Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024501.1 Corchorus olitorius cultivar O-4 contig24534, 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: 57526
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:1708 original size:11 final size:11
Alignment explanation
Indices: 1692--1717 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1682 AGATAATTTC
1692 TTTTCTTCTAG
1 TTTTCTTCTAG
1703 TTTTCTTCTAG
1 TTTTCTTCTAG
1714 TTTT
1 TTTT
1718 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:2507 original size:15 final size:15
Alignment explanation
Indices: 2477--2518 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
2467 TTACTTTGCT
2477 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
2493 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
2508 TTGCTTTCTGT
1 TTGTTTTCTGT
2519 CAATCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:3359 original size:24 final size:23
Alignment explanation
Indices: 3319--3364 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3309 CTGGTCTGGC
3319 CTTCCTCCACAACATTGATTTTGG
1 CTTCCTCCACAACATTG-TTTTGG
*
3343 CTTCCT-CAGAACTATTGTTTTG
1 CTTCCTCCACAAC-ATTGTTTTG
3365 TTCATGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (23 bp):
CTTCCTCCACAACATTGTTTTGG
Found at i:5729 original size:28 final size:29
Alignment explanation
Indices: 5686--5767 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 29
5676 ACAGCATCCG
*
5686 ACGTGGCATGCCACATGGCATTTTT-AAC
1 ACGTGGCACGCCACATGGCATTTTTGAAC
* * * *
5714 ACGTGGCACGCTACATGTCCTTTTTGTAC
1 ACGTGGCACGCCACATGGCATTTTTGAAC
** * *
5743 ACGTGGCGTGCCACGTGTCATTTTT
1 ACGTGGCACGCCACATGGCATTTTT
5768 TGGTAACGTG
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
28 21 0.49
29 22 0.51
ACGTcount: A:0.18, C:0.26, G:0.23, T:0.33
Consensus pattern (29 bp):
ACGTGGCACGCCACATGGCATTTTTGAAC
Found at i:9707 original size:32 final size:32
Alignment explanation
Indices: 9666--9730 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
9656 AGACACGCGG
*
9666 TAGTTTAAGAAATAACGCGCCACATGAATTTT
1 TAGTCTAAGAAATAACGCGCCACATGAATTTT
* * * * *
9698 TAGTCTAAGAGATAATGCGTCACGTGGATTTT
1 TAGTCTAAGAAATAACGCGCCACATGAATTTT
9730 T
1 T
9731 TTTGGCCACG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (32 bp):
TAGTCTAAGAAATAACGCGCCACATGAATTTT
Found at i:10149 original size:21 final size:21
Alignment explanation
Indices: 10099--10149 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
10089 TTGATTGGGA
*
10099 TTTTCGCAATGGAAGGAGGAT
1 TTTTCGCAGTGGAAGGAGGAT
10120 TTTTCGCAGTGGAAGGAGGAT
1 TTTTCGCAGTGGAAGGAGGAT
10141 TTTTCGCAG
1 TTTTCGCAG
10150 CAAAAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (21 bp):
TTTTCGCAGTGGAAGGAGGAT
Found at i:10449 original size:14 final size:14
Alignment explanation
Indices: 10430--10456 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10420 TATATTATAT
10430 TTTGCATTGCATAC
1 TTTGCATTGCATAC
10444 TTTGCATTGCATA
1 TTTGCATTGCATA
10457 ATAAAGGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (14 bp):
TTTGCATTGCATAC
Found at i:10643 original size:45 final size:45
Alignment explanation
Indices: 10579--10670 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
10569 AATTTGCACT
* *
10579 TGGACTTACTTTTAGGATTAGGAATAGCTCGGTTCTTTACACCTA
1 TGGACTTACTTTTAAGATTAGGAATAGCCCGGTTCTTTACACCTA
*
10624 TGGACTTATTTTTAAGATTAGGAATAGCCCGGTTCTTTACACCTA
1 TGGACTTACTTTTAAGATTAGGAATAGCCCGGTTCTTTACACCTA
10669 TG
1 TG
10671 TTTACAGGGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (45 bp):
TGGACTTACTTTTAAGATTAGGAATAGCCCGGTTCTTTACACCTA
Found at i:12308 original size:2 final size:2
Alignment explanation
Indices: 12301--12328 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12291 TCAAAACAGC
12301 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
12329 CATAAAAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14142 original size:54 final size:53
Alignment explanation
Indices: 14071--14840 Score: 894
Period size: 54 Copynumber: 14.4 Consensus size: 53
14061 AAATCAGAGC
* * * * *
14071 AATTAAACTAAATAGTAAAAGAAGGAGTAAACATTACTTAGTTTAATTCTGGGC
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACA-GAGTTAGTTTAATTCTGGGT
* *
14125 AATTAAACTAAAGAGTAAGAGAAGAAGTAAATAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-GTTAGTTTAATTCTGGGT
** *
14179 AATTAAACTAAAGAGTTTAAGAAGAAGTAAACAGAGGTTAGTTTAATTTTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-GTTAGTTTAATTCTGGGT
**
14233 AATTAAACTAAAGAGTTTAAGAAGAAGTAAACAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-GTTAGTTTAATTCTGGGT
* *
14287 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACATAGACTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAG-TTAGTTTAATTCTGGGT
* *
14341 AATTAAACTAAAAAGTAAAAGAAGAAGGAAACAGAGGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-GTTAGTTTAATTCTGGGT
* * * *
14395 AATTAAACTAAAGACTAAAAGAACAAGTAAACAGAGACTAGTTTAATTCTTGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAG-TTAGTTTAATTCTGGGT
*
14449 AATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGATGTTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGA-GTTAGTTTAATTCTGGGT
* * * * *
14503 AACTAAACTAAAAAGTAAGAGAAGGAGT----A-A-TTAGTTTAATTCTGGGG
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGTTAGTTTAATTCTGGGT
* * *
14550 AATTAAACTAAAGAGTAAAAGAAGAAGCAAACAGAGACTAGTTTAATTATGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAG-TTAGTTTAATTCTGGGT
* * * *
14604 AATTAAACTAAATAGTAAAAGAAGGAGTAAACAGTAATCAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAG-AGTTAGTTTAATTCTGGGT
* * *
14658 AATTAAACTAAATAGTAAAAGAAGGAA-TAAACAGTAATCAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAA-GAAGTAAACAG-AGTTAGTTTAATTCTGGGT
* * * *
14712 AATTAAACTAAAGAGTAAAGGAA-AGGGTAAACAATAATTAGTTTAATTCTGGGT
1 AATTAAACTAAAGAGTAAAAGAAGA-AGTAAAC-AGAGTTAGTTTAATTCTGGGT
* * * * *
14766 AATTAAGCTAAAGAGTAAAAGAA-AGAGTAAGCAGTAATTAGTTTAGTT-TAGAGT
1 AATTAAACTAAAGAGTAAAAGAAGA-AGTAAACAG-AGTTAGTTTAATTCT-GGGT
*
14820 AATTAAACTAAAAAAGTAAAA
1 AATTAAACT-AAAGAGTAAAA
14841 AGTAGCAATA
Statistics
Matches: 630, Mismatches: 66, Indels: 39
0.86 0.09 0.05
Matches are distributed among these distances:
47 39 0.06
49 1 0.00
50 1 0.00
51 1 0.00
52 2 0.00
53 5 0.01
54 565 0.90
55 16 0.03
ACGTcount: A:0.47, C:0.06, G:0.20, T:0.27
Consensus pattern (53 bp):
AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGTTAGTTTAATTCTGGGT
Found at i:27193 original size:16 final size:16
Alignment explanation
Indices: 27172--27204 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27162 GAGGTTCCAG
27172 AATTAAGATCTGCCCA
1 AATTAAGATCTGCCCA
*
27188 AATTAAGATCTGTCCA
1 AATTAAGATCTGCCCA
27204 A
1 A
27205 GTGTGAAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (16 bp):
AATTAAGATCTGCCCA
Found at i:28685 original size:50 final size:50
Alignment explanation
Indices: 28612--28724 Score: 190
Period size: 50 Copynumber: 2.3 Consensus size: 50
28602 ACACACACAC
* **
28612 ACACACACACACAGATCATTCAATAAAAATAAATAAATCAGGTTATCTGG
1 ACACACACACACAGATCAATCAATAAAAATAAATAAATCAGGACATCTGG
*
28662 ACACACACACACAGATCAATCAATAAAAATAAATAAATCTGGACATCTGG
1 ACACACACACACAGATCAATCAATAAAAATAAATAAATCAGGACATCTGG
28712 ACACACACACACA
1 ACACACACACACA
28725 CACACACACA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.50, C:0.24, G:0.09, T:0.18
Consensus pattern (50 bp):
ACACACACACACAGATCAATCAATAAAAATAAATAAATCAGGACATCTGG
Found at i:28719 original size:2 final size:2
Alignment explanation
Indices: 28712--28736 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28702 GGACATCTGG
28712 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
28737 AAATTAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:28745 original size:50 final size:50
Alignment explanation
Indices: 28608--28748 Score: 160
Period size: 50 Copynumber: 2.7 Consensus size: 50
28598 TAAAACACAC
**
28608 ACACACACACACACACAGATCATTCAATAAAAATAAATAAATCAGGTTATCTGG
1 ACACACACACACACACA-ATCA--C-ATAAAAATAAATAAATCAGGACATCTGG
* *
28662 ACACACACACACAGATCAATCA-ATAAAAATAAATAAATCTGGACATCTGG
1 ACACACACACACACA-CAATCACATAAAAATAAATAAATCAGGACATCTGG
* *
28712 ACACACACACACACACACA-CACACAAAATTAAATAAA
1 ACACACACACACACACA-ATCACATAAAAATAAATAAA
28749 AAAAAATTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
49 4 0.05
50 53 0.69
54 18 0.23
55 2 0.03
ACGTcount: A:0.52, C:0.25, G:0.07, T:0.16
Consensus pattern (50 bp):
ACACACACACACACACAATCACATAAAAATAAATAAATCAGGACATCTGG
Found at i:29203 original size:251 final size:250
Alignment explanation
Indices: 28760--29261 Score: 943
Period size: 251 Copynumber: 2.0 Consensus size: 250
28750 AAAAATTAAC
28760 CAAAATAGAACTGAAACTTCAGAATGTAAAGTGGACAAAAGAAGCAAACTAACCTGCAAATGAAT
1 CAAAATAGAACTGAAACTTCAGAATGTAAAGTGGACAAAAGAAGCAAACTAACCTGCAAATGAAT
28825 TAAAAACAAAACCTGAAAATATAAAGAGAAACAAATATATGAATATCATATAAACCTGAAAATAT
66 TAAAAACAAAACCTGAAAATATAAAGAGAAACAAATATATGAATATCATATAAACCTGAAAATAT
28890 AAAGATTGTACACAAAAGAGGAAGAACTAACCTCAAGCACATCATACTCTTGGCACTAAAAAAGG
131 AAAGATTGTACACAAAAGAGGAAGAACTAACCTCAAGCACATCATACTCTTGGCACTAAAAAAGG
*
28955 AGGAAGGAAACTCGAAAAAAAGGCACAAAACAAACCTCTCAACGAAATGGATTAGT
196 AGGAAAGAAACTCG-AAAAAAGGCACAAAACAAACCTCTCAACGAAATGGATTAGT
* *
29011 CAAAATAGAACTGAAACTTCAGAATGTAAAGTGGACAATAGAAG-AACACTGACCTGCAAATGAA
1 CAAAATAGAACTGAAACTTCAGAATGTAAAGTGGACAAAAGAAGCAA-ACTAACCTGCAAATGAA
*
29075 TTGAAAACAAAACCTGAAAATATAAAGAGAAACAAATATATGAATATCATATAAACCTGAAAATA
65 TTAAAAACAAAACCTGAAAATATAAAGAGAAACAAATATATGAATATCATATAAACCTGAAAATA
29140 TAAAGATTGTACACAAAAGAGGAAGAACTAACCTCAAGCACATCATACTCTTGGCACTAAAAAAG
130 TAAAGATTGTACACAAAAGAGGAAGAACTAACCTCAAGCACATCATACTCTTGGCACTAAAAAAG
29205 GAGGAAAGAAACTCGAAAAAAGGCACAAAACAAACCTCTCAACGAAATGGATTAGT
195 GAGGAAAGAAACTCGAAAAAAGGCACAAAACAAACCTCTCAACGAAATGGATTAGT
29261 C
1 C
29262 GTAAAAGAGG
Statistics
Matches: 246, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
250 44 0.18
251 202 0.82
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.17
Consensus pattern (250 bp):
CAAAATAGAACTGAAACTTCAGAATGTAAAGTGGACAAAAGAAGCAAACTAACCTGCAAATGAAT
TAAAAACAAAACCTGAAAATATAAAGAGAAACAAATATATGAATATCATATAAACCTGAAAATAT
AAAGATTGTACACAAAAGAGGAAGAACTAACCTCAAGCACATCATACTCTTGGCACTAAAAAAGG
AGGAAAGAAACTCGAAAAAAGGCACAAAACAAACCTCTCAACGAAATGGATTAGT
Found at i:29996 original size:2 final size:2
Alignment explanation
Indices: 29989--30019 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29979 GAGAATCACA
29989 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
30020 CTCCCCCCCC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:33497 original size:33 final size:34
Alignment explanation
Indices: 33455--33523 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 34
33445 ATTAAGGCAG
** *
33455 AAAATGGGGGCGAAAGTTGAAAAGCAGCAGC-GC
1 AAAATGGGGGCGAAAGTCAAAAAGCAACAGCTGC
33488 AAAATGGGGGCGAAAGTCAAAAAGCAACAGCTGC
1 AAAATGGGGGCGAAAGTCAAAAAGCAACAGCTGC
33522 AA
1 AA
33524 TCGTGGGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 28 0.88
34 4 0.12
ACGTcount: A:0.43, C:0.16, G:0.32, T:0.09
Consensus pattern (34 bp):
AAAATGGGGGCGAAAGTCAAAAAGCAACAGCTGC
Found at i:39410 original size:26 final size:24
Alignment explanation
Indices: 39381--39434 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
39371 TAAAAACCCA
39381 AAAAGAAAAAG-AAAATAGAGTATTTC
1 AAAAGAAAAAGTAAAA-AG-GT-TTTC
**
39407 AAAATTAAAAGTAAAAAGGTTTTC
1 AAAAGAAAAAGTAAAAAGGTTTTC
39431 AAAA
1 AAAA
39435 TCCAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 8 0.32
25 2 0.08
26 11 0.44
27 4 0.16
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (24 bp):
AAAAGAAAAAGTAAAAAGGTTTTC
Found at i:39540 original size:52 final size:52
Alignment explanation
Indices: 39467--39593 Score: 184
Period size: 52 Copynumber: 2.4 Consensus size: 52
39457 AATAAAAAAG
*
39467 AATTCCCTTCAAAGTTTTCAAAGTATCCAATTCAGCTCTTTTCAAATTGGAAA
1 AATTCCCATC-AAGTTTTCAAAGTATCCAATTCAGCTCTTTTCAAATTGGAAA
* * *
39520 AATTCCCATCAAGTTTTCAAAGTATTCAATTTAGCTCTTTTCAAATTGGGAA
1 AATTCCCATCAAGTTTTCAAAGTATCCAATTCAGCTCTTTTCAAATTGGAAA
* *
39572 AGTTTCCATCAAG-TTTCAAAGT
1 AATTCCCATCAAGTTTTCAAAGT
39594 TTTCAAATTG
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 9 0.13
52 50 0.74
53 9 0.13
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (52 bp):
AATTCCCATCAAGTTTTCAAAGTATCCAATTCAGCTCTTTTCAAATTGGAAA
Found at i:39642 original size:37 final size:37
Alignment explanation
Indices: 39557--39692 Score: 229
Period size: 37 Copynumber: 3.7 Consensus size: 37
39547 AATTTAGCTC
* **
39557 TTTTCAAATTGGGAAAGTTTCCATCAAGT-TTCAAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGG
39593 TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGG
39630 TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGG
*
39667 TTTTCAAATTTGGAAAGTTCCCATCA
1 TTTTCAAATTGGGAAAGTTCCCATCA
39693 GGTTTTAGTT
Statistics
Matches: 95, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 28 0.29
37 67 0.71
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (37 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTCTTCATGG
Found at i:44449 original size:2 final size:2
Alignment explanation
Indices: 44442--44469 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44432 AAAGGCTCCC
44442 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44470 TATTTTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46823 original size:70 final size:69
Alignment explanation
Indices: 46710--46846 Score: 195
Period size: 70 Copynumber: 2.0 Consensus size: 69
46700 CTTGAAATGC
* * * * *
46710 ATTGTCTTTTTATTTAATTTTAGCATTTGGATGTAATGAATGGTGTTCCTACGATTTTTTTCCTT
1 ATTGTCTTTATATATAATTTTAGCATTTGGATGTAATGAATGGTGCTCCCACCA-TTTTTTCCTT
46775 AGTGT
65 AGTGT
*
46780 ATTGTCTTTATATATAATTTTAGCA-TTGAGATGTAATTAATGGTGCTCCCACCATTTTTTCCTT
1 ATTGTCTTTATATATAATTTTAGCATTTG-GATGTAATGAATGGTGCTCCCACCATTTTTTCCTT
46844 AGT
65 AGT
46847 TGTTAGTTTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
69 16 0.27
70 44 0.73
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (69 bp):
ATTGTCTTTATATATAATTTTAGCATTTGGATGTAATGAATGGTGCTCCCACCATTTTTTCCTTA
GTGT
Found at i:47814 original size:23 final size:22
Alignment explanation
Indices: 47763--47867 Score: 92
Period size: 23 Copynumber: 4.7 Consensus size: 22
47753 TTGAGGTCAC
47763 AAGTGGTCGAGCGCC-GCGTTATGG
1 AAGTGGTCG-GCGCCAG-GTT-TGG
47787 AAGTGGTCGGTCGCCAGGTTTGG
1 AAGTGGTCGG-CGCCAGGTTTGG
* *
47810 AAGTGGTCGG-G-C-GCTATGG
1 AAGTGGTCGGCGCCAGGTTTGG
*
47829 AAGTGGTTGGTCGCCAGGTTTGG
1 AAGTGGTCGG-CGCCAGGTTTGG
*
47852 AAGTGGTTGGGCGCCA
1 AAGTGG-TCGGCGCCA
47868 AGCAATTGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
19 14 0.21
20 1 0.01
21 2 0.03
22 1 0.01
23 30 0.44
24 19 0.28
25 1 0.01
ACGTcount: A:0.15, C:0.17, G:0.44, T:0.24
Consensus pattern (22 bp):
AAGTGGTCGGCGCCAGGTTTGG
Found at i:47841 original size:42 final size:42
Alignment explanation
Indices: 47782--47865 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
47772 AGCGCCGCGT
47782 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
* *
47824 TATGGAAGTGGTTGGTCGCCAGGTTTGGAAGTGGTTGGGCGC
1 TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
47866 CAAGCAATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.14, C:0.14, G:0.45, T:0.26
Consensus pattern (42 bp):
TATGGAAGTGGTCGGTCGCCAGGTTTGGAAGTGGTCGGGCGC
Found at i:48362 original size:71 final size:70
Alignment explanation
Indices: 48278--48426 Score: 253
Period size: 71 Copynumber: 2.1 Consensus size: 70
48268 AGCGCCAACA
* *
48278 TTTTTTTTTGGTGGTCGACCGCCTAGATCCATTTGGGCGCTCAACCACATGTGTGTGTGTGTGTG
1 TTTTTTTTGGGTGGTCGACCGCCTAGATCCATTTGGGAGCTCAACCACATGTGTGTGTGTGTGTG
48343 TGTTG
66 TGTTG
*
48348 TTTTTTTTGGGGTGGTCGACCGCCTAGATCCATTTGGGAGCTCGACCACATGTGTGTGTGTGTGT
1 TTTTTTTT-GGGTGGTCGACCGCCTAGATCCATTTGGGAGCTCAACCACATGTGTGTGTGTGTGT
*
48413 GTGTTT
65 GTGTTG
48419 TTTTTTTT
1 TTTTTTTT
48427 TTTGCGTTTA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
70 8 0.11
71 66 0.89
ACGTcount: A:0.11, C:0.17, G:0.30, T:0.43
Consensus pattern (70 bp):
TTTTTTTTGGGTGGTCGACCGCCTAGATCCATTTGGGAGCTCAACCACATGTGTGTGTGTGTGTG
TGTTG
Found at i:50184 original size:128 final size:126
Alignment explanation
Indices: 49873--50256 Score: 565
Period size: 128 Copynumber: 3.0 Consensus size: 126
49863 GGGGATTCGT
* * *
49873 CGTTGAGCCCCTTGGGGGCGTTCATTACTTTCCGTACTTGTGCAAGGATCGCTTCTTGGCGACCG
1 CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAGGGATCGCTTCTTGGCGACCG
* *
49938 CCCACAAGTCGGGGGCCATGCTAACTCGGGTTCGGATCCTTC-CCGATCGCCCCGCCTGCTAGG
66 CCCACAAGTCGGGGGCCATGCTAAGTCGGGTT-GGAT-CTTCGTCGATCGCCCCGCCTGCT-GG
* *
50001 -GTTGAGCCCTTCGCGGGCGTTCATTACTTTCCGTACTTGTGCAGGGATCGCTTCTTGACGACCG
1 CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAGGGATCGCTTCTTGGCGACCG
*
50065 CCCACAAGTCGGGGGCCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCCCCGCTTGCTGG
66 CCCACAAGTCGGGGGCCATGCTAAGTC-GGGTTGGATCTTCGTCGATCG-CCCCGCCTGCTGG
* * * * *
50128 CGTTGAGCCCTTTGCGGGTGATCATTACTTTCCGTACTTGTGGAGGGATCGCTTCTTGGCCACTG
1 CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAGGGATCGCTTCTTGGCGACCG
* *
50193 CCCACAAGTCGGGGGTCATGCTAAGTCAGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGG
66 CCCACAAGTCGGGGGCCATGCTAAGTC-GGGTTGGATCTTCGTCGATCGCCCCGCCTGCTGG
50255 CG
1 CG
50257 CTGTCGGGGG
Statistics
Matches: 233, Mismatches: 19, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
126 4 0.02
127 110 0.47
128 119 0.51
ACGTcount: A:0.13, C:0.30, G:0.30, T:0.27
Consensus pattern (126 bp):
CGTTGAGCCCTTTGCGGGCGTTCATTACTTTCCGTACTTGTGCAGGGATCGCTTCTTGGCGACCG
CCCACAAGTCGGGGGCCATGCTAAGTCGGGTTGGATCTTCGTCGATCGCCCCGCCTGCTGG
Found at i:50271 original size:59 final size:59
Alignment explanation
Indices: 50200--50318 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
50190 CTGCCCACAA
*
50200 GTCGGGGGTCATGCTAAGTCAGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGGCGCT
1 GTCGGGGGTCATGCTAAGTCAGGGTTAGATCTTCGTCGATCGCCTCGCCTGCTGGCGCT
*
50259 GTCGGGGGTCATGCTAAGTCGGGGTTAGATCTTCGTCGATCGCCTCGCCTGCTGGCGCT
1 GTCGGGGGTCATGCTAAGTCAGGGTTAGATCTTCGTCGATCGCCTCGCCTGCTGGCGCT
50318 G
1 G
50319 AGCCCTTTGC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.10, C:0.27, G:0.36, T:0.27
Consensus pattern (59 bp):
GTCGGGGGTCATGCTAAGTCAGGGTTAGATCTTCGTCGATCGCCTCGCCTGCTGGCGCT
Found at i:50684 original size:16 final size:17
Alignment explanation
Indices: 50646--50683 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
50636 GCTTTCTTCG
50646 GGGGGTCATGCTAAGTC
1 GGGGGTCATGCTAAGTC
50663 GGGGGTCATGCTAAGTC
1 GGGGGTCATGCTAAGTC
50680 GGGG
1 GGGG
50684 TTGGATCTTC
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:0.16, C:0.16, G:0.47, T:0.21
Consensus pattern (17 bp):
GGGGGTCATGCTAAGTC
Found at i:50753 original size:59 final size:59
Alignment explanation
Indices: 50661--50775 Score: 230
Period size: 59 Copynumber: 1.9 Consensus size: 59
50651 TCATGCTAAG
50661 TCGGGGGTCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGGCGCTA
1 TCGGGGGTCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGGCGCTA
50720 TCGGGGGTCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGGCG
1 TCGGGGGTCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGGCG
50776 TTGAGCCCTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.10, C:0.27, G:0.37, T:0.27
Consensus pattern (59 bp):
TCGGGGGTCATGCTAAGTCGGGGTTGGATCTTCGTCGATCGCCTCGCCTGCTGGCGCTA
Found at i:51675 original size:12 final size:13
Alignment explanation
Indices: 51653--51682 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
51643 ACTAGCAATT
51653 AAAATCAATCAAG
1 AAAATCAATCAAG
51666 AAAA-CAATCAAG
1 AAAATCAATCAAG
51678 AAAAT
1 AAAAT
51683 TAAAGAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (13 bp):
AAAATCAATCAAG
Found at i:55037 original size:25 final size:25
Alignment explanation
Indices: 54973--55058 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
54963 TCATAAATGT
* * *
54973 AGAACGCCCGCCGAATACGAAGCGG
1 AGAACGCCCGCCGAGTGCCAAGCGG
* *
54998 AGAACGCTCGTCGAGTGCCAAGCGG
1 AGAACGCCCGCCGAGTGCCAAGCGG
*
55023 AGAACACCCGCCGAGTGAGTGCCAAGCGG
1 AGAACGCCCGCC----GAGTGCCAAGCGG
55052 AGAACGC
1 AGAACGC
55059 TTACCGAGCA
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
25 29 0.60
29 19 0.40
ACGTcount: A:0.29, C:0.30, G:0.34, T:0.07
Consensus pattern (25 bp):
AGAACGCCCGCCGAGTGCCAAGCGG
Found at i:55129 original size:181 final size:181
Alignment explanation
Indices: 54910--55364 Score: 669
Period size: 181 Copynumber: 2.5 Consensus size: 181
54900 AGTGCAAAAC
* *
54910 GTAGATCCCCAAGGAGAGGAGAATGCTCCCCATGAGAGGATGGCGATCGCCGATCATAAATGTAG
1 GTAGAT-CCCAAGGAGAGGAGAATGCTCCCCATGAGAGGAGGGCGATCGCCGATCGTAAATGTAG
*
54975 AACGCCCGCCGAATACGAAGCGGAGAACGCTCGTCGAGTGCCAAGCGGAGAACACCCGCCGAGTG
65 AACGCCCGCCGAATACGAAGCGGAGAACGCTCGTCGAGCGCCAAGCGGAGAACACCCGCCGAGTG
* * *
55040 AGTGCCAAGCGGAGAACGCTTACCGAGCACAAAGCGTAGATCC-CTAAAGAGT
130 AGTGCCAAGCGAAGAACGCTCACCGAGCACAAAGCGTAGATCCTC-AAAGAGA
* * * *
55092 GTAGATCCCGAGGAGAGGAGAATGCTCCCCGTGAGAGGAGGGCAATCGCCGATCGCAAATGTAGA
1 GTAGATCCCAAGGAGAGGAGAATGCTCCCCATGAGAGGAGGGCGATCGCCGATCGTAAATGTAGA
* ** * *
55157 ACGCCCGCTGAATGTGAAGCGGAGAACGCTCGTCGAGCGCCAAGCGGAGAACGCTCGCCGAGTGA
66 ACGCCCGCCGAATACGAAGCGGAGAACGCTCGTCGAGCGCCAAGCGGAGAACACCCGCCGAGTGA
* *
55222 GTGCCAAGCGAAGAACGCTCGCCGAGCGCAAAGCGTAGATCCTCAAAGAGA
131 GTGCCAAGCGAAGAACGCTCACCGAGCACAAAGCGTAGATCCTCAAAGAGA
* *
55273 GTAGATCCCAAGGAGAGGAGAATGCTCCCTATGAGAGGAGGGCGATCGCCGATCGTATATGTAGA
1 GTAGATCCCAAGGAGAGGAGAATGCTCCCCATGAGAGGAGGGCGATCGCCGATCGTAAATGTAGA
** * * *
55338 ACGCTTGCCGAACACGAAACAGAGAAC
66 ACGCCCGCCGAATACGAAGCGGAGAAC
55365 ACTTGCCGAG
Statistics
Matches: 241, Mismatches: 31, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
181 234 0.97
182 7 0.03
ACGTcount: A:0.30, C:0.25, G:0.32, T:0.13
Consensus pattern (181 bp):
GTAGATCCCAAGGAGAGGAGAATGCTCCCCATGAGAGGAGGGCGATCGCCGATCGTAAATGTAGA
ACGCCCGCCGAATACGAAGCGGAGAACGCTCGTCGAGCGCCAAGCGGAGAACACCCGCCGAGTGA
GTGCCAAGCGAAGAACGCTCACCGAGCACAAAGCGTAGATCCTCAAAGAGA
Found at i:55201 original size:25 final size:25
Alignment explanation
Indices: 55173--55256 Score: 96
Period size: 25 Copynumber: 3.2 Consensus size: 25
55163 GCTGAATGTG
*
55173 AAGCGGAGAACGCTCGTCGAGCGCC
1 AAGCGGAGAACGCTCGCCGAGCGCC
*
55198 AAGCGGAGAACGCTCGCCGAGTGAGTGCC
1 AAGCGGAGAACGCTCGCC----GAGCGCC
* *
55227 AAGCGAAGAACGCTCGCCGAGCGCA
1 AAGCGGAGAACGCTCGCCGAGCGCC
55252 AAGCG
1 AAGCG
55257 TAGATCCTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
25 27 0.54
29 23 0.46
ACGTcount: A:0.27, C:0.30, G:0.36, T:0.07
Consensus pattern (25 bp):
AAGCGGAGAACGCTCGCCGAGCGCC
Found at i:55278 original size:17 final size:16
Alignment explanation
Indices: 55256--55289 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55246 AGCGCAAAGC
55256 GTAGATCCTCAAAGAGA
1 GTAGATCC-CAAAGAGA
*
55273 GTAGATCCCAAGGAGA
1 GTAGATCCCAAAGAGA
55289 G
1 G
55290 GAGAATGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.38, C:0.18, G:0.29, T:0.15
Consensus pattern (16 bp):
GTAGATCCCAAAGAGA
Found at i:55516 original size:118 final size:118
Alignment explanation
Indices: 55380--55670 Score: 422
Period size: 118 Copynumber: 2.5 Consensus size: 118
55370 CCGAGTGAGT
* * * *
55380 GCCAAGTGGAGAACGCTCGCTGAGCGCAAAGCGGAGATCCCTAAGGAGAGGAGAATGCTCCCCGT
1 GCCAAGTGGAGAATGCTCGCTGAGCGCAAAGCGTAGATCCCAAAGGAGAGGAGAATGCTCCCCGG
* * *
55445 GAGAGGAGAACGATAACGCTCGCCGAACGCGAATCGTAGAACGCTTGTCGAGC
66 GAGAGGAGAACGATAACGCTCGCCGAACACGAAGCGTAGAACGCTTGCCGAGC
* * * * *
55498 GCCAAGTGGAGAATGCTCGCCT-AGTGCTAAGTGTAGATCCCAAAAGAAAGGAGAATGCTCCCCG
1 GCCAAGTGGAGAATGCTCG-CTGAGCGCAAAGCGTAGATCCCAAAGGAGAGGAGAATGCTCCCCG
*
55562 GGAGAGGAGAACGATAACGCTCGCCGAACACGAAGCGTAGAACGCTTGCCTAGC
65 GGAGAGGAGAACGATAACGCTCGCCGAACACGAAGCGTAGAACGCTTGCCGAGC
* * *
55616 GCCAAGTGGAGAATGCTCGCCGAGCGCCAAGCGTAGATCCCCAAGGAGAGGAGAA
1 GCCAAGTGGAGAATGCTCGCTGAGCGCAAAGCGTAGATCCCAAAGGAGAGGAGAA
55671 CGCTTGCCCA
Statistics
Matches: 151, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
117 1 0.01
118 148 0.98
119 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.32, T:0.13
Consensus pattern (118 bp):
GCCAAGTGGAGAATGCTCGCTGAGCGCAAAGCGTAGATCCCAAAGGAGAGGAGAATGCTCCCCGG
GAGAGGAGAACGATAACGCTCGCCGAACACGAAGCGTAGAACGCTTGCCGAGC
Found at i:55820 original size:36 final size:36
Alignment explanation
Indices: 55780--55860 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
55770 CGAGGTTACG
*
55780 AATGGAGAATGCTCCCCATAAAGGAGTAGATCGCGC
1 AATGGAGAATGCTCCCCATAAAGGAGTAGATCACGC
**
55816 AATGGAGAATGCTCCCCATATGGGAGTAGATCACGC
1 AATGGAGAATGCTCCCCATAAAGGAGTAGATCACGC
*
55852 AATGAAGAA
1 AATGGAGAA
55861 CGTTGATCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.17
Consensus pattern (36 bp):
AATGGAGAATGCTCCCCATAAAGGAGTAGATCACGC
Found at i:55905 original size:58 final size:58
Alignment explanation
Indices: 55824--55933 Score: 139
Period size: 58 Copynumber: 1.9 Consensus size: 58
55814 GCAATGGAGA
* * * * **
55824 ATGCTCCCCATATGGGAGTAGATCACGCAATGAAGAACGTTGATCGTGCGAATAGAGT
1 ATGCTCCCCATAAGGGAGCAGATCACGAAATGAAAAACGCCGATCGTGCGAATAGAGT
* * *
55882 ATGCTCCTCATAAGGGAGCAGATCGCGAAATGAAAAATGCCGATCGTGCGAA
1 ATGCTCCCCATAAGGGAGCAGATCACGAAATGAAAAACGCCGATCGTGCGAA
55934 AAGAAGTTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.27, T:0.20
Consensus pattern (58 bp):
ATGCTCCCCATAAGGGAGCAGATCACGAAATGAAAAACGCCGATCGTGCGAATAGAGT
Done.