Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012976.1 Corchorus olitorius cultivar O-4 contig13009, 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: 36994
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1205 original size:26 final size:23
Alignment explanation
Indices: 1175--1221 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
1165 CTTGAAAATT
1175 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
1201 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
1222 AATAGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:1231 original size:28 final size:26
Alignment explanation
Indices: 1175--1231 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
1165 CTTGAAAATT
* *
1175 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGATAGATGAGATGAA
1201 TGAAAAACTTGATGATAGATGA-ATAGAA
1 TGAAAAACTT--TGATAGATGAGAT-GAA
1229 TGA
1 TGA
1232 TAGATTTACC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 2 0.08
28 14 0.54
ACGTcount: A:0.44, C:0.04, G:0.26, T:0.26
Consensus pattern (26 bp):
TGAAAAACTTTGATAGATGAGATGAA
Found at i:3674 original size:33 final size:33
Alignment explanation
Indices: 3631--3757 Score: 146
Period size: 33 Copynumber: 3.8 Consensus size: 33
3621 CTTGGCAACT
* * *
3631 CAATAGTTTTAGCATCGATCTAAACTGAGAGTC
1 CAATAATTTTAGCATCGATCTAAGCTGAGAGCC
* *
3664 CAATAATTTTAGCATCGATTTAAGTTGAGAGCC
1 CAATAATTTTAGCATCGATCTAAGCTGAGAGCC
* * *
3697 CAATAACTTTAGCGTCGATCTAAGCTAAGAGCC
1 CAATAATTTTAGCATCGATCTAAGCTGAGAGCC
* * * *
3730 CAAAAATTTTAGCGTCGATTTGAGCTGA
1 CAATAATTTTAGCATCGATCTAAGCTGA
3758 TCGTCTTTGG
Statistics
Matches: 79, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (33 bp):
CAATAATTTTAGCATCGATCTAAGCTGAGAGCC
Found at i:6473 original size:2 final size:2
Alignment explanation
Indices: 6466--6500 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6456 GTCCGAGGTG
6466 AT AT 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 AT AT A
6501 ATCTTAAGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6559 original size:35 final size:35
Alignment explanation
Indices: 6507--6663 Score: 145
Period size: 35 Copynumber: 4.5 Consensus size: 35
6497 TATAATCTTA
* *
6507 AGCTTGGAACCGAGGTGAACACGTTTAAGACCTCG
1 AGCTTGGAACTGAGGTGAACACATTTAAGACCTCG
* * ** **
6542 AGCTTGGAATTGGGGTGAATGCATTTAAGACCTTT
1 AGCTTGGAACTGAGGTGAACACATTTAAGACCTCG
* * * *
6577 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCG
1 AGCTTGGAACTGAGGTGAACACATTTAAGACCTCG
*** *
6612 AGCTTGGAACTGAGGTGAATGTATTTAAGACCTTG
1 AGCTTGGAACTGAGGTGAACACATTTAAGACCTCG
*
6647 AGCTCGGAAGC-GAGGTG
1 AGCTTGGAA-CTGAGGTG
6664 GACGAGTTTA
Statistics
Matches: 94, Mismatches: 27, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
35 93 0.99
36 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (35 bp):
AGCTTGGAACTGAGGTGAACACATTTAAGACCTCG
Found at i:6680 original size:35 final size:35
Alignment explanation
Indices: 6641--6735 Score: 109
Period size: 35 Copynumber: 2.7 Consensus size: 35
6631 TGTATTTAAG
* * * *
6641 ACCTTGAGCTCGGAAGCGAGGTGGACGAGTTTAGA
1 ACCTTGAGCTCGGAACCAAAGTGAACGAGTTTAGA
* * *
6676 ACCTTGAGCTCGGATCCAAAGTGAATGCGTTTAGA
1 ACCTTGAGCTCGGAACCAAAGTGAACGAGTTTAGA
* *
6711 ACCTTGAGCTTGGAACCAAGGTGAA
1 ACCTTGAGCTCGGAACCAAAGTGAA
6736 ACACACTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.28, C:0.19, G:0.31, T:0.22
Consensus pattern (35 bp):
ACCTTGAGCTCGGAACCAAAGTGAACGAGTTTAGA
Found at i:6685 original size:70 final size:70
Alignment explanation
Indices: 6507--6663 Score: 233
Period size: 70 Copynumber: 2.2 Consensus size: 70
6497 TATAATCTTA
* * * * * *
6507 AGCTTGGAACCGAGGTGAACACGTTTAAGACCTCGAGCTTGGAATTGGGGTGAATGCATTTAAGA
1 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTTGGAACTGAGGTGAATGCATTTAAGA
*
6572 CCTTT
66 CCTTG
*
6577 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTTGGAACTGAGGTGAATGTATTTAAGA
1 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTTGGAACTGAGGTGAATGCATTTAAGA
6642 CCTTG
66 CCTTG
*
6647 AGCTCGGAAGCGAGGTG
1 AGCTCGGAACCGAGGTG
6664 GACGAGTTTA
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 78 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (70 bp):
AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTTGGAACTGAGGTGAATGCATTTAAGA
CCTTG
Found at i:6700 original size:70 final size:70
Alignment explanation
Indices: 6507--6740 Score: 193
Period size: 70 Copynumber: 3.3 Consensus size: 70
6497 TATAATCTTA
* * * * * *****
6507 AGCTTGGAACCGAGGTGAACACGTTTAAGACCTCGAGCTTGGAATTGGGGTGAATGCATTTAAGA
1 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTCGGAACCAAAGTGAATGCATTTAAGA
*
6572 CCTTT
66 CCTTG
* ** * *
6577 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTTGGAACTGAGGTGAATGTATTTAAGA
1 AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTCGGAACCAAAGTGAATGCATTTAAGA
6642 CCTTG
66 CCTTG
* * * * * * * *
6647 AGCTCGGAAGCGAGGTGGACGA-GTTTAGAACCTTGAGCTCGGATCCAAAGTGAATGCGTTT-AG
1 AGCTCGGAACCGAGGTGAAC-ACATTGAAAACCTCGAGCTCGGAACCAAAGTGAATGCATTTAAG
6710 AACCTTG
65 -ACCTTG
* *
6717 AGCTTGGAACCAAGGTGAAACACA
1 AGCTCGGAACCGAGGTG-AACACA
6741 CTAATGGGAA
Statistics
Matches: 134, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
69 2 0.01
70 129 0.96
71 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (70 bp):
AGCTCGGAACCGAGGTGAACACATTGAAAACCTCGAGCTCGGAACCAAAGTGAATGCATTTAAGA
CCTTG
Found at i:7764 original size:45 final size:45
Alignment explanation
Indices: 7681--7768 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
7671 TAGCTTGGGA
* ** **
7681 CCAATGTGAGATTCATGTAATGTCTTTAGCTCGGCCATGAGGTTG
1 CCAATGTGAGATTCATGTAATATCTTTAAATCACCCATGAGGTTG
7726 CCAATGTGAGATTCATGTAATATCTTTAAATCACCCATGAGGT
1 CCAATGTGAGATTCATGTAATATCTTTAAATCACCCATGAGGT
7769 CAAATCTTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (45 bp):
CCAATGTGAGATTCATGTAATATCTTTAAATCACCCATGAGGTTG
Found at i:9074 original size:28 final size:28
Alignment explanation
Indices: 9032--9118 Score: 95
Period size: 28 Copynumber: 3.1 Consensus size: 28
9022 TTTGCAACAA
* *
9032 GATTCTTGCTCGAGGAGTGTTGAACATG
1 GATTCTCGCTCGAGGAGCGTTGAACATG
* *
9060 GATTCTCGCTTGAGGAGCGTTGAGCATG
1 GATTCTCGCTCGAGGAGCGTTGAACATG
* * *
9088 GACTCTCACTCGAGGAGCATT-AAGCATG
1 GATTCTCGCTCGAGGAGCGTTGAA-CATG
9116 GAT
1 GAT
9119 ATTAGCGCTT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
27 1 0.02
28 47 0.98
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
GATTCTCGCTCGAGGAGCGTTGAACATG
Found at i:9180 original size:28 final size:28
Alignment explanation
Indices: 9149--9239 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 28
9139 TCTTGCTTGG
9149 GGAGCGTTGAGCATGGATTCTAGCTCGA
1 GGAGCGTTGAGCATGGATTCTAGCTCGA
* * *
9177 GGAGC-ATG-G-AT-TA-TC-A-CTTGA
1 GGAGCGTTGAGCATGGATTCTAGCTCGA
* *
9198 GGAGCGTTAAGCATGGATTCTCGCTCGA
1 GGAGCGTTGAGCATGGATTCTAGCTCGA
*
9226 GGAGCATTGAGCAT
1 GGAGCGTTGAGCAT
9240 AGTGTAGTAG
Statistics
Matches: 46, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
21 9 0.20
22 2 0.04
23 3 0.07
24 3 0.07
25 3 0.07
26 3 0.07
27 2 0.04
28 21 0.46
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (28 bp):
GGAGCGTTGAGCATGGATTCTAGCTCGA
Found at i:9813 original size:151 final size:148
Alignment explanation
Indices: 9405--9905 Score: 693
Period size: 151 Copynumber: 3.3 Consensus size: 148
9395 GCTCATAAGA
* * * *
9405 CCAGCTCTTAGAGGGTTTTAGGGGC-TTCTTAGAGAGAGAGAATTTAAATCGAAGTT-CATTGTT
1 CCAGCTCTGAGAGCGTTTTAGGGGCTTTTTTAGAGAGGGAGAATTTAAATCGAA-TTGC--TG-T
* *
9468 TTTGAGTCCATTCTTTAGGGCCGCTATGGCAACAGATTGCTCTAAGTCTTTGACCTGGAGAGCTT
62 TTTGAGTCCGTTCTTTAGGGCCGCTATGGCGACAGATTGCTCTAAGTCTTTGACCTGGAGAGCTT
9533 TGGTTGGTCTCGACCTCTCTCC
127 TGGTTGGTCTCGACCTCTCTCC
* * *
9555 CCAGCTCTGAGAGCGTTTTAGGGGCTTTTTTAGATAAGGAGAATTTAAATCGGAATTCGCTATTT
1 CCAGCTCTGAGAGCGTTTTAGGGGCTTTTTTAGAGAGGGAGAATTTAAATC-GAATT-GCTGTTT
* * *
9620 TGAGTCCGTTCTTTAGGGCCACTATGGCGACAAATTGCTCTAAGTCTTTCACCTGGAGAGCTTTG
64 TGAGTCCGTTCTTTAGGGCCGCTATGGCGACAGATTGCTCTAAGTCTTTGACCTGGAGAGCTTTG
*
9685 GCTTGGT-TTGACCTCTCTCC
129 G-TTGGTCTCGACCTCTCTCC
* * *
9705 TCAGGTCTGAGAGCGTTTTAGGGGCTTTTTTTAGAGAGGGAGAATTTGAATCAGAACTTGCTGTT
1 CCAGCTCTGAGAGCGTTTTAGGGGC-TTTTTTAGAGAGGGAGAATTTAAATC-GAA-TTGCTGTT
* * * *
9770 TTGAGTTCGTTCTTCAGGGCCGCTATGGCGACAGATTGCTCTAAGTCTTTGACCTAGAGTGCTTT
63 TTGAGTCCGTTCTTTAGGGCCGCTATGGCGACAGATTGCTCTAAGTCTTTGACCTGGAGAGCTTT
9835 GGTTGGTCTCGACCTCTCTCC
128 GGTTGGTCTCGACCTCTCTCC
* *
9856 CCAACTCTGAGAGCGTTTTAGGGGCTTTTTAAGAGAGGGAGAATTTAAAT
1 CCAGCTCTGAGAGCGTTTTAGGGGCTTTTTTAGAGAGGGAGAATTTAAAT
9906 TGGATCTCAT
Statistics
Matches: 310, Mismatches: 33, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
150 150 0.48
151 154 0.50
152 5 0.02
153 1 0.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (148 bp):
CCAGCTCTGAGAGCGTTTTAGGGGCTTTTTTAGAGAGGGAGAATTTAAATCGAATTGCTGTTTTG
AGTCCGTTCTTTAGGGCCGCTATGGCGACAGATTGCTCTAAGTCTTTGACCTGGAGAGCTTTGGT
TGGTCTCGACCTCTCTCC
Found at i:16304 original size:65 final size:64
Alignment explanation
Indices: 16200--16378 Score: 239
Period size: 56 Copynumber: 2.9 Consensus size: 64
16190 GTGATTCTTA
* *
16200 TCTTATAGAGATTAATCGTATTATAGAAAGATTAACACGTCAAATGGATGAGTTTTTTTTTTTTT
1 TCTTATAGAGATTAATCGTA-T-TAGAAAGATTAACACGTCAAATGGATGAGTTTTTTTTTCTAT
16265 AG
64 -G
16267 TCTTATAGAGATTAATCGTATTAGAAAGATTAACACGTCAAATGGATGAG------TTTCTATG
1 TCTTATAGAGATTAATCGTATTAGAAAGATTAACACGTCAAATGGATGAGTTTTTTTTTCTATG
* *
16325 TC-T-TAGAGATTGATCGTATTAGAAAGATTAATACGTCAAATGGATGAGTTTTTT
1 TCTTATAGAGATTAATCGTATTAGAAAGATTAACACGTCAAATGGATGAGTTTTTT
16379 GTTAACCATT
Statistics
Matches: 102, Mismatches: 4, Indels: 17
0.83 0.03 0.14
Matches are distributed among these distances:
56 43 0.42
57 1 0.01
58 3 0.03
59 5 0.05
65 29 0.28
66 1 0.01
67 20 0.20
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (64 bp):
TCTTATAGAGATTAATCGTATTAGAAAGATTAACACGTCAAATGGATGAGTTTTTTTTTCTATG
Found at i:16788 original size:64 final size:64
Alignment explanation
Indices: 16686--16814 Score: 231
Period size: 64 Copynumber: 2.0 Consensus size: 64
16676 AAACAGAATC
* *
16686 TGTAAGTTCAGATGAGTACACAGACAACTCTAAAACACAAACTATAGTTGAATGTTTATATTCT
1 TGTAAGTTCAGATGAGTACACAGACAACTCCAAAACACAAACTATAGTTGAATGTTCATATTCT
*
16750 TGTAAGTTCAGATGAGTACACAGACAACTCCAATACACAAACTATAGTTGAATGTTCATATTCT
1 TGTAAGTTCAGATGAGTACACAGACAACTCCAAAACACAAACTATAGTTGAATGTTCATATTCT
16814 T
1 T
16815 CTTCGCCGCT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (64 bp):
TGTAAGTTCAGATGAGTACACAGACAACTCCAAAACACAAACTATAGTTGAATGTTCATATTCT
Found at i:17001 original size:25 final size:25
Alignment explanation
Indices: 16972--17022 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
16962 TTGTATTTTG
16972 AAGCAAGTCCAAATCACATCAGAGT
1 AAGCAAGTCCAAATCACATCAGAGT
16997 AAGCAAGTCCAAATCACATCAGAGT
1 AAGCAAGTCCAAATCACATCAGAGT
17022 A
1 A
17023 TGGAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.16
Consensus pattern (25 bp):
AAGCAAGTCCAAATCACATCAGAGT
Found at i:18565 original size:51 final size:54
Alignment explanation
Indices: 18462--18567 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 54
18452 TCTTGGAGTG
* *
18462 TGGCTCCCAATCTTCAAAACTCTTTACCGTACCAAAATGAGTATGTTGTTGATGAA
1 TGGCTACCAATCTTCAAAACTCTTTA-CG-ACCAAAATGAGTATGCTGTTGATGAA
*
18518 TGGCTACCAATCTTCAAAACT-TTT-C-AGCAAAATGAGTATGCTGTTGATGA
1 TGGCTACCAATCTTCAAAACTCTTTACGACCAAAATGAGTATGCTGTTGATGA
18568 TCAATGATAC
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
51 23 0.49
53 1 0.02
55 3 0.06
56 20 0.43
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (54 bp):
TGGCTACCAATCTTCAAAACTCTTTACGACCAAAATGAGTATGCTGTTGATGAA
Found at i:21229 original size:16 final size:17
Alignment explanation
Indices: 21204--21248 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
21194 CAACAAAAGC
21204 AAAACGAAAACGAAACA
1 AAAACGAAAACGAAACA
* *
21221 AAAAC-AAAAC-ACAGA
1 AAAACGAAAACGAAACA
21236 AAAACGAAAACGA
1 AAAACGAAAACGA
21249 TGCCAAACGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 8 0.33
16 10 0.42
17 6 0.25
ACGTcount: A:0.71, C:0.18, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAACGAAAACGAAACA
Found at i:21781 original size:21 final size:21
Alignment explanation
Indices: 21755--21800 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
21745 CATGTGCAAG
21755 GCACGTGCATTATATATATAT
1 GCACGTGCATTATATATATAT
21776 GCACGTGCATTATATATATAT
1 GCACGTGCATTATATATATAT
21797 GCAC
1 GCAC
21801 TAGTTTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (21 bp):
GCACGTGCATTATATATATAT
Found at i:29532 original size:22 final size:22
Alignment explanation
Indices: 29371--29552 Score: 122
Period size: 22 Copynumber: 8.1 Consensus size: 22
29361 TGAATATTTT
*
29371 TATGAAATTTTGATAACTACCC
1 TATGAAATTTTGATAACTTCCC
* ** *
29393 TATCAAATTTTGATAACCACGC
1 TATGAAATTTTGATAACTTCCC
*
29415 TATGAAAATTTTTGATAA-TTACC
1 TATG-AAA-TTTTGATAACTTCCC
* * *
29438 TATGAAATTGTGATAAATTCCA
1 TATGAAATTTTGATAACTTCCC
* * **
29460 TATGAAAACTTTGATAACCTAAC
1 TATG-AAATTTTGATAACTTCCC
29483 TATGAAATTTTAAGA-AATCTT-CC
1 TATGAAATTTT--GATAA-CTTCCC
29506 TATGAAATTTTG-TAACCTTCCC
1 TATGAAATTTTGATAA-CTTCCC
* *
29528 TATGAGATTTTGTTAA-TCTCCC
1 TATGAAATTTTGATAACT-TCCC
29550 TAT
1 TAT
29553 AATTTTTTTA
Statistics
Matches: 126, Mismatches: 23, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
21 15 0.12
22 58 0.46
23 40 0.32
24 13 0.10
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACTTCCC
Found at i:29532 original size:68 final size:68
Alignment explanation
Indices: 29371--29532 Score: 172
Period size: 68 Copynumber: 2.4 Consensus size: 68
29361 TGAATATTTT
* * * * *
29371 TATGAAATTTTGATAACTACCCTAT-CAAATTTTGATAACCACGCTATGAAAATTTTTGATAATT
1 TATGAAATTTTGATAACTTCCCTATGAAAACTTTGATAACCACACTATGAAAATTTTAGATAATT
29435 ACC
66 ACC
* * *
29438 TATGAAATTGTGATAAATTCCATATGAAAACTTTGATAACCTA-ACTATG-AAATTTTAAGA-AA
1 TATGAAATTTTGATAACTTCCCTATGAAAACTTTGATAACC-ACACTATGAAAATTTT-AGATAA
*
29500 TCTTCC
64 T-TACC
29506 TATGAAATTTTG-TAACCTTCCCTATGA
1 TATGAAATTTTGATAA-CTTCCCTATGA
29533 GATTTTGTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
67 34 0.44
68 43 0.55
69 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (68 bp):
TATGAAATTTTGATAACTTCCCTATGAAAACTTTGATAACCACACTATGAAAATTTTAGATAATT
ACC
Found at i:30552 original size:31 final size:31
Alignment explanation
Indices: 30514--30575 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
30504 TATGTCTTGA
*
30514 AACCTAAATATGATATTTTAAGGGCCCAATT
1 AACCTAAATATGATATTCTAAGGGCCCAATT
30545 AACCTAAATATGATATTCTAAGGGCCCAATT
1 AACCTAAATATGATATTCTAAGGGCCCAATT
30576 CATTAATATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (31 bp):
AACCTAAATATGATATTCTAAGGGCCCAATT
Found at i:31228 original size:40 final size:43
Alignment explanation
Indices: 31160--31274 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 43
31150 TTTATGAAAT
* * * *
31160 TTTGATAA-CTACCCTATTAAATTTTGATAATCA-CCATATG-A-
1 TTTGATAACCTA-ACTATAAAATTTTGATAA-AATCCATAAGAAC
* *
31201 TTTGATAA-TTAACTATAAAATTGTGATAAAATCCATAAGAAAC
1 TTTGATAACCTAACTATAAAATTTTGATAAAATCCATAAG-AAC
31244 TTTGATAACCTAACTATAAAATTTTGATAAA
1 TTTGATAACCTAACTATAAAATTTTGATAAA
31275 CTTTCCTAAG
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 21 0.34
41 10 0.16
42 1 0.02
43 8 0.13
44 20 0.33
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (43 bp):
TTTGATAACCTAACTATAAAATTTTGATAAAATCCATAAGAAC
Found at i:31302 original size:20 final size:22
Alignment explanation
Indices: 31263--31302 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
31253 CTAACTATAA
*
31263 AATTTTGATAAACTTTCCTAAG
1 AATTTTGATAAACATTCCTAAG
31285 AATTTTG-T-AACATTCCTA
1 AATTTTGATAAACATTCCTA
31303 TGATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 1 0.06
22 7 0.41
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (22 bp):
AATTTTGATAAACATTCCTAAG
Found at i:32695 original size:22 final size:22
Alignment explanation
Indices: 32668--32875 Score: 141
Period size: 22 Copynumber: 9.7 Consensus size: 22
32658 CAGATCATCG
*
32668 AAATTTCATAGTGTAGCTATCA
1 AAATTTCATAGTGTAGTTATCA
* * *
32690 AAATTTCATAATGTGGTTGTCA
1 AAATTTCATAGTGTAGTTATCA
* *
32712 AAATTTCATAATGTGGTTA-CAA
1 AAATTTCATAGTGTAGTTATC-A
*
32734 AAATTTCAAAG-GTA---ATCA
1 AAATTTCATAGTGTAGTTATCA
*
32752 AAATTTCATATTGT-GCTTATCA
1 AAATTTCATAGTGTAG-TTATCA
* *
32774 AAATTTCATAGT-TAGATTAACG
1 AAATTTCATAGTGTAG-TTATCA
* *
32796 AAA-TTCTATAGGGAAGTTATCA
1 AAATTTC-ATAGTGTAGTTATCA
* *
32818 ACA-TTCTATAG-GGAGGTTATCA
1 AAATTTC-ATAGTGTA-GTTATCA
* *
32840 AAATTTCATAGTAT-GTTATCC
1 AAATTTCATAGTGTAGTTATCA
32861 AAATTTCATAGTGTA
1 AAATTTCATAGTGTA
32876 CCAAATCAGC
Statistics
Matches: 147, Mismatches: 25, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
18 11 0.07
19 3 0.02
21 28 0.19
22 100 0.68
23 5 0.03
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGTGTAGTTATCA
Found at i:32881 original size:17 final size:20
Alignment explanation
Indices: 32833--32871 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
32823 CTATAGGGAG
*
32833 GTTATCAAAATTTCATAGTAT
1 GTTATCCAAATTTCATAG-AT
32854 GTTATCCAAATTTCATAG
1 GTTATCCAAATTTCATAG
32872 TGTACCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (20 bp):
GTTATCCAAATTTCATAGAT
Found at i:33449 original size:22 final size:22
Alignment explanation
Indices: 33412--33654 Score: 146
Period size: 22 Copynumber: 11.2 Consensus size: 22
33402 AGTTGAACTT
* *
33412 TGTAGATTATCGAAATTTCATAG
1 TGTAG-TTATCAAAATTTCATAA
*
33435 TGTAGCTATCAAAATTTCATAA
1 TGTAGTTATCAAAATTTCATAA
* *
33457 TGTGGTTGTCAAAATTTCATAA
1 TGTAGTTATCAAAATTTCATAA
* *
33479 TGTGGTTGTCAAAATTTCATAA
1 TGTAGTTATCAAAATTTCATAA
*
33501 TGTCGTTA-CAAAAATTTCA-AA
1 TGTAGTTATC-AAAATTTCATAA
* *
33522 -G--GTAATCAAAATTTCATAT
1 TGTAGTTATCAAAATTTCATAA
*
33541 TGT-GCTTATCAAAATTTCATAG
1 TGTAG-TTATCAAAATTTCATAA
* * *
33563 T-TAGATTAACGAAA-TTCTATAG
1 TGTAG-TTATCAAAATTTC-ATAA
* * *
33585 GGAAGTTATCAACA-TTCTATAA
1 TGTAGTTATCAAAATTTC-ATAA
* *
33607 -GGAGGTTATCAAAATTTCATAG
1 TGTA-GTTATCAAAATTTCATAA
* * * *
33629 TATGGTTATCCAAATTTCATAG
1 TGTAGTTATCAAAATTTCATAA
33651 TGTA
1 TGTA
33655 CCAAATCAAC
Statistics
Matches: 178, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
18 12 0.07
19 2 0.01
20 2 0.01
21 10 0.06
22 142 0.80
23 10 0.06
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (22 bp):
TGTAGTTATCAAAATTTCATAA
Found at i:33780 original size:21 final size:21
Alignment explanation
Indices: 33714--33878 Score: 136
Period size: 22 Copynumber: 7.6 Consensus size: 21
33704 GTCATAAAAA
*
33714 AAAATTTCATATAGAGGTTATC
1 AAAATTTCATA-GGAGGTTATC
* * * *
33736 ACAGTTTTATAGTGTGGTTATC
1 AAAATTTCATAG-GAGGTTATC
33758 AAAATTTCATAGGATGG-TATC
1 AAAATTTCATAGGA-GGTTATC
33779 AAAATTTCATAGGATGGTTATC
1 AAAATTTCATAGGA-GGTTATC
*
33801 AAAGTTTCATAGGGAGGTTATC
1 AAAATTTCATA-GGAGGTTATC
* * *
33823 ACAATTTCTTAGAGAGGATATC
1 AAAATTTCATAG-GAGGTTATC
* * *
33845 AAAATAAT-ATAGCAAGATTATC
1 AAAAT-TTCATAG-GAGGTTATC
33867 AAAATTTCATAG
1 AAAATTTCATAG
33879 TAAGAAGGAG
Statistics
Matches: 114, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
21 24 0.21
22 86 0.75
23 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.35
Consensus pattern (21 bp):
AAAATTTCATAGGAGGTTATC
Found at i:33798 original size:65 final size:66
Alignment explanation
Indices: 33714--33849 Score: 170
Period size: 65 Copynumber: 2.1 Consensus size: 66
33704 GTCATAAAAA
* * * *
33714 AAAATTTCATATAGAGGTTATCACAGTTTTATAGTGTGGTTATCAAAATTTCATAG-GATGG-TA
1 AAAATTTCATATAGAGGTTATCAAAGTTTCATAGGGAGGTTATCAAAATTTCATAGAGA-GGATA
33777 TC
65 TC
* * *
33779 AAAATTTCATA-GGATGGTTATCAAAGTTTCATAGGGAGGTTATCACAATTTCTTAGAGAGGATA
1 AAAATTTCATATAGA-GGTTATCAAAGTTTCATAGGGAGGTTATCAAAATTTCATAGAGAGGATA
33843 TC
65 TC
33845 AAAAT
1 AAAAT
33850 AATATAGCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
64 2 0.03
65 48 0.79
66 11 0.18
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (66 bp):
AAAATTTCATATAGAGGTTATCAAAGTTTCATAGGGAGGTTATCAAAATTTCATAGAGAGGATAT
C
Found at i:34136 original size:44 final size:44
Alignment explanation
Indices: 34078--34161 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
34068 TTCATAGAAA
* * *
34078 AGTTTATTAAAATTTAATA-GTTAAGTTATCAAAGTTTCATTGGG
1 AGTTTATCAAAATTTAATAGGATAA-TTATCAAAATTTCATTGGG
*
34122 AGTTTATCAGAATTTAATAGGATAATTATCAAAATTTCAT
1 AGTTTATCAAAATTTAATAGGATAATTATCAAAATTTCAT
34162 AGTATGATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
44 31 0.89
45 4 0.11
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (44 bp):
AGTTTATCAAAATTTAATAGGATAATTATCAAAATTTCATTGGG
Found at i:34249 original size:2 final size:2
Alignment explanation
Indices: 34242--34270 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
34232 GCTCAGACTA
34242 AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34271 CATGTATGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34260 original size:15 final size:15
Alignment explanation
Indices: 34240--34270 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
34230 AAGCTCAGAC
34240 TAATATATATATATA
1 TAATATATATATATA
34255 TAATATATATATATA
1 TAATATATATATATA
34270 T
1 T
34271 CATGTATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATATATATATA
Found at i:34262 original size:13 final size:13
Alignment explanation
Indices: 34244--34269 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
34234 TCAGACTAAT
34244 ATATATATATATA
1 ATATATATATATA
34257 ATATATATATATA
1 ATATATATATATA
34270 TCATGTATGT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:34663 original size:6 final size:6
Alignment explanation
Indices: 34654--34678 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
34644 GGCTCGTTCA
34654 AGCTCG AGCTCG AGCTCG AGCTCG A
1 AGCTCG AGCTCG AGCTCG AGCTCG A
34679 AATTTTTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
AGCTCG
Found at i:34798 original size:28 final size:28
Alignment explanation
Indices: 34758--34813 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
34748 ACAACTACAC
34758 CAAATGATAATCAAGTCCAAACCAATTA
1 CAAATGATAATCAAGTCCAAACCAATTA
* *
34786 CAAATGATAATCAATTCCATACCAATTA
1 CAAATGATAATCAAGTCCAAACCAATTA
34814 TACCACAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.48, C:0.21, G:0.05, T:0.25
Consensus pattern (28 bp):
CAAATGATAATCAAGTCCAAACCAATTA
Done.