Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020001.1 Corchorus olitorius cultivar O-4 contig20034, 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: 81283
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4495 original size:9 final size:9
Alignment explanation
Indices: 4481--4510 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
4471 CATCTTATCC
4481 TTTCTTTCT
1 TTTCTTTCT
4490 TTTCTTTCT
1 TTTCTTTCT
4499 TTTCTTTCT
1 TTTCTTTCT
4508 TTT
1 TTT
4511 TTTGGCCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTCT
Found at i:5677 original size:29 final size:29
Alignment explanation
Indices: 5635--5692 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5625 CTGCTGCCTA
5635 CTTGAAAATAATATATTCACCAAAGCAAT
1 CTTGAAAATAATATATTCACCAAAGCAAT
5664 CTTGAAAATAATATATTCACCAAAGCAAT
1 CTTGAAAATAATATATTCACCAAAGCAAT
5693 GGATATATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (29 bp):
CTTGAAAATAATATATTCACCAAAGCAAT
Found at i:10234 original size:23 final size:24
Alignment explanation
Indices: 10204--10248 Score: 83
Period size: 23 Copynumber: 1.9 Consensus size: 24
10194 GTAGGCTCGT
10204 CGAGCCTAATCGAG-CCCCTCTGA
1 CGAGCCTAATCGAGTCCCCTCTGA
10227 CGAGCCTAATCGAGTCCCCTCT
1 CGAGCCTAATCGAGTCCCCTCT
10249 AATATTACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (24 bp):
CGAGCCTAATCGAGTCCCCTCTGA
Found at i:13170 original size:21 final size:22
Alignment explanation
Indices: 13135--13216 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 22
13125 CACAGAGAGA
*
13135 TTACAAAA-ATCATAGGAAGG-
1 TTACAAAATTTCATAGGAAGGT
13155 TTACAAAATTTCATAGGAAGGT
1 TTACAAAATTTCATAGGAAGGT
*
13177 TTATTAAAATTTCATAGG-AGGAT
1 TTA-CAAAATTTCATAGGAAGG-T
*
13200 TTATTAAAATTTCATAG
1 TTA-CAAAATTTCATAG
13217 TTAGGTTATT
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
20 8 0.14
21 11 0.20
22 6 0.11
23 31 0.55
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (22 bp):
TTACAAAATTTCATAGGAAGGT
Found at i:13189 original size:23 final size:23
Alignment explanation
Indices: 13144--13216 Score: 107
Period size: 23 Copynumber: 3.3 Consensus size: 23
13134 ATTACAAAAA
*
13144 TCATAGGAAGG-TTA-CAAAATT
1 TCATAGGAAGGTTTATTAAAATT
13165 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
13188 TCATAGG-AGGATTTATTAAAATT
1 TCATAGGAAGG-TTTATTAAAATT
13211 TCATAG
1 TCATAG
13217 TTAGGTTATT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
21 11 0.23
22 6 0.12
23 31 0.65
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (23 bp):
TCATAGGAAGGTTTATTAAAATT
Found at i:13276 original size:22 final size:22
Alignment explanation
Indices: 13251--13311 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
13241 CATAGGTAAA
* *
13251 TTATCAAAATTCCATAACATGG
1 TTATCAAAATTTCATAACATAG
* **
13273 TTATCAAAATTTAATAAGGTAG
1 TTATCAAAATTTCATAACATAG
13295 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
13312 AAATATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAACATAG
Found at i:13388 original size:14 final size:14
Alignment explanation
Indices: 13369--13444 Score: 54
Period size: 14 Copynumber: 5.4 Consensus size: 14
13359 TTAAAACTAG
13369 TATATATATAAAAT
1 TATATATATAAAAT
13383 TATATATATTAAACCAT
1 TATATATA-TAAA--AT
*
13400 GTATA-ATAT-ATA-
1 -TATATATATAAAAT
13412 TATA-ATATAAAAT
1 TATATATATAAAAT
*
13425 TATATAAATATAAA-
1 TATATATATA-AAAT
13439 TATATA
1 TATATA
13445 GTTAGAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
11 8 0.16
12 2 0.04
13 5 0.10
14 18 0.35
15 8 0.16
16 1 0.02
17 5 0.10
18 4 0.08
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (14 bp):
TATATATATAAAAT
Found at i:13444 original size:16 final size:17
Alignment explanation
Indices: 13404--13444 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
13394 AACCATGTAT
13404 AATATATATATAATATA
1 AATATATATATAATATA
13421 AA-AT-TATATAAATATA
1 AATATATATAT-AATATA
13437 AATATATA
1 AATATATA
13445 GTTAGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.24
16 10 0.48
17 4 0.19
18 2 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATATATATAATATA
Found at i:25860 original size:631 final size:631
Alignment explanation
Indices: 24657--25921 Score: 2530
Period size: 631 Copynumber: 2.0 Consensus size: 631
24647 ACTCCCTTTG
24657 GGTATTCGATCGAGTGCAAATTTGTAAATACAACGAGCTCTCTCAGTTTCCTTGCACCGCTCCTC
1 GGTATTCGATCGAGTGCAAATTTGTAAATACAACGAGCTCTCTCAGTTTCCTTGCACCGCTCCTC
24722 AAACTCAGCAAAGGCAATAAATAATTGCTCTGAATCTTCTTCATCCGCCAGCTTCGCCGCCGCAC
66 AAACTCAGCAAAGGCAATAAATAATTGCTCTGAATCTTCTTCATCCGCCAGCTTCGCCGCCGCAC
24787 GTTCATAAACATCCCTTGCCCTTACAATTTCCCCGTTCTTCATCTCAAATTTGGCATATTTGATC
131 GTTCATAAACATCCCTTGCCCTTACAATTTCCCCGTTCTTCATCTCAAATTTGGCATATTTGATC
24852 CAAGCGCCGACTTTGGGGTGGCACTGAACGAGCCGTTCGTAAATTGCACGCGCGCGTTCGACTTC
196 CAAGCGCCGACTTTGGGGTGGCACTGAACGAGCCGTTCGTAAATTGCACGCGCGCGTTCGACTTC
24917 GTTGTAACGAAGCTCGAACTTGATGAAGGAAAGCCAGCCTTGTTGGTCCGGCATCCACGACATTC
261 GTTGTAACGAAGCTCGAACTTGATGAAGGAAAGCCAGCCTTGTTGGTCCGGCATCCACGACATTC
24982 ATCGTTCGAAAATCTGGCGAGCTCCGGCAACGTTCCCTAACATTTCTTCCATGTGGATATATTTA
326 ATCGTTCGAAAATCTGGCGAGCTCCGGCAACGTTCCCTAACATTTCTTCCATGTGGATATATTTA
25047 TACCACAGCTGGTCGACGCGCGGGAGGAGCGTGACGGCGCGGTCCCAGACGTTCCTTGCGTGGTT
391 TACCACAGCTGGTCGACGCGCGGGAGGAGCGTGACGGCGCGGTCCCAGACGTTCCTTGCGTGGTT
25112 GATGAACTTGTTCTTCATCTCTGATTCGGCGTATTTGAGCCATAAAGTGTGGGTTTGGTAATCGA
456 GATGAACTTGTTCTTCATCTCTGATTCGGCGTATTTGAGCCATAAAGTGTGGGTTTGGTAATCGA
25177 CTTCGAGTGCTCGCTCCCACACGCTACGTGCTCGATTGAAATCCTTTTGAGACTCTTCCCATTGC
521 CTTCGAGTGCTCGCTCCCACACGCTACGTGCTCGATTGAAATCCTTTTGAGACTCTTCCCATTGC
25242 GCGTACTTGATCCAGACGGTGACATTCCACCGTACACGGCGAATTT
586 GCGTACTTGATCCAGACGGTGACATTCCACCGTACACGGCGAATTT
25288 GGTATTCGATCGAGTGCAAATTTGTAAATACAACGAGCTCTCTCAGTTTCCTTGCACCGCTCCTC
1 GGTATTCGATCGAGTGCAAATTTGTAAATACAACGAGCTCTCTCAGTTTCCTTGCACCGCTCCTC
25353 AAACTCAGCAAAGGCAATAAATAATTGCTCTGAATCTTCTTCATCCGCCAGCTTCGCCGCCGCAC
66 AAACTCAGCAAAGGCAATAAATAATTGCTCTGAATCTTCTTCATCCGCCAGCTTCGCCGCCGCAC
25418 GTTCATAAACATCCCTTGCCCTTACAATTTCCCCGTTCTTCATCTCAAATTTGGCATATTTGATC
131 GTTCATAAACATCCCTTGCCCTTACAATTTCCCCGTTCTTCATCTCAAATTTGGCATATTTGATC
25483 CAAGCGCCGACTTTGGGGTGGCACTGAACGAGCCGTTCGTAAATTGCACGCGCGCGTTCGACTTC
196 CAAGCGCCGACTTTGGGGTGGCACTGAACGAGCCGTTCGTAAATTGCACGCGCGCGTTCGACTTC
25548 GTTGTAACGAAGCTCGAACTTGATGAAGGAAAGCCAGCCTTGTTGGTCCGGCATCCACGACATTC
261 GTTGTAACGAAGCTCGAACTTGATGAAGGAAAGCCAGCCTTGTTGGTCCGGCATCCACGACATTC
25613 ATCGTTCGAAAATCTGGCGAGCTCCGGCAACGTTCCCTAACATTTCTTCCATGTGGATATATTTA
326 ATCGTTCGAAAATCTGGCGAGCTCCGGCAACGTTCCCTAACATTTCTTCCATGTGGATATATTTA
25678 TACCACAGCTGGTCGACGCGCGGGAGGAGCGTGACGGCGCGGTCCCAGACGTTCCTTGCGTGGTT
391 TACCACAGCTGGTCGACGCGCGGGAGGAGCGTGACGGCGCGGTCCCAGACGTTCCTTGCGTGGTT
25743 GATGAACTTGTTCTTCATCTCTGATTCGGCGTATTTGAGCCATAAAGTGTGGGTTTGGTAATCGA
456 GATGAACTTGTTCTTCATCTCTGATTCGGCGTATTTGAGCCATAAAGTGTGGGTTTGGTAATCGA
25808 CTTCGAGTGCTCGCTCCCACACGCTACGTGCTCGATTGAAATCCTTTTGAGACTCTTCCCATTGC
521 CTTCGAGTGCTCGCTCCCACACGCTACGTGCTCGATTGAAATCCTTTTGAGACTCTTCCCATTGC
25873 GCGTACTTGATCCAGACGGTGACATTCCACCGTACACGGCGAATTT
586 GCGTACTTGATCCAGACGGTGACATTCCACCGTACACGGCGAATTT
25919 GGT
1 GGT
25922 CCTCGAATTC
Statistics
Matches: 634, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
631 634 1.00
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (631 bp):
GGTATTCGATCGAGTGCAAATTTGTAAATACAACGAGCTCTCTCAGTTTCCTTGCACCGCTCCTC
AAACTCAGCAAAGGCAATAAATAATTGCTCTGAATCTTCTTCATCCGCCAGCTTCGCCGCCGCAC
GTTCATAAACATCCCTTGCCCTTACAATTTCCCCGTTCTTCATCTCAAATTTGGCATATTTGATC
CAAGCGCCGACTTTGGGGTGGCACTGAACGAGCCGTTCGTAAATTGCACGCGCGCGTTCGACTTC
GTTGTAACGAAGCTCGAACTTGATGAAGGAAAGCCAGCCTTGTTGGTCCGGCATCCACGACATTC
ATCGTTCGAAAATCTGGCGAGCTCCGGCAACGTTCCCTAACATTTCTTCCATGTGGATATATTTA
TACCACAGCTGGTCGACGCGCGGGAGGAGCGTGACGGCGCGGTCCCAGACGTTCCTTGCGTGGTT
GATGAACTTGTTCTTCATCTCTGATTCGGCGTATTTGAGCCATAAAGTGTGGGTTTGGTAATCGA
CTTCGAGTGCTCGCTCCCACACGCTACGTGCTCGATTGAAATCCTTTTGAGACTCTTCCCATTGC
GCGTACTTGATCCAGACGGTGACATTCCACCGTACACGGCGAATTT
Found at i:27759 original size:25 final size:24
Alignment explanation
Indices: 27708--27764 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
27698 GTCAGTCTTG
*
27708 AATTT-TTTAATGTTTAATTCTTA
1 AATTTATTTAATGTTTAATTATTA
*
27731 AATTTATTTAATGTCTTAATTATTC
1 AATTTATTTAATGT-TTAATTATTA
27756 AATTTATTT
1 AATTTATTT
27765 TACAATCCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 5 0.17
24 8 0.27
25 17 0.57
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.60
Consensus pattern (24 bp):
AATTTATTTAATGTTTAATTATTA
Found at i:29005 original size:57 final size:57
Alignment explanation
Indices: 28934--29046 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
28924 AGCCACGAGC
** *
28934 ATAGGATAGTCCCTAACATCAACATCAAG-GAGACTCTTCACTTCAGCAGGTGGTTCG
1 ATAGGATACCCCCTAACATCAACATCAAGAAAG-CTCTTCACTTCAGCAGGTGGTTCG
* *
28991 ATAGGATACCCCCTAGCATCAACATCAATAAAGCTCTTCACTTCAGCAGGTGGTTC
1 ATAGGATACCCCCTAACATCAACATCAAGAAAGCTCTTCACTTCAGCAGGTGGTTC
29047 AAACAACAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 48 0.96
58 2 0.04
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.25
Consensus pattern (57 bp):
ATAGGATACCCCCTAACATCAACATCAAGAAAGCTCTTCACTTCAGCAGGTGGTTCG
Found at i:35600 original size:14 final size:13
Alignment explanation
Indices: 35581--35618 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
35571 CTCAACACTG
35581 ACTGACTCGAAAAA
1 ACTGACTC-AAAAA
*
35595 ACTGACTCAACAA
1 ACTGACTCAAAAA
35608 ACTGACT-AAAA
1 ACTGACTCAAAA
35619 CCCGACAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 3 0.14
13 11 0.50
14 8 0.36
ACGTcount: A:0.50, C:0.24, G:0.11, T:0.16
Consensus pattern (13 bp):
ACTGACTCAAAAA
Found at i:35611 original size:13 final size:14
Alignment explanation
Indices: 35581--35614 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
35571 CTCAACACTG
35581 ACTGACTCGAAAAA
1 ACTGACTCGAAAAA
*
35595 ACTGACTC-AACAA
1 ACTGACTCGAAAAA
35608 ACTGACT
1 ACTGACT
35615 AAAACCCGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.58
14 8 0.42
ACGTcount: A:0.44, C:0.26, G:0.12, T:0.18
Consensus pattern (14 bp):
ACTGACTCGAAAAA
Found at i:46945 original size:14 final size:14
Alignment explanation
Indices: 46926--46956 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
46916 TCTAATTAAT
46926 TCATGGGAAATGTG
1 TCATGGGAAATGTG
46940 TCATGGGAAATGTG
1 TCATGGGAAATGTG
46954 TCA
1 TCA
46957 ACCTTTGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.10, G:0.32, T:0.29
Consensus pattern (14 bp):
TCATGGGAAATGTG
Found at i:50638 original size:16 final size:17
Alignment explanation
Indices: 50615--50655 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
50605 GTTCTATTAG
50615 TGTTTAAACACTTTTTT
1 TGTTTAAACACTTTTTT
50632 T-TTTAAAAACACTTTTTT
1 TGTTT--AAACACTTTTTT
50650 TGTTTA
1 TGTTTA
50656 GCTAAAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
16 3 0.14
17 2 0.10
18 13 0.62
19 3 0.14
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.59
Consensus pattern (17 bp):
TGTTTAAACACTTTTTT
Found at i:50643 original size:18 final size:19
Alignment explanation
Indices: 50620--50655 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
50610 ATTAGTGTTT
50620 AAACACTTTTTTT-TTTAA
1 AAACACTTTTTTTGTTTAA
50638 AAACACTTTTTTTGTTTA
1 AAACACTTTTTTTGTTTA
50656 GCTAAAACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.56
Consensus pattern (19 bp):
AAACACTTTTTTTGTTTAA
Found at i:53190 original size:41 final size:41
Alignment explanation
Indices: 53133--53216 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
53123 TGGAACAGCC
53133 ATCTTATCCAAATATTCACAACAAAGAGAACGCCTCAAAGT
1 ATCTTATCCAAATATTCACAACAAAGAGAACGCCTCAAAGT
53174 ATCTTATCCAAATATTCACAACAAAGAGAACGCCTCAAAGT
1 ATCTTATCCAAATATTCACAACAAAGAGAACGCCTCAAAGT
53215 AT
1 AT
53217 ACTCGATCCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.23
Consensus pattern (41 bp):
ATCTTATCCAAATATTCACAACAAAGAGAACGCCTCAAAGT
Found at i:54106 original size:50 final size:49
Alignment explanation
Indices: 54047--54146 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 49
54037 TTTATTCCTT
54047 GTTTGCCTGGTTAAATTAAATTTTATATTTTCATTTCTAAAACCCTATGG
1 GTTTGCCTGGTTAAATTAAATTTTATATTTTCA-TTCTAAAACCCTATGG
54097 GTTTGCCTGGTTAAATTAAATTTTATATTTTCATTCTAAAACCCTATGG
1 GTTTGCCTGGTTAAATTAAATTTTATATTTTCATTCTAAAACCCTATGG
54146 G
1 G
54147 AAATGCATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 17 0.34
50 33 0.66
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.45
Consensus pattern (49 bp):
GTTTGCCTGGTTAAATTAAATTTTATATTTTCATTCTAAAACCCTATGG
Found at i:55190 original size:18 final size:19
Alignment explanation
Indices: 55153--55190 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
55143 CCCTACTAGT
55153 AGTCACATTGGATCTCCCTC
1 AGTCACATTGGA-CTCCCTC
55173 AGTCACATTGGA-TCCCTC
1 AGTCACATTGGACTCCCTC
55191 TTGAATAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (19 bp):
AGTCACATTGGACTCCCTC
Found at i:63208 original size:5 final size:5
Alignment explanation
Indices: 63194--63227 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
63184 GTTCAATATT
*
63194 TTTTC ATTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
63228 GTGCTTTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTC
Found at i:78486 original size:15 final size:15
Alignment explanation
Indices: 78459--78497 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
78449 AAAGGTCAAG
78459 CTTTTT-TTCTTTTT
1 CTTTTTCTTCTTTTT
*
78473 CTTTTTCTTTTTTTT
1 CTTTTTCTTCTTTTT
*
78488 CTTATTCTTC
1 CTTTTTCTTC
78498 AGCTTGGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (15 bp):
CTTTTTCTTCTTTTT
Found at i:80075 original size:3 final size:3
Alignment explanation
Indices: 80067--80134 Score: 111
Period size: 3 Copynumber: 22.3 Consensus size: 3
80057 ATATTTATAT
80067 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA
80113 TTA TTA TTA TTA -TA GTTA TTA T
1 TTA TTA TTA TTA TTA -TTA TTA T
80135 ATATATATAT
Statistics
Matches: 62, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.03
3 55 0.89
4 5 0.08
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:80076 original size:12 final size:12
Alignment explanation
Indices: 80049--80140 Score: 84
Period size: 12 Copynumber: 7.5 Consensus size: 12
80039 AAAAATTAAT
80049 TTATATTTA-TA
1 TTATATTTATTA
80060 TTTATATTTATTA
1 -TTATATTTATTA
80073 TTAT-TATTATTA
1 TTATAT-TTATTA
*
80085 TTATTAATTATTA
1 TTA-TATTTATTA
80098 TTAT-TATTATTA
1 TTATAT-TTATTA
80110 TTAT-TATTATTA
1 TTATAT-TTATTA
*
80122 TTATAGTTATTA
1 TTATATTTATTA
80134 TATATAT
1 T-TATAT
80141 ATATATATAT
Statistics
Matches: 69, Mismatches: 4, Indels: 13
0.80 0.05 0.15
Matches are distributed among these distances:
11 1 0.01
12 52 0.75
13 16 0.23
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (12 bp):
TTATATTTATTA
Done.