Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014542.1 Corchorus capsularis cultivar CVL-1 contig14563, 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: 66165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1237 original size:23 final size:22
Alignment explanation
Indices: 1210--1259 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
1200 CATTTTCCAA
1210 TAACCCCTTAGCAATATATCTAG
1 TAACCCCTTAG-AATATATCTAG
*
1233 TAA-CCCTTTGAATATATCTAG
1 TAACCCCTTAGAATATATCTAG
1254 TAACCC
1 TAACCC
1260 TTTGAGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 14 0.56
22 8 0.32
23 3 0.12
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (22 bp):
TAACCCCTTAGAATATATCTAG
Found at i:1248 original size:21 final size:21
Alignment explanation
Indices: 1222--1264 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1212 ACCCCTTAGC
1222 AATATATCTAGTAACCCTTTG
1 AATATATCTAGTAACCCTTTG
1243 AATATATCTAGTAACCCTTTG
1 AATATATCTAGTAACCCTTTG
1264 A
1 A
1265 GAGGGAACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (21 bp):
AATATATCTAGTAACCCTTTG
Found at i:1609 original size:11 final size:11
Alignment explanation
Indices: 1593--1635 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
1583 TATACTATAT
1593 CTAATTAATAG
1 CTAATTAATAG
*
1604 CTAATTAATAT
1 CTAATTAATAG
1615 CTAATTAATAG
1 CTAATTAATAG
*
1626 TTAATTAATA
1 CTAATTAATA
1636 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:1617 original size:22 final size:22
Alignment explanation
Indices: 1589--1635 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
1579 CCACTATACT
1589 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
1611 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
1633 ATA
1 ATA
1636 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:7784 original size:18 final size:18
Alignment explanation
Indices: 7761--7795 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
7751 CTCCTATTTA
*
7761 ACATATACATATTCATAC
1 ACATATACATATGCATAC
*
7779 ACATATATATATGCATA
1 ACATATACATATGCATA
7796 ATTAGTGGAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (18 bp):
ACATATACATATGCATAC
Found at i:9799 original size:128 final size:127
Alignment explanation
Indices: 9637--10016 Score: 654
Period size: 128 Copynumber: 3.0 Consensus size: 127
9627 GCTTGACTCC
*
9637 TATATGTTATAACATCATGAAGAGCACAAAATTGTTAATA-CCAACACATAACAAGTTGAAAATT
1 TATATGTTATAACATCAGGAAGAGCACAAAATTGTTAATATCCAACACATAACAAGTTGAAAA--
* * * *
9701 CTAGTCTTGCCTTTCATTATTGAATGTTTGAGAGATGGACTTACCAAAAAGAGAACAGTTTTGT
64 CTAGTCTTGCCTTTCATTATTCAATGTTTGAAAGGTGGACTTACCAAAAAAAGAACAGTTTTGT
9765 TATATGTTATAACATCAGGAAGAGCACAAAATTGTTAATTATCCAACACATAACAAGTTGAAAAC
1 TATATGTTATAACATCAGGAAGAGCACAAAATTGTTAA-TATCCAACACATAACAAGTTGAAAAC
9830 TAGTCTTGCCTTTCATTATTCAATGTTTGAAAGGTGGACTTACCAAAAAAAGAACAGTTTTGT
65 TAGTCTTGCCTTTCATTATTCAATGTTTGAAAGGTGGACTTACCAAAAAAAGAACAGTTTTGT
*
9893 TATATGTTATAACATCAGGAAGAGCACAAAATTGTTGATTATCCAACACATAACAAGTTGAAAAC
1 TATATGTTATAACATCAGGAAGAGCACAAAATTGTT-AATATCCAACACATAACAAGTTGAAAAC
*
9958 TAGTCTTGCCATTCATTATTCAATGTTTGAAAGGTGGACTTACCAAAAAAAGAACAGTT
65 TAGTCTTGCCTTTCATTATTCAATGTTTGAAAGGTGGACTTACCAAAAAAAGAACAGTT
10017 GCACAATGCT
Statistics
Matches: 242, Mismatches: 7, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
128 217 0.90
129 3 0.01
130 22 0.09
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (127 bp):
TATATGTTATAACATCAGGAAGAGCACAAAATTGTTAATATCCAACACATAACAAGTTGAAAACT
AGTCTTGCCTTTCATTATTCAATGTTTGAAAGGTGGACTTACCAAAAAAAGAACAGTTTTGT
Found at i:14448 original size:56 final size:56
Alignment explanation
Indices: 14373--14480 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
14363 CACAAAGCAA
*
14373 AAACATTATTAGCATTCAAAGAGATTGATTTTTCGTGGAGTTCAAGTCAATAATTT
1 AAACATTAATAGCATTCAAAGAGATTGATTTTTCGTGGAGTTCAAGTCAATAATTT
* * *
14429 AAACGTTAATAGCATTCAAAGAGATTGATTTTTCTTGTAGTTCAAGTCAATA
1 AAACATTAATAGCATTCAAAGAGATTGATTTTTCGTGGAGTTCAAGTCAATA
14481 GTTTTATTAG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (56 bp):
AAACATTAATAGCATTCAAAGAGATTGATTTTTCGTGGAGTTCAAGTCAATAATTT
Found at i:23406 original size:1 final size:1
Alignment explanation
Indices: 23402--23441 Score: 71
Period size: 1 Copynumber: 40.0 Consensus size: 1
23392 GGTAAAAATT
*
23402 AAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
23442 CTACTACTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:29526 original size:11 final size:11
Alignment explanation
Indices: 29510--29542 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
29500 TAATTATCAT
29510 CGACAAAGTTA
1 CGACAAAGTTA
29521 CGACAAAGTTA
1 CGACAAAGTTA
*
29532 CAACAAAGTTA
1 CGACAAAGTTA
29543 TAAAGGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (11 bp):
CGACAAAGTTA
Found at i:29564 original size:25 final size:26
Alignment explanation
Indices: 29529--29587 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
29519 TACGACAAAG
*
29529 TTACAACAAAGTT-ATAAAGGATGAA
1 TTACAAAAAAGTTAATAAAGGATGAA
*
29554 TTACAAAAAAGTTAATAAAGGATGCA
1 TTACAAAAAAGTTAATAAAGGATGAA
*
29580 TAACAAAA
1 TTACAAAA
29588 GCGGCTATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 12 0.40
26 18 0.60
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (26 bp):
TTACAAAAAAGTTAATAAAGGATGAA
Found at i:35805 original size:322 final size:319
Alignment explanation
Indices: 35182--36965 Score: 1744
Period size: 322 Copynumber: 5.6 Consensus size: 319
35172 GTGTTTAACT
*
35182 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGTCTCAATTTT
1 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTT
* * * *
35247 GCATGATTTTTGGCACAAAAACTCCTTGAAATTTCTATAATTATCGAATCAAATCTCAACAATAT
66 GCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTTATCGAATCAAATCTCAGCAATAT
** * *
35312 TGGATATAAGCTTTTGTTTTTTCGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTTG
131 TGGATATAAGGATTTGTTTTTT-GACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAA-TTC
* * *
35377 GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGTCCGTCAATATTTTTGGCATTGAATTAT
194 GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTAT
* * * *
35442 -TATTTTTTTTGTGTATTGTGCCAAAAAATTGAGAAAAAAAAAATTTCAAGTCAGTTTTTTGCC
259 ATATTTTTTCTGTGTATTGTGGC-AAAAATTGAG--AAAAAAATTTTCAAGTCAGTTTTTAGCC
35505 GAAATCGTGTACTAACCATCAC-GTTTTTGGCTAAAAACGCGTTCC-AGAGCCCCGACTCAATTT
1 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGA-AGCCCCGACTCAATTT
** * *
35568 TATATGATTTTTGGCACAAAGACTCTTTGAAATATCTATATTTATCGAATCAAATCTCATCAATA
65 TGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTTATCGAATCAAATCTCAGCAATA
*
35633 TTGGATATAAGGAATTGTCTTTTTGACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC
130 TTGGATATAAGGATTTGT-TTTTTGACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC
35698 AGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTA
194 -GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTA
35763 TATATTTTTTCTGTGTATTGTGGCAAAAAATTTGAGAAAAAAATTTTTCGAA-TCAGTTTTTAGC
258 TATATTTTTTCTGTGTATTGTGGC-AAAAA-TTGAGAAAAAAA-TTTTC-AAGTCAGTTTTTAGC
35827 C
319 C
** * * * *
35828 GAAATAATGTACTAAACCATTACGGTTTTTTGCTAAAAACGCGTTCTGAAACCCCGACTCAATTT
1 GAAATCGTGTACT-AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTT
* * * * * * *
35893 TCCATGATTTTTGGAAAAAAAGACTCCTTTAAATATCTATATTCATTGAACCAAATCTCAGCAAT
65 TGCATGATTTTTGG-CACAAAGACTCCTTGAAATATCTATATTTATCGAATCAAATCTCAGCAAT
* *
35958 ATTGGATATAAGGATTTGTTTTTTTGAGCATCTCAATCTTGTTTCGATTTAAGTAGAAA-TAATT
129 ATTGGATATAAGGATTTG-TTTTTTGACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAA-T
* *
36022 TCGGAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATT
192 TCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATT
* * * * ** *** * *
36086 ATATATTTTTTCCGTGTATCGTGGCAAAAATTGTGATAAACGTTTTTGGGTCAGTTTTTAACT
257 ATATATTTTTTCTGTGTATTGTGGCAAAAATTGAGAAAAAAATTTTCAAGTCAGTTTTTAGCC
* * *
36149 GAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGTCTCAATCTT
1 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTT
** * * * * * *
36214 GCATGATTTTTTACGCAAAGACTCCTTGAAATATCCATATTCATCGAATCAAATGTCAGCCACAT
66 GCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTTATCGAATCAAATCTCAGCAATAT
* * * *
36279 TGGATATAAGGATTTGTTTTTACGAACATCTGAATCTTGTTTCGATTTAATTAAAAATTAATTCG
131 TGGATATAAGGATTTGTTTTT-TGACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCG
* * * * * * *
36344 AAAAAAAATGAAAAAACAATATTAGATGTGTGAAAAGCCCGTTAATCTTTTTGGTGTTGGATTAT
195 -AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTAT
** * * * ** *
36409 ATA-TTTTTCTCAGTATTATGGCCAAAATTTGAG-AAAAACTTTT-GGGCCAGTTTTTAGCC
259 ATATTTTTTCTGTGTATTGTGG-CAAAAATTGAGAAAAAAATTTTCAAGTCAGTTTTTAGCC
* ** * * * * * * * *
36468 GAAATCGTGTAATAATTATCACGAG-TTTTGACTAAAAACGCCTTCAG-GGACACGGCTCTATTT
1 GAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTT
* * ** * * * *
36531 TGCATGATTTTTTGCGCCGAGACTCCTTGAAATATCTTTA-TTAGTCTAATCAAATCTCAGCCAC
65 TGCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTTA-TCGAATCAAATCTCAGCAAT
* * * ** ** *
36595 ATCGGATTTAAGGATTT-TTTTTACGTGCATCAGAATCTTG-TTCGATTTAAATAGAAATTAATT
129 ATTGGATATAAGGATTTGTTTTT-TGACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAA-T
* * * ** * * *
36658 TAGAAAAAATAT-GAAGAACGATATTAAAAGCGTGAAAAGTGCTTTAATCTTTTT-GCGTTGACT
192 TCGAAAAAA-ATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAAT
* * ** * *
36721 TATATATATTTTTATGAGTGT-TTTTACCAAAAATTGAG-GAAAAATCTTTC-GGATCA-TTTTT
256 TATATAT-TTTTTCT--GTGTATTGTGGCAAAAATTGAGAAAAAAAT-TTTCAAG-TCAGTTTTT
36782 ----
316 AGCC
** * *
36782 ---A-C---TA-T---CAT---GGTTTTTTACTAAAAACGCGTTCCG-GGCCCCGGCTCAATTTT
1 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTT
* * * * **
36832 GCATGATTTTTGGCACTAAGACTCCTTAAAATATCTGTA-TTATCTAATCAAATCTCAGGTATAT
66 GCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTTATCGAATCAAATCTCAGCAATAT
* * * * * ** * *
36896 TGGTTTTAAGGATTTATTTTAATAAGTA-CTTAAATCTTGTTTCGATTTAATTAAAAATTAATTC
131 TGGATATAAGGATTTGTTTT-TTGACCATC-TCAATCTTGTTTCGATTTAATTAGAAATTAATTC
36960 -AAAAAA
194 GAAAAAA
36966 TATTAAACAA
Statistics
Matches: 1248, Mismatches: 178, Indels: 94
0.82 0.12 0.06
Matches are distributed among these distances:
299 40 0.03
300 85 0.07
301 19 0.02
303 2 0.00
306 1 0.00
307 2 0.00
310 1 0.00
311 1 0.00
315 12 0.01
316 58 0.05
317 48 0.04
318 96 0.08
319 147 0.12
320 85 0.07
321 91 0.07
322 225 0.18
323 85 0.07
324 91 0.07
325 58 0.05
326 100 0.08
327 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (319 bp):
GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGACTCAATTTT
GCATGATTTTTGGCACAAAGACTCCTTGAAATATCTATATTTATCGAATCAAATCTCAGCAATAT
TGGATATAAGGATTTGTTTTTTGACCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGA
AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAATTATAT
ATTTTTTCTGTGTATTGTGGCAAAAATTGAGAAAAAAATTTTCAAGTCAGTTTTTAGCC
Found at i:43204 original size:13 final size:13
Alignment explanation
Indices: 43186--43211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43176 TGTTTCCCTC
43186 TTATAATTGTCCT
1 TTATAATTGTCCT
43199 TTATAATTGTCCT
1 TTATAATTGTCCT
43212 AATTGGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TTATAATTGTCCT
Found at i:44138 original size:39 final size:39
Alignment explanation
Indices: 44084--44160 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
44074 CGTTTTATCA
* * *
44084 CGACATACCTTTCAAATTTTTCAATCCACTGATTGATCT
1 CGACAAACCCTTCAAATGTTTCAATCCACTGATTGATCT
*
44123 CGACAAACCCTTCAAATGTTTCAATCGACTGATTGATC
1 CGACAAACCCTTCAAATGTTTCAATCCACTGATTGATC
44161 GTCACATATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (39 bp):
CGACAAACCCTTCAAATGTTTCAATCCACTGATTGATCT
Found at i:48795 original size:30 final size:29
Alignment explanation
Indices: 48746--48803 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
48736 CATTTTTTAC
*
48746 AACATAAAGGATTTATTTGTCTAAAAAAAA
1 AACATAAAGAATTTATTTGT-TAAAAAAAA
*
48776 AACATAAAGAA-TTATTTTGTTCAAAAAA
1 AACATAAAGAATTTA-TTTGTTAAAAAAA
48804 TGTAAGGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (29 bp):
AACATAAAGAATTTATTTGTTAAAAAAAA
Found at i:50209 original size:21 final size:21
Alignment explanation
Indices: 50183--50224 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
50173 GGAAGGCGAG
50183 GTTACAAAATCGATTGATCTC
1 GTTACAAAATCGATTGATCTC
* *
50204 GTTACAGAGTCGATTGATCTC
1 GTTACAAAATCGATTGATCTC
50225 CATGAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
GTTACAAAATCGATTGATCTC
Found at i:60703 original size:2 final size:2
Alignment explanation
Indices: 60696--60748 Score: 52
Period size: 2 Copynumber: 26.0 Consensus size: 2
60686 ATCATACTAT
* * * *
60696 TA TA TA TA TG GA TCA TA TA TA TG CA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
60739 TA TA TC TA TA
1 TA TA TA TA TA
60749 CTAATATAAG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (2 bp):
TA
Found at i:62561 original size:2 final size:2
Alignment explanation
Indices: 62554--62584 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
62544 TAATTTCAAG
62554 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
62585 GCCAGGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:66034 original size:2 final size:2
Alignment explanation
Indices: 66027--66126 Score: 60
Period size: 2 Copynumber: 54.5 Consensus size: 2
66017 CATTTTCAAT
* *
66027 TA TA TA TA TA TA TT TA -A T- TA TT TA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
66065 -A TA TA -A TA TA -A TA -A TT TA GTT TT TA GT- TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
66103 -A 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 T
66127 CAAAACAACG
Statistics
Matches: 77, Mismatches: 8, Indels: 26
0.69 0.07 0.23
Matches are distributed among these distances:
1 11 0.14
2 64 0.83
3 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66051 original size:43 final size:39
Alignment explanation
Indices: 65951--66050 Score: 137
Period size: 39 Copynumber: 2.6 Consensus size: 39
65941 ATATATACAT
* * *
65951 TATATATTCACTTATTTACTTAAACTCCATTTTCAATTA
1 TATATATTTAATTATTTATTTAAACTCCATTTTCAATTA
*
65990 TATACATTTAATTATTTATTTAAACTCCATTTTCAATTA
1 TATATATTTAATTATTTATTTAAACTCCATTTTCAATTA
* * *
66029 TATATATATATTTAATTATTTA
1 TATATATTTAATTATTTATTTA
66051 TATAATATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (39 bp):
TATATATTTAATTATTTATTTAAACTCCATTTTCAATTA
Found at i:66060 original size:5 final size:5
Alignment explanation
Indices: 66050--66077 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
66040 TTAATTATTT
66050 ATATA ATATA ATATA ATATA ATATA ATA
1 ATATA ATATA ATATA ATATA ATATA ATA
66078 ATTTAGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:66116 original size:8 final size:8
Alignment explanation
Indices: 66027--66126 Score: 60
Period size: 7 Copynumber: 13.6 Consensus size: 8
66017 CATTTTCAAT
66027 TATATATA
1 TATATATA
*
66035 TATATTTA
1 TATATATA
*
66043 -AT-TATT
1 TATATATA
66049 TATATA-A
1 TATATATA
66056 TATA-ATA
1 TATATATA
66063 TA-ATATA
1 TATATATA
66070 -ATATA-A
1 TATATATA
*
66076 TA-ATTTA
1 TATATATA
* *
66083 GTTTTTAGT-
1 -TATATA-TA
66092 TATAT-TA
1 TATATATA
66099 TATA-ATA
1 TATATATA
66106 TATATATA
1 TATATATA
66114 TATATATA
1 TATATATA
66122 TATAT
1 TATAT
66127 CAAAACAACG
Statistics
Matches: 69, Mismatches: 10, Indels: 26
0.66 0.10 0.25
Matches are distributed among these distances:
6 9 0.13
7 29 0.42
8 29 0.42
9 1 0.01
10 1 0.01
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (8 bp):
TATATATA
Done.