Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007524.1 Corchorus capsularis cultivar CVL-1 contig07545, 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: 92921
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1442 original size:13 final size:13
Alignment explanation
Indices: 1412--1475 Score: 51
Period size: 13 Copynumber: 5.1 Consensus size: 13
1402 TAATCTACTT
*
1412 AAATCTTCAGAT-
1 AAATCTTCAGTTG
* *
1424 -AATCTTGATTTG
1 AAATCTTCAGTTG
1436 AAATCTTCAGTTG
1 AAATCTTCAGTTG
* *
1449 AAATCTTCTGATG
1 AAATCTTCAGTTG
* *
1462 ATATCTTCTGTTG
1 AAATCTTCAGTTG
1475 A
1 A
1476 TAATATTCTC
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
11 8 0.20
13 33 0.80
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (13 bp):
AAATCTTCAGTTG
Found at i:1477 original size:13 final size:13
Alignment explanation
Indices: 1433--1475 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
1423 TAATCTTGAT
*
1433 TTGAAATCTTCAG
1 TTGAAATCTTCTG
1446 TTGAAATCTTCTG
1 TTGAAATCTTCTG
* *
1459 ATGATATCTTCTG
1 TTGAAATCTTCTG
1472 TTGA
1 TTGA
1476 TAATATTCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.44
Consensus pattern (13 bp):
TTGAAATCTTCTG
Found at i:14154 original size:2 final size:2
Alignment explanation
Indices: 14149--14199 Score: 61
Period size: 2 Copynumber: 26.0 Consensus size: 2
14139 TATACATAAA
* *
14149 AT AT AT AT ACT AT GT AT AT AT AT AT AT AT AT AT AT AT TT AT -T
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14191 A- AT AT AT AT
1 AT AT AT AT AT
14200 GTTTTTTTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 2 0.05
2 38 0.90
3 2 0.05
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:14296 original size:20 final size:18
Alignment explanation
Indices: 14271--14315 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14261 ACACATGTTT
14271 TACTAATAAATAATAATATA
1 TACTAATAAAT-A-AATATA
* *
14291 TACTAACAAATAAATATT
1 TACTAATAAATAAATATA
14309 TACTAAT
1 TACTAAT
14316 TTTGCTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 11 0.50
19 1 0.05
20 10 0.45
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.36
Consensus pattern (18 bp):
TACTAATAAATAAATATA
Found at i:17490 original size:31 final size:29
Alignment explanation
Indices: 17455--17528 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
17445 TCGATAATGG
*
17455 AGGGTGCAACGTGGAACAAAAATAAAACATA
1 AGGGTGCAAAGTGGAAC-AAAATAAAA-ATA
*
17486 AGGGTGCAAAAGT-GATCAAAATAAAAATA
1 AGGGTGC-AAAGTGGAACAAAATAAAAATA
*
17515 AGAGTGCAAAGTGG
1 AGGGTGCAAAGTGG
17529 CAGTCCGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.13
29 10 0.26
30 9 0.24
31 10 0.26
32 4 0.11
ACGTcount: A:0.50, C:0.09, G:0.26, T:0.15
Consensus pattern (29 bp):
AGGGTGCAAAGTGGAACAAAATAAAAATA
Found at i:22426 original size:53 final size:53
Alignment explanation
Indices: 22346--22524 Score: 288
Period size: 53 Copynumber: 3.4 Consensus size: 53
22336 CCCAATAATT
22346 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTATATCA
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTATATCA
* * *
22399 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCACCTCTCTCAA
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTATATC-A
* *
22453 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATTTACATC-
1 AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTATATCA
*
22505 AAAGTCCTCAAGCACAAGGG
1 AAAGTCCTCAAACACAAGGG
22525 CATCCATATT
Statistics
Matches: 116, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
52 19 0.16
53 49 0.42
54 48 0.41
ACGTcount: A:0.39, C:0.28, G:0.15, T:0.19
Consensus pattern (53 bp):
AAAGTCCTCAAACACAAGGGTATTCATCCCTAAACACAGAGGCATCTATATCA
Found at i:38492 original size:18 final size:19
Alignment explanation
Indices: 38456--38498 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
38446 ACTCATACTC
*
38456 AAACT-AACTGATTCAAAA
1 AAACTGAACTGACTCAAAA
38474 AAACTGAACTGACTC-AAA
1 AAACTGAACTGACTCAAAA
38492 AAACTGA
1 AAACTGA
38499 CTAAACCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.53, C:0.19, G:0.09, T:0.19
Consensus pattern (19 bp):
AAACTGAACTGACTCAAAA
Found at i:38552 original size:26 final size:26
Alignment explanation
Indices: 38523--38574 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
38513 TCAATAGATC
38523 CGGGGACTTTATTCTAAAATAAAAGT
1 CGGGGACTTTATTCTAAAATAAAAGT
38549 CGGGGACTTTATTCTAAAATAAAAGT
1 CGGGGACTTTATTCTAAAATAAAAGT
38575 AAAAAAAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (26 bp):
CGGGGACTTTATTCTAAAATAAAAGT
Found at i:40088 original size:3 final size:3
Alignment explanation
Indices: 40080--40152 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
40070 TGTAGTCTAT
*
40080 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
40128 ATA ATA ATA ATA ATA ACA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40153 GTTATATTAG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:41981 original size:74 final size:74
Alignment explanation
Indices: 41900--42051 Score: 252
Period size: 74 Copynumber: 2.1 Consensus size: 74
41890 GAAGGGAAAT
*
41900 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAAT-GGTTGAAACTCATAGAGGGGCTTTTTAGT
1 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGG-GGAAACTCATAGAGGGGCTTTTTAGT
*
41964 CATTCAAAAA
65 CACTCAAAAA
*
41974 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATGGAGGGGCTTTTTAGTC
1 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
*
42039 ACTCGAAAA
66 ACTCAAAAA
42048 GTGT
1 GTGT
42052 GAAAAGACCA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
74 71 0.97
75 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.23
Consensus pattern (74 bp):
GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
ACTCAAAAA
Found at i:42154 original size:3 final size:3
Alignment explanation
Indices: 42148--42198 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
42138 TATAGTATAT
42148 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42196 ATA
1 ATA
42199 TATTTATTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:53221 original size:16 final size:17
Alignment explanation
Indices: 53189--53221 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
53179 AAAAATTACT
*
53189 AAAAATTAGATTTGAAC
1 AAAAATTAGATTAGAAC
53206 AAAAATTA-ATTAGAAC
1 AAAAATTAGATTAGAAC
53222 GAAATTGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (17 bp):
AAAAATTAGATTAGAAC
Found at i:55894 original size:18 final size:20
Alignment explanation
Indices: 55868--55921 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
55858 AAAGAAGGAG
55868 AAGAGGAAAAAAAAGAA-AA
1 AAGAGGAAAAAAAAGAATAA
*
55887 TAAG-GAAAAGAAAAAGAATAA
1 -AAGAGGAAA-AAAAAGAATAA
55908 AAGAGGAAAAAAAA
1 AAGAGGAAAAAAAA
55922 AGAAGGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 19 0.66
21 6 0.21
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (20 bp):
AAGAGGAAAAAAAAGAATAA
Found at i:55936 original size:20 final size:18
Alignment explanation
Indices: 55874--55951 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 18
55864 GGAGAAGAGG
55874 AAAAAAAAGAAAATAAGGA
1 AAAAAAAAGAAAA-AAGGA
55893 AAAGAAAAAGAATAAAAGAGGA
1 AAA-AAAAAG-A-AAAA-AGGA
*
55915 AAAAAAAAGAAGGAAAATGA
1 AAAAAAAAGAA--AAAAGGA
55935 AAAAGAAAA-AAAAAAGG
1 AAAA-AAAAGAAAAAAGG
55952 CCATGTCAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
18 5 0.10
19 4 0.08
20 16 0.32
21 15 0.30
22 10 0.20
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAGGA
Found at i:62742 original size:20 final size:20
Alignment explanation
Indices: 62719--62756 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
62709 AAGATTCTCT
62719 AATTCCTCA-TCCCCTTCTTC
1 AATTCCTCACT-CCCTTCTTC
*
62739 AATTTCTCACTCCCTTCT
1 AATTCCTCACTCCCTTCT
62757 ACTATTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.16, C:0.42, G:0.00, T:0.42
Consensus pattern (20 bp):
AATTCCTCACTCCCTTCTTC
Found at i:65070 original size:20 final size:20
Alignment explanation
Indices: 65033--65071 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
65023 TCTCTAATTC
* * *
65033 CTCATCCCCTTTTTCTATTT
1 CTCACCCCCTTCTACTATTT
65053 CTCACCCCCTTCTACTATT
1 CTCACCCCCTTCTACTATT
65072 CTATCAATCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.41, G:0.00, T:0.46
Consensus pattern (20 bp):
CTCACCCCCTTCTACTATTT
Found at i:68559 original size:12 final size:13
Alignment explanation
Indices: 68542--68574 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
68532 TGTATAATTG
68542 TAATTGTACT-TA
1 TAATTGTACTGTA
*
68554 TAATTGTATTGTA
1 TAATTGTACTGTA
68567 TAATTGTA
1 TAATTGTA
68575 ATTTGTCAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (13 bp):
TAATTGTACTGTA
Found at i:70662 original size:21 final size:21
Alignment explanation
Indices: 70636--70697 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
70626 TAATCCTATG
70636 TTGGAGGTTTCTTATTTATAT
1 TTGGAGGTTTCTTATTTATAT
70657 TTGGAGGTTTCTTATTTATAT
1 TTGGAGGTTTCTTATTTATAT
*
70678 TTAGAGGTTTCTTATTTATA
1 TTGGAGGTTTCTTATTTATA
70698 ATTAGGTTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.56
Consensus pattern (21 bp):
TTGGAGGTTTCTTATTTATAT
Found at i:70702 original size:21 final size:21
Alignment explanation
Indices: 70639--70710 Score: 110
Period size: 21 Copynumber: 3.5 Consensus size: 21
70629 TCCTATGTTG
*
70639 GAGGTTTCTTATTTATATTTG
1 GAGGTTTCTTATTTATATTTA
70660 GAGGTTTCTTATTTATATTTA
1 GAGGTTTCTTATTTATATTTA
*
70681 GAGGTTTCTTATTTATAATTA
1 GAGGTTTCTTATTTATATTTA
*
70702 G-GTTTTCTT
1 GAGGTTTCTT
70711 TATAATTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 7 0.15
21 41 0.85
ACGTcount: A:0.21, C:0.06, G:0.17, T:0.57
Consensus pattern (21 bp):
GAGGTTTCTTATTTATATTTA
Found at i:80025 original size:14 final size:14
Alignment explanation
Indices: 79992--80030 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
79982 AAATTTCCTT
*
79992 AACCCGAAACTAACCT
1 AACCC-AAA-TAACCG
80008 AACCCAAATAACCG
1 AACCCAAATAACCG
80022 AACCCAAAT
1 AACCCAAAT
80031 CCAATCCGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.49, C:0.36, G:0.05, T:0.10
Consensus pattern (14 bp):
AACCCAAATAACCG
Found at i:85826 original size:60 final size:60
Alignment explanation
Indices: 85755--85901 Score: 249
Period size: 60 Copynumber: 2.5 Consensus size: 60
85745 AATGCACGCG
*
85755 TCTTCTCTTTATAACTATAATTTGAAAAAATGTATAACAACTTTTTATTGCGCGCTCGAA
1 TCTTCTCTTTATAACTATAATTTAAAAAAATGTATAACAACTTTTTATTGCGCGCTCGAA
***
85815 TCTTCTCTTTATAACTATAATTTAAAAAAATGTATAATGGCTTTTTATTGCGCGCTCGAA
1 TCTTCTCTTTATAACTATAATTTAAAAAAATGTATAACAACTTTTTATTGCGCGCTCGAA
*
85875 TCTTCTCTTTATAACTATATTTTAAAA
1 TCTTCTCTTTATAACTATAATTTAAAA
85902 GCTCAACTCC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.43
Consensus pattern (60 bp):
TCTTCTCTTTATAACTATAATTTAAAAAAATGTATAACAACTTTTTATTGCGCGCTCGAA
Found at i:88240 original size:818 final size:815
Alignment explanation
Indices: 86107--88462 Score: 2803
Period size: 818 Copynumber: 2.8 Consensus size: 815
86097 CACTTAATTT
* * *
86107 CGTTACAAAGAAGCTTTTTGTCTTATTCGAGTCGGGTCGGTCCACTATGAGGCCAAAACTCTC-C
1 CGTTACAAAGAAGTTTTTTGTCTTATT-AAGTCGGGTCGGTCCATTATGAGGCCAAAACTCTCTC
* * * *
86171 CAAATATAATTTTCTCCATTCATAAGACTTAAACTCGAGACCTTAG-CTAACA-AAACAAGTGCA
65 CACA-ATAATTTTCTCCATTCATAAGACTCAAACTCGACACCTT-GTCTAA-AGGAACAAGTGCA
* **
86234 TAACCAAGTAGATTCTTTTACAAGGCTGCTTTTATGCAATGAAAAATTGCTATTCTTTGATCTTT
127 TAACCACGTAGATTCTTTTACAAAACTGCTTTTATGCAATGAAAAATTGCTATTCTTTGA-CTTT
* * *
86299 ACGCCAAACCAACTCCTATTGTAACGTACA-AGTTAATGGTTGCTTATTAATTGGATT-CTTGGC
191 ACGCCAAACCAA-TCCTACTGTAACGTACAGAATTAATGGTTTCTTATTAATTGGATTCCTTGGC
* * *
86362 TACTTTCTTCGTATATTAATTA-----TG-TTT-TTTTATAGTATTTTTTTTTG-TGTTGTTTAT
255 TGCTTTCTTCATATATTAATTATGTTTTGTTTTGTTTTATAGTATTTTTTTTTGTTGTTGTTTGT
* * *
86419 TGGAGTCTTCCTGCAAAACTTTCATGATTCCAATGGCTATCTAAGCTTTACTTGCCTTAATTTGT
320 TGGAG------T----AA----C-----TCCAATGGCTATATGAGCTTTACTTTCCTTAATTTGT
* *
86484 GAAAGAC-AATAAAAGAGTACTCATTAATTATTACCTAGTTGTTCACAATTACTTCCTTTCCATC
366 GAAAG-CTAATAAAAG-GTACTCATTAATTATTGCCTAGTTGTTCACAATTACTTCCTTTCCATA
* *
86548 TATTTCCTCTACAATCAGATTCTCCATAGATTTACCAATAAAGATAATGAAACTTTTTTGAGAAT
429 TATTTCCTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAATGAAACTTTTTTGAGGAT
* * * * * * *
86613 TTTGAGAGCGGTCAACATCTGTGGTTTGCCCCTGTGGCATTGCCCAATAAATGCTTTCTAGCCTT
494 TTTGAGAGCGGTCAAAATCTGTGGTTTGCCCCTGTGGCAATGCCTAATAATTACTTTCTAGTCTA
* * *
86678 AAATGGATTCGACCCTATCATT-ATAAGAAGCCAGATTAAACCCTTACATATTCACAACTTCAAA
559 AAATGGAGTCGACCCT-TCGTTGATAAGAAGCTAGATTAAACCC-T-C--ATT--CAACTTCAAA
86742 TTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATAGGGAATTGTTTAATTTG---T--
617 TTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATAGGGAATTGTTTAATTTGTAATAA
* *
86802 GAATATCATAAAATTTCAAGTTCAATAACTTGTGCAAATTAACATTGCATATAAGAAAATATAGA
682 GAATATCATAAAATTTCAAGTTCAATAACTTGTGCAAATAAACATTGCATATAAGAAAATACAGA
*
86867 ACGCACATTTACATTCTATATATACTTTATTATATTATTAGAAAATTAATATTAAACCCTTCATG
747 AC-CACA--TACATTCTATACATACTTTATTATATTATTAGAAAATTAATATTAAACCCTTCATG
86932 ATTCTTC
809 ATTCTTC
* * * *
86939 TGTTACAAAGGAGTTTTTAGTCTT-TTCAAGTCGGGTCGGTCAACTATATATAAGGCCAAAACTC
1 CGTTACAAAGAAGTTTTTTGTCTTATT-AAGTCGGGTCGGTC--C-AT-TATGAGGCCAAAACTC
* * * * * * *
87003 TATCAACAATAATTTTCTCCATTGACAAGAATCAAACTCGACACCTTATCTAAAGGAACATGTGC
61 TCTCCACAATAATTTTCTCCATTCATAAGACTCAAACTCGACACCTTGTCTAAAGGAACAAGTGC
* * *
87068 ATAACCACGTAGATTCTTTTACAAAACTGCTTTTATGCAATGAAAAATTGCAATTCTCTGATTTT
126 ATAACCACGTAGATTCTTTTACAAAACTGCTTTTATGCAATGAAAAATTGCTATTCTTTGA-CTT
* *
87133 TACG-----CC--TCCTACTGTAATGTAC-GAATTAATGGTTTCCTATTAATTGGATTCCTTGGC
190 TACGCCAAACCAATCCTACTGTAACGTACAGAATTAATGGTTTCTTATTAATTGGATTCCTTGGC
87190 TGCTTTCTTCATATATTAATTATGTTTTGTTTTGTTTTATAGTATTTTTTTTATGTTGTT-TATT
255 TGCTTTCTTCATATATTAATTATGTTTTGTTTTGTTTTATAGTATTTTTTTT-TGTTGTTGT-TT
** * * *
87254 GGATTCTTCCTACAAAACTTTCATGACTCCAATGGCTATATGTGCTTTACTTTCCTTAATTTATG
318 -G-----T--T---GGA--GT-A--ACTCCAATGGCTATATGAGCTTTACTTTCCTTAATTTGTG
* * *
87319 AAA--TACCATAAAAGGGTACTCATTAATTATTGCCTGGTTGTACACAATCACTTCCTTTCCATC
367 AAAGCTA--ATAAAA-GGTACTCATTAATTATTGCCTAGTTGTTCACAATTACTTCCTTTCCAT-
* * * * * *
87382 A-AATTCCTCTACAACCAGATTCCCCAAAGATTTTCCAATAAAGATGATGAAACTTTTTTAAGGA
428 ATATTTCCTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAATGAAACTTTTTTGAGGA
*
87446 TTTTGAGAGCGGTCAAAATCTATGGTTTGCCCCTGTGGCAATGCCTAATAATTACTTTCTAGTCT
493 TTTTGAGAGCGGTCAAAATCTGTGGTTTGCCCCTGTGGCAATGCCTAATAATTACTTTCTAGTCT
* * *
87511 AAAATGGAGTCGACCCATTCGTTGATAAAAAGCTAGATTAGA-CC-C-TT-AACTTCAAAATTTG
558 AAAATGGAGTCGACCC-TTCGTTGATAAGAAGCTAGATTAAACCCTCATTCAACTTCAAATTTTG
* *
87572 CTTGATCTTTATCCTCTCAATGTCTATGTACTTAATAGGGAATTGTTTAATTTGTAATAAGAATA
622 CTTGATCTTTATCCTCTCAATGGCTATGAACTTAATAGGGAATTGTTTAATTTGTAATAAGAATA
* *
87637 TCATAAAGTTTCAAGTTCAATAACTTGTGCAAATAAACATTGCATATGAGAAAATACAGAA-CAC
687 TCATAAAATTTCAAGTTCAATAACTTGTGCAAATAAACATTGCATATAAGAAAATACAGAACCAC
* *
87701 A-AGCATTCTATACATACTTTATTATATTATTAGAAAATTAATATTAAACCCTTCGTGATTTTTC
752 ATA-CATTCTATACATACTTTATTATATTATTAGAAAATTAATATTAAACCCTTCATGATTCTTC
* *
87765 CGTTACAAATAAGTTTTTTGTCTTATTATAGTCGGGTCGGTCCATTATGAGGCCAAATCTCTCTC
1 CGTTACAAAGAAGTTTTTTGTCTTATTA-AGTCGGGTCGGTCCATTATGAGGCCAAAACTCTCTC
* * * * *
87830 CACAATAATTTTTTCCCGTTCATAAGTCCCAAACTCGACACCTTGTCTAAAGGAACAAGTGTATA
65 CACAATAATTTTCT-CCATTCATAAGACTCAAACTCGACACCTTGTCTAAAGGAACAAGTGCATA
* * * ** * *
87895 ACCACTTAGATTCTTTTAAAAAACCGCTTTTATGCAATGAATTATAGTTATTCTTTGACTTGTAC
129 ACCACGTAGATTCTTTTACAAAACTGCTTTTATGCAATGAAAAATTGCTATTCTTTGACTT-TAC
*
87960 GCCAAACCAAGTCCTACTGTAACGTACGAGATATATAATGGTTTCTTATAAATTGGATTCCTTGG
193 GCCAAACCAA-TCCTACTGTAACGTAC-AGA-AT-TAATGGTTTCTTATTAATTGGATTCCTTGG
*
88025 CTGCTTTCTTCATATATTAATTATGTTTTGTTTTGTTTTATAGTAATTTTTTTTGTTGTTGTTTG
254 CTGCTTTCTTCATATATTAATTATGTTTTGTTTTGTTTTATAGTATTTTTTTTTGTTGTTGTTTG
*
88090 TTGGAGT-ACTCCAATGGCTATTTGAGCTTTACTTTCCTTAATTTGTGAAAGCTAATAAAATGGT
319 TTGGAGTAACTCCAATGGCTATATGAGCTTTACTTTCCTTAATTTGTGAAAGCTAATAAAA-GGT
*
88154 ACTCATTAATTATTGCCTAGTTGTTCACAATTACTTCATTTCCATATATTTCCTCTACAACCAGA
383 ACTCATTAATTATTGCCTAGTTGTTCACAATTACTTCCTTTCCATATATTTCCTCTACAACCAGA
* * *
88219 TTCTCCATAGATTTACCAATAAAGATAAAGAAACTTTTTTGAGGATTTTGAGAACGGTCAAAGTC
448 TTCTCCATAGATTTACCAATAAAGATAATGAAACTTTTTTGAGGATTTTGAGAGCGGTCAAAATC
*
88284 TGTGGTTTGCCCCTGTGCCAATGCCTAATAATTACTTTCTAGTCTAAAATGGAGTCGACCCTTTC
513 TGTGGTTTGCCCCTGTGGCAATGCCTAATAATTACTTTCTAGTCTAAAATGGAGTCGACCC-TTC
*
88349 GTTGATAAGAAGCTAGATTAAACCCTTACATAGTCAGAACTTCAAATTTTGCTTGGTCTTTATCC
577 GTTGATAAGAAGCTAGATTAAACCC-T-CAT--TC--AACTTCAAATTTTGCTTGATCTTTATCC
88414 TCTCAATGGCTATGAACTTAATAGGGAATTGTTTAATTTGTAATAAGAA
636 TCTCAATGGCTATGAACTTAATAGGGAATTGTTTAATTTGTAATAAGAA
88463 AATATAGAGA
Statistics
Matches: 1309, Mismatches: 138, Indels: 158
0.82 0.09 0.10
Matches are distributed among these distances:
817 1 0.00
818 246 0.19
819 2 0.00
820 2 0.00
822 2 0.00
823 32 0.02
824 97 0.07
825 68 0.05
826 79 0.06
827 54 0.04
828 106 0.08
829 3 0.00
830 64 0.05
831 17 0.01
832 36 0.03
833 3 0.00
834 226 0.17
835 171 0.13
836 87 0.07
837 6 0.00
839 1 0.00
841 1 0.00
843 2 0.00
844 1 0.00
845 1 0.00
848 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.38
Consensus pattern (815 bp):
CGTTACAAAGAAGTTTTTTGTCTTATTAAGTCGGGTCGGTCCATTATGAGGCCAAAACTCTCTCC
ACAATAATTTTCTCCATTCATAAGACTCAAACTCGACACCTTGTCTAAAGGAACAAGTGCATAAC
CACGTAGATTCTTTTACAAAACTGCTTTTATGCAATGAAAAATTGCTATTCTTTGACTTTACGCC
AAACCAATCCTACTGTAACGTACAGAATTAATGGTTTCTTATTAATTGGATTCCTTGGCTGCTTT
CTTCATATATTAATTATGTTTTGTTTTGTTTTATAGTATTTTTTTTTGTTGTTGTTTGTTGGAGT
AACTCCAATGGCTATATGAGCTTTACTTTCCTTAATTTGTGAAAGCTAATAAAAGGTACTCATTA
ATTATTGCCTAGTTGTTCACAATTACTTCCTTTCCATATATTTCCTCTACAACCAGATTCTCCAT
AGATTTACCAATAAAGATAATGAAACTTTTTTGAGGATTTTGAGAGCGGTCAAAATCTGTGGTTT
GCCCCTGTGGCAATGCCTAATAATTACTTTCTAGTCTAAAATGGAGTCGACCCTTCGTTGATAAG
AAGCTAGATTAAACCCTCATTCAACTTCAAATTTTGCTTGATCTTTATCCTCTCAATGGCTATGA
ACTTAATAGGGAATTGTTTAATTTGTAATAAGAATATCATAAAATTTCAAGTTCAATAACTTGTG
CAAATAAACATTGCATATAAGAAAATACAGAACCACATACATTCTATACATACTTTATTATATTA
TTAGAAAATTAATATTAAACCCTTCATGATTCTTC
Found at i:90485 original size:818 final size:831
Alignment explanation
Indices: 88456--90938 Score: 3406
Period size: 818 Copynumber: 3.0 Consensus size: 831
88446 TTAATTTGTA
* * *
88456 ATAAGAAAATATAGAGAGCACATGTACATTCTATATATACTTTACTATATTATTAGAAAATAAAT
1 ATAAGAAAATATAGAAAGCACATGTACATTCTATACATACTTTATTATATTATTAGAAAATAAAT
* * * *
88521 ATTAAACCCTTCGTGATTCTTCCATTACAAAGAAGCTTTTAGTCTTTTCGAGTC-GGGTCGGTCC
66 ATTAAACCCTTCGTGATTCTTCCGTTACAAAGCAGCTTTTAGGCTTTTCGA-TCAGGGTCAGTCC
* * * * * *
88585 ATTATGAGGCCAAAACTCTCTCAATAATAAATT-TCTCCGTTCACAAGACTTAAACTCGAGACCT
130 ACTATGAGGCCAAAACTCTCTCAACAATAATTTATCTCTGTTCAAAAGACTCAAACTCGAGACCT
* *
88649 TGCCTAAAGGAACAAGTGCATAACCACTTAGATTCTTTTATAAAGTTGCTTTTATGCAATGAAAA
195 TGCCTAAAGGAACAAGTGCATAACCACTTAGATTCTTTTACAAAGCTGCTTTTATGCAATGAAAA
* * * * * ** ** *
88714 ATTGTTATTTCTCGATCTTTACGCCAAACCAACTCCTTTTGTAACGTACGAGTTAATGGTTTCTT
260 ATAGCTA-TTCTTGAACTCTACGCCAAACCAACTCCTACTGTAACGTACGACATAATAGTTTCTT
* * * * *
88779 ATTAATTGGATTTCTCCGATGCTTTCTTCTTATATTAATTATGTTTTGTTTTGTCTTATAGTAAT
324 ATTAATTAGATTCCTCCGCTACTTTCTTCATATATTAATTATGTTTTGTTTTGTCTTATAG---T
* * * * *
88844 ATTTTTTTGTGTGTTGTTTATTGGATTTTTCCTGTAAAACTTTCATGATTCC-ATTGCCAACTGA
386 A-TTTTAT-TGTGTTGTTTATTGG----TT-CTG--AAAC-GTCA-GATTCCAATCGCTAACTAA
*
88908 TCTTTACTTGCCTTAAGTTATGAAAGACCATAAAAGGGTACTCATTAATTATTGCCTAGTTGTTC
440 TCTTTACTTGCCTTAATTTATGAAAGACCATAAAAGGGTACTCATTAATTATTGCCTAGTTGTTC
*
88973 ACAATTACTTCCTTTCCATCTATTTCTTCTATAACCAGATTCTCCATAGATTTACCAATAAAGAT
505 A-AATTACTTCCTTTCCATCTATTTCTTCTACAACCAGATTCTCCATAGATTTACCAATAAAGAT
*
89038 AATGAAACTTTTTTTAGGATTTTGAGAGCGGTCAAAATCTATGGTTTGCCCATGTGGCATTGCCT
569 AATGAAACTTTTTTGAGGATTTTGAGAGCGGTCAAAATCTATGGTTTGCCCATGTGGCATTGCCT
*
89103 AATAAGTACTTTCTAGCCTAAAATGGATTCGACCCTTTCGTTATAAGAAGCTAGATTAGA-CCTT
634 AATAAGTACTTTCTAGCCTAAAATGGATTTGACCCTTTCGTTATAAGAAGCTAGATTAGACCCTT
* * *
89167 ACATAGTCAGAATTTCAAATTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACGTAATAGAGA
699 ACATAGTAAGAACTTCAAATTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATAG-GA
* * *
89232 ATTGTTTAATTTGTAATAAGAATATCATAAATTTTCAAGTTCAATAACTTGCGCAAATTAACATT
763 ATTGTTTAATTTGTAATAAGAATTTCATAAAATTTCAAGTTCAATAACTTGCGCAAATTAACACT
*
89297 ACGT
828 ACAT
89301 ATAAGAAAATATAGAAAGCACATGTACATTCTATACATACTTTATTATATTATTAGAAAATAAAT
1 ATAAGAAAATATAGAAAGCACATGTACATTCTATACATACTTTATTATATTATTAGAAAATAAAT
*
89366 ATTAAACCCTTCGTGATTCTTCCGTTACAAAGCAGCTTTTAGGCTTTTCGATCCGGGTCAGTCCA
66 ATTAAACCCTTCGTGATTCTTCCGTTACAAAGCAGCTTTTAGGCTTTTCGATCAGGGTCAGTCCA
* *
89431 TTATGAGGCCAAAACTCTCTCAACAATAATTTATTTCTGTTCAAAAGACTCAAACTCGAGACCTT
131 CTATGAGGCCAAAACTCTCTCAACAATAATTTATCTCTGTTCAAAAGACTCAAACTCGAGACCTT
* * *
89496 GCCTAAAGTAACAAGTGCATAACCACTTAGATTCTTTTACAGAGCTGCTTTTATTCAATGAAAAA
196 GCCTAAAGGAACAAGTGCATAACCACTTAGATTCTTTTACAAAGCTGCTTTTATGCAATGAAAAA
* **
89561 TAGCTATTCTTTAACCTCTACGCCAAACCAACTCCTACTGTAACGTACGGGATAATAGTTTCTTA
261 TAGCTATTCTTGAA-CTCTACGCCAAACCAACTCCTACTGTAACGTACGACATAATAGTTTCTTA
* **
89626 TTAATTGGATTCCTTGGCTACTTTCTTCATATATTAATTATGTTTTGTTTTGT-TT-T-GT-TTT
325 TTAATTAGATTCCTCCGCTACTTTCTTCATATATTAATTATGTTTTGTTTTGTCTTATAGTATTT
* * * * *
89687 ATATT-T-TT-TTT-TT-G-T-TG-GA-GT-A-A-TCCAATTGCTATCTGAGT-TTTACTTTCCT
390 -TATTGTGTTGTTTATTGGTTCTGAAACGTCAGATTCCAATCGCTAACT-AATCTTTACTTGCCT
* * * * * *
89739 TAATTTGTGAAAG-CTAATAAAAAGGTAATCATTAATTATTGCCTTGTTGTTCAATGTTACTTCC
453 TAATTTATGAAAGAC-CATAAAAGGGTACTCATTAATTATTGCCTAGTTGTTCAA-ATTACTTCC
* *
89803 TTTCCATATATTTCCTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAATGAAACTTTT
516 TTTCCATCTATTTCTTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAATGAAACTTTT
* * *
89868 TTGAGGATTTTGAGAGCGGTCAAAATCTGTGGTTTGTCCC-TGTGGCATTGCCCAATAAATACTT
581 TTGAGGATTTTGAGAGCGGTCAAAATCTATGGTTTG-CCCATGTGGCATTGCCTAATAAGTACTT
* * *
89932 TCTAGCCTTAAATGGATTTGACCCTTTCGTTATAAGAAGCTAAATTAGACCCTTACATAGTAACA
645 TCTAGCCTAAAATGGATTTGACCCTTTCGTTATAAGAAGCTAGATTAGACCCTTACATAGTAAGA
89997 ACTTCAAATTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATATGGAATTGTTTAATT
710 ACTTCAAATTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATA-GGAATTGTTTAATT
*
90062 TGTAATAAGAATTTCATAAAATTTCAAGTTCAATAACTTGTGCAAATTAACACTACAT
774 TGTAATAAGAATTTCATAAAATTTCAAGTTCAATAACTTGCGCAAATTAACACTACAT
* *
90120 ATAAGAAAATATAGAAAGCACATGTACATTCTATATATACTTTATTATATTATTAGAACATAAAT
1 ATAAGAAAATATAGAAAGCACATGTACATTCTATACATACTTTATTATATTATTAGAAAATAAAT
* * * * **
90185 ATTAAACCCTTCGTGATTTTTCCGTTACAAAG-ATGTTTTTAGTCTTTTTGAGT-AGGGTTGGTC
66 ATTAAACCCTTCGTGATTCTTCCGTTACAAAGCA-GCTTTTAGGCTTTTCGA-TCAGGGTCAGTC
90248 CACTATGAGGCCAAAACTCTCTCAACAATAATTT-TCTCTGTTCAAAAGACTCAAACTCGAGACC
129 CACTATGAGGCCAAAACTCTCTCAACAATAATTTATCTCTGTTCAAAAGACTCAAACTCGAGACC
* *
90312 TTGCTTAAAGGAACAAGTGCATAACCACTTAGATTCTTTTACAAAGTTGCTTTTATGCAATGAAA
194 TTGCCTAAAGGAACAAGTGCATAACCACTTAGATTCTTTTACAAAGCTGCTTTTATGCAATGAAA
* * * *
90377 AATAGGTATTTCTTGATA-TTTACGCCAAACCAACTCCTACTGTAACGTACGACTTACT-GATTT
259 AATAGCTA-TTCTTGA-ACTCTACGCCAAACCAACTCCTACTGTAACGTACGACATAATAG-TTT
*
90440 CTTATTAATTAGATTCCTCCGCTACTTTCTTCTTATATTAATTATGTTTTGTTTTGTCTTATAGT
321 CTTATTAATTAGATTCCTCCGCTACTTTCTTCATATATTAATTATGTTTTGTTTTGTCTTATAGT
* *
90505 ATTTTTTTGTGTTGTTTATTGGATTTTTCCTGCAAAACTTTCATGATTCCAATCGCTAACTAATC
386 ATTTTATTGTGTTGTTTATTGG----TT-CTG--AAAC-GTCA-GATTCCAATCGCTAACTAATC
*
90570 TTTACTTGCCTTAATTTATGAAAGACCATAAAAGGGTACTCATTTATTATTGCCTAGTTGTTCAA
442 TTTACTTGCCTTAATTTATGAAAGACCATAAAAGGGTACTCATTAATTATTGCCTAGTTGTTC-A
90635 AATTACTTCCTTTCCATCTATTTCTTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAA
506 AATTACTTCCTTTCCATCTATTTCTTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAA
* *
90700 TGAAACTTTTTTGAGGATTTTGAGAGTGGTCAAAATCTATGGTTTCCCCATGTGGCATTGCCTAA
571 TGAAACTTTTTTGAGGATTTTGAGAGCGGTCAAAATCTATGGTTTGCCCATGTGGCATTGCCTAA
* * *
90765 TAAGTACTTTCTAGTCTAAAATGGATTCT-ACTCTTTCATTATAAGAAGCTAGATTAGACCCTTA
636 TAAGTACTTTCTAGCCTAAAATGGATT-TGACCCTTTCGTTATAAGAAGCTAGATTAGACCCTTA
* * * *
90829 CATAGTGAGAACTTCAAATTTTGCTTGATCTTGATCCTGTCAATGGTTATGAACTTAATAGGGAA
700 CATAGTAAGAACTTCAAATTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATA-GGAA
* *
90894 TTGTATAATTTGTAATAAGAATATT-ATAAAATTTCAAGTTTAATA
764 TTGTTTAATTTGTAATAAGAAT-TTCATAAAATTTCAAGTTCAATA
90939 GGGATTCCTC
Statistics
Matches: 1461, Mismatches: 130, Indels: 97
0.87 0.08 0.06
Matches are distributed among these distances:
817 6 0.00
818 424 0.29
819 287 0.20
820 5 0.00
821 6 0.00
822 4 0.00
823 3 0.00
824 3 0.00
825 2 0.00
826 3 0.00
828 1 0.00
831 1 0.00
833 3 0.00
834 2 0.00
835 3 0.00
836 3 0.00
837 1 0.00
838 5 0.00
839 3 0.00
840 1 0.00
841 6 0.00
842 339 0.23
843 7 0.00
844 3 0.00
845 157 0.11
846 183 0.13
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.38
Consensus pattern (831 bp):
ATAAGAAAATATAGAAAGCACATGTACATTCTATACATACTTTATTATATTATTAGAAAATAAAT
ATTAAACCCTTCGTGATTCTTCCGTTACAAAGCAGCTTTTAGGCTTTTCGATCAGGGTCAGTCCA
CTATGAGGCCAAAACTCTCTCAACAATAATTTATCTCTGTTCAAAAGACTCAAACTCGAGACCTT
GCCTAAAGGAACAAGTGCATAACCACTTAGATTCTTTTACAAAGCTGCTTTTATGCAATGAAAAA
TAGCTATTCTTGAACTCTACGCCAAACCAACTCCTACTGTAACGTACGACATAATAGTTTCTTAT
TAATTAGATTCCTCCGCTACTTTCTTCATATATTAATTATGTTTTGTTTTGTCTTATAGTATTTT
ATTGTGTTGTTTATTGGTTCTGAAACGTCAGATTCCAATCGCTAACTAATCTTTACTTGCCTTAA
TTTATGAAAGACCATAAAAGGGTACTCATTAATTATTGCCTAGTTGTTCAAATTACTTCCTTTCC
ATCTATTTCTTCTACAACCAGATTCTCCATAGATTTACCAATAAAGATAATGAAACTTTTTTGAG
GATTTTGAGAGCGGTCAAAATCTATGGTTTGCCCATGTGGCATTGCCTAATAAGTACTTTCTAGC
CTAAAATGGATTTGACCCTTTCGTTATAAGAAGCTAGATTAGACCCTTACATAGTAAGAACTTCA
AATTTTGCTTGATCTTTATCCTCTCAATGGCTATGAACTTAATAGGAATTGTTTAATTTGTAATA
AGAATTTCATAAAATTTCAAGTTCAATAACTTGCGCAAATTAACACTACAT
Found at i:90523 original size:22 final size:23
Alignment explanation
Indices: 90486--90532 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
90476 ATTAATTATG
* *
90486 TTTTGTTTTGTCTTATAGTATTT
1 TTTTGTGTTGTCTTATAGGATTT
*
90509 TTTTGTGTTGT-TTATTGGATTT
1 TTTTGTGTTGTCTTATAGGATTT
90531 TT
1 TT
90533 CCTGCAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.11, C:0.02, G:0.17, T:0.70
Consensus pattern (23 bp):
TTTTGTGTTGTCTTATAGGATTT
Found at i:91210 original size:41 final size:41
Alignment explanation
Indices: 91153--91233 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
91143 TTATAACTAT
* *
91153 GGGCTAAACCTGAATTTATTTTCTTACCTTAATTATTAGGG
1 GGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAGGG
*
91194 GGGCTAAACCTGAATTTAATTTATTTCCTTAATTATTAGG
1 GGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAGG
91234 AGGGAAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (41 bp):
GGGCTAAACCTGAATTTAATTTATTACCTTAATTATTAGGG
Done.