Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold541
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: 143301
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:956 original size:77 final size:77
Alignment explanation
Indices: 843--1022 Score: 245
Period size: 77 Copynumber: 2.3 Consensus size: 77
833 CCGGCTAAGT
* * * * *
843 CCCGAAGGCTTTTGTGCTAAGTGACTATATCCGGTAAGATCTGAAGGCATTT-TGCGAGTTACTA
1 CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGTAAG-TCCGAAGGCATTTGTGCGAGTTACTA
*
907 TATCCGGGCCAAAA
64 AATCCGGGCCAAAA
921 CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
1 CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
* **
986 TCCGGGCTAAGT
66 TCCGGGCCAAAA
*
998 CCCGAAGGCAATTGTGCGAGTTACT
1 CCCGAAGGCATTTGTGCGAGTTACT
1023 CTAACCGGGC
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
76 12 0.13
77 63 0.69
78 16 0.18
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (77 bp):
CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGTAAGTCCGAAGGCATTTGTGCGAGTTACTAAA
TCCGGGCCAAAA
Found at i:972 original size:37 final size:38
Alignment explanation
Indices: 831--1050 Score: 214
Period size: 40 Copynumber: 5.7 Consensus size: 38
821 TTCGAATGAT
* * * *
831 ATCCGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTAT
1 ATCCGGCTAAGT-CCGAAGGCATTTGTGC-GAGTTACTAA
* *
871 ATCCGG-TAAGATCTGAAGGCATTT-TGCGAGTTACTAT
1 ATCCGGCTAAG-TCCGAAGGCATTTGTGCGAGTTACTAA
* **
908 ATCCGGGCCAAAACCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCC-GG-CTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
948 ATCCGG-TAAGTCCGAAGGCATTTGTGCGAGTTACTAA
1 ATCCGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
* *
985 ATCCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACTCTA
1 ATCC-GGCTAAGT-CCGAAGGCATTTGTGCGAGTTACT-AA
* *
1026 A-CCGGGCTATGTCCCAAGGCATTTG
1 ATCC-GGCTAAGTCCGAAGGCATTTG
1051 AGCAAGCTAT
Statistics
Matches: 154, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
37 44 0.29
38 7 0.05
39 43 0.28
40 58 0.38
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (38 bp):
ATCCGGCTAAGTCCGAAGGCATTTGTGCGAGTTACTAA
Found at i:3452 original size:15 final size:15
Alignment explanation
Indices: 3413--3482 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
3403 GTATCTTGGG
*
3413 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
3428 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
3443 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
3457 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
3472 TTTCTTTATTC
1 TTTCTTTATTC
3483 GTTTTCTTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 2 0.04
14 9 0.20
15 32 0.71
16 2 0.04
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:3476 original size:29 final size:29
Alignment explanation
Indices: 3404--3483 Score: 90
Period size: 29 Copynumber: 2.7 Consensus size: 29
3394 CATAGTATCG
* * *
3404 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATCTCTC
* *
3434 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATCTCTC
3463 TATCTTGGATTTCTTTATTCG
1 TATCTTGGATTTCTTTATTCG
3484 TTTTCTTGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 26 0.60
30 17 0.40
ACGTcount: A:0.11, C:0.17, G:0.16, T:0.55
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATCTCTC
Found at i:9346 original size:42 final size:43
Alignment explanation
Indices: 9295--9393 Score: 141
Period size: 43 Copynumber: 2.3 Consensus size: 43
9285 AATTCTTAAA
9295 TGGTCCAAGTTCATGATAT-ATGT-AGCATCCGAGCTCATTGAG
1 TGGTCCAAGTTCATGAT-TGATGTGAGCATCCGAGCTCATTGAG
* *
9337 TGGTCCAAGTTCATTATTGATGTGAGCATCCGAGCTCGTTGAG
1 TGGTCCAAGTTCATGATTGATGTGAGCATCCGAGCTCATTGAG
9380 TGGTCCGAA-TTCAT
1 TGGTCC-AAGTTCAT
9394 AATGGATGCG
Statistics
Matches: 52, Mismatches: 2, Indels: 5
0.88 0.03 0.08
Matches are distributed among these distances:
41 1 0.02
42 20 0.38
43 29 0.56
44 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.32
Consensus pattern (43 bp):
TGGTCCAAGTTCATGATTGATGTGAGCATCCGAGCTCATTGAG
Found at i:13492 original size:58 final size:59
Alignment explanation
Indices: 13392--13503 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 59
13382 TCGAGTCAAA
* * *
13392 GAATCATGTATGTAATTGAATATGTATAAGGCTAGATGAAAAAAATAGGAAAAATAAAT
1 GAATCATGTATGTAATTAAATATGTATAAGGCCAGATGAAAAAAAAAGGAAAAATAAAT
* * * *
13451 GAAT-ATGTTTGTAATTAAGTATGTATAAGGCCAGATTAAAAAAAAAGGGAAAA
1 GAATCATGTATGTAATTAAATATGTATAAGGCCAGATGAAAAAAAAAGGAAAAA
13504 CAGAGTTAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 42 0.91
59 4 0.09
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.27
Consensus pattern (59 bp):
GAATCATGTATGTAATTAAATATGTATAAGGCCAGATGAAAAAAAAAGGAAAAATAAAT
Found at i:17664 original size:22 final size:22
Alignment explanation
Indices: 17639--17695 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
17629 AAACAGGGTC
17639 ACACGCCCGTGTGGACATAGGG
1 ACACGCCCGTGTGGACATAGGG
17661 ACACGCCCGTGTGGACATAGGG
1 ACACGCCCGTGTGGACATAGGG
17683 ACACGCCCGTGTG
1 ACACGCCCGTGTG
17696 CCTTTGGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.21, C:0.30, G:0.35, T:0.14
Consensus pattern (22 bp):
ACACGCCCGTGTGGACATAGGG
Found at i:19776 original size:46 final size:47
Alignment explanation
Indices: 19648--19812 Score: 153
Period size: 46 Copynumber: 3.5 Consensus size: 47
19638 AGGCCGACGC
* * *
19648 CATGTCCTAGACATGGTGTTACACTAGCTTTGACATATCTGT-GCCGATG
1 CATGTCCCAGACATGGTCTTACACTAGC-TT-ACATCT-TGTAGCCGATG
* * *
19697 CCATATCCCAGACATGGTCTTACACTAAC--ACATCTTGTAACCGATG
1 -CATGTCCCAGACATGGTCTTACACTAGCTTACATCTTGTAGCCGATG
* * * *
19743 CATGTCCTAGACAT-GTCTTACACTGGCTTACATCTCG-AGGCCAATG
1 CATGTCCCAGACATGGTCTTACACTAGCTTACATCTTGTA-GCCGATG
19789 CATGTCCCAGACAT-GTCTTACACT
1 CATGTCCCAGACATGGTCTTACACT
19813 GGCAACACAA
Statistics
Matches: 97, Mismatches: 14, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
44 11 0.11
45 16 0.16
46 46 0.47
50 24 0.25
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACTAGCTTACATCTTGTAGCCGATG
Found at i:31574 original size:17 final size:17
Alignment explanation
Indices: 31552--31598 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
31542 AACCGCAACC
31552 AATATTCTTTGGTTTTT
1 AATATTCTTTGGTTTTT
*
31569 AATATTCCATTT-ATTTTT
1 AATATT-C-TTTGGTTTTT
31587 -ATATTCTTTGGT
1 AATATTCTTTGGT
31599 ATGTAACCGT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
15 3 0.12
16 2 0.08
17 11 0.44
18 6 0.24
19 3 0.12
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (17 bp):
AATATTCTTTGGTTTTT
Found at i:35844 original size:26 final size:27
Alignment explanation
Indices: 35807--35858 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
35797 AATTCAAATC
35807 TTTATGAGTCATAATATATTTTAAGCT
1 TTTATGAGTCATAATATATTTTAAGCT
35834 TTTATGA-TCATAATATATTTTAAGC
1 TTTATGAGTCATAATATATTTTAAGC
35859 CAAATTTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 18 0.72
27 7 0.28
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (27 bp):
TTTATGAGTCATAATATATTTTAAGCT
Found at i:39883 original size:42 final size:42
Alignment explanation
Indices: 39824--39979 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
39814 CCTAAGATTA
* *
39824 CGTGTAAGACCATATCTGGGATAT-AGCATCGATATGAGACTT
1 CGTGTAAGACCATATCTGAGATATGA-CATCGATAGGAGACTT
* *
39866 CGTGTAAGACCATATCTGAGCTATGACATCGTTAGGAGACTT
1 CGTGTAAGACCATATCTGAGATATGACATCGATAGGAGACTT
* * * *
39908 TGTGTAAGACCATAGCT-AGACTATTGGCATCGATACGAGA-TT
1 CGTGTAAGACCATATCTGAGA-TA-TGACATCGATAGGAGACTT
* * *
39950 ACATGCAAGACCATATCTGATATATGACAT
1 -CGTGTAAGACCATATCTGAGATATGACAT
39980 TGGTACGATA
Statistics
Matches: 93, Mismatches: 16, Indels: 10
0.78 0.13 0.08
Matches are distributed among these distances:
41 2 0.02
42 60 0.65
43 29 0.31
44 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGAGATATGACATCGATAGGAGACTT
Found at i:45626 original size:32 final size:32
Alignment explanation
Indices: 45557--45662 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
45547 CAGTTCTGTG
* * *
45557 AAATGGTAACAAATATCAACTTTTCATTTTGTG
1 AAATGATAACAAATATCAAC-TTTAATTTTGTA
45590 AAATGATAACAAAT-TACAACTTTAATTTTGTA
1 AAATGATAACAAATAT-CAACTTTAATTTTGTA
* * *
45622 AAATGATAACAAATATTAGCTTTAATTTTTTA
1 AAATGATAACAAATATCAACTTTAATTTTGTA
45654 AAATGATAA
1 AAATGATAA
45663 TAATATTCCT
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
32 47 0.72
33 18 0.28
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (32 bp):
AAATGATAACAAATATCAACTTTAATTTTGTA
Found at i:47837 original size:12 final size:13
Alignment explanation
Indices: 47796--47842 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
47786 GAATTAATTT
47796 TTAAT-AAAAATA
1 TTAATAAAAAATA
** *
47808 TTTTTAGAAAATA
1 TTAATAAAAAATA
47821 TTAATAAAAAATA
1 TTAATAAAAAATA
47834 -TAATAAAAA
1 TTAATAAAAA
47843 TCTAATATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
TTAATAAAAAATA
Found at i:49460 original size:19 final size:18
Alignment explanation
Indices: 49436--49471 Score: 63
Period size: 18 Copynumber: 1.9 Consensus size: 18
49426 TATTAATATC
49436 TTTTTCTTAGTTTTGGCCT
1 TTTTTC-TAGTTTTGGCCT
49455 TTTTTCTAGTTTTGGCC
1 TTTTTCTAGTTTTGGCC
49472 AATTGCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.06, C:0.17, G:0.17, T:0.61
Consensus pattern (18 bp):
TTTTTCTAGTTTTGGCCT
Found at i:50694 original size:16 final size:18
Alignment explanation
Indices: 50668--50701 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
50658 TCTAATTAGA
50668 TAAATTAAATTTC-CAAT
1 TAAATTAAATTTCTCAAT
50685 TAAA-TAAATTTCTCAAT
1 TAAATTAAATTTCTCAAT
50702 CCAATTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTAAATTTCTCAAT
Found at i:53368 original size:34 final size:35
Alignment explanation
Indices: 53320--53400 Score: 130
Period size: 34 Copynumber: 2.4 Consensus size: 35
53310 ATCAAGATAT
* *
53320 ATCATTTTAGAAGGCAATATATACACCAAACTAA-
1 ATCATTTTACAAGGCAATATACACACCAAACTAAC
53354 ATCATTTTACAAGGCAATATACACACCAAACTAAC
1 ATCATTTTACAAGGCAATATACACACCAAACTAAC
53389 ATCATTTT-CAAG
1 ATCATTTTACAAG
53401 CCATATCTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
34 36 0.82
35 8 0.18
ACGTcount: A:0.44, C:0.21, G:0.07, T:0.27
Consensus pattern (35 bp):
ATCATTTTACAAGGCAATATACACACCAAACTAAC
Found at i:62951 original size:40 final size:40
Alignment explanation
Indices: 62906--63086 Score: 267
Period size: 40 Copynumber: 4.5 Consensus size: 40
62896 TTATTTGATG
62906 TGGAATGGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATGGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
62946 TGGAATCGTATCCGAGCTTAAAGACCCGCAGGCTTCGTGC
1 TGGAATGGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
62986 TGGAAAT-GTATCCAGGCTTAAAGACCCGCAAGCTTCGTGC
1 TGG-AATGGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
* *
63026 TGGAATTGTATCCGGGCTTAAAGACCCGCAGGCTTTGTGC
1 TGGAATGGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
**
63066 TGGAATGACATCCGGG-TTAAA
1 TGGAATGGTATCCGGGCTTAAA
63087 AACCTACAGG
Statistics
Matches: 128, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
39 8 0.06
40 117 0.91
41 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (40 bp):
TGGAATGGTATCCGGGCTTAAAGACCCGCAGGCTTCGTGC
Found at i:67289 original size:47 final size:46
Alignment explanation
Indices: 67005--67311 Score: 216
Period size: 47 Copynumber: 6.6 Consensus size: 46
66995 TTGCCGATGC
* *
67005 CATGTCCCAGACATGGTCTTACACTGGCTCTCATATATGTGTGCTGACG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCTCATA-ATGTG-GCCGAAG
* * * * * * *
67054 CATGTCCTAGACATGTCTTACACTAG--CACA-ACTCTTAGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAAT-GTGGCCGAAG
* * * * *
67098 CGTGTCTCAGACACGTCTTACACTGGCTATC-T-CTGTCAAGGCC-AATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGT---GGCCGAA-G
* * * * * *
67145 CATGTCCCAGGCATGTCTTACTCTGGCACTCATAATATAGCTGAAG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCCGAAG
* * * * *
67191 CATGTCCCAGACATGTCTTACACTAGCCCTCGT-CTG-GAAGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTG--GCCGAAG
67237 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCCGAAG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGTGGCCGAAG
*
67285 CATGTCCCAAACATGTCTTACACTGGC
1 CATGTCCCAGACATGTCTTACACTGGC
67312 GCACAAATGA
Statistics
Matches: 196, Mismatches: 45, Indels: 37
0.71 0.16 0.13
Matches are distributed among these distances:
44 28 0.14
45 5 0.03
46 54 0.28
47 57 0.29
48 34 0.17
49 17 0.09
50 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCCGAAG
Found at i:71432 original size:40 final size:40
Alignment explanation
Indices: 71388--71611 Score: 290
Period size: 40 Copynumber: 5.8 Consensus size: 40
71378 GGATATAGCT
* * * *
71388 ACTCGCTCAAATGCCTTTGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
71428 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
71468 ACTCGCACAAATGCCTTCGGGACTTA--CCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
71506 ACTCGCACAAATGCCTTCGGG--TTAGCCCGGA-TTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
71543 ACTCGCACAAATGCCTTC--GACTTAG-CCGGA-ATAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
*
71579 ACTAGCACAAA-GCCTTCGGGACTTAGCCCGGAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAT
71612 ATCATTCGAA
Statistics
Matches: 166, Mismatches: 9, Indels: 19
0.86 0.05 0.10
Matches are distributed among these distances:
35 7 0.04
36 22 0.13
37 35 0.21
38 43 0.26
40 57 0.34
41 2 0.01
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:73780 original size:36 final size:37
Alignment explanation
Indices: 73737--73811 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
73727 AATCTAAGTA
*
73737 TCTTTTT-CAAGGTGAAACTTTAAGAAACACTTTATC
1 TCTTTTTCCAAGGTGAAACCTTAAGAAACACTTTATC
*
73773 TCTTTTTCCAAGGTGAAACCTTAAGAAACACTTTGTC
1 TCTTTTTCCAAGGTGAAACCTTAAGAAACACTTTATC
73810 TC
1 TC
73812 CCACCTGATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 7 0.19
37 29 0.81
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (37 bp):
TCTTTTTCCAAGGTGAAACCTTAAGAAACACTTTATC
Found at i:79541 original size:40 final size:40
Alignment explanation
Indices: 79496--79726 Score: 349
Period size: 40 Copynumber: 5.8 Consensus size: 40
79486 GGATATAGCT
* * *
79496 ACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTAGAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
*
79536 ACTCGCACAATTGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
79576 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
79616 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
** *
79656 ACTCGCACAAATGCCTTCGGGACTT-GCCCGGAACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
79695 ACTAGCGCAGATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
79727 TTATCATCCA
Statistics
Matches: 178, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 33 0.19
40 143 0.80
41 2 0.01
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:82668 original size:20 final size:20
Alignment explanation
Indices: 82643--82692 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 20
82633 TTCTTTTTCA
82643 CTTTTTTTCTTTTTC-C-TT
1 CTTTTTTTCTTTTTCACTTT
*
82661 CTCTTTTTCTTTTTCACTTT
1 CTTTTTTTCTTTTTCACTTT
82681 CTTTTTTTCTTT
1 CTTTTTTTCTTT
82693 CACACTCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 13 0.46
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (20 bp):
CTTTTTTTCTTTTTCACTTT
Found at i:82669 original size:18 final size:20
Alignment explanation
Indices: 82646--82692 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
82636 TTTTTCACTT
82646 TTTTTCTTTTTC-C-TTCTC
1 TTTTTCTTTTTCACTTTCTC
*
82664 TTTTTCTTTTTCACTTTCTT
1 TTTTTCTTTTTCACTTTCTC
82684 TTTTTCTTT
1 TTTTTCTTT
82693 CACACTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 12 0.46
19 1 0.04
20 13 0.50
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTCTTTTTCACTTTCTC
Found at i:82693 original size:18 final size:17
Alignment explanation
Indices: 82636--82695 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
82626 TCTCACATTC
*
82636 TTTTTCACTTT-TTTTC
1 TTTTTCACTTTCTTTTT
82652 TTTTTC-CTTCTCTTTTT
1 TTTTTCACTT-TCTTTTT
82669 CTTTTTCACTTTCTTTTT
1 -TTTTTCACTTTCTTTTT
82687 TTCTTTCAC
1 TT-TTTCAC
82696 ACTCTTTCTC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
15 3 0.08
16 7 0.18
17 6 0.16
18 19 0.50
19 3 0.08
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTCACTTTCTTTTT
Found at i:82698 original size:20 final size:20
Alignment explanation
Indices: 82659--82698 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
82649 TTCTTTTTCC
**
82659 TTCTCTTTTTCTTTTTCACT
1 TTCTCTTTTTCTTTCACACT
*
82679 TTCTTTTTTTCTTTCACACT
1 TTCTCTTTTTCTTTCACACT
82699 CTTTCTCACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCTCTTTTTCTTTCACACT
Found at i:82701 original size:18 final size:18
Alignment explanation
Indices: 82633--82702 Score: 58
Period size: 18 Copynumber: 4.0 Consensus size: 18
82623 TCTTCTCACA
*
82633 TTCTTTTT--CACTTTTT
1 TTCTTTTTCACACTCTTT
*
82649 TTCTTTTTC-CTTCTCTTT
1 TTCTTTTTCAC-ACTCTTT
**
82667 TTCTTTTTCACTTTCTTT
1 TTCTTTTTCACACTCTTT
82685 TT-TTCTTTCACACTCTTT
1 TTCTT-TTTCACACTCTTT
82703 CTCACATGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
16 8 0.18
17 3 0.07
18 33 0.73
19 1 0.02
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (18 bp):
TTCTTTTTCACACTCTTT
Found at i:82704 original size:34 final size:33
Alignment explanation
Indices: 82633--82702 Score: 79
Period size: 34 Copynumber: 2.0 Consensus size: 33
82623 TCTTCTCACA
*
82633 TTCTTTTTCACTTTTTTTCTTTTTCCTTCTCTTT
1 TTCTTTTTCACTTTTTTTCTTTTTCCTACTC-TT
*
82667 TTCTTTTTCACTTTCTTTTTTTCTTTCAC-ACTCTT
1 TTCTTTTTCACTTT-TTTTCTT-TTTC-CTACTCTT
82702 T
1 T
82703 CTCACATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 14 0.45
35 9 0.29
36 7 0.23
37 1 0.03
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.70
Consensus pattern (33 bp):
TTCTTTTTCACTTTTTTTCTTTTTCCTACTCTT
Found at i:95766 original size:57 final size:59
Alignment explanation
Indices: 95639--95781 Score: 168
Period size: 57 Copynumber: 2.5 Consensus size: 59
95629 TTGTTAGAAA
* * * *
95639 AAGGATTTAGCCCAGACGGGTAATCCCAATATAATACCTCTCGAGCATACATTATGATT
1 AAGGATTTAGCCTAGACTGGTAATCCTAATAGAATACCTCTCGAGCATACATTATGATT
* * * *
95698 -AGGGTTTAGCCTAGACTGGTAATCCTAATCGAGCT-CCTCT-GAGCGTACATTAT-ATT
1 AAGGATTTAGCCTAGACTGGTAATCCTAATAGA-ATACCTCTCGAGCATACATTATGATT
*
95754 AAGGATTTAGCCTGGACTGGTAATCCTA
1 AAGGATTTAGCCTAGACTGGTAATCCTA
95782 TTATATGACA
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
56 3 0.04
57 37 0.51
58 31 0.43
59 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (59 bp):
AAGGATTTAGCCTAGACTGGTAATCCTAATAGAATACCTCTCGAGCATACATTATGATT
Found at i:106215 original size:15 final size:15
Alignment explanation
Indices: 106197--106228 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
106187 GTCCAATTCA
106197 GAAAAGGCTAATTTT
1 GAAAAGGCTAATTTT
106212 GAAAAGGCTAATTTT
1 GAAAAGGCTAATTTT
106227 GA
1 GA
106229 GGGCTCTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (15 bp):
GAAAAGGCTAATTTT
Found at i:112026 original size:46 final size:47
Alignment explanation
Indices: 111748--112109 Score: 192
Period size: 46 Copynumber: 7.6 Consensus size: 47
111738 GGTATAATGT
* * *
111748 CGATGCCATGTCCCAGATATGGTGTTACACTGGC-T-CATCCATCAA-GT
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACAT-C-TCAAGGC
** ** ** *
111795 CGATGCCATGTCCCAGACATGGTCTTACACTAACTATTGAAATCGAGGC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCT-TACATCTCAAGGC
* * ** * *
111844 CAACGCCATGTCTGAGACATGGTCTTACACTAGCTGTCACATATTC--GTGC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCT-T-ACAT-CTCAAG-GC
* * * * * *
111894 CAATGGCATGTCCTAGACATGGTCTTACACTGGC--ACCTCTATATATGC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACATCT-CA-AGGC
* * * *
111942 CGATGTCATCTCCCAGACATGGTCTTACACTGAC--ACATCTCGTA-GC
1 CGATGCCATGTCCCAGACAT-GTCTTACACTGGCTTACATCTC-AAGGC
* *
111988 CGATG-CATATCCCAAACATGTCTTACACTGGCTTACATCTCAAGGC
1 CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAGGC
* * * * *
112034 CGATG-CATGTCCTAGACATGTCTTATACTAGCTCT-CGTCTCAATGC
1 CGATGCCATGTCCCAGACATGTCTTACACTGGCT-TACATCTCAAGGC
112080 CGATGCCATGTCCCAGACATGTCTTACACT
1 CGATGCCATGTCCCAGACATGTCTTACACT
112110 ACCTCTCATA
Statistics
Matches: 249, Mismatches: 49, Indels: 34
0.75 0.15 0.10
Matches are distributed among these distances:
44 12 0.05
45 14 0.06
46 61 0.24
47 54 0.22
48 39 0.16
49 34 0.14
50 33 0.13
51 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGTCTTACACTGGCTTACATCTCAAGGC
Found at i:112104 original size:47 final size:45
Alignment explanation
Indices: 111899--112158 Score: 196
Period size: 46 Copynumber: 5.6 Consensus size: 45
111889 CGTGCCAATG
* * * *
111899 GCATGTCCTAGACATGGTCTTACACTGGCAC-CTCTATATATGCCGAT
1 GCATGTCCCAGACAT-GTCTTACACTAGCTCTCTCT-CA-ATGCCGAT
* *
111946 GTCATCTCCCAGACATGGTCTTACACT-GACACATCTCGT--A-GCCGAT
1 G-CATGTCCCAGACAT-GTCTTACACTAG-CTC-TCTC-TCAATGCCGAT
* * * *
111992 GCATATCCCAAACATGTCTTACACTGGCT-TACATCTCAAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCTCT-C-TCTCAATGCCGAT
* *
112038 GCATGTCCTAGACATGTCTTATACTAGCTCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCTCTC-TCTCAATGCCGAT
112084 GCCATGTCCCAGACATGTCTTACACTA-C-CTCTCAT-AATGTGGCCGAT
1 G-CATGTCCCAGACATGTCTTACACTAGCTCTCTC-TCAA--T-GCCGAT
*
112131 GCATGTTCCAGACATGTCTTACACTAGC
1 GCATGTCCCAGACATGTCTTACACTAGC
112159 ACACAAATAA
Statistics
Matches: 180, Mismatches: 15, Indels: 36
0.78 0.06 0.16
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 17 0.09
45 18 0.10
46 77 0.43
47 35 0.19
48 26 0.14
50 3 0.02
51 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (45 bp):
GCATGTCCCAGACATGTCTTACACTAGCTCTCTCTCAATGCCGAT
Found at i:114282 original size:13 final size:13
Alignment explanation
Indices: 114264--114291 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
114254 TTAGATTATA
114264 CATAACCAAAATC
1 CATAACCAAAATC
114277 CATAACCAAAATC
1 CATAACCAAAATC
114290 CA
1 CA
114292 ACATTCCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.32, G:0.00, T:0.14
Consensus pattern (13 bp):
CATAACCAAAATC
Found at i:114890 original size:16 final size:16
Alignment explanation
Indices: 114869--114907 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
114859 TCTTACTCAC
114869 ACACATATATCGAAGT
1 ACACATATATCGAAGT
*
114885 ACACATATATCGGAGT
1 ACACATATATCGAAGT
114901 -CACATAT
1 ACACATAT
114908 CAATGCCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.41, C:0.21, G:0.13, T:0.26
Consensus pattern (16 bp):
ACACATATATCGAAGT
Found at i:114932 original size:72 final size:72
Alignment explanation
Indices: 114813--114950 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
114803 TCTTACTCAC
*
114813 ACACATATATCAAAGTCACATATCGATGCCAAAATAGAAAACATGGTCTTACTCACACACATATA
1 ACACATATATCAAAGTCACATATCAATGCCAAAATAGAAAACATGGTCTTACTCACACACATATA
114878 TCGAAGT
66 TCGAAGT
** ** * * *
114885 ACACATATATCGGAGTCACATATCAATGCCAACGTATAAAACCTGGTCTTACTCGCACACATATA
1 ACACATATATCAAAGTCACATATCAATGCCAAAATAGAAAACATGGTCTTACTCACACACATATA
114950 T
66 T
114951 TAGAGTCACA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 58 1.00
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.25
Consensus pattern (72 bp):
ACACATATATCAAAGTCACATATCAATGCCAAAATAGAAAACATGGTCTTACTCACACACATATA
TCGAAGT
Found at i:116602 original size:648 final size:648
Alignment explanation
Indices: 115361--116671 Score: 2595
Period size: 648 Copynumber: 2.0 Consensus size: 648
115351 ATAAATGGAC
*
115361 AAATTACCATTTTACCCCTAACAGTTTACGCTTTTTACAATTTAGTCTAAATTGCATAAAACACA
1 AAATTTCCATTTTACCCCTAACAGTTTACGCTTTTTACAATTTAGTCTAAATTGCATAAAACACA
115426 AAACATGCAAAATTTGCACATACTATGCTTAGGCCGAATACTCCAAGTGTTCATACAAGTCCACA
66 AAACATGCAAAATTTGCACATACTATGCTTAGGCCGAATACTCCAAGTGTTCATACAAGTCCACA
115491 CATTTCATTTATTTTACATTTTAGTCCCTCAATTTATTATTTTTTCAATTTAGTCCTAATTACTC
131 CATTTCATTTATTTTACATTTTAGTCCCTCAATTTATTATTTTTTCAATTTAGTCCTAATTACTC
115556 AAAATCATCAAAAATTCCAATACAAAACATGTTAATCTATCACATATCTTTCAACAATGGCATAA
196 AAAATCATCAAAAATTCCAATACAAAACATGTTAATCTATCACATATCTTTCAACAATGGCATAA
115621 CTCAAAATATTCACCAAAATAAAAATTTCAAGCATGAGTCTTGTAGATAACTTAGCAACGATCTC
261 CTCAAAATATTCACCAAAATAAAAATTTCAAGCATGAGTCTTGTAGATAACTTAGCAACGATCTC
115686 AAAAACGTAAAAATTATCAAAAACCGAACAAAAACTAACCTTGAATCAAGCTTGAATAAGGCTGA
326 AAAAACGTAAAAATTATCAAAAACCGAACAAAAACTAACCTTGAATCAAGCTTGAATAAGGCTGA
115751 ATACCCTAAGCTTATTTTCTTTTCTTTATTTCTCAACTTTCGGTCAAAAAGATGAACAAATGCAT
391 ATACCCTAAGCTTATTTTCTTTTCTTTATTTCTCAACTTTCGGTCAAAAAGATGAACAAATGCAT
115816 GGTTGTTTTATTTTTATGTTTTATTATAACATTATTAATTTATAATTTACCAAATTAACCTTAAG
456 GGTTGTTTTATTTTTATGTTTTATTATAACATTATTAATTTATAATTTACCAAATTAACCTTAAG
*
115881 ATAAAAATATAAAACCATTTTAATGCATGGTCACAACCGTTCATTACTTATTATCATGGACAAAT
521 ATAAAAATATAAAACCATTTTAATGCATGGTCACAACCGTTCATTACTTATTATCATGGAAAAAT
115946 TAAATATTAAATACCTTAACTTACAAAGACAAACACAATTCAGCCCTTACACATTAAACCACT
586 TAAATATTAAATACCTTAACTTACAAAGACAAACACAATTCAGCCCTTACACATTAAACCACT
116009 AAATTTCCATTTTACCCCTAACAGTTTACGCTTTTTACAATTTAGTCTAAATTGCATAAAACACA
1 AAATTTCCATTTTACCCCTAACAGTTTACGCTTTTTACAATTTAGTCTAAATTGCATAAAACACA
116074 AAACATGCAAAATTTGCACATACTATGCTTAGGCCGAATACTCCAAGTGTTCATACAAGTCCACA
66 AAACATGCAAAATTTGCACATACTATGCTTAGGCCGAATACTCCAAGTGTTCATACAAGTCCACA
116139 CATTTCATTTATTTTACATTTTAGTCCCTCAATTTATTATTTTTTCAATTTAGTCCTAATTACTC
131 CATTTCATTTATTTTACATTTTAGTCCCTCAATTTATTATTTTTTCAATTTAGTCCTAATTACTC
116204 AAAATCATCAAAAATTCCAATACAAAACATGTTAATCTATCACATATCTTTCAACAATGGCATAA
196 AAAATCATCAAAAATTCCAATACAAAACATGTTAATCTATCACATATCTTTCAACAATGGCATAA
116269 CTCAAAATATTCACCAAAATAAAAATTTCAAGCATGAGTCTTGTAGATAACTTAGCAACGATCTC
261 CTCAAAATATTCACCAAAATAAAAATTTCAAGCATGAGTCTTGTAGATAACTTAGCAACGATCTC
116334 AAAAACGTAAAAATTATCAAAAACCGAACAAAAACTAACCTTGAATCAAGCTTGAATAAGGCTGA
326 AAAAACGTAAAAATTATCAAAAACCGAACAAAAACTAACCTTGAATCAAGCTTGAATAAGGCTGA
116399 ATACCCTAAGCTTATTTTCTTTTCTTTATTTCTCAACTTTCGGTCAAAAAGATGAACAAATGCAT
391 ATACCCTAAGCTTATTTTCTTTTCTTTATTTCTCAACTTTCGGTCAAAAAGATGAACAAATGCAT
116464 GGTTGTTTTATTTTTATGTTTTATTATAACATTATTAATTTATAATTTACCAAATTAACCTTAAG
456 GGTTGTTTTATTTTTATGTTTTATTATAACATTATTAATTTATAATTTACCAAATTAACCTTAAG
116529 ATAAAAATATAAAACCATTTTAATGCATGGTCACAACCGTTCATTACTTATTATCATGGAAAAAT
521 ATAAAAATATAAAACCATTTTAATGCATGGTCACAACCGTTCATTACTTATTATCATGGAAAAAT
*
116594 TAAATATTAAATACCTTAACTTACAAAGACAAACACAATTCGGCCCTTACACATTAAACCACT
586 TAAATATTAAATACCTTAACTTACAAAGACAAACACAATTCAGCCCTTACACATTAAACCACT
116657 AAATTTCCATTTTAC
1 AAATTTCCATTTTAC
116672 GCGATTAAGC
Statistics
Matches: 660, Mismatches: 3, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
648 660 1.00
ACGTcount: A:0.39, C:0.19, G:0.08, T:0.34
Consensus pattern (648 bp):
AAATTTCCATTTTACCCCTAACAGTTTACGCTTTTTACAATTTAGTCTAAATTGCATAAAACACA
AAACATGCAAAATTTGCACATACTATGCTTAGGCCGAATACTCCAAGTGTTCATACAAGTCCACA
CATTTCATTTATTTTACATTTTAGTCCCTCAATTTATTATTTTTTCAATTTAGTCCTAATTACTC
AAAATCATCAAAAATTCCAATACAAAACATGTTAATCTATCACATATCTTTCAACAATGGCATAA
CTCAAAATATTCACCAAAATAAAAATTTCAAGCATGAGTCTTGTAGATAACTTAGCAACGATCTC
AAAAACGTAAAAATTATCAAAAACCGAACAAAAACTAACCTTGAATCAAGCTTGAATAAGGCTGA
ATACCCTAAGCTTATTTTCTTTTCTTTATTTCTCAACTTTCGGTCAAAAAGATGAACAAATGCAT
GGTTGTTTTATTTTTATGTTTTATTATAACATTATTAATTTATAATTTACCAAATTAACCTTAAG
ATAAAAATATAAAACCATTTTAATGCATGGTCACAACCGTTCATTACTTATTATCATGGAAAAAT
TAAATATTAAATACCTTAACTTACAAAGACAAACACAATTCAGCCCTTACACATTAAACCACT
Found at i:118505 original size:9 final size:9
Alignment explanation
Indices: 118491--118515 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
118481 AATTAGGGAC
118491 TAAATTGAA
1 TAAATTGAA
118500 TAAATTGAA
1 TAAATTGAA
118509 TAAATTG
1 TAAATTG
118516 CAAAACTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (9 bp):
TAAATTGAA
Found at i:124337 original size:33 final size:33
Alignment explanation
Indices: 124268--124365 Score: 108
Period size: 33 Copynumber: 2.9 Consensus size: 33
124258 CTATACCCAT
* * *
124268 CTATGCCGAATGCATAGATACATACACTTATTTTCAC
1 CTATGCCGAATGCAT--ACACATA-A-ATATATTCAC
124305 CTATGCCGAATGCATACACATAAATATATTCAC
1 CTATGCCGAATGCATACACATAAATATATTCAC
* *
124338 CTATGCCGAATGCA-ACATATATATATAT
1 CTATGCCGAATGCATACACATAAATATAT
124366 ACATATCTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
32 12 0.21
33 22 0.39
34 1 0.02
35 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (33 bp):
CTATGCCGAATGCATACACATAAATATATTCAC
Found at i:124625 original size:41 final size:41
Alignment explanation
Indices: 124580--124735 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
124570 ACCGGCTCTT
*
124580 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
124621 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
124662 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * * *
124703 AGCCTGCTAGACGTAAAGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
124736 TAACGATAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 98 0.92
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:125240 original size:21 final size:23
Alignment explanation
Indices: 125216--125263 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
125206 ATAATATATA
125216 TATTTC-AC-TCATACTTTTAAT
1 TATTTCAACATCATACTTTTAAT
*
125237 TATTTCAACTATCATATTTTTAAT
1 TATTTCAAC-ATCATACTTTTAAT
125261 TAT
1 TAT
125264 ATTTCATCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 2 0.09
24 15 0.65
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTCAACATCATACTTTTAAT
Found at i:131970 original size:32 final size:31
Alignment explanation
Indices: 131932--131995 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 31
131922 ACACTTATTT
131932 TCACCTATGCCGAATGCATACACATAAATATA
1 TCACCTATGCCGAATGCA-ACACATAAATATA
* *
131964 TCACCTATGCCGAATGCAACATATATATATA
1 TCACCTATGCCGAATGCAACACATAAATATA
131995 T
1 T
131996 ACATATCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.39, C:0.23, G:0.09, T:0.28
Consensus pattern (31 bp):
TCACCTATGCCGAATGCAACACATAAATATA
Found at i:132253 original size:41 final size:41
Alignment explanation
Indices: 132208--132362 Score: 235
Period size: 41 Copynumber: 3.8 Consensus size: 41
132198 ACCGGCTCTT
*
132208 AGCCTGCTAGACTTATAGTCCGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
132249 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
132290 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTG-A-AATGTGTCACCGGCATTA
* * *
132331 AGCCTGCTAGACGTA-AGTCTGAATTATGTCAC
1 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAC
132363 TAACGATAAA
Statistics
Matches: 107, Mismatches: 3, Indels: 9
0.90 0.03 0.08
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 10 0.09
41 88 0.82
42 2 0.02
43 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCTGAAATGTGTCACCGGCATTA
Found at i:139937 original size:42 final size:41
Alignment explanation
Indices: 139891--139988 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 41
139881 ACCGGCTCTT
139891 AGCCTGCTAGACTTATAGTCCGAAATGCTGTTC-ACCGGCA-TA
1 AGCCTGCTAGACTTATAGTCCGAAATG-TG-TCAACC-GCATTA
*
139933 AGCCTGCTAGACTTATAGTCTGAAATGTGTCAACCGCATTA
1 AGCCTGCTAGACTTATAGTCCGAAATGTGTCAACCGCATTA
139974 AGCC-GCTAGACTTAT
1 AGCCTGCTAGACTTAT
139989 CTGATAATTC
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
40 16 0.30
41 11 0.21
42 26 0.49
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACTTATAGTCCGAAATGTGTCAACCGCATTA
Done.