Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015455.1 Corchorus olitorius cultivar O-4 contig15488, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62729
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1123 original size:17 final size:17
Alignment explanation
Indices: 1086--1133 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
1076 GTAATCTTTA
*
1086 ATCACCGGTGATCTTGC
1 ATCACTGGTGATCTTGC
1103 ATCACTGGTGATCTTAG-
1 ATCACTGGTGATCTT-GC
*
1120 ATCACTAGTGATCT
1 ATCACTGGTGATCT
1134 GGGGGTGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 27 0.96
18 1 0.04
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (17 bp):
ATCACTGGTGATCTTGC
Found at i:13599 original size:60 final size:60
Alignment explanation
Indices: 13506--13728 Score: 277
Period size: 60 Copynumber: 3.9 Consensus size: 60
13496 TAGACAGAAA
13506 CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTC
1 CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTC
** * *
13566 CTGAAGGGTGACATGTGAACTTTGGAGCAATT-C--C----T-ATTGCCAGAC-AGG-TC
1 CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTC
* *
13616 CTGAACGGTGACATGTGAACTTTGGAGCAATTCCTATATAATAATTGGAAGCCGCGGTTC
1 CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTC
*** * *
13676 CTGAAGGGTGACATGTGAACTTCAAAGCAATTCTTATATAATAATTGGAAGCC
1 CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCC
13729 ATGAAATCAC
Statistics
Matches: 138, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
50 33 0.24
51 3 0.02
52 7 0.05
53 1 0.01
57 2 0.01
58 7 0.05
59 3 0.02
60 82 0.59
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (60 bp):
CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTC
Found at i:13705 original size:110 final size:110
Alignment explanation
Indices: 13506--13708 Score: 361
Period size: 110 Copynumber: 1.8 Consensus size: 110
13496 TAGACAGAAA
*
13506 CTGAAGGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTCCTGAA
1 CTGAACGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTCCTGAA
***
13571 GGGTGACATGTGAACTTTGGAGCAATTCCTATTGCCAGACAGGTC
66 GGGTGACATGTGAACTTCAAAGCAATTCCTATTGCCAGACAGGTC
*
13616 CTGAACGGTGACATGTGAACTTTGGAGCAATTCCTATATAATAATTGGAAGCCGCGGTTCCTGAA
1 CTGAACGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTCCTGAA
13681 GGGTGACATGTGAACTTCAAAGCAATTC
66 GGGTGACATGTGAACTTCAAAGCAATTC
13709 TTATATAATA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
110 88 1.00
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (110 bp):
CTGAACGGTGACATGTGAACTTTGGAGCAATTCCTACATAATAATTGGAAGCCGCGGTTCCTGAA
GGGTGACATGTGAACTTCAAAGCAATTCCTATTGCCAGACAGGTC
Found at i:17004 original size:38 final size:38
Alignment explanation
Indices: 16953--17191 Score: 190
Period size: 38 Copynumber: 5.9 Consensus size: 38
16943 GGTTGTACTT
*
16953 GCATGGATTATATTGAATTCTGACTAATTCGGAGTTGA
1 GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
* * *
16991 GCATGGATTATATTGGATTCTGACTAATTTGGAGGCAAGTCA
1 GCATGGATTATATTGAATTCTGACTAATTTGGA-G---TTGA
* * *
17033 TTGCATGGATTACATTAAATTCTGACTAATTCGGAGTTGA
1 --GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
* * * * *
17073 GCATGGATTGTATTGGATTCTGGCTAATTTGGAATCAAGTCA
1 GCATGGATTATATTGAATTCTGACTAATTTGGAGT----TGA
* * *
17115 TTGCATGGATTATGTTGAATTCTAACTAATTAGGAGTTGA
1 --GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
* * *
17155 GCATGAATTATATATTGGATTCTAACTAATTTGGAGT
1 GCATGGA-T-TATATTGAATTCTGACTAATTTGGAGT
17192 CAAAGTCATG
Statistics
Matches: 157, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
38 65 0.41
39 2 0.01
40 28 0.18
42 4 0.03
43 1 0.01
44 57 0.36
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.37
Consensus pattern (38 bp):
GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
Found at i:17088 original size:82 final size:82
Alignment explanation
Indices: 16951--17200 Score: 374
Period size: 82 Copynumber: 3.0 Consensus size: 82
16941 ATGGTTGTAC
16951 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
1 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
*
17016 AATTTGGAGGCAAGTCA
66 AATTTGGAGTCAAGTCA
* * * *
17033 TTGCATGGATTACATTAAATTCTGACTAATTCGGAGTTGAGCATGGATTGTATTGGATTCTGGCT
1 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
*
17098 AATTTGGAATCAAGTCA
66 AATTTGGAGTCAAGTCA
* * * * *
17115 TTGCATGGATTATGTTGAATTCTAACTAATTAGGAGTTGAGCATGAATTATATATTGGATTCTAA
1 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGA-T-TATATTGGATTCTGA
17180 CTAATTTGGAGTCAAAGTCA
64 CTAATTTGGAGTC-AAGTCA
17200 T
1 T
17201 GTCACTTATG
Statistics
Matches: 149, Mismatches: 16, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
82 117 0.79
83 1 0.01
84 24 0.16
85 7 0.05
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (82 bp):
TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
AATTTGGAGTCAAGTCA
Found at i:19532 original size:144 final size:144
Alignment explanation
Indices: 19260--19542 Score: 458
Period size: 144 Copynumber: 2.0 Consensus size: 144
19250 AGCCTATTAT
* *
19260 TTTGCTGAAAAGCGCAGAAGTTTTTGGCTGGTGCCCATTTCCTCAAAGTTAGAAGCTTATCTGGT
1 TTTGCTGAAAAGCGCAGAAGTTTTTGACGGGTGCCCATTTCCTCAAAGTTAGAAGCTTATCTGGT
* * * *
19325 ACTAACCATCCGGTATCCGGTAATCATATTTATTTTCACCTATTTTAGAGTTTCAAGTCAGGTTC
66 ACTAACCATCCGATATCCGGTAATCATATTTATTTTCACCTATTTTAGAGTCTCAAATAAGGTTC
19390 TAGACTATTAGTAA
131 TAGACTATTAGTAA
** * * *
19404 TTTGCTGAAAAGTTCAGAAGTTTTTGACGGGTGCCCATTTCCTCGAATTTAGAAGCTTATTTGGT
1 TTTGCTGAAAAGCGCAGAAGTTTTTGACGGGTGCCCATTTCCTCAAAGTTAGAAGCTTATCTGGT
*
19469 ACTAATCATCCGATATCCGGTAATCATATTTATTTTCACCTATTTTAGAGTCTCAAATAAGGTTC
66 ACTAACCATCCGATATCCGGTAATCATATTTATTTTCACCTATTTTAGAGTCTCAAATAAGGTTC
19534 TAGACTATT
131 TAGACTATT
19543 TTAGTAATAA
Statistics
Matches: 127, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
144 127 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (144 bp):
TTTGCTGAAAAGCGCAGAAGTTTTTGACGGGTGCCCATTTCCTCAAAGTTAGAAGCTTATCTGGT
ACTAACCATCCGATATCCGGTAATCATATTTATTTTCACCTATTTTAGAGTCTCAAATAAGGTTC
TAGACTATTAGTAA
Found at i:23973 original size:21 final size:21
Alignment explanation
Indices: 23948--24029 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 21
23938 TATCTTAGAT
23948 ATAATATATATTATTAAATAA
1 ATAATATATATTATTAAATAA
23969 ATAATAAATATATT-TTAAAT-A
1 ATAAT--ATATATTATTAAATAA
*
23990 ATAA-ATA-ATGAGTTCAAAATAA
1 ATAATATATATTA-TT--AAATAA
*
24012 ATAGATATATATTTTTAA
1 ATA-ATATATATTATTAA
24030 TTACTAAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 19
0.69 0.04 0.27
Matches are distributed among these distances:
17 2 0.04
18 3 0.06
19 2 0.04
21 14 0.29
22 12 0.25
23 8 0.17
24 5 0.10
25 2 0.04
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (21 bp):
ATAATATATATTATTAAATAA
Found at i:23981 original size:25 final size:25
Alignment explanation
Indices: 23950--23998 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
23940 TCTTAGATAT
*
23950 AATATATATT-ATTAAATAAATAATA
1 AATATATATTAAAT-AATAAATAATA
*
23975 AATATATTTTAAATAATAAATAAT
1 AATATATATTAAATAATAAATAAT
23999 GAGTTCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
AATATATATTAAATAATAAATAATA
Found at i:26051 original size:11 final size:11
Alignment explanation
Indices: 26019--26062 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
26009 TCAACCTTTA
* *
26019 TATATAGTATA
1 TATATTGTATG
26030 TATATTGGTATG
1 TATATT-GTATG
26042 TATATTGTATG
1 TATATTGTATG
*
26053 TATAATGTAT
1 TATATTGTAT
26063 AATGTATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 19 0.66
12 10 0.34
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (11 bp):
TATATTGTATG
Found at i:26262 original size:2 final size:2
Alignment explanation
Indices: 26255--26293 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
26245 AAGATTGAAC
26255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26294 TCCTAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:26437 original size:13 final size:13
Alignment explanation
Indices: 26421--26457 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
26411 GATAATTCTT
26421 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
26434 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
26447 CTTGACCCTCC
1 TTTGACCCTCC
26458 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:26518 original size:40 final size:40
Alignment explanation
Indices: 26461--26537 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
26451 ACCCTCCTAA
*
26461 TAATTAAGGAAATAAATTAAATCCAGGTTTAGCCCCTTAC
1 TAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCCTTAC
* *
26501 TAATTAAGGTAAGAAATTAAATTCAGGTTTAGCCCCT
1 TAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCCT
26538 AGTTATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (40 bp):
TAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCCCTTAC
Found at i:33341 original size:45 final size:44
Alignment explanation
Indices: 33291--33376 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 44
33281 TATATTGTGT
33291 AGTTCCCAAAGCCCTTTCTGGCCAAACAAAAAAAAGTTACCGTGA
1 AGTTCCCAAAGCCCTTTCTGGCCAAAC-AAAAAAAGTTACCGTGA
33336 AGTTCCCAAAGCCCTTTCTGGCCAAACAAAAAAAGTTACCG
1 AGTTCCCAAAGCCCTTTCTGGCCAAACAAAAAAAGTTACCG
33377 AAGCCATGGC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 14 0.34
45 27 0.66
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (44 bp):
AGTTCCCAAAGCCCTTTCTGGCCAAACAAAAAAAGTTACCGTGA
Found at i:34397 original size:25 final size:25
Alignment explanation
Indices: 34363--34450 Score: 76
Period size: 25 Copynumber: 3.4 Consensus size: 25
34353 AACATGTGTC
34363 AATGAAAATGGGTATACTTTTGGAA
1 AATGAAAATGGGTATACTTTTGGAA
* *
34388 AATGAAAAT-GGCA-A-TTGAGTGG-A
1 AATGAAAATGGGTATACTT--TTGGAA
34411 AATGGAAAAAAATGGGTATACTTTTGGAA
1 AAT-G---AAAATGGGTATACTTTTGGAA
34440 AATGAAAATGG
1 AATGAAAATGG
34451 CAATTGAGTG
Statistics
Matches: 49, Mismatches: 4, Indels: 20
0.67 0.05 0.27
Matches are distributed among these distances:
22 2 0.04
23 5 0.10
24 7 0.14
25 16 0.33
27 5 0.10
28 7 0.14
29 5 0.10
30 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.26
Consensus pattern (25 bp):
AATGAAAATGGGTATACTTTTGGAA
Found at i:34418 original size:24 final size:23
Alignment explanation
Indices: 34387--34471 Score: 57
Period size: 24 Copynumber: 3.4 Consensus size: 23
34377 TACTTTTGGA
34387 AAATGAAAATGGCAATTGAGTGG
1 AAATGAAAATGGCAATTGAGTGG
* *
34410 AAATGGAAAAAAATGGGTATACTT--TTGG
1 AAAT-G---AAAAT-GGCA-A-TTGAGTGG
34438 AAAATGAAAATGGCAATTGAGTGG
1 A-AATGAAAATGGCAATTGAGTGG
34462 AAATGGAAAA
1 AAAT-GAAAA
34472 CATTTTTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 21
0.65 0.06 0.29
Matches are distributed among these distances:
22 2 0.04
23 8 0.17
24 13 0.28
25 5 0.11
27 5 0.11
28 8 0.17
29 4 0.09
30 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.27, T:0.22
Consensus pattern (23 bp):
AAATGAAAATGGCAATTGAGTGG
Found at i:34441 original size:52 final size:52
Alignment explanation
Indices: 34367--34471 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
34357 TGTGTCAATG
34367 AAAATGGGTATACTTTTGGAAAATGAAAATGGCAATTGAGTGGAAATGGAAA
1 AAAATGGGTATACTTTTGGAAAATGAAAATGGCAATTGAGTGGAAATGGAAA
34419 AAAATGGGTATACTTTTGGAAAATGAAAATGGCAATTGAGTGGAAATGGAAA
1 AAAATGGGTATACTTTTGGAAAATGAAAATGGCAATTGAGTGGAAATGGAAA
34471 A
1 A
34472 CATTTTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.45, C:0.04, G:0.27, T:0.25
Consensus pattern (52 bp):
AAAATGGGTATACTTTTGGAAAATGAAAATGGCAATTGAGTGGAAATGGAAA
Found at i:41970 original size:11 final size:11
Alignment explanation
Indices: 41954--41979 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41944 ATATTACTAT
41954 TAATTAATTAA
1 TAATTAATTAA
41965 TAATTAATTAA
1 TAATTAATTAA
41976 TAAT
1 TAAT
41980 AATCAGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAATTAATTAA
Found at i:41972 original size:15 final size:14
Alignment explanation
Indices: 41952--41982 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
41942 ATATATTACT
41952 ATTAATTAATTAATA
1 ATTAATTAA-TAATA
41967 ATTAATTAATAATA
1 ATTAATTAATAATA
41981 AT
1 AT
41983 CAGTTTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAATTAATAATA
Found at i:53461 original size:18 final size:18
Alignment explanation
Indices: 53438--53484 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
53428 TGACATTGCC
53438 ACGTGGCATTTTGATCCA
1 ACGTGGCATTTTGATCCA
* *
53456 ACGTGGCATGTTTTATCCG
1 ACGTGGCAT-TTTGATCCA
*
53475 ACATGGCATT
1 ACGTGGCATT
53485 GCCACATCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (18 bp):
ACGTGGCATTTTGATCCA
Found at i:54166 original size:2 final size:2
Alignment explanation
Indices: 54159--54188 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54149 TTTAGGAAAC
54159 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54189 CTTATCTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54589 original size:31 final size:31
Alignment explanation
Indices: 54527--54610 Score: 125
Period size: 31 Copynumber: 2.6 Consensus size: 31
54517 CAGTCTAAAC
*
54527 TCTAAACTGGGTTTTACTTTTGGGGCAAAAAG
1 TCTAAACTGGGTTTT-TTTTTGGGGCAAAAAG
54559 TCTAAACT-GGTTTTTTTTTGGGGCAGAAAAG
1 TCTAAACTGGGTTTTTTTTTGGGGCA-AAAAG
54590 TCTAAACTGGGATTTTTTTTT
1 TCTAAACTGGG-TTTTTTTTT
54611 TTGGCAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
30 10 0.21
31 19 0.40
32 10 0.21
33 9 0.19
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.42
Consensus pattern (31 bp):
TCTAAACTGGGTTTTTTTTTGGGGCAAAAAG
Found at i:55234 original size:32 final size:31
Alignment explanation
Indices: 55198--55304 Score: 133
Period size: 32 Copynumber: 3.4 Consensus size: 31
55188 CATCATGTTG
*
55198 TGCCACGTCAGACCATAATGATGATGTGGCAT
1 TGCCACGTCGGACCA-AATGATGATGTGGCAT
* *
55230 TGCCACGTCGGACCAAACCGATGACGTGGCAT
1 TGCCACGTCGGACCAAA-TGATGATGTGGCAT
* * *
55262 TGACACGTTGGACCAAATCAATGATGTGGCAT
1 TGCCACGTCGGACCAAAT-GATGATGTGGCAT
55294 TGCCACGTCGG
1 TGCCACGTCGG
55305 CTTTTGGCGC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.03
32 61 0.97
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.21
Consensus pattern (31 bp):
TGCCACGTCGGACCAAATGATGATGTGGCAT
Found at i:60932 original size:26 final size:25
Alignment explanation
Indices: 60850--60940 Score: 146
Period size: 25 Copynumber: 3.6 Consensus size: 25
60840 CATCGTCACA
60850 TAGTTGCATATTCAGTAGGGCCATG
1 TAGTTGCATATTCAGTAGGGCCATG
*
60875 TAGTTTCATATTCAGTAGGGCCATG
1 TAGTTGCATATTCAGTAGGGCCATG
* *
60900 TAATTGCATATTCAGTAGGGTTCATG
1 TAGTTGCATATTCAGTAGGG-CCATG
60926 TAGTTGCATATTCAG
1 TAGTTGCATATTCAG
60941 CCAAAAACTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
25 42 0.70
26 18 0.30
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.36
Consensus pattern (25 bp):
TAGTTGCATATTCAGTAGGGCCATG
Found at i:62152 original size:331 final size:331
Alignment explanation
Indices: 61261--62712 Score: 1778
Period size: 333 Copynumber: 4.4 Consensus size: 331
61251 ACCCCAACAT
* * ** *
61261 GATTTCGGCTAAAATTTTGTAAAAACT-AACCTGAAATTTTTTTCCTCAATATAAGGCCATAATA
1 GATTTCGGCTAAAATTTTGCAAAAACTGAACC-GAAAATTTTTTCCTCAATATTCGGCCACAATA
* * * * *
61325 CTCGTAAAAAATATATAATTTAAAGCCAAAAACATTGAATGACTTTTCACGCTTCTAATATCGTT
65 CTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATT
* * * **
61390 TCTCTTATTTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTAATAATCGTAAAAAC
130 TTTCCTA-TTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
* * *
61455 AAATCCTTAAATCCAATCTGAATGAGATTTGGCCAGATTAATATAAATATTTCAAGGAGTCTTGG
194 AAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTCAAGGAGTCTTGG
* * * * * * * * *
61520 TGTCCAAAATCATGCAAAACTAAGCTGGTGCGCCGGAACACGTTTTTAGCAAAAAACTGTGATGG
259 CGCCCAAAATCATGCAAAACTGAGCCGG-ACCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
61585 TTATTACAC
323 TTATTACAC
* * ** * *
61594 GATTTCGGCAAAAATTTTACAAAAACTGAGTC-AAAATTTTTTTCCTTAATATTCGGCCATAATA
1 GATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAA-TTTTTTCCTCAATATTCGGCCACAATA
* * * * * ** *
61658 CTGGTTAAAAGTATATAATTTAATGCCAAAAAGATTGAAGGGTTTTTCACGTTTCTAATATCATT
65 CTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATT
* * *
61723 TTTCCTATTTTTTTTCGAATGAATTTCTAATAAAATCAAAACAAGATTCTGATGCTCGTAAAAAC
130 TTTCCTA-TTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
*
61788 AAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATGAATATAGATATTTCAAGGAGTCTTGG
194 AAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTCAAGGAGTCTTGG
* ** * **
61853 CACCCAAAATCAACCAAAACTGTGCCAGGACCCCGGAACGCGTTTTTAGCCAAAAACAATGATGG
259 CGCCCAAAATCATGCAAAACTGAGCC-GGACCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
*
61918 ATA-T-CAC
323 TTATTACAC
* * *
61925 GATTTTGGCTAAAAAATTTTGCAAAAACTGAACC-AAAAATTATTCCTCAATATTCGGCCACAAT
1 GATTTCGGCT--AAAATTTTGCAAAAACTGAACCGAAAATTTTTTCCTCAATATTCGGCCACAAT
* * *
61989 AGTCGTAAAAAATATATAATTCAACGCTAAAAAGATTGAA-GACTTTTCAGGCTTCTAATATCAT
64 ACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCAT
* * * * *
62053 TTTTCCTATTTATACTGAATT-ATTTCTAACAAAATCGAAACAAGATTTTGATGCTCGTTAAAAA
129 TTTTCCTATTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCG-T-AAAA
*
62117 ACAAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTTAAGGAGTCTT
192 ACAAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTCAAGGAGTCTT
* * * * *
62182 TGTGCCCAAAATCATGC-AAACTGAGTCGGGGCCCCGGAACGTG-TTTTAGCCAAAAACCGTGAT
257 GGCGCCCAAAATCATGCAAAACTGAG-CCGGACCCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
62245 GGTTATTACAC
321 GGTTATTACAC
* * * *
62256 GATTTCGGCTAAATTTTTGCAAAAAAATG-ACTCGAAAATTTTTTCCTTAATATTTGGCCACAAT
1 GATTTCGGCTAAAATTTTGC-AAAAACTGAAC-CGAAAATTTTTTCCTCAATATTCGGCCACAAT
* * * *
62320 ACTTGTAAAAAATATATAATTCAACGACAAAAAGATGGAAGAACTTTTCACGCTTCTAATATCAT
64 ACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCAT
* * * *
62385 TTTTCCTGTTTTTTCCGAATTAATTTCTAGTAAAATCGAAACAAGATTCTGATTCTCGTTAAAAC
129 TTTTCCTATTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAAC
* * * * * *
62450 AAATCGTTAAATCCAATTTGTCAGAGATTTGGTCAGATTAATATAGATATTTCAAGGAGTATTGC
194 AAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTCAAGGAGTCTTGG
* * * * *
62515 CTCCCAAAGTCTTGCAAAACTGTGCCGAGACCCCGGAACGCGTTTTTAGTCAAAAACCGTGATGG
259 CGCCCAAAATCATGCAAAACTGAGCCG-GACCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGG
62580 TTATTACAC
323 TTATTACAC
* *
62589 GATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATATTCGAG-CACAATA
1 GATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAATTTTTTCCTCAATATTCG-GCCACAATA
** * * * *
62653 CTATTAAAAAATATATAATTCAACG-CAAAAA-AATGTAGGGCTTTTCACGCGTCTAATATC
65 CTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATC
62713 GTTATTATTA
Statistics
Matches: 957, Mismatches: 142, Indels: 43
0.84 0.12 0.04
Matches are distributed among these distances:
329 66 0.07
330 61 0.06
331 273 0.29
332 176 0.18
333 377 0.39
334 4 0.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (331 bp):
GATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAATTTTTTCCTCAATATTCGGCCACAATAC
TCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCATTT
TTCCTATTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTGATGCTCGTAAAAACAA
ATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTCAAGGAGTCTTGGCG
CCCAAAATCATGCAAAACTGAGCCGGACCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
TTACAC
Found at i:62535 original size:662 final size:666
Alignment explanation
Indices: 61261--62712 Score: 1921
Period size: 662 Copynumber: 2.2 Consensus size: 666
61251 ACCCCAACAT
* ** ** *
61261 GATTTCGGCTAAAATTTTGTAAAAACT-AACCTGAAATTTTTTTCCTCAATATAAGGCCATAATA
1 GATTTCGGCTAAAATTTTGCAAAAACTGAACC-GAAAAATTTTTCCTCAATATTCGGCCACAATA
* * * *
61325 CTCGTAAAAAATATATAATTTAAAGCCAAAAACATTGAATGACTTTTCACGCTTCTAATATCGTT
65 CTCGTAAAAAATATATAATTCAACGCAAAAAACATTGAATGACTTTTCACGCTTCTAATATCATT
* * * *
61390 TCTCTTATTTTTTTCCGAATTAATTTCTAATAAAATCGAAACAAGATTCTAATAATCGTAAAAAC
130 TCTCCTATTTTATACCGAATTAATTTCTAACAAAATCGAAACAAGATTCTAATAATCGTAAAAAC
61455 AAATCCTTAAATCCAATCTGAATGAGATTTGGCCAGATTAATATAAATATTTCAAGGAGTCTTGG
195 AAATCCTTAAATCCAATCTGAATGAGATTTGGCCAGATTAATATAAATATTTCAAGGAGTCTTGG
* * * *
61520 TGTCCAAAATCATGCAAAACTAAGCTGGTGCGCCGGAACACGTTTTTAGCAAAAAACTGTGATGG
260 TGCCCAAAATCATGCAAAACTAAGCTGGGGCCCCGGAACACGTTTTTAGCAAAAAACCGTGATGG
* *
61585 TTATTACACGATTTCGGCAAAAATTTTACAAAAACTGAGTCAAAATTTTTTTCCTTAATATTCGG
325 TTATTACACGATTTCGGCAAAAATTTTACAAAAAATGACTCAAAATTTTTTTCCTTAATATTCGG
* * * * * * * *** *
61650 CCATAATACTGGTTAAAAGTATATAATTTAATGCCAAAAAGATTGAAGGGTTTTTCACGTTTCTA
390 CCACAATACTGGTAAAAAATATATAATTCAACGACAAAAAGATGGAAGAACTTTTCACGCTTCTA
* *
61715 ATATCATTTTTCCTATTTTTTTTCGAATGAATTTCTAATAAAATCAAAACAAGATTCTGATGCTC
455 ATATCATTTTTCCTAGTTTTTTCCGAATGAATTTCTAATAAAATCAAAACAAGATTCTGATGCTC
*
61780 GTAAAAACAAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATGAATATAGATATTTCAAGG
520 GTAAAAACAAATCCTTAAATCCAATCTGACAGAGATTTGGTCAGATGAATATAGATATTTCAAGG
* *
61845 AGTCTTGGCACCCAAAATCAACCAAAACTGTGCC-AGGACCCCGGAACGCGTTTTTAGCCAAAAA
585 AGTATTGCCACCCAAAATCAACCAAAACTGTGCCGA-GACCCCGGAACGCGTTTTTAGCCAAAAA
61909 CAATGATGGATA-T-CAC
649 CAATGATGGATATTACAC
* *
61925 GATTTTGGCTAAAAAATTTTGCAAAAACTGAACC-AAAAATTATTCCTCAATATTCGGCCACAAT
1 GATTTCGGCT--AAAATTTTGCAAAAACTGAACCGAAAAATTTTTCCTCAATATTCGGCCACAAT
* * * *
61989 AGTCGTAAAAAATATATAATTCAACGCTAAAAAGATTGAA-GACTTTTCAGGCTTCTAATATCAT
64 ACTCGTAAAAAATATATAATTCAACGCAAAAAACATTGAATGACTTTTCACGCTTCTAATATCAT
* * * * **
62053 TTTTCCTA-TTTATACTGAATT-ATTTCTAACAAAATCGAAACAAGATTTTGATGCTCGTTAAAA
129 TTCTCCTATTTTATACCGAATTAATTTCTAACAAAATCGAAACAAGATTCTAATAATCG-T-AAA
* * * *
62116 AACAAATCCTTAAATCCAATCTGACTGAGATTTGGTCAGATTAATATAGATATTTTAAGGAGTCT
192 AACAAATCCTTAAATCCAATCTGAATGAGATTTGGCCAGATTAATATAAATATTTCAAGGAGTCT
* * *
62181 TTGTGCCCAAAATCATGC-AAACTGAG-TCGGGGCCCCGG-A-ACGTGTTTTAGCCAAAAACCGT
257 TGGTGCCCAAAATCATGCAAAACTAAGCT-GGGGCCCCGGAACACGT-TTTTAGCAAAAAACCGT
* * *
62242 GATGGTTATTACACGATTTCGGCTAAATTTTTGCAAAAAAATGACTCGAAAA-TTTTTTCCTTAA
320 GATGGTTATTACACGATTTCGGCAAAAATTTTAC-AAAAAATGACTC-AAAATTTTTTTCCTTAA
* *
62306 TATTTGGCCACAATACTTGTAAAAAATATATAATTCAACGACAAAAAGATGGAAGAACTTTTCAC
383 TATTCGGCCACAATACTGGTAAAAAATATATAATTCAACGACAAAAAGATGGAAGAACTTTTCAC
* * *
62371 GCTTCTAATATCATTTTTCCT-GTTTTTTCCGAATTAATTTCTAGTAAAATCGAAACAAGATTCT
448 GCTTCTAATATCATTTTTCCTAGTTTTTTCCGAATGAATTTCTAATAAAATCAAAACAAGATTCT
* * * * * *
62435 GATTCTCGTTAAAACAAATCGTTAAATCCAATTTGTCAGAGATTTGGTCAGATTAATATAGATAT
513 GATGCTCGTAAAAACAAATCCTTAAATCCAATCTGACAGAGATTTGGTCAGATGAATATAGATAT
* * *** *
62500 TTCAAGGAGTATTGCCTCCCAAAGTCTTGCAAAACTGTGCCGAGACCCCGGAACGCGTTTTTAGT
578 TTCAAGGAGTATTGCCACCCAAAATCAACCAAAACTGTGCCGAGACCCCGGAACGCGTTTTTAGC
** *
62565 CAAAAACCGTGATGGTTATTACAC
643 CAAAAACAATGATGGATATTACAC
*
62589 GATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATATTCGAG-CACAATA
1 GATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAAATTTTTCCTCAATATTCG-GCCACAATA
** * * * *
62653 CTATTAAAAAATATATAATTCAACGCAAAAAA-A-TGTAGGGCTTTTCACGCGTCTAATATC
65 CTCGTAAAAAATATATAATTCAACGCAAAAAACATTGAATGACTTTTCACGCTTCTAATATC
62713 GTTATTATTA
Statistics
Matches: 685, Mismatches: 88, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
661 7 0.01
662 286 0.42
663 179 0.26
664 134 0.20
665 59 0.09
666 16 0.02
667 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (666 bp):
GATTTCGGCTAAAATTTTGCAAAAACTGAACCGAAAAATTTTTCCTCAATATTCGGCCACAATAC
TCGTAAAAAATATATAATTCAACGCAAAAAACATTGAATGACTTTTCACGCTTCTAATATCATTT
CTCCTATTTTATACCGAATTAATTTCTAACAAAATCGAAACAAGATTCTAATAATCGTAAAAACA
AATCCTTAAATCCAATCTGAATGAGATTTGGCCAGATTAATATAAATATTTCAAGGAGTCTTGGT
GCCCAAAATCATGCAAAACTAAGCTGGGGCCCCGGAACACGTTTTTAGCAAAAAACCGTGATGGT
TATTACACGATTTCGGCAAAAATTTTACAAAAAATGACTCAAAATTTTTTTCCTTAATATTCGGC
CACAATACTGGTAAAAAATATATAATTCAACGACAAAAAGATGGAAGAACTTTTCACGCTTCTAA
TATCATTTTTCCTAGTTTTTTCCGAATGAATTTCTAATAAAATCAAAACAAGATTCTGATGCTCG
TAAAAACAAATCCTTAAATCCAATCTGACAGAGATTTGGTCAGATGAATATAGATATTTCAAGGA
GTATTGCCACCCAAAATCAACCAAAACTGTGCCGAGACCCCGGAACGCGTTTTTAGCCAAAAACA
ATGATGGATATTACAC
Done.