Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016460.1 Corchorus olitorius cultivar O-4 contig16493, 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: 137082
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:10653 original size:26 final size:26
Alignment explanation
Indices: 10623--10703 Score: 76
Period size: 26 Copynumber: 3.1 Consensus size: 26
10613 TAAAGCTACT
10623 AACCACATAAAACAAAGAGATATCCA
1 AACCACATAAAACAAAGAGATATCCA
** * *
10649 AACCA-ATTCAAGGCAAAG-TATAGCCA
1 AACCACA-T-AAAACAAAGAGATATCCA
* *
10675 AACCACATAAATCAAAGAGATATTCA
1 AACCACATAAAACAAAGAGATATCCA
10701 AAC
1 AAC
10704 AAATAGAAGG
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
25 8 0.19
26 26 0.62
27 8 0.19
ACGTcount: A:0.53, C:0.22, G:0.10, T:0.15
Consensus pattern (26 bp):
AACCACATAAAACAAAGAGATATCCA
Found at i:10696 original size:52 final size:53
Alignment explanation
Indices: 10594--10703 Score: 168
Period size: 52 Copynumber: 2.1 Consensus size: 53
10584 CTATAAAAAT
*
10594 AAACCAATTCAAGGCAAAGTAAAGCTACTAACCACATAAAACAAAGAGATATCC
1 AAACCAATTCAAGGCAAAGTAAAGC-ACAAACCACATAAAACAAAGAGATATCC
* * *
10648 AAACCAATTCAAGGCAAAGTATAGC-CAAACCACATAAATCAAAGAGATATTC
1 AAACCAATTCAAGGCAAAGTAAAGCACAAACCACATAAAACAAAGAGATATCC
10700 AAAC
1 AAAC
10704 AAATAGAAGG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 28 0.54
54 24 0.46
ACGTcount: A:0.52, C:0.22, G:0.11, T:0.15
Consensus pattern (53 bp):
AAACCAATTCAAGGCAAAGTAAAGCACAAACCACATAAAACAAAGAGATATCC
Found at i:10966 original size:3 final size:3
Alignment explanation
Indices: 10949--10982 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
10939 CCATATATGC
10949 ATA ATA CAT- ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
10983 CATATTAGGC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:30451 original size:2 final size:2
Alignment explanation
Indices: 30444--30470 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30434 TTCAAACACC
30444 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 T
30471 TAAAACCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:33713 original size:2 final size:2
Alignment explanation
Indices: 33706--33740 Score: 52
Period size: 2 Copynumber: 16.5 Consensus size: 2
33696 ATTTTTGATC
33706 AT AT AT AT AT AT GAT CAT 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 A
33741 CGTTAAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
2 27 0.87
3 4 0.13
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:33720 original size:16 final size:16
Alignment explanation
Indices: 33701--33733 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
33691 CCTATATTTT
33701 TGATCATATATATATA
1 TGATCATATATATATA
33717 TGATCATATATATATA
1 TGATCATATATATATA
33733 T
1 T
33734 ATATATACGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (16 bp):
TGATCATATATATATA
Found at i:36512 original size:14 final size:14
Alignment explanation
Indices: 36489--36518 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36479 TTATTATTAC
36489 TAGTACTATATATA
1 TAGTACTATATATA
*
36503 TAGTATTATATATA
1 TAGTACTATATATA
36517 TA
1 TA
36519 CTTGTATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (14 bp):
TAGTACTATATATA
Found at i:42593 original size:30 final size:29
Alignment explanation
Indices: 42557--42699 Score: 144
Period size: 30 Copynumber: 4.8 Consensus size: 29
42547 CAACCCTGGG
* **
42557 GAAGTACTCGTTGTCCTTGGTAATCCGGCC
1 GAAGTACTCGAT-TCCGAGGTAATCCGGCC
** **
42587 GAAGTACTCGTATTCCTG-GACAATCCGGTA
1 GAAGTACTCG-ATTCC-GAGGTAATCCGGCC
42617 GAAGTACTCGGATTCCGAGGTAATCCGGCC
1 GAAGTACTC-GATTCCGAGGTAATCCGGCC
*
42647 GAAGTACTCGAATTCCGAGGTAATCCTGCC
1 GAAGTACTCG-ATTCCGAGGTAATCCGGCC
*
42677 GAAGTACTCGAATTCCGGGGTAA
1 GAAGTACTCG-ATTCCGAGGTAA
42700 ACCAGAGGAA
Statistics
Matches: 96, Mismatches: 12, Indels: 10
0.81 0.10 0.08
Matches are distributed among these distances:
29 2 0.02
30 92 0.96
31 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (29 bp):
GAAGTACTCGATTCCGAGGTAATCCGGCC
Found at i:42672 original size:60 final size:60
Alignment explanation
Indices: 42575--42699 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
42565 CGTTGTCCTT
* * *
42575 GGTAATCCGGCCGAAGTACTCGTATTCCTGGACAATCCGGTAGAAGTACTCGGATTCCGA
1 GGTAATCCGGCCGAAGTACTCGAATTCCTGGACAATCCGGCAGAAGTACTCGAATTCCGA
** * * *
42635 GGTAATCCGGCCGAAGTACTCGAATTCC-GAGGTAATCCTGCCGAAGTACTCGAATTCCGG
1 GGTAATCCGGCCGAAGTACTCGAATTCCTG-GACAATCCGGCAGAAGTACTCGAATTCCGA
42695 GGTAA
1 GGTAA
42700 ACCAGAGGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (60 bp):
GGTAATCCGGCCGAAGTACTCGAATTCCTGGACAATCCGGCAGAAGTACTCGAATTCCGA
Found at i:44146 original size:14 final size:14
Alignment explanation
Indices: 44124--44175 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
44114 GTTGTACTCA
*
44124 ATTTTTATGCATTG
1 ATTTATATGCATTG
44138 ATTTATATG-ATTTTG
1 ATTTATATGCA--TTG
44153 CATTT-TATGCATTG
1 -ATTTATATGCATTG
44167 ATTTATATG
1 ATTTATATG
44176 ATTTTGCAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
13 5 0.16
14 15 0.47
15 7 0.22
16 5 0.16
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.56
Consensus pattern (14 bp):
ATTTATATGCATTG
Found at i:44158 original size:29 final size:29
Alignment explanation
Indices: 44126--44188 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
44116 TGTACTCAAT
44126 TTTTATGCATTGATTTATATGATTTTGCA
1 TTTTATGCATTGATTTATATGATTTTGCA
44155 TTTTATGCATTGATTTATATGATTTTGCA
1 TTTTATGCATTGATTTATATGATTTTGCA
*
44184 ATTTA
1 TTTTA
44189 GATTATCATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.56
Consensus pattern (29 bp):
TTTTATGCATTGATTTATATGATTTTGCA
Found at i:51397 original size:19 final size:18
Alignment explanation
Indices: 51373--51413 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
51363 ACTATACTCG
*
51373 TTTTTTTTT-AATCTTTCT
1 TTTTTTTTTCTATCTTT-T
51391 TTTTTTTTTCTATCTTTT
1 TTTTTTTTTCTATCTTTT
51409 TTTTT
1 TTTTT
51414 GTTCTCTTCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTCTATCTTTT
Found at i:51412 original size:15 final size:16
Alignment explanation
Indices: 51373--51413 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
51363 ACTATACTCG
*
51373 TTTTTTTTTAATCTTTC
1 TTTTTTTTT-ATCTATC
51390 TTTTTTTTT-TCTATC
1 TTTTTTTTTATCTATC
51405 TTTTTTTTT
1 TTTTTTTTT
51414 GTTCTCTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.61
17 9 0.39
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTTTATCTATC
Found at i:57410 original size:3 final size:3
Alignment explanation
Indices: 57397--57432 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
57387 GAATGACAAA
*
57397 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
57433 TTGAGGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.03
Consensus pattern (3 bp):
AAG
Found at i:57909 original size:4 final size:4
Alignment explanation
Indices: 57900--57924 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57890 CGTAGTCATT
57900 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
57925 CGCTTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:58283 original size:17 final size:17
Alignment explanation
Indices: 58253--58290 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
58243 AATTTTATTT
*
58253 ATAT-TATTTTAAAAAA
1 ATATCTATTTAAAAAAA
*
58269 TTATCTATTTAAAAAAA
1 ATATCTATTTAAAAAAA
58286 ATATC
1 ATATC
58291 AAAAACTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
ATATCTATTTAAAAAAA
Found at i:59435 original size:3 final size:3
Alignment explanation
Indices: 59429--59460 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
59419 TGAGTCCTCC
59429 TTA TTA TTA TTA TTA TTA TTA TTA TTA GTTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA T
59461 GGGTTTATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:62741 original size:12 final size:12
Alignment explanation
Indices: 62724--62775 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
62714 GGGATTTTAT
62724 AAAATCCATCCC
1 AAAATCCATCCC
*
62736 AAAATCCATGCC
1 AAAATCCATCCC
* *
62748 AATAGATTCATTCC
1 AA-A-ATCCATCCC
*
62762 AAAATCTATCCC
1 AAAATCCATCCC
62774 AA
1 AA
62776 TGGTGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 21 0.66
13 2 0.06
14 9 0.28
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.23
Consensus pattern (12 bp):
AAAATCCATCCC
Found at i:72419 original size:8 final size:7
Alignment explanation
Indices: 72371--72436 Score: 64
Period size: 7 Copynumber: 9.1 Consensus size: 7
72361 TGATTATTAG
*
72371 ATAATAT
1 ATAATAA
72378 AT-ATAA
1 ATAATAA
72384 ACTAATAA
1 A-TAATAA
*
72392 ATAATTA
1 ATAATAA
72399 ATAA-AA
1 ATAATAA
72405 ATAAATAA
1 AT-AATAA
72413 ATTAATAA
1 A-TAATAA
72421 ATAATTAA
1 ATAA-TAA
72429 ATAATAA
1 ATAATAA
72436 A
1 A
72437 ATGGGTGAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
6 7 0.14
7 21 0.42
8 21 0.42
9 1 0.02
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (7 bp):
ATAATAA
Found at i:81542 original size:17 final size:17
Alignment explanation
Indices: 81515--81565 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
81505 TCTGAAATTG
81515 AGAAAAAAAAAAA-AAA
1 AGAAAAAAAAAAAGAAA
*
81531 AGCAAAACAAAAAAGAAA
1 AG-AAAAAAAAAAAGAAA
81549 AGAAAAGAAAAGAAAGA
1 AGAAAA-AAAA-AAAGA
81566 TAAACCCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 2 0.07
17 14 0.48
18 8 0.28
19 5 0.17
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAAAGAAA
Found at i:83178 original size:29 final size:27
Alignment explanation
Indices: 83141--83238 Score: 65
Period size: 29 Copynumber: 3.3 Consensus size: 27
83131 CAAGTGTTAC
83141 AATTTCAAATTCAAGGGGCAATCATCCT
1 AATTTCAAATTCAAGGGGCAAT-ATCCT
* *
83169 AATTTGCAAAGTAT-ATGGGGCAA-AGTGGCAT
1 AATTT-CAAA-T-TCAAGGGGCAATA-T--CCT
*
83200 AATTTCAAATTCAAGGGACAATTTATCCT
1 AATTTCAAATTCAAGGGGCAA--TATCCT
83229 AATTTGCAAA
1 AATTT-CAAA
83239 GTATAGGGGA
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
28 7 0.13
29 20 0.37
30 17 0.31
31 9 0.17
32 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (27 bp):
AATTTCAAATTCAAGGGGCAATATCCT
Found at i:83204 original size:59 final size:60
Alignment explanation
Indices: 83141--83257 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
83131 CAAGTGTTAC
*
83141 AATTTCAAATTCAAGGGGCAA-TCATCCTAATTTGCAAAGTATATGGGG-CAAAGTGGCAT
1 AATTTCAAATTCAAGGGACAATTCATCCTAATTTGCAAAGTATA-GGGGACAAAGTGGCAT
*
83200 AATTTCAAATTCAAGGGACAATTTATCCTAATTTGCAAAGTATAGGGGACAAAGTGGC
1 AATTTCAAATTCAAGGGACAATTCATCCTAATTTGCAAAGTATAGGGGACAAAGTGGC
83258 TATTCAACCA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
59 24 0.44
60 30 0.56
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (60 bp):
AATTTCAAATTCAAGGGACAATTCATCCTAATTTGCAAAGTATAGGGGACAAAGTGGCAT
Found at i:83250 original size:31 final size:31
Alignment explanation
Indices: 83164--83254 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 31
83154 AGGGGCAATC
83164 ATCCTAATTTGCAAAGTATATGGGG-CAAAGT
1 ATCCTAATTTGCAAAGTATA-GGGGACAAAGT
** * * **
83195 GGCATAATTT-CAAA-T-TCAAGGGACAATTT
1 ATCCTAATTTGCAAAGTAT-AGGGGACAAAGT
83224 ATCCTAATTTGCAAAGTATAGGGGACAAAGT
1 ATCCTAATTTGCAAAGTATAGGGGACAAAGT
83255 GGCTATTCAA
Statistics
Matches: 43, Mismatches: 12, Indels: 10
0.66 0.18 0.15
Matches are distributed among these distances:
28 4 0.09
29 13 0.30
30 8 0.19
31 17 0.40
32 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (31 bp):
ATCCTAATTTGCAAAGTATAGGGGACAAAGT
Found at i:88513 original size:34 final size:34
Alignment explanation
Indices: 88475--88544 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
88465 AATTGAGAAT
88475 TGGAAATGAAAACCAAAAATGCCTAAACTCAATC
1 TGGAAATGAAAACCAAAAATGCCTAAACTCAATC
*
88509 TGGAAATGAAAACCAGAAATGCCTAAACTCAATC
1 TGGAAATGAAAACCAAAAATGCCTAAACTCAATC
88543 TG
1 TG
88545 TCAAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.19
Consensus pattern (34 bp):
TGGAAATGAAAACCAAAAATGCCTAAACTCAATC
Found at i:89055 original size:21 final size:19
Alignment explanation
Indices: 89030--89087 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
89020 GCTGCTCTAA
89030 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
89051 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
*
89070 TAATCTCATATGTACAGT
1 TAATCTCATCTGTACAGT
89088 TGCTAAACAG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.48
21 17 0.52
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:90762 original size:43 final size:43
Alignment explanation
Indices: 90701--90784 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
90691 AGACTGCAAT
90701 GGAAGATACACTTGGTTAAATGGATTTCTACAGTAATACTAAA
1 GGAAGATACACTTGGTTAAATGGATTTCTACAGTAATACTAAA
90744 GGAAGATACACTTGGTTAAATGGATTTCTACAGTAATACTA
1 GGAAGATACACTTGGTTAAATGGATTTCTACAGTAATACTA
90785 TATTTGGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (43 bp):
GGAAGATACACTTGGTTAAATGGATTTCTACAGTAATACTAAA
Found at i:97129 original size:7 final size:7
Alignment explanation
Indices: 97117--97148 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
97107 CACTTGAGAG
97117 TTTTTTC
1 TTTTTTC
97124 TTTTTTC
1 TTTTTTC
97131 TTTTTTC
1 TTTTTTC
97138 TTTTTT-
1 TTTTTTC
97144 TTTTT
1 TTTTT
97149 AGAGTTTACG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (7 bp):
TTTTTTC
Found at i:111389 original size:13 final size:14
Alignment explanation
Indices: 111359--111391 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
111349 ATATAAGGAT
*
111359 ATTATCAGAATCAA
1 ATTAACAGAATCAA
111373 ATTAACAGAAT-AA
1 ATTAACAGAATCAA
111386 ATTAAC
1 ATTAAC
111392 TATTATTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.55, C:0.12, G:0.06, T:0.27
Consensus pattern (14 bp):
ATTAACAGAATCAA
Found at i:112810 original size:3 final size:3
Alignment explanation
Indices: 112802--112829 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
112792 CAAACATTTG
112802 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
112830 ATACCTAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:130014 original size:121 final size:121
Alignment explanation
Indices: 129800--130048 Score: 471
Period size: 121 Copynumber: 2.1 Consensus size: 121
129790 TAGTTTTTTA
*
129800 GATATTTTATTTGTGGTCTATTGATGCAGCATATTGGATCTCTATATGTTTATATGCCCTTTCTT
1 GATATTTTATTTGTGGTCTATTGATGCAACATATTGGATCTCTATATGTTTATATGCCCTTTCTT
129865 GATATTAATATGTTTTAGCATGTTTTATTAATATTTTTTGGTATGCTGAACTAAAC
66 GATATTAATATGTTTTAGCATGTTTTATTAATATTTTTTGGTATGCTGAACTAAAC
129921 GATATTTTATTTGTGGTCTATTGATGCAACATATTGGATCTCTATATGTTTATATGCCCTTTCTT
1 GATATTTTATTTGTGGTCTATTGATGCAACATATTGGATCTCTATATGTTTATATGCCCTTTCTT
*
129986 GATATTAATATGTTTTAGCATGTTTTATTTATATTTTTTGGTATGCTGAACTAAAC
66 GATATTAATATGTTTTAGCATGTTTTATTAATATTTTTTGGTATGCTGAACTAAAC
*
130042 TATATTT
1 GATATTT
130049 AGGATACAAA
Statistics
Matches: 125, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 125 1.00
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (121 bp):
GATATTTTATTTGTGGTCTATTGATGCAACATATTGGATCTCTATATGTTTATATGCCCTTTCTT
GATATTAATATGTTTTAGCATGTTTTATTAATATTTTTTGGTATGCTGAACTAAAC
Found at i:135604 original size:116 final size:116
Alignment explanation
Indices: 135400--135631 Score: 446
Period size: 116 Copynumber: 2.0 Consensus size: 116
135390 AAGGTTGAAT
*
135400 TGAATGTAGCGTCTAAGAAACGACGCCGTGTATGTAAGTCCCGCCCACCCTTGAGTTTGAAATTA
1 TGAATGTAGCGTCTAAGAAACGACGCCGTGTATGTAAGTCCCGCCCACCCTTGAGTTCGAAATTA
*
135465 GACACAGCCGATTCCTTTTCTTCGCTTTATCGGGCGCCTGAGAGATCGAAC
66 GACACAACCGATTCCTTTTCTTCGCTTTATCGGGCGCCTGAGAGATCGAAC
135516 TGAATGTAGCGTCTAAGAAACGACGCCGTGTATGTAAGTCCCGCCCACCCTTGAGTTCGAAATTA
1 TGAATGTAGCGTCTAAGAAACGACGCCGTGTATGTAAGTCCCGCCCACCCTTGAGTTCGAAATTA
135581 GACACAACCGATTCCTTTTCTTCGCTTTATCGGGCGCCTGAGAGATCGAAC
66 GACACAACCGATTCCTTTTCTTCGCTTTATCGGGCGCCTGAGAGATCGAAC
135632 GAGAACATTA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (116 bp):
TGAATGTAGCGTCTAAGAAACGACGCCGTGTATGTAAGTCCCGCCCACCCTTGAGTTCGAAATTA
GACACAACCGATTCCTTTTCTTCGCTTTATCGGGCGCCTGAGAGATCGAAC
Found at i:136580 original size:321 final size:323
Alignment explanation
Indices: 135975--137076 Score: 1543
Period size: 321 Copynumber: 3.4 Consensus size: 323
135965 CAAGATTTTT
* *
135975 GGCCCCGGTTCAGTTTTGTAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAA
1 GGCCCAGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAA
*
136040 CCAAATCTCAGCCACAAAAGATCTAAAGATATATTTTTACGAGTATCTGAATTTTGTTTCGATTT
66 CCAAATCTCAGCCACAAAAGATTTAAAGATATA-TTTTACGAGTATCTGAATTTTGTTTCGATTT
136105 AATTAGAAATAATTCGAAAAAATTTGAAAATAATAATAGAAGCATGAAAAGCCCTTGAATCCTTT
130 AATTAGAAATAATTCGAAAAAATTTG---A-AATAATAGAAGCATGAAAAGCCCTTGAATCCTTT
* * * *
136170 TGGCATTGAATTATATATTTTTAATGAGTATTGTGGCCAAAAATTGTGAAAAACATTTTTGGATC
191 TGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAACATTTTCGGATC
*
136235 AGTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTGCTAAAATCGCATTT
256 AGTTTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTGCTAAAATCGCGTTT
136300 CGG
321 CGG
* * * * * *
136303 GGCTCC-GGTTCACTTTTGCAATATTTCTGGAGACAAGACTCATTGAAATATCTATATTCATCAA
1 GGC-CCAGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTA
* * * * *
136367 ATCAAATCTCAGCCACATAAGATTTAAAGATAGATCTTTACGAGTTTCTGAATTTTGTTTCGAAT
65 ACCAAATCTCAGCCACAAAAGATTTAAAGATATAT-TTTACGAGTATCTGAATTTTGTTTCGATT
* *
136432 TAATTAGAAATAATTCG-AAAAA-TTG-AGTAATAGAAGCGTGAAAAGCCCTTGAATCCTTTTGG
129 TAATTAGAAATAATTCGAAAAAATTTGAAATAATAGAAGCATGAAAAGCCCTTGAATCCTTTTGG
* * * * *
136494 CGTTGAATTATATATTTTTTATAAGTACTATGGCCGAAAATTGCGAAAAACATTTTCGGGTCAGT
194 CGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAACATTTTCGGATCAGT
* * * *
136559 TTTTGCAAAATTTTAGCCGAAACCGTGTACTAACCATCACGGTTTTTTCCAAAATCGCGTTTCGG
259 TTTTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGG
* * * * * *
136624 GGCCCTGGTTCAGTTTTGTAAGATTTTTGGTGCCAACACTCATTCAGATATCTATATTCCTCTAA
1 GGCCCAGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAA
136689 CCAAATCTCAGCCACAAAAGATTTAAAGATATATTCTTACGAGTATCTGAATTTTGTTTCGATTT
66 CCAAATCTCAGCCACAAAAGATTTAAAGATATATT-TTACGAGTATCTGAATTTTGTTTCGATTT
* * *
136754 AATTAGAAATAATTCGAAAAAATTTGAAAAATAATAATAGAAGCCTGAAAAGACCTTGAACCCTT
130 AATTAGAAATAATTCGAAAAAATTTG----A-AATAATAGAAGCATGAAAAGCCCTTGAATCCTT
* *
136819 TTGGCGTTGGATTATATA-TTTTTATGAGTATTGTAGCCAAAAATTGCGAAACAA-ATTTTCGGA
190 TTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAA-AACATTTTCGGA
*
136882 TCAGTTTTTGCAAAATTTTAGCCGAAAACCTTGTACTAACTAACCATCACGGTTTTTGCTAAAAT
254 TCAGTTTTTGCAAAATTTTAGCCG-AAA--TCGTA-T-ACTAACCATCACGGTTTTTGCTAAAAT
136947 -GACGTTTCGG
314 CG-CGTTTCGG
* *
136957 GGCCCAGGTTCAATTTTGCAAGATTATTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAA
1 GGCCCAGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAA
* * * *
137022 CCAAATCTAAGCCACATAAGATTTAAAGATATATTTTTCGTGTATCTGAATTTTG
66 CCAAATCTCAGCCACAAAAGATTTAAAGATATATTTTACGAGTATCTGAATTTTG
137077 GCGTTG
Statistics
Matches: 682, Mismatches: 73, Indels: 34
0.86 0.09 0.04
Matches are distributed among these distances:
320 3 0.00
321 276 0.40
322 5 0.01
323 3 0.00
326 3 0.00
327 6 0.01
328 188 0.28
329 53 0.08
331 2 0.00
332 20 0.03
333 123 0.18
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (323 bp):
GGCCCAGGTTCAGTTTTGCAAGATTTTTGGTGCCAAGACTCATTGAAATATCTATATTCATCTAA
CCAAATCTCAGCCACAAAAGATTTAAAGATATATTTTACGAGTATCTGAATTTTGTTTCGATTTA
ATTAGAAATAATTCGAAAAAATTTGAAATAATAGAAGCATGAAAAGCCCTTGAATCCTTTTGGCG
TTGAATTATATATTTTTTATGAGTATTGTGGCCAAAAATTGCGAAAAACATTTTCGGATCAGTTT
TTGCAAAATTTTAGCCGAAATCGTATACTAACCATCACGGTTTTTGCTAAAATCGCGTTTCGG
Done.