Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000533.1 Hibiscus syriacus cultivar Beakdansim tig00001028_pilon, 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: 60067
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:1253 original size:14 final size:14
Alignment explanation
Indices: 1234--1269 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
1224 GCTTGTTTAA
1234 TGATTTGTAAAAGT
1 TGATTTGTAAAAGT
1248 TGATTTGTAAAAGT
1 TGATTTGTAAAAGT
1262 TGATTTGT
1 TGATTTGT
1270 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGT
Found at i:1260 original size:75 final size:76
Alignment explanation
Indices: 1172--1314 Score: 245
Period size: 76 Copynumber: 1.9 Consensus size: 76
1162 GCTTGTTTAA
*
1172 TTGATTTGTAAAAGTTGA-TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGCTTGTTTAA-T
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTA-TTGTGCTTATTTAATT
1235 GATTTGTAAAAG
65 GATTTGTAAAAG
*
1247 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTGTTCTTATTTAATTG
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTGTGCTTATTTAATTG
1312 ATT
66 ATT
1315 GAAATGTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
75 30 0.47
76 34 0.53
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.52
Consensus pattern (76 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTGTGCTTATTTAATTG
ATTTGTAAAAG
Found at i:1427 original size:20 final size:20
Alignment explanation
Indices: 1402--1462 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
1392 CGCTAAACTC
*
1402 AAATCGCAATACGAAAGTCA
1 AAATCGCAATGCGAAAGTCA
*
1422 AAATCGCAATGCGAAAGCCA
1 AAATCGCAATGCGAAAGTCA
*
1442 AAATCGCAACGCGAAAGTCA
1 AAATCGCAATGCGAAAGTCA
1462 A
1 A
1463 TTCGCGTTGC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (20 bp):
AAATCGCAATGCGAAAGTCA
Found at i:1525 original size:20 final size:20
Alignment explanation
Indices: 1452--1704 Score: 195
Period size: 20 Copynumber: 13.7 Consensus size: 20
1442 AAATCGCAAC
*
1452 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
1471 GCGATAGTCTAA-TCGCTTT
1 GCGATAGTCAAATTCGCGTT
*
1490 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
1504 GCGATAGTCAAATTCCCGTT
1 GCGATAGTCAAATTCGCGTT
* * * *
1524 GCAATAATCAAATTCACGCT
1 GCGATAGTCAAATTCGCGTT
1544 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1564 GCGATAGTCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1584 GCGAT--T----TTGGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1598 GCGATAGTCATATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1618 GCGATAGTCAAATTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
1638 GCGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
* **
1652 ACGATAGTCAAATTCATGTT
1 GCGATAGTCAAATTCGCGTT
1672 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
1692 GCGATATTCAAAT
1 GCGATAGTCAAAT
1705 GAATGTGTAA
Statistics
Matches: 187, Mismatches: 27, Indels: 39
0.74 0.11 0.15
Matches are distributed among these distances:
14 33 0.18
16 3 0.02
17 1 0.01
18 2 0.01
19 19 0.10
20 129 0.69
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:1625 original size:54 final size:54
Alignment explanation
Indices: 1543--1696 Score: 245
Period size: 54 Copynumber: 2.9 Consensus size: 54
1533 AAATTCACGC
*
1543 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTGGCGT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTGGAGT
* *
1597 TGCGATAGTCATATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTTGAGT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTGGAGT
* ** *
1651 TACGATAGTCAAATTCATGTTGCGATAGTCAAATTCGCGTTGCGAT
1 TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGAT
1697 ATTCAAATGA
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 92 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (54 bp):
TGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTTGCGTTGCGATTTTGGAGT
Found at i:4166 original size:24 final size:23
Alignment explanation
Indices: 4132--4184 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
4122 TCTGAACATC
4132 ATCAAAATCCGAG-ATTTGACCAAG
1 ATCAAAATCCG-GTA-TTGACCAAG
*
4156 ATCAAAGTCCGGTATTGACCAAG
1 ATCAAAATCCGGTATTGACCAAG
4179 ATCAAA
1 ATCAAA
4185 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.21
Consensus pattern (23 bp):
ATCAAAATCCGGTATTGACCAAG
Found at i:4856 original size:17 final size:17
Alignment explanation
Indices: 4834--4871 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
4824 CGGATGGGGA
4834 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
4851 AGGATGTCGTTGGATAT
1 AGGATGTCGTTGGATAT
4868 AGGA
1 AGGA
4872 ACGGATGTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.26, C:0.05, G:0.37, T:0.32
Consensus pattern (17 bp):
AGGATGTCGTTGGATAT
Found at i:4880 original size:22 final size:20
Alignment explanation
Indices: 4831--4881 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 20
4821 TGCCGGATGG
4831 GGAAGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
4851 ---AGGATGTCGTTGGATAT
1 GGAAGGATGTCGTTGGATAT
4868 AGGAACGGATGTCG
1 -GGAA-GGATGTCG
4882 CCGAAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 17 0.65
21 1 0.04
22 8 0.31
ACGTcount: A:0.25, C:0.08, G:0.39, T:0.27
Consensus pattern (20 bp):
GGAAGGATGTCGTTGGATAT
Found at i:5065 original size:20 final size:20
Alignment explanation
Indices: 5019--5065 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
5009 AAATTCAACA
*
5019 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
5039 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
5059 TTGCGAT
1 TTGCGAT
5066 TATGTATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:5164 original size:20 final size:19
Alignment explanation
Indices: 5139--5184 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
5129 GGAAACTAAT
*
5139 TTGCGATACTAGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
5159 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
5178 TTGCGAT
1 TTGCGAT
5185 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:5172 original size:19 final size:19
Alignment explanation
Indices: 5148--5186 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5138 TTTGCGATAC
*
5148 TAGAGATCGCGTTGCGATT
1 TAGAGATCGCATTGCGATT
5167 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTGCGATT
5186 T
1 T
5187 TGTTGGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (19 bp):
TAGAGATCGCATTGCGATT
Found at i:16165 original size:15 final size:15
Alignment explanation
Indices: 16145--16176 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
16135 ATTAGCATTG
16145 GCTAAAATCACTTGT
1 GCTAAAATCACTTGT
*
16160 GCTAAAATCGCTTGT
1 GCTAAAATCACTTGT
16175 GC
1 GC
16177 AATCTATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (15 bp):
GCTAAAATCACTTGT
Found at i:21486 original size:14 final size:14
Alignment explanation
Indices: 21460--21529 Score: 63
Period size: 14 Copynumber: 5.0 Consensus size: 14
21450 GTTTTTTTCG
21460 TTATT-TTATTATTA
1 TTATTATTA-TATTA
21474 TTATTATTATATTA
1 TTATTATTATATTA
* *
21488 TTATTATTATCGTCA
1 TTATTATTAT-ATTA
* *
21503 -TCTTATTATTTTA
1 TTATTATTATATTA
*
21516 TTATTAATATATTA
1 TTATTATTATATTA
21530 CAAAATTTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 2 0.04
14 38 0.84
15 5 0.11
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (14 bp):
TTATTATTATATTA
Found at i:21486 original size:17 final size:17
Alignment explanation
Indices: 21460--21519 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
21450 GTTTTTTTCG
*
21460 TTATTTTATTATTATTA
1 TTATTATATTATTATTA
21477 TTATTATATTATTATTA
1 TTATTATATTATTATTA
*
21494 TTATCGTCATCTTATTATT-
1 TTAT--T-ATATTATTATTA
21513 TTATTAT
1 TTATTAT
21520 TAATATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.05
17 21 0.55
19 5 0.13
20 10 0.26
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (17 bp):
TTATTATATTATTATTA
Found at i:21512 original size:3 final size:3
Alignment explanation
Indices: 21460--21497 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
21450 GTTTTTTTCG
21460 TTA TT- TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
21498 CGTCATCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:23113 original size:2 final size:2
Alignment explanation
Indices: 23106--23136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
23096 GTTATTGTCA
23106 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
23137 GGTGCATGTT
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:23599 original size:58 final size:55
Alignment explanation
Indices: 23487--23612 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 55
23477 TTCTACATTT
* *
23487 TATATTCGATTCATTATTTTAGTTTATTTTGTTGTATGTAAACATCAAAATTTTTATG
1 TATATTCGATTCATTATTTTAATTTATTTTGTTGTATGAAAACATC--AATTTTT-TG
* * * *
23545 TATATTCGATTTATTTTTTATCAATTTATTTTGTTGTATGAAAATATC-GTTTTTTG
1 TATATTCGATTCATTATTT-T-AATTTATTTTGTTGTATGAAAACATCAATTTTTTG
*
23601 TATATTCCATTC
1 TATATTCGATTC
23613 GTATCTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
56 12 0.21
57 5 0.09
58 17 0.29
59 1 0.02
60 23 0.40
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.56
Consensus pattern (55 bp):
TATATTCGATTCATTATTTTAATTTATTTTGTTGTATGAAAACATCAATTTTTTG
Found at i:28928 original size:4 final size:4
Alignment explanation
Indices: 28919--28986 Score: 63
Period size: 4 Copynumber: 17.2 Consensus size: 4
28909 TCACAAATCA
* *
28919 ACAT ACAT ACAT -CAAT ACAA ACAT ATAT -CAAT ACAT ACAT ACAT -CAAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT
28967 ACAT ACAT ACAT A-AT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
28987 AAATTTGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
3 5 0.09
4 45 0.85
5 3 0.06
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:28948 original size:16 final size:16
Alignment explanation
Indices: 28919--28986 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
28909 TCACAAATCA
28919 ACATACATACATCAAT
1 ACATACATACATCAAT
* *
28935 ACAAACATATATCAAT
1 ACATACATACATCAAT
28951 ACATACATACATCAAT
1 ACATACATACATCAAT
28967 ACATACATACAT-AAT
1 ACATACATACATCAAT
28982 ACATA
1 ACATA
28987 AAATTTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
15 8 0.17
16 40 0.83
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (16 bp):
ACATACATACATCAAT
Found at i:29309 original size:34 final size:34
Alignment explanation
Indices: 29271--29372 Score: 125
Period size: 35 Copynumber: 3.0 Consensus size: 34
29261 TGAGGGTGTT
* *
29271 TTTCTTGAAAC-AATTTTGTCTCGCTTGAGACAGC
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACA-A
* *
29305 TTTCTAAAAACAAATTTTGTCTCGTTTGAGACAA
1 TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAA
* *
29339 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACA
1 TT-TCTTAAAACAAATTTTGTCTCGCTTGAGACA
29373 TTTTTCCTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
34 11 0.19
35 47 0.81
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (34 bp):
TTTCTTAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:29455 original size:105 final size:105
Alignment explanation
Indices: 29339--29535 Score: 290
Period size: 105 Copynumber: 1.9 Consensus size: 105
29329 TTTGAGACAA
* *
29339 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACC-AATTTTGAATTT
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGAT-CCAAATTTCGAATTT
29403 GATTCAC-TTAAAACAAAATTAATCTCACCTTAGATTGTTGT
65 GATTCACATT-AAACAAAATTAATCTCACCTTAGATTGTTGT
* * *
29444 TTCTTTTAAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTG
1 TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
* * *
29509 TTTCACATTAAACAAAGTTGATCTCAC
66 ATTCACATTAAACAAAATTAATCTCAC
29536 TTGAGATCGT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 2 0.02
105 78 0.95
106 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (105 bp):
TTCTCTTAAAACAAACTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATCCAAATTTCGAATTTG
ATTCACATTAAACAAAATTAATCTCACCTTAGATTGTTGT
Found at i:29904 original size:28 final size:27
Alignment explanation
Indices: 29857--29958 Score: 116
Period size: 28 Copynumber: 3.6 Consensus size: 27
29847 TCTGGAGACA
* *
29857 GTTTCTCTTGAGATAAATCTTTGAGTCT
1 GTTTCTTTTGA-AAAAATCTTTGAGTCT
*
29885 GTTCCTTTTGAATAAAATCTTTGAGT-T
1 GTTTCTTTTGAA-AAAATCTTTGAGTCT
29912 GTTTCTTTTGAAACAAATATCTTTGAGTCT
1 GTTTCTTTTG-AA-AAA-ATCTTTGAGTCT
*
29942 ATTTCTTTTGAAAAAAT
1 GTTTCTTTTGAAAAAAT
29959 TTATCTCCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
27 13 0.20
28 29 0.45
29 12 0.19
30 10 0.16
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (27 bp):
GTTTCTTTTGAAAAAATCTTTGAGTCT
Found at i:29958 original size:29 final size:29
Alignment explanation
Indices: 29873--29958 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
29863 CTTGAGATAA
* *
29873 ATCTTTGAGTCTGTTCCTTTTGAATAAA-
1 ATCTTTGAGTCTGTTTCTTTTGAAAAAAT
29901 ATCTTTGAGT-TGTTTCTTTTGAAACAAAT
1 ATCTTTGAGTCTGTTTCTTTTGAAA-AAAT
*
29930 ATCTTTGAGTCTATTTCTTTTGAAAAAAT
1 ATCTTTGAGTCTGTTTCTTTTGAAAAAAT
29959 TTATCTCCTA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
27 12 0.23
28 13 0.25
29 14 0.27
30 13 0.25
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (29 bp):
ATCTTTGAGTCTGTTTCTTTTGAAAAAAT
Found at i:30012 original size:60 final size:63
Alignment explanation
Indices: 29913--30050 Score: 151
Period size: 62 Copynumber: 2.2 Consensus size: 63
29903 CTTTGAGTTG
*
29913 TTTCTTTTGAAACAAATATCTTTGAGTCTATTTCTTTTG-AA-AAAATTTATCTC-CTAAAGACA
1 TTTCTTTTG-AA-AAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTT-TCTCTCTAAAGACA
29975 A
63 A
* * **
29976 TTTCTTTTGAAAAA-ATCTTTGAGT-TGGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAA
1 TTTCTTTTGAAAAATATCTTTGAGTCT-ATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
*
30038 CTTCTTTTGAAAA
1 TTTCTTTTGAAAA
30051 TACCCACCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
59 1 0.02
60 18 0.28
61 8 0.12
62 29 0.45
63 9 0.14
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
TTTCTTTTGAAAAATATCTTTGAGTCTATTTCCTTTGAAACAAAATTTTCTCTCTAAAGACAA
Found at i:30200 original size:15 final size:14
Alignment explanation
Indices: 30166--30208 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
30156 TTTTGAGTCG
*
30166 TTTCACTTGAAACA
1 TTTCTCTTGAAACA
30180 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
*
30194 TTTTCTCTTAAAACA
1 -TTTCTCTTGAAACA
30209 AGATCATCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.42
Consensus pattern (14 bp):
TTTCTCTTGAAACA
Found at i:30691 original size:40 final size:40
Alignment explanation
Indices: 30633--30997 Score: 211
Period size: 40 Copynumber: 8.7 Consensus size: 40
30623 CCAGTCGTCC
* * *
30633 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
* * * * *
30673 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * * *
30716 TCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
30762 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
30802 TCATCACGTATGAGCCGTGTCA-CCCTAGATAACCAG-CCGTCC
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATC-TCT
* * *
30844 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAGCCGTGTCATC-CC--TAGA---CCAGATCTCT
* *
30890 TCATCACGTATGAGCCGTGTCATTCCC-CGACCAGATCTCT
1 TCATCACGTAGGAGCCGTGTCA-TCCCTAGACCAGATCTCT
* * *
30930 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCA-AACTCT
1 TCATCACGTAGGAGCCGTGTCATCCCTAG---ACCAGATCTCT
* * *
30972 TCATCACGTACGAGCAGTGTCGTCCC
1 TCATCACGTAGGAGCCGTGTCATCCC
30998 CAACAACCAA
Statistics
Matches: 250, Mismatches: 45, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
38 3 0.01
39 3 0.01
40 85 0.34
41 1 0.00
42 53 0.21
43 37 0.15
44 3 0.01
46 59 0.24
47 6 0.02
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (40 bp):
TCATCACGTAGGAGCCGTGTCATCCCTAGACCAGATCTCT
Found at i:30981 original size:128 final size:129
Alignment explanation
Indices: 30633--30965 Score: 589
Period size: 128 Copynumber: 2.6 Consensus size: 129
30623 CCAGTCGTCC
* * *
30633 TCATCATGTAGGAACCGTGTCA-TCCCCAGACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
1 TCATCACGTATGAGCCGTGTCATTCCCC-GACCAGATCTCTTCATCACGTATGAGCCGTGTCAAC
*
30697 CATAGATAACCAGCCGTCCTCATCACATAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
65 CATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
30762 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTC-ACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
*
30826 CTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
66 ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
*
30890 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTAGGAGCCGTGTCAACC
1 TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
30955 ATAGATAACCA
66 ATAGATAACCA
30966 AACTCTTCAT
Statistics
Matches: 195, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
128 125 0.64
129 65 0.33
130 5 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (129 bp):
TCATCACGTATGAGCCGTGTCATTCCCCGACCAGATCTCTTCATCACGTATGAGCCGTGTCAACC
ATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
Found at i:31192 original size:3 final size:3
Alignment explanation
Indices: 31148--31177 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
31138 GTTTTTTTCG
31148 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31178 CGTCATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:33268 original size:57 final size:55
Alignment explanation
Indices: 33158--33282 Score: 144
Period size: 59 Copynumber: 2.2 Consensus size: 55
33148 TTCTACATTT
* *
33158 TATATTCGATTCATTATTTTAGTTTATTTTGTTGTATGTAAACATCAAATTTTTATG
1 TATATTCGATTCATTATTTTAATTTATTTTGTTGTATGAAAACATC-AATTTTT-TG
* * * *
33215 TATATTCGATTTATTTTTTATCAATTTATTTTGTTGTATGAAAATATC-GTTTTTTG
1 TATATTCGATTCATTATTT-T-AATTTATTTTGTTGTATGAAAACATCAATTTTTTG
*
33271 TATATTCCATTC
1 TATATTCGATTC
33283 GTATCTTTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
56 12 0.21
57 22 0.38
58 1 0.02
59 23 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (55 bp):
TATATTCGATTCATTATTTTAATTTATTTTGTTGTATGAAAACATCAATTTTTTG
Found at i:37505 original size:16 final size:16
Alignment explanation
Indices: 37484--37526 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
37474 CTTCAGAAAG
37484 AAATCCAAATCGTGGC
1 AAATCCAAATCGTGGC
37500 AAATCCAAATCGTGGC
1 AAATCCAAATCGTGGC
*
37516 AAATCGAAATC
1 AAATCCAAATC
37527 TAGAAGGGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.42, C:0.23, G:0.16, T:0.19
Consensus pattern (16 bp):
AAATCCAAATCGTGGC
Found at i:40154 original size:29 final size:29
Alignment explanation
Indices: 40111--40174 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
40101 AATTATTTGT
* *
40111 TTTTTTTAAAATTTAATGACTTAGTTAAC
1 TTTTTATAAAATTTAAAGACTTAGTTAAC
* * *
40140 TTTTTATAAAGTTTAAAGATTTATTTAAC
1 TTTTTATAAAATTTAAAGACTTAGTTAAC
*
40169 CTTTTA
1 TTTTTA
40175 AGAAAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.53
Consensus pattern (29 bp):
TTTTTATAAAATTTAAAGACTTAGTTAAC
Found at i:41314 original size:207 final size:207
Alignment explanation
Indices: 40957--41360 Score: 661
Period size: 207 Copynumber: 1.9 Consensus size: 207
40947 TATTTTTATA
40957 TTTTTAATCTTTTTAAAATAAACTTTTAAGTATTTTATACTTTTATTTTTTAAAAAACTTTTATC
1 TTTTTAATCTTTTTAAAATAAACTTTTAAGTATTTTATACTTTTATTTTTTAAAAAACTTTTATC
* *
41022 ATATTAAATTTTAAATAATTTCTTAATTTTTTTTATTGAAATGTTAACTAGATTTTCGAACTTTA
66 ATATTAAATTTTAAATAAATTCTTAA--TTTTTTATTGAAATGTTAACTAGATTTTCAAACTTTA
* *
41087 CAAAAAAATCAATTAAACATTCGAAATTTCTAACATCCCAATTAAATCAATAGTGTATACAAACT
129 CAAAAAAATCAATTAAACATTCGAAATTTCTAAAAACCCAATTAAATCAATAGTGTATACAAACT
41152 TTATAATTTGTAAT
194 TTATAATTTGTAAT
* * *
41166 TTTTTAATCTTTTTAAAATAAACTTTTAAGTATTTTTTTACTTTTATATTTTT-TAAAATTTTTA
1 TTTTTAATCTTTTTAAAATAAACTTTTAAGTA-TTTTATACTTTTAT-TTTTTAAAAAACTTTTA
41230 TCATATTAAATTTTAAATAAATTCTTAA-TTTTTATTGAAATGTTGAA-TAGATTTTCAAACTTT
64 TCATATTAAATTTTAAATAAATTCTTAATTTTTTATTGAAATGTT-AACTAGATTTTCAAACTTT
* *
41293 ACAAAAAAATCAATTAAACATTGGAAATTTCTAAAAACCCAATTAAATCAATAGTGTATACCAAC
128 ACAAAAAAATCAATTAAACATTCGAAATTTCTAAAAACCCAATTAAATCAATAGTGTATACAAAC
41358 TTT
193 TTT
41361 TCAAATGTTG
Statistics
Matches: 183, Mismatches: 9, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
207 95 0.52
208 2 0.01
209 32 0.17
210 49 0.27
211 5 0.03
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (207 bp):
TTTTTAATCTTTTTAAAATAAACTTTTAAGTATTTTATACTTTTATTTTTTAAAAAACTTTTATC
ATATTAAATTTTAAATAAATTCTTAATTTTTTATTGAAATGTTAACTAGATTTTCAAACTTTACA
AAAAAATCAATTAAACATTCGAAATTTCTAAAAACCCAATTAAATCAATAGTGTATACAAACTTT
ATAATTTGTAAT
Found at i:45626 original size:46 final size:46
Alignment explanation
Indices: 45528--45650 Score: 169
Period size: 46 Copynumber: 2.7 Consensus size: 46
45518 TTGGACCTTT
* *
45528 AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAC
* * *
45573 AGTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCAC
*
45619 AGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATCAAATGCATTCGATGTT
45651 CAATTTATTC
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
45 28 0.41
46 38 0.55
47 3 0.04
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (46 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAC
Found at i:46305 original size:2 final size:2
Alignment explanation
Indices: 46298--46369 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
46288 CCAAACCAAT
46298 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
46340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46370 AGTTCAAAAT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54236 original size:17 final size:18
Alignment explanation
Indices: 54214--54249 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
54204 GTGCACTAAG
54214 AGTGCA-TCGATGTATCA
1 AGTGCATTCGATGTATCA
*
54231 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTATCA
54249 A
1 A
54250 AATAGCCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (18 bp):
AGTGCATTCGATGTATCA
Found at i:54348 original size:65 final size:65
Alignment explanation
Indices: 54215--54374 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
54205 TGCACTAAGA
* * *
54215 GTGCATCGATGTATCAAGTGCATTCGATG-TTTCAAAATAGCCAAAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTG
* **
54279 GTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCA-AAATAGCCAAAGTGCATCGATGCATGGCT
*
54342 AT
65 -G
*
54344 GTGCATTGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
54375 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 27 0.32
65 55 0.65
66 3 0.04
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAGCCAAAGTGCATCGATGCATGGCTG
Found at i:54413 original size:65 final size:64
Alignment explanation
Indices: 54215--54422 Score: 199
Period size: 65 Copynumber: 3.2 Consensus size: 64
54205 TGCACTAAGA
* * * * * ** *
54215 GTGCATCGATGTATCAAGTGCATTCGATGTTTCA-AAATAGCCAAAGTGCATCGATGCATGGCTG
1 GTGCATTGATGCATGAAATGCATTCGATGTTTCATAAA-ATCCTCAGTGCATCGATGCATGGTTG
*
54279 GTGCATCGATGCATGAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATTGATGCATGAAATGCATTCGATG-TTTCATAAAATCCTCAGTGCATCGATGCATGGT-T
54344 -
64 G
** * * *
54344 GTGCATTGATGCATGAAATGCATTCGATG-TTCAATTTATTCCAT-GGTGCATCGATGTATGGAT
1 GTGCATTGATGCATGAAATGCATTCGATGTTTC-ATAAAATCC-TCAGTGCATCGATGCATGG-T
54407 TG
63 TG
*
54409 GTGCATTGGTGCAT
1 GTGCATTGATGCAT
54423 CACTTTGAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
63 3 0.02
64 48 0.39
65 68 0.55
66 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.33
Consensus pattern (64 bp):
GTGCATTGATGCATGAAATGCATTCGATGTTTCATAAAATCCTCAGTGCATCGATGCATGGTTG
Found at i:58858 original size:20 final size:21
Alignment explanation
Indices: 58828--58875 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
58818 TGATAAATGA
58828 ATTTGAATATA-TAATGTGTTT
1 ATTT-AATATATTAATGTGTTT
*
58849 ATTTAATATATTTATGTGTTT
1 ATTTAATATATTAATGTGTTT
*
58870 CTTTAA
1 ATTTAA
58876 AATGATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (21 bp):
ATTTAATATATTAATGTGTTT
Done.