at i:24166597 original size:27 final size:27
Alignment explanation
Indices: 24166542--24166598 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
24166532 AACAAAGCTG
*
24166542 CCAGTAACAGTATATGTGGCCAAGTCA
1 CCAGTAACAGTATATGTGGCCAAGCCA
24166569 CCAGTAACAGTGAT-TGTGG-CAGAGCCA
1 CCAGTAACAGT-ATATGTGGCCA-AGCCA
24166596 CCA
1 CCA
24166599 ATATAGTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 23 0.85
28 2 0.07
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCCAAGCCA
Found at i:24166737 original size:24 final size:24
Alignment explanation
Indices: 24166670--24166730 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
24166660 CCATGCTTAG
* *
24166670 AATCGGTCATACAAATCACAGACA
1 AATCAGTCATACAAATCATAGACA
*
24166694 AATCAGTCATAAAAATCATAGACA
1 AATCAGTCATACAAATCATAGACA
*
24166718 AATTAGTCATACA
1 AATCAGTCATACA
24166731 TAACATAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.21
Consensus pattern (24 bp):
AATCAGTCATACAAATCATAGACA
Found at i:24166949 original size:27 final size:27
Alignment explanation
Indices: 24166909--24167373 Score: 423
Period size: 27 Copynumber: 17.3 Consensus size: 27
24166899 ATCATGGTCT
* *
24166909 TTTTACCC-TACAGGGATACTTCGGTAA
1 TTTTACCCAT-CAGGGGTATTTCGGTAA
* **
24166936 TTTTGCCCATCAGGGGTATTTTAGTAA
1 TTTTACCCATCAGGGGTATTTCGGTAA
*
24166963 TTTTACCCATC-GGAGGTATTTCGATAA
1 TTTTACCCATCAGG-GGTATTTCGGTAA
*
24166990 TTTTACCCATCAGGGGTATTTCGATAA
1 TTTTACCCATCAGGGGTATTTCGGTAA
* * *
24167017 TTTTACCCAT-TGACGGTATTTCGATAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
* *
24167044 TTTTACCTATC-GAGGGTATTTCGATAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
* *
24167071 TTTTATCCATC-GAGGGTATTTCGATAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
* * *
24167098 TTTTACCTATCGGGGGTATTTCAGTAA
1 TTTTACCCATCAGGGGTATTTCGGTAA
** *
24167125 TTTTACCCATTGGGGGTATTTCGATAA
1 TTTTACCCATCAGGGGTATTTCGGTAA
*
24167152 TTTTACCCATCGGGGGTATTTCGGTAA
1 TTTTACCCATCAGGGGTATTTCGGTAA
* * *
24167179 TTTTAACCATC-GAAGGTATTTCGATAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
*
24167206 TTTTACCCATC-GAGAGTATTTC-GTAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
* *
24167232 TTTTACCTATC-GAGGGTATTTCAGTAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
24167259 TTTTACCCAT-AGAGGGTATTTCGGTAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
* *
24167286 TTTTACCCTTC-GAGGGTATTTCAGTAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
* * **
24167313 TTTTACCCTTCAAGGGTATTTTAGTAA
1 TTTTACCCATCAGGGGTATTTCGGTAA
* * *
24167340 TTTTACCCTTC-GAGGGTATTTTGATAA
1 TTTTACCCATCAG-GGGTATTTCGGTAA
24167367 TTTTACC
1 TTTTACC
24167374 TATAAGGCCC
Statistics
Matches: 383, Mismatches: 43, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
26 27 0.07
27 352 0.92
28 4 0.01
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (27 bp):
TTTTACCCATCAGGGGTATTTCGGTAA
Found at i:24166999 original size:54 final size:54
Alignment explanation
Indices: 24166928--24167373 Score: 505
Period size: 54 Copynumber: 8.3 Consensus size: 54
24166918 ACAGGGATAC
* *
24166928 TTCGGTAATTTTGCCCATCAGGGGTATTTTAGTAATTTTACCCATCG-GAGGTAT
1 TTCGATAATTTTACCCATCAGGGGTATTTTAGTAATTTTACCCATCGAG-GGTAT
* * *
24166982 TTCGATAATTTTACCCATCAGGGGTA-TTTCGATAATTTTACCCATTGACGGTAT
1 TTCGATAATTTTACCCATCAGGGGTATTTTAG-TAATTTTACCCATCGAGGGTAT
* * *
24167036 TTCGATAATTTTACCTATC-GAGGGTA-TTTCGATAATTTTATCCATCGAGGGTAT
1 TTCGATAATTTTACCCATCAG-GGGTATTTTAG-TAATTTTACCCATCGAGGGTAT
* * * * *
24167090 TTCGATAATTTTACCTATCGGGGGTATTTCAGTAATTTTACCCATTGGGGGTAT
1 TTCGATAATTTTACCCATCAGGGGTATTTTAGTAATTTTACCCATCGAGGGTAT
* ** * *
24167144 TTCGATAATTTTACCCATCGGGGGTATTTCGGTAATTTTAACCATCGAAGGTAT
1 TTCGATAATTTTACCCATCAGGGGTATTTTAGTAATTTTACCCATCGAGGGTAT
* * *
24167198 TTCGATAATTTTACCCATC-GAGAGTA-TTTCGTAATTTTACCTATCGAGGGTAT
1 TTCGATAATTTTACCCATCAG-GGGTATTTTAGTAATTTTACCCATCGAGGGTAT
** *
24167251 TTC-AGTAATTTTACCCAT-AGAGGGTATTTCGGTAATTTTACCCTTCGAGGGTAT
1 TTCGA-TAATTTTACCCATCAG-GGGTATTTTAGTAATTTTACCCATCGAGGGTAT
* * *
24167305 TTC-AGTAATTTTACCCTTCAAGGGTATTTTAGTAATTTTACCCTTCGAGGGTAT
1 TTCGA-TAATTTTACCCATCAGGGGTATTTTAGTAATTTTACCCATCGAGGGTAT
*
24167359 TTTGATAATTTTACC
1 TTCGATAATTTTACC
24167374 TATAAGGCCC
Statistics
Matches: 345, Mismatches: 36, Indels: 22
0.86 0.09 0.05
Matches are distributed among these distances:
52 1 0.00
53 50 0.14
54 288 0.83
55 6 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (54 bp):
TTCGATAATTTTACCCATCAGGGGTATTTTAGTAATTTTACCCATCGAGGGTAT
Found at i:24167018 original size:81 final size:81
Alignment explanation
Indices: 24166909--24167373 Score: 472
Period size: 81 Copynumber: 5.8 Consensus size: 81
24166899 ATCATGGTCT
* * * *
24166909 TTTTACCC-TACAGGGATACTTCGGTAATTTTGCCCATC-AGGGGTATTTTAG-TAATTTTACCC
1 TTTTACCCAT-CAGGGGTATTTCGATAATTTTACCCATCGA-GGGTATTTTAGATAATTTTACCC
24166971 ATCGGAGGTATTTCGATAA
64 ATC-GAGGTATTTCGATAA
* * * *
24166990 TTTTACCCATCAGGGGTATTTCGATAATTTTACCCATTGACGGTA-TTTCGATAATTTTACCTAT
1 TTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAGATAATTTTACCCAT
24167054 CGAGGGTATTTCGATAA
66 CGA-GGTATTTCGATAA
* * * *
24167071 TTTTATCCATC-GAGGGTATTTCGATAATTTTACCTATCGGGGGTATTTCAG-TAATTTTACCCA
1 TTTTACCCATCAG-GGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAGATAATTTTACCCA
* *
24167134 TTGGGGGTATTTCGATAA
65 -TCGAGGTATTTCGATAA
* * * * *
24167152 TTTTACCCATCGGGGGTATTTCGGTAATTTTAACCATCGAAGGTA-TTTCGATAATTTTACCCAT
1 TTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAGATAATTTTACCCAT
24167216 CGAGAGTATTTCG-TAA
66 CGAG-GTATTTCGATAA
* * * *
24167232 TTTTACCTATC-GAGGGTATTTC-AGTAATTTTACCCATAGAGGGTA-TTTCGGTAATTTTACCC
1 TTTTACCCATCAG-GGGTATTTCGA-TAATTTTACCCATCGAGGGTATTTTAGATAATTTTACCC
*
24167294 TTCGAGGGTATTTC-AGTAA
64 ATCGA-GGTATTTCGA-TAA
* * * *
24167313 TTTTACCCTTCAAGGGTATTT-TAGTAATTTTACCCTTCGAGGGTATTTT-GATAATTTTACC
1 TTTTACCCATCAGGGGTATTTCGA-TAATTTTACCCATCGAGGGTATTTTAGATAATTTTACC
24167374 TATAAGGCCC
Statistics
Matches: 325, Mismatches: 41, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
79 1 0.00
80 80 0.25
81 233 0.72
82 11 0.03
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (81 bp):
TTTTACCCATCAGGGGTATTTCGATAATTTTACCCATCGAGGGTATTTTAGATAATTTTACCCAT
CGAGGTATTTCGATAA
Found at i:24173247 original size:11 final size:11
Alignment explanation
Indices: 24173231--24173264 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
24173221 GTGCAGATTC
24173231 AAAAAAA-CAA
1 AAAAAAATCAA
*
24173241 AAAAAAATCCA
1 AAAAAAATCAA
24173252 AAAAAAATCAA
1 AAAAAAATCAA
24173263 AA
1 AA
24173265 TCAAAGTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 7 0.33
11 14 0.67
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.06
Consensus pattern (11 bp):
AAAAAAATCAA
Found at i:24174173 original size:6 final size:6
Alignment explanation
Indices: 24174152--24174190 Score: 51
Period size: 6 Copynumber: 6.0 Consensus size: 6
24174142 AAAAAAAGGG
24174152 TGAAAA GTGAAAAA TGAAAA TGAAAAA TGAAAA TGAAAA
1 TGAAAA -TG-AAAA TGAAAA TG-AAAA TGAAAA TGAAAA
24174191 AGTAAAAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 16 0.53
7 10 0.33
8 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (6 bp):
TGAAAA
Found at i:24174191 original size:7 final size:7
Alignment explanation
Indices: 24174152--24174200 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
24174142 AAAAAAAGGG
*
24174152 TGAAAAG
1 TGAAAAA
24174159 TGAAAAA
1 TGAAAAA
24174166 TG-AAAA
1 TGAAAAA
24174172 TGAAAAA
1 TGAAAAA
24174179 TG-AAAA
1 TGAAAAA
24174185 TGAAAAA
1 TGAAAAA
24174192 -GTAAAAA
1 TG-AAAAA
24174199 TG
1 TG
24174201 GAGAGGCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
6 13 0.35
7 23 0.62
8 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:24174191 original size:20 final size:19
Alignment explanation
Indices: 24174152--24174200 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
24174142 AAAAAAAGGG
*
24174152 TGAAAAGTGAAAAATGAAAA
1 TGAAAAATG-AAAATGAAAA
24174172 TGAAAAATGAAAATGAAAA
1 TGAAAAATGAAAATGAAAA
*
24174191 AGTAAAAATG
1 TG-AAAAATG
24174201 GAGAGGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.65, C:0.00, G:0.18, T:0.16
Consensus pattern (19 bp):
TGAAAAATGAAAATGAAAA
Found at i:24174197 original size:13 final size:13
Alignment explanation
Indices: 24174152--24174191 Score: 71
Period size: 13 Copynumber: 3.0 Consensus size: 13
24174142 AAAAAAAGGG
24174152 TGAAAAGTGAAAAA
1 TGAAAA-TGAAAAA
24174166 TGAAAATGAAAAA
1 TGAAAATGAAAAA
24174179 TGAAAATGAAAAA
1 TGAAAATGAAAAA
24174192 GTAAAAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (13 bp):
TGAAAATGAAAAA
Found at i:24175772 original size:88 final size:88
Alignment explanation
Indices: 24175418--24175897 Score: 615
Period size: 88 Copynumber: 5.5 Consensus size: 88
24175408 CCCTAGGGAA
* * *
24175418 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACA-AAGCCTTGCCTCCATCGGTT
1 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTCGGTT
*
24175482 GCAGTGGAGCTGGTTAAAGATAG
66 GCAGTGGAGCAGGTTAAAGATAG
* * *
24175505 CAGATCTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAA-ACA-AAGCCTTGCCTCCATCGGTT
1 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTCGGTT
*
24175568 GCAGTGGAGCGGGTTAAAGATAG
66 GCAGTGGAGCAGGTTAAAGATAG
* * * * * *
24175591 TAGATCTTGCCTTCCTGCGTTGACAACAAAGCAGATCGAAGAAATAAAGCCTTGCCTCCCTCAGT
1 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGACA-CAAGCCTTGCCTCCCTCGGT
*
24175656 TGCAGTGGAGCAGGTTGAAGATAG
65 TGCAGTGGAGCAGGTTAAAGATAG
* * * * * *
24175680 CAGATCTTGCCTTCTTACGCTGACAACGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTCGGTT
1 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTCGGTT
* *
24175745 GCAGTGGAGTAGGTTAAAGATAA
66 GCAGTGGAGCAGGTTAAAGATAG
* * * *
24175768 CAGATCTTGCCTTCCTGCGTAGACAGTGAAGCGGATCGAAGACACCAGCCTTGCCTCCCTCGGTT
1 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTCGGTT
* *
24175833 GCAGTGGAGCAGGTTGAGGATAG
66 GCAGTGGAGCAGGTTAAAGATAG
* *** * *
24175856 CAAATCTTGCCTTCCTGTACTGACGGCAAAGCAGATCGAAGA
1 CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGA
24175898 TGGCAGATTT
Statistics
Matches: 347, Mismatches: 43, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
86 82 0.24
87 41 0.12
88 147 0.42
89 77 0.22
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCGTTGACAGCGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTCGGTT
GCAGTGGAGCAGGTTAAAGATAG
Found at i:24175916 original size:265 final size:261
Alignment explanation
Indices: 24175418--24175897 Score: 658
Period size: 263 Copynumber: 1.8 Consensus size: 261
24175408 CCCTAGGGAA
* * *
24175418 CAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
1 CAGATCTTGCCTTCCTACACTGACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
* *
24175483 CAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAACA
66 CAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGATCGAAACA
* * * **
24175548 AAGCCTTGCCTCCATCGGTTGCAGTGGAGCGGGTTAAAGATAGTAGATCTTGCCTTCCTGCGTTG
131 AAGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAATCTTGCCTTCCTGCACTG
*
24175613 ACAACAAAGCAGATCGAAGAAATAAAGCCTTGCCTCCCTCAGTTGCAGTGGAGCAGGTTGAAGAT
196 ACAACAAAGCAGATCGAAG-AATAAAGCCTTACCTCCCTCAGTTGCAGTGGAGCAGGTTGAAGAT
24175678 AG
260 AG
* * * *
24175680 CAGATCTTGCCTTCTTACGCTGACAACGAAGCAGATCGAAGATAC-CAGCCTTGCCTCCCTCGGT
1 CAGATCTTGCCTTCCTACACTGACAACGAAGCAGATCGAA-A-ACAAAGCCTTGCCTCCATCGGT
* ** *
24175744 TGCAGTGGAG-TAGGTTAAAGATAACAGATCTTGCCTTCCTGCGTAGACAGTGAAGCGGATCGAA
64 TGCAGTGGAGCT-GGTTAAAGATAACAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGATCGAA
* * * *
24175808 GACACCAGCCTTGCCTCCCTCGGTTGCAGTGGAGCAGGTTGAGGATAGCAAATCTTGCCTTCCTG
128 -ACA-AAGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAATCTTGCCTTCCTG
* **
24175873 TACTGACGGCAAAGCAGATCGAAGA
191 CACTGACAACAAAGCAGATCGAAGA
24175898 TGGCAGATTT
Statistics
Matches: 188, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
262 36 0.19
263 74 0.39
264 6 0.03
265 72 0.38
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.23
Consensus pattern (261 bp):
CAGATCTTGCCTTCCTACACTGACAACGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTG
CAGTGGAGCTGGTTAAAGATAACAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGATCGAAACA
AAGCCTTGCCTCCATCGGTTGCAGTGGAGCAGGTTAAAGATAGCAAATCTTGCCTTCCTGCACTG
ACAACAAAGCAGATCGAAGAATAAAGCCTTACCTCCCTCAGTTGCAGTGGAGCAGGTTGAAGATA
G
Found at i:24176145 original size:73 final size:74
Alignment explanation
Indices: 24176026--24176163 Score: 251
Period size: 73 Copynumber: 1.9 Consensus size: 74
24176016 AGCAGATCAA
*
24176026 AGACGGGGGATTTTACCTCCCTGTGGTTACAGTTGAGTACATTGAAGCCAGTAATTCTAT-TTCC
1 AGACGGGGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCC
24176090 CTAGGCAGC
66 CTAGGCAGC
*
24176099 AGACGGGGGATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCC
1 AGACGGGGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCC
24176164 TGAGTGGTGC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
73 58 0.94
74 4 0.06
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (74 bp):
AGACGGGGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCC
CTAGGCAGC
Found at i:24176236 original size:50 final size:50
Alignment explanation
Indices: 24176182--24176391 Score: 188
Period size: 50 Copynumber: 4.2 Consensus size: 50
24176172 GCAGTGGAAC
* * *
24176182 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTACAGTTAAAA
* ** * ** ** *
24176232 AGATTAAAGCTACAACAGCGAATCTTATTTCCCTGGA-AGAACAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCC-CGACATTACAGTTAAAA
* * * * *
24176282 AGATTAATGCCACAACGGCGAATCTTGCTTCTCCGACATTGCAATTAAAAA
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTACAGTT-AAAA
* * * * * *
24176333 AGATTAAAGCTACGACAGCGAATCTTGCTTCCTCAACATCACAGTTAAAC
1 AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTACAGTTAAAA
24176383 AGATTAAAG
1 AGATTAAAG
24176392 TTACGAGTTA
Statistics
Matches: 120, Mismatches: 37, Indels: 6
0.74 0.23 0.04
Matches are distributed among these distances:
49 2 0.02
50 78 0.65
51 40 0.33
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTTGCTTCCCCGACATTACAGTTAAAA
Found at i:24176295 original size:100 final size:101
Alignment explanation
Indices: 24176173--24176358 Score: 302
Period size: 100 Copynumber: 1.9 Consensus size: 101
24176163 CTGAGTGGTG
* * *
24176173 CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTT-AAAAAGATT
1 CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAATTAAAAAAGATT
24176237 AAAGCTACAACAGCGAATCTTATTTCCCTGGAAGAA
66 AAAGCTACAACAGCGAATCTTATTTCCCTGGAAGAA
* * *
24176273 CAGTGGAACAGATTAATGCCACAACGGCGAATCTTGCTTCTCCGACATTGCAATTAAAAAAGATT
1 CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAATTAAAAAAGATT
*
24176338 AAAGCTACGACAGCGAATCTT
66 AAAGCTACAACAGCGAATCTT
24176359 GCTTCCTCAA
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 49 0.63
101 29 0.37
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (101 bp):
CAGTGGAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAATTAAAAAAGATT
AAAGCTACAACAGCGAATCTTATTTCCCTGGAAGAA
Found at i:24176388 original size:101 final size:100
Alignment explanation
Indices: 24176173--24176391 Score: 271
Period size: 100 Copynumber: 2.2 Consensus size: 100
24176163 CTGAGTGGTG
* * * *
24176173 CAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTACAGTTAAAAAGATTA
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAATTAAAAAGATTA
* * *
24176238 AAGCTACAACAGCGAATCTTATTTCCCTGGAAGAA
66 AAGCTACAACAGCGAATCTTACTTCCCTGCAACAA
* * * *
24176273 CAGTGGAACAGATTAATGCCACAACGGCGAATCTTGCTTCTCCGACATTGCAATTAAAAAAGATT
1 CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAATT-AAAAAGATT
* *
24176338 AAAGCTACGACAGCGAATCTTGCTT-CCT-CAACATCA
65 AAAGCTACAACAGCGAATCTTACTTCCCTGCAACA--A
*
24176374 CAGTTAAACAGATTAAAG
1 CAGTGAAACAGATTAAAG
24176392 TTACGAGTTA
Statistics
Matches: 102, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
99 3 0.03
100 52 0.51
101 47 0.46
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (100 bp):
CAGTGAAACAGATTAAAGCCACAACGGCGAATCTTGCTTCCCCGACATTACAATTAAAAAGATTA
AAGCTACAACAGCGAATCTTACTTCCCTGCAACAA
Found at i:24185205 original size:13 final size:13
Alignment explanation
Indices: 24185189--24185236 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
24185179 TTCATTTAGC
*
24185189 TTTTTTATTTTAA
1 TTTTTCATTTTAA
*
24185202 -TTTTAATTTTAA
1 TTTTTCATTTTAA
*
24185214 TTTTTCATTATAA
1 TTTTTCATTTTAA
24185227 TTTTTCATTT
1 TTTTTCATTT
24185237 GTTTGTTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTCATTTTAA
Found at i:24188227 original size:6 final size:6
Alignment explanation
Indices: 24188187--24188220 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
24188177 TGTTTTTGTT
*
24188187 TTTTTC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTT
24188221 TACTTTTTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.15, G:0.12, T:0.74
Consensus pattern (6 bp):
TTTTGC
Found at i:24207887 original size:4 final size:4
Alignment explanation
Indices: 24207864--24207904 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
24207854 AATCCTAGTC
*
24207864 AAAT AAAA AAAT -AA- AAAT AAAT AAAT AAAT AAGAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AA
24207905 GTACAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 4 0.12
4 24 0.75
5 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:24207913 original size:13 final size:12
Alignment explanation
Indices: 24207864--24207904 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 12
24207854 AATCCTAGTC
*
24207864 AAATAAAAAAAT
1 AAATAAATAAAT
24207876 -AA-AAATAAAT
1 AAATAAATAAAT
24207886 AAATAAATAAGAT
1 AAATAAATAA-AT
24207899 AAATAA
1 AAATAA
24207905 GTACAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.28
11 4 0.16
12 6 0.24
13 8 0.32
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (12 bp):
AAATAAATAAAT
Found at i:24209521 original size:15 final size:14
Alignment explanation
Indices: 24209501--24209550 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
24209491 AATTATATTT
24209501 TTAATAGATTTTTTA
1 TTAATA-ATTTTTTA
24209516 TTAAT-ATTTTTTA
1 TTAATAATTTTTTA
**
24209529 AAAAT-ATTTTTTA
1 TTAATAATTTTTTA
*
24209542 TTAAAAATT
1 TTAATAATT
24209551 AATTCGTGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 21 0.72
14 3 0.10
15 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TTAATAATTTTTTA
Found at i:24209524 original size:13 final size:13
Alignment explanation
Indices: 24209508--24209545 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
24209498 TTTTTAATAG
24209508 ATTTTTTATTAAT
1 ATTTTTTATTAAT
**
24209521 ATTTTTTAAAAAT
1 ATTTTTTATTAAT
24209534 ATTTTTTATTAA
1 ATTTTTTATTAA
24209546 AAATTAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTTTTTATTAAT
Found at i:24211774 original size:32 final size:32
Alignment explanation
Indices: 24211731--24211842 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
24211721 TTTTAAATGA
24211731 ATATTT-TTATCATTTAACAAAATTAAAGTTG
1 ATATTTGTTATCATTTAACAAAATTAAAGTTG
* *
24211762 ATATTTGTTATCATTTTACAAAATTAACGTTG
1 ATATTTGTTATCATTTAACAAAATTAAAGTTG
* * * *
24211794 -TAATTTATTATCATTTCACAAAATGAAAACTTG
1 AT-ATTTGTTATCATTTAACAAAAT-TAAAGTTG
*
24211827 AAATTTGTTATCATTT
1 ATATTTGTTATCATTT
24211843 CATAGAACCG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
31 7 0.10
32 43 0.63
33 18 0.26
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.46
Consensus pattern (32 bp):
ATATTTGTTATCATTTAACAAAATTAAAGTTG
Found at i:24217648 original size:17 final size:19
Alignment explanation
Indices: 24217626--24217707 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 19
24217616 TATGGAAACA
24217626 TAATCTT-CA-AGGATATG
1 TAATCTTACATAGGATATG
* *
24217643 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
* *
24217662 TAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
* * *
24217681 CAATCTTAGATATGATATG
1 TAATCTTACATAGGATATG
24217700 TAATCTTA
1 TAATCTTA
24217708 GAAGATATGA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
17 7 0.12
18 1 0.02
19 51 0.86
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (19 bp):
TAATCTTACATAGGATATG
Found at i:24217661 original size:19 final size:19
Alignment explanation
Indices: 24217637--24217732 Score: 138
Period size: 19 Copynumber: 4.8 Consensus size: 19
24217627 AATCTTCAAG
24217637 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
24217656 GATATGTAATCTTAGATAT
1 GATATGTAATCTTAGATAT
*
24217675 GATATGCAATCTTAGATAT
1 GATATGTAATCTTAGATAT
24217694 GATATGTAATCTTAGAAGATAT
1 GATATGTAATCTT---AGATAT
*
24217716 GATTTTGTAATCTTAGA
1 GA-TATGTAATCTTAGA
24217733 GATTTAATTT
Statistics
Matches: 70, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
19 49 0.70
20 3 0.04
22 8 0.11
23 10 0.14
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.41
Consensus pattern (19 bp):
GATATGTAATCTTAGATAT
Found at i:24217742 original size:22 final size:23
Alignment explanation
Indices: 24217698--24217742 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
24217688 AGATATGATA
*
24217698 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
24217721 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
24217743 GTAGATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:24218204 original size:3 final size:3
Alignment explanation
Indices: 24218198--24218250 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
24218188 CATAATAATA
24218198 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24218246 ATT AT
1 ATT AT
24218251 ATTCATGTGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:24218575 original size:8 final size:8
Alignment explanation
Indices: 24218529--24218576 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
24218519 TTTTCAACAC
24218529 ATATGTTAT
1 ATAT-TTAT
*
24218538 AATATATAT
1 -ATATTTAT
* *
24218547 ATATATGT
1 ATATTTAT
24218555 ATATTTAT
1 ATATTTAT
24218563 ATATTTAT
1 ATATTTAT
24218571 ATATTT
1 ATATTT
24218577 TTCTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 27 0.79
9 3 0.09
10 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (8 bp):
ATATTTAT
Found at i:24219297 original size:79 final size:79
Alignment explanation
Indices: 24219108--24219268 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 79
24219098 ACAAATATTT
* *
24219108 TTTTTAAAAAAATAATAACAAAGGAAATATTCCAAGTTTAGGATTTTGAGAAATTGTGCCCTAAC
1 TTTTTAAAAAAATAATAACAAATGAAATATTCCAAGTTTAGAATTTTGAGAAATTGTGCCCTAAC
24219173 GTATTGGGCCGCAA
66 GTATTGGGCCGCAA
24219187 TTTTTAAAAAAATAATAACAAATGAAATATTCCAAGTTTAGAATTTTGAGAAATTGTGCCCTAAC
1 TTTTTAAAAAAATAATAACAAATGAAATATTCCAAGTTTAGAATTTTGAGAAATTGTGCCCTAAC
24219252 GTATTGGGCCGCAA
66 GTATTGGGCCGCAA
24219266 TTT
1 TTT
24219269 CTTTCTAAAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.32
Consensus pattern (79 bp):
TTTTTAAAAAAATAATAACAAATGAAATATTCCAAGTTTAGAATTTTGAGAAATTGTGCCCTAAC
GTATTGGGCCGCAA
Found at i:24222618 original size:13 final size:13
Alignment explanation
Indices: 24222600--24222624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24222590 CTAGGATCTA
24222600 AAACACAAGCAAC
1 AAACACAAGCAAC
24222613 AAACACAAGCAA
1 AAACACAAGCAA
24222625 ATTCATCTTA
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:0.64, C:0.28, G:0.08, T:0.00
Consensus pattern (13 bp):
AAACACAAGCAAC
Found at i:24224177 original size:22 final size:22
Alignment explanation
Indices: 24224152--24224200 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
24224142 ATCATGTATG
*
24224152 GTTCTGTCATTCGAGCTCCTAT
1 GTTCTGTCATCCGAGCTCCTAT
24224174 GTTCTGTCATCCGAGCTCCTAT
1 GTTCTGTCATCCGAGCTCCTAT
24224196 GTTCT
1 GTTCT
24224201 TCCTTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (22 bp):
GTTCTGTCATCCGAGCTCCTAT
Found at i:24225498 original size:46 final size:46
Alignment explanation
Indices: 24225405--24225502 Score: 144
Period size: 46 Copynumber: 2.1 Consensus size: 46
24225395 TTTCTAATTT
* *
24225405 TTTGTGTGATTCAATGGATTGGGTTTATTTTGGGAGTGGATCGGTG
1 TTTGTGTGAGTCAATGGATTGGGTTTATTTTGGGAGTGGATCAGTG
* *
24225451 TTTGTGTGAGTCAGTGGATTGGGTTTATTTTGGGAGTAGG-TTAGTG
1 TTTGTGTGAGTCAATGGATTGGGTTTATTTTGGGAGT-GGATCAGTG
24225497 TTTGTG
1 TTTGTG
24225503 GCCTGGTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
46 45 0.96
47 2 0.04
ACGTcount: A:0.14, C:0.03, G:0.38, T:0.45
Consensus pattern (46 bp):
TTTGTGTGAGTCAATGGATTGGGTTTATTTTGGGAGTGGATCAGTG
Found at i:24225805 original size:30 final size:30
Alignment explanation
Indices: 24225770--24225842 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
24225760 TTTTCAGTGG
*
24225770 CACACGGCCGTGTCACTAGCTCGTATGTGA
1 CACACGGCCGTGTCACTAACTCGTATGTGA
**
24225800 CACACGGCCAAGTCACTAACTCGTATGTGA
1 CACACGGCCGTGTCACTAACTCGTATGTGA
* *
24225830 GACATGGCCGTGT
1 CACACGGCCGTGT
24225843 GGCCAGATCG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.23, C:0.29, G:0.26, T:0.22
Consensus pattern (30 bp):
CACACGGCCGTGTCACTAACTCGTATGTGA
Found at i:24238555 original size:46 final size:46
Alignment explanation
Indices: 24238497--24238588 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
24238487 CCCAGATGCT
24238497 TAGATACCTATCCCAACTTATAGCACATGATCACAAGACCCTAAAA
1 TAGATACCTATCCCAACTTATAGCACATGATCACAAGACCCTAAAA
*
24238543 TAGATACTTATCCCAACTTATAGCACATGATCACAAGACCCTAAAA
1 TAGATACCTATCCCAACTTATAGCACATGATCACAAGACCCTAAAA
24238589 CCCATTCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.27, G:0.09, T:0.23
Consensus pattern (46 bp):
TAGATACCTATCCCAACTTATAGCACATGATCACAAGACCCTAAAA
Found at i:24243004 original size:10 final size:10
Alignment explanation
Indices: 24242989--24243015 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
24242979 TTAAGTTTAG
24242989 TGTGTTTAAA
1 TGTGTTTAAA
24242999 TGTGTTTAAA
1 TGTGTTTAAA
24243009 TGTGTTT
1 TGTGTTT
24243016 GTTAATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (10 bp):
TGTGTTTAAA
Found at i:24263736 original size:5 final size:5
Alignment explanation
Indices: 24263726--24263799 Score: 148
Period size: 5 Copynumber: 14.8 Consensus size: 5
24263716 TAATACATGC
24263726 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
24263776 ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATAT
24263800 ACAATATTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 69 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:24267328 original size:14 final size:14
Alignment explanation
Indices: 24267311--24267340 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
24267301 AATGGTTTGG
*
24267311 GAAAAATAAAATGA
1 GAAAAATAAAAAGA
24267325 GAAAAATAAAAAGA
1 GAAAAATAAAAAGA
24267339 GA
1 GA
24267341 TTCCAGGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (14 bp):
GAAAAATAAAAAGA
Found at i:24267692 original size:20 final size:19
Alignment explanation
Indices: 24267667--24267714 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
24267657 TAAAATTATA
24267667 ATTTTTAGTTTTTGTATTTC
1 ATTTTTA-TTTTTGTATTTC
24267687 ATTTTTATTTTTGTATTTC
1 ATTTTTATTTTTGTATTTC
24267706 -TTTTT-TTTT
1 ATTTTTATTTT
24267715 GTTATAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.14
18 5 0.18
19 12 0.43
20 7 0.25
ACGTcount: A:0.12, C:0.04, G:0.06, T:0.77
Consensus pattern (19 bp):
ATTTTTATTTTTGTATTTC
Found at i:24268355 original size:7 final size:7
Alignment explanation
Indices: 24268343--24268517 Score: 88
Period size: 7 Copynumber: 24.6 Consensus size: 7
24268333 ATTATTCCTC
24268343 AAACCCT
1 AAACCCT
24268350 AAACCCCT
1 AAA-CCCT
24268358 -AACCCT
1 AAACCCT
*
24268364 TAACCCT
1 AAACCCT
*
24268371 TAACCACT
1 AAACC-CT
24268379 -AACCCTT
1 AAACCC-T
24268386 AAACCCT
1 AAACCCT
*
24268393 AAACCTT
1 AAACCCT
*
24268400 AAACCCC
1 AAACCCT
* *
24268407 AATCCTT
1 AAACCCT
*
24268414 AAACCAT
1 AAACCCT
*
24268421 AAACCAT
1 AAACCCT
*
24268428 AATCCCT
1 AAACCCT
24268435 AAACCCAT
1 AAACCC-T
* *
24268443 AATCCAT
1 AAACCCT
*
24268450 AAACCTT
1 AAACCCT
*
24268457 AAA--AT
1 AAACCCT
*
24268462 AGTAACTCTT
1 A--AAC-CCT
*
24268472 AAACCTT
1 AAACCCT
24268479 AAACCCT
1 AAACCCT
*
24268486 AAACCAT
1 AAACCCT
* *
24268493 ATACCTT
1 AAACCCT
*
24268500 AAACCAT
1 AAACCCT
24268507 AAACCCT
1 AAACCCT
24268514 AAAC
1 AAAC
24268518 TATAATGGTC
Statistics
Matches: 133, Mismatches: 24, Indels: 22
0.74 0.13 0.12
Matches are distributed among these distances:
5 2 0.02
6 5 0.04
7 105 0.79
8 19 0.14
10 2 0.02
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:24268678 original size:14 final size:14
Alignment explanation
Indices: 24268661--24268715 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
24268651 CATAAAACAA
24268661 AAACCATAAACCTT
1 AAACCATAAACCTT
* *
24268675 AAACCCTTAACCCTT
1 AAA-CCATAAACCTT
* * *
24268690 AAATCACAACCCTT
1 AAACCATAAACCTT
24268704 AAACCATAAACC
1 AAACCATAAACC
24268716 ATAATCCTTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCATAAACCTT
Found at i:24268713 original size:21 final size:21
Alignment explanation
Indices: 24268661--24268734 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
24268651 CATAAAACAA
24268661 AAACCATAAACCTTA-AACCCTT
1 AAACCATAAACC--ACAACCCTT
* * *
24268683 AACCCTTAAATCACAACCCTT
1 AAACCATAAACCACAACCCTT
* *
24268704 AAACCATAAACCATAATCCTT
1 AAACCATAAACCACAACCCTT
*
24268725 AAATCATAAA
1 AAACCATAAA
24268735 GCTCAATCTA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
20 1 0.02
21 32 0.76
22 9 0.21
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (21 bp):
AAACCATAAACCACAACCCTT
Found at i:24268796 original size:40 final size:39
Alignment explanation
Indices: 24268735--24269278 Score: 235
Period size: 40 Copynumber: 14.0 Consensus size: 39
24268725 AAATCATAAA
* *
24268735 GCTCAATCTATAACGGCGTTTTTCAAAAGCTGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTCAAAAGC-GCCGCTAAT
* *
24268775 GCTCGATCTATAGCGGTGTTTTTCAAGATGCGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTCAA-AAGCGCCGCTAAT
* * * * * *
24268815 ACTCGATCTATAGCTGCGTTTTTGAAAAACACAGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTCAAAAGCGCCGCTAAT
* * ** * **
24268854 GC-C-A-CTA-A--AGC-----TCAAATG-GTAGTGTTGT
1 GCTCGATCTATAGCGGCGTTTTTCAAAAGCGCCG-CTAAT
** * * * *
24268882 GCTTAATTTTTTTGCGGCATTTTTCAAAAAGCGCCGCTAAT
1 GCTCGA-TCTATAGCGGCGTTTTTC-AAAAGCGCCGCTAAT
* * * * *
24268923 GGTTGACCTATAGCGGCGCTTTTTCAAAAAGCACTGCTAAT
1 GCTCGATCTATAGCGGCG-TTTTTC-AAAAGCGCCGCTAAT
*
24268964 GCTCGATCTATAGCGGCATTTTTCAAGAAGCGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTCAA-AAGCGCCGCTAAT
24269004 GCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTCAA-AAGCGCCGCTAAT
** **
24269044 GCTCGATCTATAGCAACGTTTTTCAAAAAATGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTC-AAAAGCGCCGCTAAT
* * **** ** * **
24269084 GC-C-A-CTAAAGC-TC-AACAT-AAAA-CGATGGTGTTGT
1 GCTCGATCTATAGCGGCGTTTTTCAAAAGCG-CCG-CTAAT
** * * * ** * *
24269118 GCTTAATTTTTTTTGCTACGTTTTTTAAAAAGCGCTGCTAAT
1 GCTCGA--TCTATAGCGGCG-TTTTTCAAAAGCGCCGCTAAT
* * *
24269160 GGTCGACCTATAGCGACGTTTTTCAAAAAGCGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTC-AAAAGCGCCGCTAAT
* * *
24269200 GCTCGATCTGTAACGGTGTTTTTCAAGAAGCGCCGCTAAT
1 GCTCGATCTATAGCGGCGTTTTTCAA-AAGCGCCGCTAAT
* * *
24269240 GCTCAACCTATAGCGGCGTTTTTTAAAAAGCGCCGCTAA
1 GCTCGATCTATAGCGGCG-TTTTTCAAAAGCGCCGCTAA
24269279 AAATGTCGCT
Statistics
Matches: 368, Mismatches: 102, Indels: 68
0.68 0.19 0.13
Matches are distributed among these distances:
27 2 0.01
28 8 0.02
30 1 0.00
32 2 0.01
33 7 0.02
34 4 0.01
35 4 0.01
36 5 0.01
37 7 0.02
38 2 0.01
39 23 0.06
40 232 0.63
41 56 0.15
42 8 0.02
43 5 0.01
44 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (39 bp):
GCTCGATCTATAGCGGCGTTTTTCAAAAGCGCCGCTAAT
Found at i:24269000 original size:81 final size:80
Alignment explanation
Indices: 24268895--24269278 Score: 278
Period size: 80 Copynumber: 4.8 Consensus size: 80
24268885 TAATTTTTTT
* * *
24268895 GCGGCATTTTTCAAAAAGCGCCGCTAATGGTTGACCTATAGCGGCGCTTTTTCAAAAAGCACTGC
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCG-TTTTTCAAAAAGCACCGC
24268960 TAATGCTCGATCTATA
65 TAATGCTCGATCTATA
* * * *
24268976 GCGGCATTTTTCAAGAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCT
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCT
24269041 AATGCTCGATCTATA
66 AATGCTCGATCTATA
** * ** * * **** * ** *
24269056 GCAACGTTTTTCAAAAAATGCCGCTAATGC-C-A-CTAAAGC-TC-AACAT-AAAACG-ATGGTG
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAAAAGCACCG-C
** ** * * *
24269114 TTGTGCTTAATTTTTTTT
65 TAATGCTCGA--TCTATA
** * * * * * *
24269132 GCTACGTTTTTTAAAAAGCGCTGCTAATGGTCGACCTATAGCGACGTTTTTCAAAAAGCGCCGCT
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCT
*
24269197 AATGCTCGATCTGTA
66 AATGCTCGATCTATA
* ** * * * *
24269212 ACGGTGTTTTTCAAGAAGCGCCGCTAATGCTCAACCTATAGCGGCGTTTTTTAAAAAGCGCCGCT
1 GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCT
24269277 AA
66 AA
24269279 AAATGTCGCT
Statistics
Matches: 226, Mismatches: 67, Indels: 21
0.72 0.21 0.07
Matches are distributed among these distances:
73 1 0.00
74 10 0.04
75 1 0.00
76 28 0.12
77 7 0.03
78 2 0.01
79 7 0.03
80 115 0.51
81 43 0.19
82 11 0.05
83 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (80 bp):
GCGGCATTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCT
AATGCTCGATCTATA
Found at i:24279843 original size:6 final size:6
Alignment explanation
Indices: 24279832--24279876 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
24279822 GTCTCTCAGC
* *
24279832 AAAATA AAAATA AAAATA AATAATA AGAA-A AAAATA AAATTA AAA
1 AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA AAA
24279877 TGTGTATTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 4 0.12
6 25 0.74
7 5 0.15
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:24289449 original size:41 final size:41
Alignment explanation
Indices: 24289378--24289476 Score: 128
Period size: 41 Copynumber: 2.4 Consensus size: 41
24289368 TTTTCAAATA
* * *
24289378 CAACCTTTCCATTTGTTATCCTATATGGATAACTCCCTTTT
1 CAACATTTTCATTTGTTATCCTATACGGATAACTCCCTTTT
* *
24289419 CCACATTTTCATTTGTTATCC-ATTACGGATAACTTCCTTTT
1 CAACATTTTCATTTGTTATCCTA-TACGGATAACTCCCTTTT
*
24289460 CAACCTTTTCATTTGTT
1 CAACATTTTCATTTGTT
24289477 CAGAAATGCG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 1 0.02
41 49 0.98
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.46
Consensus pattern (41 bp):
CAACATTTTCATTTGTTATCCTATACGGATAACTCCCTTTT
Found at i:24291452 original size:14 final size:14
Alignment explanation
Indices: 24291433--24291462 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
24291423 AATGTATACT
24291433 TGAAACTCTAATTG
1 TGAAACTCTAATTG
24291447 TGAAACTCTAATTG
1 TGAAACTCTAATTG
24291461 TG
1 TG
24291463 GTTCAAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (14 bp):
TGAAACTCTAATTG
Found at i:24291677 original size:29 final size:30
Alignment explanation
Indices: 24291634--24291715 Score: 103
Period size: 29 Copynumber: 2.7 Consensus size: 30
24291624 GAATTGGATC
*
24291634 AAATCAAAATTTCATGTATAAAATTGCACA-
1 AAATC-AAAGTTCATGTATAAAATTGCACAT
*
24291664 AAATCAAAGTTCATGTATACAATTGCACATT
1 AAATCAAAGTTCATGTATAAAATTGCACA-T
* *
24291695 AAACCATAGTTCATGTATAAA
1 AAATCAAAGTTCATGTATAAA
24291716 TTTGGTATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 22 0.49
30 5 0.11
31 18 0.40
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.30
Consensus pattern (30 bp):
AAATCAAAGTTCATGTATAAAATTGCACAT
Found at i:24297279 original size:3 final size:3
Alignment explanation
Indices: 24297271--24297305 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
24297261 AATTTTTATA
24297271 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
24297306 AAGTATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24297477 original size:21 final size:21
Alignment explanation
Indices: 24297453--24297505 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
24297443 AACGGTGGCG
*
24297453 GTGAGATTAGTTACTGTAGCA
1 GTGAGATTAGATACTGTAGCA
* *
24297474 GTGAGATTGGATACTGTAGCG
1 GTGAGATTAGATACTGTAGCA
*
24297495 GTGAAATTAGA
1 GTGAGATTAGA
24297506 AACAATGGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.32, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACTGTAGCA
Found at i:24302212 original size:9 final size:9
Alignment explanation
Indices: 24302189--24302239 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
24302179 AAGTTAAATG
*
24302189 AATCAAGTT
1 AATCGAGTT
*
24302198 ATTCGAGTT
1 AATCGAGTT
24302207 AATCGAGTT
1 AATCGAGTT
*
24302216 ATTCGAGTT
1 AATCGAGTT
24302225 AATCGAGTT
1 AATCGAGTT
*
24302234 ATTCGA
1 AATCGA
24302240 ATCAACTCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 36 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (9 bp):
AATCGAGTT
Found at i:24302215 original size:18 final size:18
Alignment explanation
Indices: 24302189--24302239 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
24302179 AAGTTAAATG
*
24302189 AATCAAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
24302207 AATCGAGTTATTCGAGTT
1 AATCGAGTTATTCGAGTT
24302225 AATCGAGTTATTCGA
1 AATCGAGTTATTCGA
24302240 ATCAACTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (18 bp):
AATCGAGTTATTCGAGTT
Found at i:24319129 original size:9 final size:9
Alignment explanation
Indices: 24319115--24319142 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
24319105 TATAGTTTGA
24319115 TATTCGAAT
1 TATTCGAAT
24319124 TATTCGAAT
1 TATTCGAAT
24319133 TATTCGAAT
1 TATTCGAAT
24319142 T
1 T
24319143 CGAAAACTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:24319214 original size:9 final size:9
Alignment explanation
Indices: 24319197--24319227 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
24319187 TCGAGTTGAT
24319197 TCGAATAAC
1 TCGAATAAC
*
24319206 TCGATTAAC
1 TCGAATAAC
24319215 TCGAATAAC
1 TCGAATAAC
24319224 TCGA
1 TCGA
24319228 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:24320018 original size:19 final size:20
Alignment explanation
Indices: 24319947--24320046 Score: 64
Period size: 19 Copynumber: 5.2 Consensus size: 20
24319937 GAAGAAATTC
24319947 AAATATTATA-AAATTTATA
1 AAATATTATAGAAATTTATA
* * * ** *
24319966 AAAAATTAAAAAAAGATACA
1 AAATATTATAGAAATTTATA
** *
24319986 AAA-ATCGTAAAAATTTATA
1 AAATATTATAGAAATTTATA
*
24320005 AAATA-TATAGAAATATA-A
1 AAATATTATAGAAATTTATA
* *
24320023 AAAAATTATAGAATTTTATA
1 AAATATTATAGAAATTTATA
24320043 AAAT
1 AAAT
24320047 TGAAAATTAT
Statistics
Matches: 58, Mismatches: 19, Indels: 7
0.69 0.23 0.08
Matches are distributed among these distances:
18 5 0.09
19 39 0.67
20 14 0.24
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
AAATATTATAGAAATTTATA
Found at i:24320027 original size:38 final size:39
Alignment explanation
Indices: 24319956--24320046 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 39
24319946 CAAATATTAT
* * *
24319956 AAAATTTATAAAAAATTAAAAAAAGATACAAAAATCGTA
1 AAAATTTATAAAATATTAAAAAAAGATAAAAAAATCATA
* * * *
24319995 AAAATTTATAAAATA-TATAGAAATATAAAAAAATTATA
1 AAAATTTATAAAATATTAAAAAAAGATAAAAAAATCATA
* *
24320033 GAATTTTATAAAAT
1 AAAATTTATAAAAT
24320047 TGAAAATTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
38 29 0.67
39 14 0.33
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (39 bp):
AAAATTTATAAAATATTAAAAAAAGATAAAAAAATCATA
Found at i:24326296 original size:27 final size:28
Alignment explanation
Indices: 24326231--24326300 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
24326221 GGATAATGAG
*
24326231 ATTGTTGGATTTTGATATATGTCTTGAA
1 ATTGTTGGATATTGATATATGTCTTGAA
* * * *
24326259 TTTTTTAGATATTGAT-TATGT-TTTAA
1 ATTGTTGGATATTGATATATGTCTTGAA
24326285 CATTGTTGGATATTGA
1 -ATTGTTGGATATTGA
24326301 ATTGATTATT
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
26 4 0.12
27 17 0.52
28 12 0.36
ACGTcount: A:0.26, C:0.03, G:0.19, T:0.53
Consensus pattern (28 bp):
ATTGTTGGATATTGATATATGTCTTGAA
Found at i:24327706 original size:14 final size:14
Alignment explanation
Indices: 24327683--24327724 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
24327673 ACAGAAAAGT
*
24327683 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
24327697 AAATCATTTTACGG
1 AAAACATTTTACAG
24327711 AAAACATTTTACAG
1 AAAACATTTTACAG
24327725 CCAATCAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.31
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:24333173 original size:45 final size:45
Alignment explanation
Indices: 24333124--24333380 Score: 300
Period size: 45 Copynumber: 5.7 Consensus size: 45
24333114 CTGGCAAAAA
* * * *
24333124 AAGATTCATAGATATGGTGAACTCATACATGCGGTTTCATGGTAG
1 AAGATTCATAGATATGGCGAACTCATACATGCGGATTCATAGAAG
* * * *
24333169 AAGATTCAT-GAATATGGCAAACTCGTATATGCGGATTCATAGTAG
1 AAGATTCATAG-ATATGGCGAACTCATACATGCGGATTCATAGAAG
* * *
24333214 AAGATTCATAGATATGACGAACTCATACATGTGGATTCATAGCAG
1 AAGATTCATAGATATGGCGAACTCATACATGCGGATTCATAGAAG
* * * *
24333259 AAGATTTATAGATATGGTGGACTCATACATGCGGATTCATAGAAA
1 AAGATTCATAGATATGGCGAACTCATACATGCGGATTCATAGAAG
** * *
24333304 AAGATTCATAGATATGATGGACTCATACATGCGGATTCATAAAAG
1 AAGATTCATAGATATGGCGAACTCATACATGCGGATTCATAGAAG
* * *
24333349 AAGATTCATAAATATGGCGGACTAATACATGC
1 AAGATTCATAGATATGGCGAACTCATACATGC
24333381 AAACTGTGTC
Statistics
Matches: 183, Mismatches: 27, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
44 1 0.01
45 181 0.99
46 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (45 bp):
AAGATTCATAGATATGGCGAACTCATACATGCGGATTCATAGAAG
Found at i:24333340 original size:135 final size:133
Alignment explanation
Indices: 24333124--24333379 Score: 334
Period size: 135 Copynumber: 1.9 Consensus size: 133
24333114 CTGGCAAAAA
* * * *
24333124 AAGATTCATAGATATGGTGAACTCATACATGCGGTTTCATGGTAGAAGATTCATGAATATGGCAA
1 AAGATTCATAGATATGGTGAACTCATACATGCGGATTCATAGAAAAAGATTCATGAATATGG--A
* * ** * *
24333189 ACTCGTATATGCGGATTCATAGTAGAAGATTCATAGATATGACGAACTCATACATGTGGATTCAT
64 ACTCATACATGCGGATTCATAAAAGAAGATTCATAAATATGACGAACTAATACATGTGGATTCAT
24333254 AGCAG
129 AGCAG
* *
24333259 AAGATTTATAGATATGGTGGACTCATACATGCGGATTCATAGAAAAAGATTCATAGATATGATGG
1 AAGATTCATAGATATGGTGAACTCATACATGCGGATTCATAGAAAAAGATTCAT-GA-AT-ATGG
* *
24333324 -ACTCATACATGCGGATTCATAAAAGAAGATTCATAAATATGGCGGACTAATACATG
63 AACTCATACATGCGGATTCATAAAAGAAGATTCATAAATATGACGAACTAATACATG
24333380 CAAACTGTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
135 96 0.92
136 2 0.02
137 2 0.02
138 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.28
Consensus pattern (133 bp):
AAGATTCATAGATATGGTGAACTCATACATGCGGATTCATAGAAAAAGATTCATGAATATGGAAC
TCATACATGCGGATTCATAAAAGAAGATTCATAAATATGACGAACTAATACATGTGGATTCATAG
CAG
Found at i:24333608 original size:13 final size:13
Alignment explanation
Indices: 24333590--24333623 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
24333580 ATATATCTCA
24333590 GTACAATCCAATC
1 GTACAATCCAATC
24333603 GTACAATCCAATC
1 GTACAATCCAATC
24333616 GTACAATC
1 GTACAATC
24333624 GCAAAACCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.29, G:0.09, T:0.24
Consensus pattern (13 bp):
GTACAATCCAATC
Found at i:24339977 original size:11 final size:12
Alignment explanation
Indices: 24339956--24339994 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
24339946 AATAGAGGAC
*
24339956 TAAATTGAAATT
1 TAAAGTGAAATT
24339968 TAAA-TGAAATT
1 TAAAGTGAAATT
*
24339979 TAAAGTGAAAAT
1 TAAAGTGAAATT
24339991 TAAA
1 TAAA
24339995 AAAAAAAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.33
Consensus pattern (12 bp):
TAAAGTGAAATT
Found at i:24341170 original size:23 final size:23
Alignment explanation
Indices: 24341141--24341185 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
24341131 TTGGGCTTCT
24341141 GGGTAGTTTAGGTAATTGGGCTA
1 GGGTAGTTTAGGTAATTGGGCTA
24341164 GGGTAGTTTAGGTAATTGGGCT
1 GGGTAGTTTAGGTAATTGGGCT
24341186 TGTAAATGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.04, G:0.40, T:0.36
Consensus pattern (23 bp):
GGGTAGTTTAGGTAATTGGGCTA
Found at i:24341270 original size:2 final size:2
Alignment explanation
Indices: 24341263--24341290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24341253 GGCCATTACA
24341263 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
24341291 GTAATTAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24346932 original size:98 final size:98
Alignment explanation
Indices: 24346763--24346954 Score: 348
Period size: 98 Copynumber: 2.0 Consensus size: 98
24346753 AATAAAAATA
24346763 TTAAAAGAACATCCACTTATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCCT
1 TTAAAAGAACATCCACTTATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCCT
24346828 TTAGAATCCCGAACTCGGAATATTTCCTTTAAT
66 TTAGAATCCCGAACTCGGAATATTTCCTTTAAT
* * * *
24346861 TTAAAAGAACATCTACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGTCACGATCCCT
1 TTAAAAGAACATCCACTTATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCCT
24346926 TTAGAATCCCGAACTCGGAATATTTCCTT
66 TTAGAATCCCGAACTCGGAATATTTCCTT
24346955 CATGACTTTT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 90 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (98 bp):
TTAAAAGAACATCCACTTATCCAAAATTTAAGAAACCACACCCAATACGTTAGGGCACGATCCCT
TTAGAATCCCGAACTCGGAATATTTCCTTTAAT
Found at i:24347854 original size:22 final size:22
Alignment explanation
Indices: 24347824--24347868 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
24347814 ATTTTATTTT
24347824 CAAAACCTTCTTTTTAAAAAAA
1 CAAAACCTTCTTTTTAAAAAAA
* *
24347846 CAAATCCTTTTTTTTAAAAAAA
1 CAAAACCTTCTTTTTAAAAAAA
24347868 C
1 C
24347869 CTCTCAACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.36
Consensus pattern (22 bp):
CAAAACCTTCTTTTTAAAAAAA
Found at i:24348402 original size:5 final size:5
Alignment explanation
Indices: 24348394--24348425 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
24348384 AAAAATCTGC
*
24348394 TTGAT TTGAT TTGAT TTGGT TTGAT TTGAT TT
1 TTGAT TTGAT TTGAT TTGAT TTGAT TTGAT TT
24348426 TTGTTTCCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.22, T:0.62
Consensus pattern (5 bp):
TTGAT
Found at i:24352286 original size:17 final size:17
Alignment explanation
Indices: 24352264--24352323 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
24352254 TCTGGGCAAT
24352264 AGAAGAATAAGAGAAAA
1 AGAAGAATAAGAGAAAA
24352281 AGAAGAATAAGAGAAGAA
1 AGAAGAATAAGAGAA-AA
* *
24352299 ATGGAGAAGAAGA-AGAAA
1 A-GAAGAATAAGAGA-AAA
24352317 AGAAGAA
1 AGAAGAA
24352324 AAGGAGGAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 20 0.54
18 7 0.19
19 10 0.27
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (17 bp):
AGAAGAATAAGAGAAAA
Found at i:24352308 original size:25 final size:25
Alignment explanation
Indices: 24352280--24352339 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
24352270 ATAAGAGAAA
* * *
24352280 AAGAAGAATAAGAGAAGAAATGGAG
1 AAGAAGAAGAAAAGAAGAAAAGGAG
24352305 AAGAAGAAGAAAAGAAGAAAAGGAG
1 AAGAAGAAGAAAAGAAGAAAAGGAG
*
24352330 GAGAAGAAGA
1 AAGAAGAAGA
24352340 GAAAATGGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.03
Consensus pattern (25 bp):
AAGAAGAAGAAAAGAAGAAAAGGAG
Found at i:24352323 original size:28 final size:26
Alignment explanation
Indices: 24352274--24352344 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 26
24352264 AGAAGAATAA
*
24352274 GAGAAAAAGAAGAATAAGAGAAGAA-ATG
1 GAGAAGAAGAAGAA-AAGAGAA-AAGA-G
24352302 GAGAAGAAGAAGAAAAGAAGAAAAGGAG
1 GAGAAGAAGAAGAAAAG-AGAAAA-GAG
24352330 GAGAAGAAG-AGAAAA
1 GAGAAGAAGAAGAAAA
24352345 TGGAAGGACT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 11 0.28
28 27 0.69
29 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (26 bp):
GAGAAGAAGAAGAAAAGAGAAAAGAG
Found at i:24367855 original size:114 final size:114
Alignment explanation
Indices: 24367655--24367887 Score: 466
Period size: 114 Copynumber: 2.0 Consensus size: 114
24367645 TCTCACAAAG
24367655 TTTATTATACCTCACGATTTACAATTCCATTACTTACACCGTTTCTTCTATGAGAAATTAGACTC
1 TTTATTATACCTCACGATTTACAATTCCATTACTTACACCGTTTCTTCTATGAGAAATTAGACTC
24367720 AATAAGATTTAATTTCATATTTTGTTCATCTCTAATTTGATGTCCACAA
66 AATAAGATTTAATTTCATATTTTGTTCATCTCTAATTTGATGTCCACAA
24367769 TTTATTATACCTCACGATTTACAATTCCATTACTTACACCGTTTCTTCTATGAGAAATTAGACTC
1 TTTATTATACCTCACGATTTACAATTCCATTACTTACACCGTTTCTTCTATGAGAAATTAGACTC
24367834 AATAAGATTTAATTTCATATTTTGTTCATCTCTAATTTGATGTCCACAA
66 AATAAGATTTAATTTCATATTTTGTTCATCTCTAATTTGATGTCCACAA
24367883 TTTAT
1 TTTAT
24367888 GGCAATTTTT
Statistics
Matches: 119, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 119 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (114 bp):
TTTATTATACCTCACGATTTACAATTCCATTACTTACACCGTTTCTTCTATGAGAAATTAGACTC
AATAAGATTTAATTTCATATTTTGTTCATCTCTAATTTGATGTCCACAA
Found at i:24379078 original size:18 final size:18
Alignment explanation
Indices: 24379057--24379093 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
24379047 TGAGTTTTCG
24379057 AATTTGAATAACTCGAAT
1 AATTTGAATAACTCGAAT
*
24379075 AATTTGAATAATTCGAAT
1 AATTTGAATAACTCGAAT
24379093 A
1 A
24379094 TCACACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (18 bp):
AATTTGAATAACTCGAAT
Found at i:24379343 original size:30 final size:31
Alignment explanation
Indices: 24379307--24379366 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
24379297 AAACCTTTTA
*
24379307 TTTTT-CCTCAAAATTTTTACTCCC-TCCCAC
1 TTTTTCCCT-AAAACTTTTACTCCCTTCCCAC
*
24379337 TTTTTCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTTCCCTAAAACTTTTACTCCCTTCCCA
24379367 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.20, C:0.35, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTTTCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:24391248 original size:5 final size:5
Alignment explanation
Indices: 24391238--24391279 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
24391228 GGTAAGTTCA
24391238 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TA
24391280 TTATTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:24391430 original size:45 final size:45
Alignment explanation
Indices: 24391381--24391595 Score: 306
Period size: 45 Copynumber: 4.8 Consensus size: 45
24391371 ATCAAACGGT
*
24391381 TAAGACAATAGTTGAAAGACACTATGGCACTATACC-AGAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGA-AAATGAA
* * *
24391426 TAAGACCATAGTTGAAAGACACTATAGAAATATACCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATGAA
* * *
24391471 TAAGACCATAGTTGAAAGGCATTATGGCACTATACCAAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATGAA
* * * * *
24391516 TAAGATCATAGATGAATGACACTATGGCACTACATCGAAAATGAA
1 TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATGAA
24391561 TAAGACCATAGTTGAAAGACACTATGGCACTATAC
1 TAAGACCATAGTTGAAAGACACTATGGCACTATAC
24391596 TTGTAACAGC
Statistics
Matches: 146, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
45 145 0.99
46 1 0.01
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.21
Consensus pattern (45 bp):
TAAGACCATAGTTGAAAGACACTATGGCACTATACCGAAAATGAA
Found at i:24392474 original size:35 final size:35
Alignment explanation
Indices: 24392435--24392525 Score: 112
Period size: 35 Copynumber: 2.6 Consensus size: 35
24392425 GGACTAGCTT
24392435 TTATGAGCATTGATGTGATTT-GGAGGGATTGGCTC
1 TTATGAGCATTGATGTG-TTTCGGAGGGATTGGCTC
* *
24392470 TTATGAGCATTGGTGTGTTTCGGATGGATTGGCTC
1 TTATGAGCATTGATGTGTTTCGGAGGGATTGGCTC
** *
24392505 TTACAAGCATCTGGTGTGTTT
1 TTATGAGCAT-TGATGTGTTT
24392526 GGGTGCCTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
34 3 0.06
35 37 0.74
36 10 0.20
ACGTcount: A:0.18, C:0.11, G:0.32, T:0.40
Consensus pattern (35 bp):
TTATGAGCATTGATGTGTTTCGGAGGGATTGGCTC
Found at i:24398284 original size:21 final size:21
Alignment explanation
Indices: 24398238--24398285 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
24398228 GTGACAGGGG
24398238 TACACGACTGTGTGGCTAAGA
1 TACACGACTGTGTGGCTAAGA
* * *
24398259 GACACGACCT-TGTGGTTGAGA
1 TACACGA-CTGTGTGGCTAAGA
24398280 TACACG
1 TACACG
24398286 GTCGTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.91
22 2 0.09
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (21 bp):
TACACGACTGTGTGGCTAAGA
Found at i:24401893 original size:21 final size:21
Alignment explanation
Indices: 24401846--24401894 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24401836 TGGTACACAT
* *
24401846 TCGTATGGCTGAGAGACATGG
1 TCGTGTGGCTGAGAGACACGG
*
24401867 TCGTGTGGCTGAGATACACGG
1 TCGTGTGGCTGAGAGACACGG
*
24401888 TGGTGTG
1 TCGTGTG
24401895 ACCAAATTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.41, T:0.27
Consensus pattern (21 bp):
TCGTGTGGCTGAGAGACACGG
Found at i:24409360 original size:14 final size:15
Alignment explanation
Indices: 24409335--24409364 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
24409325 TTGAAATGTT
24409335 TTATTGATTTTTGAA
1 TTATTGATTTTTGAA
24409350 TTATT-ATTTTTGAA
1 TTATTGATTTTTGAA
24409364 T
1 T
24409365 ACTTATATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (15 bp):
TTATTGATTTTTGAA
Found at i:24410353 original size:18 final size:20
Alignment explanation
Indices: 24410318--24410358 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
24410308 ACCATGATTT
24410318 GTTAGATAATGATGTGAT-G
1 GTTAGATAATGATGTGATAG
* *
24410337 GTTAGA-AATGTTTTGATAG
1 GTTAGATAATGATGTGATAG
24410356 GTT
1 GTT
24410359 TATTACTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (20 bp):
GTTAGATAATGATGTGATAG
Found at i:24411813 original size:17 final size:18
Alignment explanation
Indices: 24411781--24411815 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
24411771 ATCAAATGAA
24411781 AAAAATGGATAGAAATGGT
1 AAAAATGGA-AGAAATGGT
24411800 AAAAATGG-AGAAATGG
1 AAAAATGGAAGAAATGG
24411816 GAAACATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (18 bp):
AAAAATGGAAGAAATGGT
Found at i:24415649 original size:34 final size:34
Alignment explanation
Indices: 24415611--24415685 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
24415601 TTACTGTGTT
* *
24415611 ATTTGGTATGATGAATGGATC-GGCTCATACTAGC
1 ATTTGGTATGATGAATGG-TCTGGCGCATACGAGC
* * *
24415645 ATTTGGTGTGCTGGATGGTCTGGCGCATACGAGC
1 ATTTGGTATGATGAATGGTCTGGCGCATACGAGC
24415679 ATTTGGT
1 ATTTGGT
24415686 GTGCTGGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.20, C:0.15, G:0.32, T:0.33
Consensus pattern (34 bp):
ATTTGGTATGATGAATGGTCTGGCGCATACGAGC
Found at i:24425624 original size:4 final size:4
Alignment explanation
Indices: 24425617--24426542 Score: 1416
Period size: 4 Copynumber: 233.2 Consensus size: 4
24425607 ATGTGATAGA
24425617 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
24425665 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
24425713 TATG TATG TATG TATG TATG TATG TATG TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
24425761 TATG TATG TATG TGTG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
24425809 TATG TATG CATG TATG CATG CATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
24425857 TATG TATG TATG TATG TATG CATG CATG -ATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
24425904 CATG GATG TATG CATG TATG TATG CATG CATG -ATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
24425951 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
24425999 CATG CATG CATG CATG -ATG TATG TATG TATG CATG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
24426046 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG GATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
24426094 TATG CATG CATG CATG CATG -ATG TATG TATA TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
24426141 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
24426189 TATG TATG TATG TATG TATG CATG CATG CATG CATG -ATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
24426236 TATG TATG TATG CATG TATG TATG TATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * *
24426284 CATG GATG TATG CATG CATG CATG -ATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
24426331 TATG TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
24426379 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
24426427 CATG CATG CATG CATG -ATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
24426474 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
24426522 TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG T
24426543 TGAGCATGTT
Statistics
Matches: 879, Mismatches: 36, Indels: 14
0.95 0.04 0.02
Matches are distributed among these distances:
3 21 0.02
4 858 0.98
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:24427347 original size:18 final size:18
Alignment explanation
Indices: 24427307--24427373 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
24427297 TTTCACGATA
*
24427307 AATAACGTTTTGAAAATT
1 AATAACGTTTTGAAAATG
*
24427325 TATAACGTTTTGAAAGA-G
1 AATAACGTTTTGAAA-ATG
* *
24427343 AATAAC-TTATGAATATG
1 AATAACGTTTTGAAAATG
*
24427360 AATCACG-TTTGAAA
1 AATAACGTTTTGAAA
24427374 TTGATCAACA
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.03
17 17 0.45
18 19 0.50
19 1 0.03
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.34
Consensus pattern (18 bp):
AATAACGTTTTGAAAATG
Found at i:24430224 original size:20 final size:20
Alignment explanation
Indices: 24430179--24430225 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24430169 GCTTGTATAG
* *
24430179 GATTGCACTTTGGTGCCTCT
1 GATTGCACTTCGATGCCTCT
24430199 -ATTTGCACTTCGATGCCTCT
1 GA-TTGCACTTCGATGCCTCT
24430219 GATTGCA
1 GATTGCA
24430226 TATTTGTGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (20 bp):
GATTGCACTTCGATGCCTCT
Found at i:24430907 original size:20 final size:21
Alignment explanation
Indices: 24430882--24430924 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
24430872 GATTGTCAGG
24430882 TTTAGAAAATTTAATCCT-TT
1 TTTAGAAAATTTAATCCTATT
24430902 TTTAGAAAATTTAATCCTATT
1 TTTAGAAAATTTAATCCTATT
24430923 TT
1 TT
24430925 CATTTTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (21 bp):
TTTAGAAAATTTAATCCTATT
Found at i:24434643 original size:51 final size:51
Alignment explanation
Indices: 24434585--24434686 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
24434575 ACGTCGGTTG
* *
24434585 ACAATGAGTCACGTTGCGACATCAAGTGGCCTGAGGTCACGACGTGACATA
1 ACAATGAGTCACGTTACGACATCAAGTGGCCTAAGGTCACGACGTGACATA
**
24434636 ACAATGAGTCACGTTACGACATTGAGTGGCCTAAGGTCACGACGTGACATA
1 ACAATGAGTCACGTTACGACATCAAGTGGCCTAAGGTCACGACGTGACATA
24434687 CTTTTATGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (51 bp):
ACAATGAGTCACGTTACGACATCAAGTGGCCTAAGGTCACGACGTGACATA
Found at i:24437728 original size:20 final size:20
Alignment explanation
Indices: 24437700--24437741 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
24437690 GACTCATTCG
24437700 CATTAATATTTTCATCAAGT
1 CATTAATATTTTCATCAAGT
*
24437720 CATTCATATTTTCATCAAGT
1 CATTAATATTTTCATCAAGT
24437740 CA
1 CA
24437742 AAATATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (20 bp):
CATTAATATTTTCATCAAGT
Found at i:24440713 original size:20 final size:20
Alignment explanation
Indices: 24440688--24440728 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
24440678 CCTTCCTTCG
24440688 TGCTGCCAGATACAGAATAT
1 TGCTGCCAGATACAGAATAT
*
24440708 TGCTGCCTGATACAGAATAT
1 TGCTGCCAGATACAGAATAT
24440728 T
1 T
24440729 ATGGTCAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
TGCTGCCAGATACAGAATAT
Found at i:24440938 original size:36 final size:36
Alignment explanation
Indices: 24440881--24440971 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
24440871 ATTTTCTGTA
*
24440881 GGCATGCTTT-ACATGCAAATCAAAACCAGTATAGT
1 GGCATGCTTTAACATGCAAATCAAAACCAGTATAAT
* * *
24440916 GGCATGCTTTAACATGCGAATCAGAATCAGTATAAT
1 GGCATGCTTTAACATGCAAATCAAAACCAGTATAAT
24440952 GGCATGC-TTAACATGCAAAT
1 GGCATGCTTTAACATGCAAAT
24440972 TAGAATATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
35 22 0.44
36 28 0.56
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (36 bp):
GGCATGCTTTAACATGCAAATCAAAACCAGTATAAT
Found at i:24444137 original size:22 final size:22
Alignment explanation
Indices: 24444109--24444154 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
24444099 TCAATTATCC
*
24444109 ATAATAATAATAAACAAATAAA
1 ATAATAATAATAAACAAACAAA
* *
24444131 ATAATAATGATAACCAAACAAA
1 ATAATAATAATAAACAAACAAA
24444153 AT
1 AT
24444155 TCGAAACCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.22
Consensus pattern (22 bp):
ATAATAATAATAAACAAACAAA
Found at i:24452086 original size:23 final size:23
Alignment explanation
Indices: 24452054--24452131 Score: 81
Period size: 23 Copynumber: 3.4 Consensus size: 23
24452044 TTCTCTTTTC
24452054 TTTTTC-TATATTTGATTCTCTA
1 TTTTTCATATATTTGATTCTCTA
24452076 TTTTTCATATATGTT-ATTCTCT-
1 TTTTTCATATAT-TTGATTCTCTA
* *
24452098 TTCCTTTCCTATATTTGATTATCTA
1 TT--TTTCATATATTTGATTCTCTA
*
24452123 TTTTCCATA
1 TTTTTCATA
24452132 AAATATTCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
22 8 0.17
23 19 0.41
24 17 0.37
25 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTCATATATTTGATTCTCTA
Found at i:24452113 original size:47 final size:48
Alignment explanation
Indices: 24452029--24452131 Score: 154
Period size: 47 Copynumber: 2.2 Consensus size: 48
24452019 AGAATACATA
* * * *
24452029 TTTCCATATCTGTTATTCTCTTTTCTTTTTCTATATTTGATTCTCTAT
1 TTTCCATATATGTTATTCTCTTTTCCTTTCCTATATTTGATTATCTAT
*
24452077 TTTTCATATATGTTATTCTC-TTTCCTTTCCTATATTTGATTATCTAT
1 TTTCCATATATGTTATTCTCTTTTCCTTTCCTATATTTGATTATCTAT
24452124 TTTCCATA
1 TTTCCATA
24452132 AAATATTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
47 31 0.63
48 18 0.37
ACGTcount: A:0.17, C:0.18, G:0.04, T:0.60
Consensus pattern (48 bp):
TTTCCATATATGTTATTCTCTTTTCCTTTCCTATATTTGATTATCTAT
Found at i:24464089 original size:28 final size:27
Alignment explanation
Indices: 24464000--24464090 Score: 83
Period size: 28 Copynumber: 3.3 Consensus size: 27
24463990 AGGGTTGGTG
* **
24464000 AATTTTTTGAAGCAAAGAGAGTTTTTGA
1 AATTTTTTGAAG-AAATAGAGTTAATGA
* ** *
24464028 AATTTTTTGAATGAAATAGGGTTCGTCA
1 AATTTTTTGAA-GAAATAGAGTTAATGA
*
24464056 ATTTTTTTGAACGAAATAGAGTTAATGA
1 AATTTTTTGAA-GAAATAGAGTTAATGA
24464084 AATTTTT
1 AATTTTT
24464091 AAAGGATATT
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
28 49 0.98
29 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (27 bp):
AATTTTTTGAAGAAATAGAGTTAATGA
Found at i:24466416 original size:21 final size:22
Alignment explanation
Indices: 24466374--24466416 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
24466364 TAAACGAAGT
* *
24466374 ACAATATTATTTAACTACATAA
1 ACAATATAATTTAACTAAATAA
24466396 ACAATATAATTT-ACTAAATAA
1 ACAATATAATTTAACTAAATAA
24466417 TTACATGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (22 bp):
ACAATATAATTTAACTAAATAA
Found at i:24468767 original size:36 final size:36
Alignment explanation
Indices: 24468727--24468914 Score: 214
Period size: 36 Copynumber: 4.9 Consensus size: 36
24468717 GGTAGCTTTA
*
24468727 GCTACACTTATCTGATCAAGGGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
24468763 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
*
24468808 AGCTACACTTATCTAATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
24468845 GTTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
24468881 GCTATACTTATCTGATCAAGTGACAAAGTGATAA
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAA
24468915 ATGGTAGCTT
Statistics
Matches: 132, Mismatches: 10, Indels: 20
0.81 0.06 0.12
Matches are distributed among these distances:
36 95 0.72
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 29 0.22
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:24468828 original size:82 final size:82
Alignment explanation
Indices: 24468691--24468881 Score: 310
Period size: 82 Copynumber: 2.3 Consensus size: 82
24468681 TTTGAGTACT
* * *
24468691 TCTGATCAATAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGGGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGGAAAAAGT
24468756 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
* *
24468773 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGTGAAAAAGT
1 TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGGAAAAAGT
* *
24468838 GATAAGTGTTATACTTA
66 GATAAGTGCTACACTTA
*
24468855 TCTGATCAAGTGAAAAAGTGATAAGTG
1 TCTGATCAAGAGAAAAAGTGATAAGTG
24468882 CTATACTTAT
Statistics
Matches: 101, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 101 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGAAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAAGGGAAAAAGT
GATAAGTGCTACACTTA
Found at i:24473162 original size:56 final size:57
Alignment explanation
Indices: 24473075--24473187 Score: 174
Period size: 56 Copynumber: 2.0 Consensus size: 57
24473065 TTGGTTTTTA
* **
24473075 TAATATATATAATATATATGCATGACTTAAATGAAGCTAAATGGAATATATATGCAT
1 TAATATATATAATATATACGCATGACTTAAATGAAGCTAAACAGAATATATATGCAT
* *
24473132 TAATATATAT-ATATATGCGCATGACTTAAATGAAGCTAAACAGTATATATATGCAT
1 TAATATATATAATATATACGCATGACTTAAATGAAGCTAAACAGAATATATATGCAT
24473188 GACTTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
56 41 0.80
57 10 0.20
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (57 bp):
TAATATATATAATATATACGCATGACTTAAATGAAGCTAAACAGAATATATATGCAT
Found at i:24473188 original size:34 final size:35
Alignment explanation
Indices: 24473139--24473206 Score: 120
Period size: 34 Copynumber: 1.9 Consensus size: 35
24473129 CATTAATATA
24473139 TATATATATGCGCATGACTTAAATGAAGCTAAACAG
1 TATATATAT-CGCATGACTTAAATGAAGCTAAACAG
24473175 TATATATAT-GCATGACTTAAATGAAGCTAAAC
1 TATATATATCGCATGACTTAAATGAAGCTAAAC
24473207 CTGCTAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
34 23 0.72
36 9 0.28
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (35 bp):
TATATATATCGCATGACTTAAATGAAGCTAAACAG
Found at i:24473256 original size:85 final size:88
Alignment explanation
Indices: 24473086--24473257 Score: 230
Period size: 90 Copynumber: 2.0 Consensus size: 88
24473076 AATATATATA
*
24473086 ATATATATGCATGACTTAAATGAAGCTAAATGGAATATATATGCATTAATATATATATATATGCG
1 ATATATATGCATGACTTAAATGAAGCTAAATGGAATATATATG-AGTAATATATATATATAT-CG
*
24473151 CATGACTTAAATGAAGCTAAACAGT
64 CATGACTTAAATGAAACTAAACAGT
*
24473176 ATATATATGCATGACTTAAATGAAGCTAAACCTGCTAATA-A-A-G-GT-ATATATATATATAT-
1 ATATATATGCATGACTTAAATGAAGCTAAA--TG-GAATATATATGAGTAATATATATATATATC
24473235 GCATGACTTAAATGAAACTAAAC
63 GCATGACTTAAATGAAACTAAAC
24473258 CTGCTAATAA
Statistics
Matches: 76, Mismatches: 3, Indels: 11
0.84 0.03 0.12
Matches are distributed among these distances:
85 22 0.29
87 14 0.18
88 1 0.01
90 31 0.41
91 1 0.01
92 3 0.04
93 4 0.05
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.31
Consensus pattern (88 bp):
ATATATATGCATGACTTAAATGAAGCTAAATGGAATATATATGAGTAATATATATATATATCGCA
TGACTTAAATGAAACTAAACAGT
Found at i:24473641 original size:21 final size:22
Alignment explanation
Indices: 24473615--24473669 Score: 87
Period size: 21 Copynumber: 2.6 Consensus size: 22
24473605 ACAACTGATG
24473615 GTGGTTGTGGCCTA-TGGAACC
1 GTGGTTGTGGCCTAGTGGAACC
24473636 GTGGTTGTGGCC-AGTGGAACC
1 GTGGTTGTGGCCTAGTGGAACC
*
24473657 GTGGTCGTGGCCT
1 GTGGTTGTGGCCT
24473670 CGTGAGACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.11, C:0.20, G:0.42, T:0.27
Consensus pattern (22 bp):
GTGGTTGTGGCCTAGTGGAACC
Found at i:24475759 original size:14 final size:14
Alignment explanation
Indices: 24475733--24475773 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
24475723 TTTACAGATA
24475733 CAGATA-ACAGAAT
1 CAGATATACAGAAT
*
24475746 CAGATATGCAGAAT
1 CAGATATACAGAAT
24475760 -AGATATACAGAAT
1 CAGATATACAGAAT
24475773 C
1 C
24475774 CTAGCCCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 18 0.75
14 6 0.25
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.20
Consensus pattern (14 bp):
CAGATATACAGAAT
Done.