Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012234.1 Corchorus capsularis cultivar CVL-1 contig12255, 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: 56376
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:94 original size:22 final size:21
Alignment explanation
Indices: 60--109 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
50 TTTAATTAAT
*
60 TAAATT-ATTAAAAAAATGGCC
1 TAAATTAATT-AAAAAATGCCC
81 TAAATTAATTAAAAAATGCCC
1 TAAATTAATTAAAAAATGCCC
102 TAAGATTA
1 TAA-ATTA
110 CCCAAACTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.30
Consensus pattern (21 bp):
TAAATTAATTAAAAAATGCCC
Found at i:462 original size:21 final size:22
Alignment explanation
Indices: 425--469 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
415 GCAAAAGTGT
425 AAAAAGTGGAGCAGTATTTAGC
1 AAAAAGTGGAGCAGTATTTAGC
*
447 AAAAAGTGG-GCGGTATTTAGC
1 AAAAAGTGGAGCAGTATTTAGC
468 AA
1 AA
470 TACCCTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.40, C:0.09, G:0.29, T:0.22
Consensus pattern (22 bp):
AAAAAGTGGAGCAGTATTTAGC
Found at i:6650 original size:28 final size:29
Alignment explanation
Indices: 6593--6650 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
6583 CGATTGTAAT
*
6593 CTTTTTTTCAAAACATATTTTAATTGTAC
1 CTTTTTTTCAAAACATATTTTAAATGTAC
6622 CTTTTTTT-AAAACATATTTCTAAAT-TAC
1 CTTTTTTTCAAAACATATTT-TAAATGTAC
6650 C
1 C
6651 ATTATTAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.50
Consensus pattern (29 bp):
CTTTTTTTCAAAACATATTTTAAATGTAC
Found at i:13780 original size:123 final size:122
Alignment explanation
Indices: 13557--13928 Score: 550
Period size: 123 Copynumber: 3.0 Consensus size: 122
13547 ATGCAATTTT
* * * *
13557 GAAAGTACCAGCTGACCTTAATTCTGATGAAGATGCCGAAGTAGTGTCTGACCAACTAA-CTCTT
1 GAAAGTACCAGCTGACC-GAATTCTGATGAAGATGCTGAAGCAATGTCTGACCAAC-AAGCTCTT
*
13621 ATAGACCATCAGAAGCTGCATGATAATACA-TCAATTGAACAGGACCAAGACCCTGATGA
64 ATAGACCATCAGAAGCTGCATGATAATACAGT-AATTGAACAGGGCCAAGACCCTGATGA
* * * *
13680 GAAAGTACCAGCTGAGCGAAATTCTGATGAAGATTCTGAAGCAAAGTCCGACCAACAAGCTCTTA
1 GAAAGTACCAGCTGACCG-AATTCTGATGAAGATGCTGAAGCAATGTCTGACCAACAAGCTCTTA
* *
13745 TAGACTATCAGAAGCTGCATGATAATACAGTAATTGAACAGGGCCAAGACCCTAATGA
65 TAGACCATCAGAAGCTGCATGATAATACAGTAATTGAACAGGGCCAAGACCCTGATGA
*
13803 GAAAGTACCAGCTGACCTGAATTCTGATGAAGATGCTGAAGCAATGTTTGACCAACAAGCTCTTA
1 GAAAGTACCAGCTGACC-GAATTCTGATGAAGATGCTGAAGCAATGTCTGACCAACAAGCTCTTA
* * *
13868 TAGACCATCAGAAGCTGCATGATAATACAGCAATTGAACAGGGCCAAAAGCCTGATGA
65 TAGACCATCAGAAGCTGCATGATAATACAGTAATTGAACAGGGCCAAGACCCTGATGA
13926 GAA
1 GAA
13929 CTTAGCAGAT
Statistics
Matches: 224, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
122 2 0.01
123 220 0.98
124 2 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (122 bp):
GAAAGTACCAGCTGACCGAATTCTGATGAAGATGCTGAAGCAATGTCTGACCAACAAGCTCTTAT
AGACCATCAGAAGCTGCATGATAATACAGTAATTGAACAGGGCCAAGACCCTGATGA
Found at i:16424 original size:18 final size:18
Alignment explanation
Indices: 16380--16435 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 18
16370 GATAATGATG
*
16380 TGAAAATTTGATAACATCA
1 TGAAAATTTGATAAC-CCA
*
16399 TTATGAAATTTCGATAACCCA
1 TGA--AAATTT-GATAACCCA
16420 TGAAAATTTGATAACC
1 TGAAAATTTGATAACC
16436 ACAAAGTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.23
19 8 0.26
21 10 0.32
22 6 0.19
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (18 bp):
TGAAAATTTGATAACCCA
Found at i:16515 original size:45 final size:44
Alignment explanation
Indices: 16422--16553 Score: 135
Period size: 45 Copynumber: 3.0 Consensus size: 44
16412 ATAACCCATG
* *
16422 AAAA-TTTGATAACCACA-AAGTAAAATTTTGATAATTTCCCTAT
1 AAAATTTTGATAACCACACCA-TAAAATTTTGATAATCTCCCTAT
* * * *
16465 GAAATTTTGATAACCGCACTATGAAAATTTTGATAATCT-CTTCAT
1 AAAATTTTGATAACCACACCAT-AAAATTTTGATAATCTCCCT-AT
* * *
16510 AAAATTTTGATAACCACACCATTAAATTTCGATAATCACCCTAT
1 AAAATTTTGATAACCACACCATAAAATTTTGATAATCTCCCTAT
16554 GAGAACGAAA
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
43 3 0.04
44 30 0.42
45 39 0.54
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (44 bp):
AAAATTTTGATAACCACACCATAAAATTTTGATAATCTCCCTAT
Found at i:16536 original size:22 final size:22
Alignment explanation
Indices: 16417--16544 Score: 82
Period size: 22 Copynumber: 5.8 Consensus size: 22
16407 TTTCGATAAC
16417 CCATGAAAA-TTTGATAACCACA
1 CCAT-AAAATTTTGATAACCACA
* ***
16439 -AAGTAAAATTTTGATAATTTC-
1 CCA-TAAAATTTTGATAACCACA
* *
16460 CCTATGAAATTTTGATAACCGCA
1 CC-ATAAAATTTTGATAACCACA
* * * *
16483 CTATGAAAATTTTGATAATCTCT
1 CCAT-AAAATTTTGATAACCACA
*
16506 TCATAAAATTTTGATAACCACA
1 CCATAAAATTTTGATAACCACA
* *
16528 CCATTAAATTTCGATAA
1 CCATAAAATTTTGATAA
16545 TCACCCTATG
Statistics
Matches: 78, Mismatches: 22, Indels: 12
0.70 0.20 0.11
Matches are distributed among these distances:
21 5 0.06
22 55 0.71
23 18 0.23
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (22 bp):
CCATAAAATTTTGATAACCACA
Found at i:16724 original size:22 final size:22
Alignment explanation
Indices: 16584--16879 Score: 146
Period size: 22 Copynumber: 13.3 Consensus size: 22
16574 ATCTTTATTT
* *
16584 AATTTTGATAACATCTCC-ATAA
1 AATTTTGATAACCT-TCCTATGA
16606 AATTTTTG-TAACCTTCCTATGA
1 AA-TTTTGATAACCTTCCTATGA
* * *
16628 AATTTTGTTAACCTCCCTAGGA
1 AATTTTGATAACCTTCCTATGA
*
16650 AACTTTGATAACCTCCCTCCCTATGA
1 AATTTTGATAACCT---T-CCTATGA
*
16676 AATTTTGATAACAACAT--TAT-A
1 AATTTTGATAAC--CTTCCTATGA
* *
16697 AATTTTGATAACCTTCGTATAA
1 AATTTTGATAACCTTCCTATGA
* ** *
16719 AATTTTGTTAA-CGACACTAAGA
1 AATTTTGATAACCTTC-CTATGA
* * **
16741 AAATTTGATAACATTTTTATGA
1 AATTTTGATAACCTTCCTATGA
* * * *
16763 AATTTTGGTAA-CGTCTGTATGG
1 AATTTTGATAACCTTC-CTATGA
*
16785 AATTTTGATAA-CTACACTATGA
1 AATTTTGATAACCTTC-CTATGA
**
16807 CGTTTTGATAACC-TCCATATGA
1 AATTTTGATAACCTTCC-TATGA
*
16829 AATTTT-ATTAACC-ACACTATGA
1 AATTTTGA-TAACCTTC-CTATGA
* *
16851 AAATTTGATAACCTTCCTATGT
1 AATTTTGATAACCTTCCTATGA
16873 AATTTTG
1 AATTTTG
16880 GTTTGATTGA
Statistics
Matches: 205, Mismatches: 48, Indels: 42
0.69 0.16 0.14
Matches are distributed among these distances:
19 2 0.01
21 29 0.14
22 146 0.71
23 9 0.04
25 1 0.00
26 17 0.08
28 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (22 bp):
AATTTTGATAACCTTCCTATGA
Found at i:17551 original size:16 final size:15
Alignment explanation
Indices: 17515--17557 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
17505 AATGGGCGGG
*
17515 TTCGGGCTCGTGTAC
1 TTCGGGCTCGGGTAC
*
17530 TTCGGGCTCGGGTATT
1 TTCGGGCTCGGGTA-C
*
17546 TTCGGGTTCGGG
1 TTCGGGCTCGGG
17558 CTCGGATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.05, C:0.21, G:0.40, T:0.35
Consensus pattern (15 bp):
TTCGGGCTCGGGTAC
Found at i:20282 original size:21 final size:21
Alignment explanation
Indices: 20258--20301 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20248 ATAAAGGTCC
20258 TAAAACACA-ATTTGAATAAAT
1 TAAAACACATATTT-AATAAAT
*
20279 TAAAATACATATTTAATAAAT
1 TAAAACACATATTTAATAAAT
20300 TA
1 TA
20302 TGACATTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAACACATATTTAATAAAT
Found at i:21181 original size:64 final size:64
Alignment explanation
Indices: 21103--21230 Score: 163
Period size: 64 Copynumber: 2.0 Consensus size: 64
21093 AAACTCTTAG
* *
21103 ATTTTTTTTCTCTCTTCTACCTCCCCTAGA-TTAATCCTAC-TCACCAAAAAAAAAATCCAGATT
1 ATTTTTATTCTCTCTTCTACCTCCCCTAGATTTAATCCCACTTCA--AAAAAAAAAA-CCAGATT
21166 TT
63 TT
* * *
21168 ATTTTTATT-TCTCTTCTTCCTTCCCTAGATTTAATCCCACTTTAAAAAAAAAAACCAGATTTT
1 ATTTTTATTCTCTCTTCTACCTCCCCTAGATTTAATCCCACTTCAAAAAAAAAAACCAGATTTT
21231 TTTGTTCTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
63 9 0.16
64 28 0.50
65 17 0.30
66 2 0.04
ACGTcount: A:0.31, C:0.25, G:0.03, T:0.41
Consensus pattern (64 bp):
ATTTTTATTCTCTCTTCTACCTCCCCTAGATTTAATCCCACTTCAAAAAAAAAAACCAGATTTT
Found at i:25714 original size:22 final size:21
Alignment explanation
Indices: 25686--25739 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
25676 ATTATACTAT
25686 TTTTGATAATGTCCTTATGAAA
1 TTTTGATAATGTCC-TATGAAA
* *
25708 TTTTGATGACTTTCCTATGAAA
1 TTTTGAT-AATGTCCTATGAAA
*
25730 TTATGATAAT
1 TTTTGATAAT
25740 TACATTATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 2 0.07
22 20 0.74
23 5 0.19
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (21 bp):
TTTTGATAATGTCCTATGAAA
Found at i:25736 original size:62 final size:62
Alignment explanation
Indices: 25639--25793 Score: 206
Period size: 62 Copynumber: 2.5 Consensus size: 62
25629 GAAATATTCA
* * * *
25639 TATGAAATTATGATAACCTTT-CTATTAAATTATGATAATTATACTATT-TTTGATAATGTCCT
1 TATGAAATTTTGATAA-CTTTCCTATGAAATTATGATAATTACACTATTGTTT-ATAACGTCCT
* * *
25701 TATGAAATTTTGATGACTTTCCTATGAAATTATGATAATTACATTATTGTTTATGACGTCCT
1 TATGAAATTTTGATAACTTTCCTATGAAATTATGATAATTACACTATTGTTTATAACGTCCT
*
25763 TATGAAATTTTGATAACCTTCCTATGAAATT
1 TATGAAATTTTGATAACTTTCCTATGAAATT
25794 TCAATAACGA
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
61 4 0.05
62 75 0.91
63 3 0.04
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (62 bp):
TATGAAATTTTGATAACTTTCCTATGAAATTATGATAATTACACTATTGTTTATAACGTCCT
Found at i:25788 original size:22 final size:22
Alignment explanation
Indices: 25763--26325 Score: 211
Period size: 22 Copynumber: 25.6 Consensus size: 22
25753 ATGACGTCCT
25763 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCTTCC
** ** *
25785 TATGAAATTTCAATAACGATAC
1 TATGAAATTTTGATAACCTTCC
* * **
25807 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTTCC
* *
25829 TAT-AAATTTTGTTTTAACCTTCT
1 TATGAAATTTTG--ATAACCTTCC
* * *
25852 TATGAAATTTTGTTTACCTCCC
1 TATGAAATTTTGATAACCTTCC
*
25874 TAAGAAATTTTGA-AGACC-TCAC
1 TATGAAATTTTGATA-ACCTTC-C
**
25896 TATGAAATTTTGATAACCAACCC
1 TATGAAATTTTGATAACC-TTCC
* *
25919 TAT-AAGATGTTGATAGCC-TCC
1 TATGAA-ATTTTGATAACCTTCC
* * *
25940 ATATGATATATTGATAA--TTACGT
1 -TATGAAATTTTGATAACCTT-C-C
* * *
25963 TATGAAAATTTAAAAACC-TCC
1 TATGAAATTTTGATAACCTTCC
* *
25984 ATATG-AATTGTCAGTAATCACATT-C
1 -TATGAAATTTTGA-TAA-C-C-TTCC
* * *
26009 --TGAAATTTTGATAATCATAC
1 TATGAAATTTTGATAACCTTCC
* *
26029 TACGAAATTGTGATAACC-TCGC
1 TATGAAATTTTGATAACCTTC-C
* *
26051 TGTGAAATTTTGATAAACCTTCG
1 TATGAAATTTTGAT-AACCTTCC
*
26074 TAT-AGAATTTTGATAAATCTTCC
1 TATGA-AATTTTGAT-AACCTTCC
* * *
26097 TATAAAATTTTGATAAATCTCCC
1 TATGAAATTTTGAT-AACCTTCC
*
26120 TATAAAATTTTGATAACC-TCC
1 TATGAAATTTTGATAACCTTCC
*
26141 TTATGAAATCTTGATAA-----C
1 -TATGAAATTTTGATAACCTTCC
* *
26159 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTTCC
** *
26180 TATGATTTTTTGATAACC-TCAT
1 TATGAAATTTTGATAACCTTC-C
* * * *
26202 TATGAGATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCTTCC
* * *
26224 TATGAAATTTTGATTTA-CATAC
1 TATGAAATTTTGA-TAACCTTCC
* * *
26246 TATAAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAACCTTCC
* **
26268 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-TCC
* *
26290 TATGATATTTTGATAACCTTCA
1 TATGAAATTTTGATAACCTTCC
26312 TATGAAATTTTGAT
1 TATGAAATTTTGAT
26326 TACTCCATAA
Statistics
Matches: 400, Mismatches: 97, Indels: 88
0.68 0.17 0.15
Matches are distributed among these distances:
16 11 0.03
17 2 0.00
18 1 0.00
19 1 0.00
20 2 0.00
21 28 0.07
22 243 0.61
23 97 0.24
24 13 0.03
25 1 0.00
26 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTCC
Found at i:25867 original size:23 final size:24
Alignment explanation
Indices: 25821--25866 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
25811 AAATTTCGAG
*
25821 AACCTTTTTAT-AAATTTTGTTTT
1 AACCTTCTTATGAAATTTTGTTTT
25844 AACCTTCTTATGAAATTTTGTTT
1 AACCTTCTTATGAAATTTTGTTT
25867 ACCTCCCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.26, C:0.11, G:0.07, T:0.57
Consensus pattern (24 bp):
AACCTTCTTATGAAATTTTGTTTT
Found at i:26082 original size:23 final size:23
Alignment explanation
Indices: 26055--26135 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
26045 CCTCGCTGTG
* *
26055 AAATTTTGATAAACCTTCGTATA
1 AAATTTTGATAAATCTTCCTATA
*
26078 GAATTTTGATAAATCTTCCTATA
1 AAATTTTGATAAATCTTCCTATA
*
26101 AAATTTTGATAAATCTCCCTATA
1 AAATTTTGATAAATCTTCCTATA
26124 AAATTTTGATAA
1 AAATTTTGATAA
26136 CCTCCTTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.41
Consensus pattern (23 bp):
AAATTTTGATAAATCTTCCTATA
Found at i:26646 original size:37 final size:36
Alignment explanation
Indices: 26605--26700 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
26595 ATATAAGCTC
* *
26605 AAATAGGACGTTGAAGACGAAGACAAAAA-GCAAAATT
1 AAATAGGACGTTGAA-ACAAAGA-AAAAAGGAAAAATT
**
26642 AAATACAACGATTGGAAACAAAGAAAAAAGGAAAAATT
1 AAATAGGACG-TT-GAAACAAAGAAAAAAGGAAAAATT
*
26680 AAATAGGAAGTTGGAAACAAA
1 AAATAGGACGTT-GAAACAAA
26701 AAATCAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
37 24 0.49
38 22 0.45
39 3 0.06
ACGTcount: A:0.58, C:0.08, G:0.20, T:0.14
Consensus pattern (36 bp):
AAATAGGACGTTGAAACAAAGAAAAAAGGAAAAATT
Found at i:27015 original size:156 final size:157
Alignment explanation
Indices: 26773--27085 Score: 576
Period size: 156 Copynumber: 2.0 Consensus size: 157
26763 AATAATTTAT
*
26773 GATTAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTTTTA
1 GATTAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTTTAA
*
26838 AAAAGGGTACAATTGGAATATATTATAAAAATAA-GG-ATACAACCGGAAAACATAAAGTTTTCC
66 AAAAGGGTACAATTGGAATATATTATAAAAATAAGGGTATACAACCGGAAAACATAAAGTTTCCC
26901 CTTATTCGTACTTTTATATATAGTATA
131 CTTATTCGTACTTTTATATATAGTATA
26928 GATTAAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTTTA
1 GATT-AAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTTTA
*
26993 AAAAAGGGTACAATTGGAATATATTTTAAAAATAAGGGTATACAACCGGAAAACATAAAGTTTCC
65 AAAAAGGGTACAATTGGAATATATTATAAAAATAAGGGTATACAACCGGAAAACATAAAGTTTCC
27058 CCTTATTCGTACTTTTATATATAGTATA
130 CCTTATTCGTACTTTTATATATAGTATA
27086 AATAATATAG
Statistics
Matches: 152, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
155 4 0.03
156 93 0.61
157 2 0.01
158 53 0.35
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (157 bp):
GATTAAAAATAATGGAATAATTAAAATATTATTTAGTAATGGCAATTTAGAAATATGTTTTTTAA
AAAAGGGTACAATTGGAATATATTATAAAAATAAGGGTATACAACCGGAAAACATAAAGTTTCCC
CTTATTCGTACTTTTATATATAGTATA
Found at i:28334 original size:2 final size:2
Alignment explanation
Indices: 28327--28368 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
28317 AACAAATTGC
* *
28327 AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT GT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28367 AT
1 AT
28369 CTCAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30463 original size:21 final size:20
Alignment explanation
Indices: 30437--30475 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
30427 ATAGGTACTT
30437 TCTCTCTCTAACATGAGAGTC
1 TCTCTCTCTAAC-TGAGAGTC
*
30458 TCTCTCTCTATCTGAGAG
1 TCTCTCTCTAACTGAGAG
30476 CTTCGCCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (20 bp):
TCTCTCTCTAACTGAGAGTC
Found at i:32545 original size:2 final size:2
Alignment explanation
Indices: 32538--32576 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32528 GATATCAGTC
32538 AT AT 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 AT AT A
32577 AGATGTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32872 original size:21 final size:20
Alignment explanation
Indices: 32852--32895 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
32842 AGATTCTCTA
*
32852 ATTCCTCATCCCCTTCTTCT
1 ATTCCTCACCCCCTTCTTCT
* *
32872 ATTTCTCACCCCCTTCTGCT
1 ATTCCTCACCCCCTTCTTCT
32892 ATTC
1 ATTC
32896 TATCAATCCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.11, C:0.43, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTCCTCACCCCCTTCTTCT
Found at i:35030 original size:20 final size:20
Alignment explanation
Indices: 35007--35045 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34997 TTCTCTAATC
* *
35007 CTCATCCCCTTCTTCTATTT
1 CTCACCCCCTTCTACTATTT
35027 CTCACCCCCTTCTACTATT
1 CTCACCCCCTTCTACTATT
35046 CTATCAATCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.44, G:0.00, T:0.44
Consensus pattern (20 bp):
CTCACCCCCTTCTACTATTT
Found at i:36027 original size:2 final size:2
Alignment explanation
Indices: 36020--36065 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
36010 CATATTCCCA
*
36020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
36062 AT AT
1 AT AT
36066 TATCATAGCT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 38 0.95
3 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:42314 original size:21 final size:21
Alignment explanation
Indices: 42290--42329 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
42280 GTACAATTTT
*
42290 TAAAAAGATTTTTTTTGTTAA
1 TAAAAAGATATTTTTTGTTAA
42311 TAAAAAGATATTTTTTGTT
1 TAAAAAGATATTTTTTGTT
42330 TGGTACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TAAAAAGATATTTTTTGTTAA
Found at i:48091 original size:6 final size:6
Alignment explanation
Indices: 48080--48104 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
48070 GATGATTGAG
48080 GATGCA GATGCA GATGCA GATGCA G
1 GATGCA GATGCA GATGCA GATGCA G
48105 GTGATATTGG
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:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GATGCA
Found at i:48496 original size:54 final size:54
Alignment explanation
Indices: 48432--48542 Score: 138
Period size: 54 Copynumber: 2.1 Consensus size: 54
48422 GATGAAGGTG
* *
48432 ATGTCGGTGAA-TTGAAGCTGACCT-CCCCTTTGTCTGAGGCTGAGTC-GATTCTCA
1 ATGTCGGTGAAGTT-AAGCTGA-ATGCCACTTTGTCTGAGGCTGAGTCAG-TTCTCA
* *
48486 ATGTTGGTGAAGTTAAGCTGAATGCCACTTTGTCTGAGGTTGAGTCAGTTCTCA
1 ATGTCGGTGAAGTTAAGCTGAATGCCACTTTGTCTGAGGCTGAGTCAGTTCTCA
48540 ATG
1 ATG
48543 AGGCAACAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
53 1 0.02
54 46 0.92
55 3 0.06
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (54 bp):
ATGTCGGTGAAGTTAAGCTGAATGCCACTTTGTCTGAGGCTGAGTCAGTTCTCA
Found at i:48806 original size:378 final size:378
Alignment explanation
Indices: 48111--48866 Score: 1059
Period size: 378 Copynumber: 2.0 Consensus size: 378
48101 GCAGGTGATA
* ** **
48111 TTGGTGAAATTGAGCTGAAATCCACTTTGTCTGAGGCTAATTTGATTCTCAATGAGGTGACAGAG
1 TTGGTGAAATTAAGCTGAAATCCACTTTGTCTGAGGCTAATCAGATTCTCAATGAGGCAACAGAG
** * *
48176 CATCAGACAGTAGATGAATCTGTTGATAATGATGTAGTGGCACCTTCTGAAGTTAAAATTGAGAC
66 CATCAGACAGTAGATGAATCTGTTGATAATGACATAGTGGCACCTTCTGAAGTTAAAATCGAAAC
* ** *
48241 TGAAATTACTACTGAAACTATGTCTTCAGGGGGCCTCTCTGAAAATGATGTGCCTCACACTCTAA
131 TGAAATTACTACTGAAACTACGTCTTCAGGGGGCAGCTCTGAAAAGGATGTGCCTCACACTCTAA
* * * * *
48306 AGTACCAGGAAAGTGCCAAGGATGATGATGCTGGTGAAGAAGTTGCAGATCTTTCTGTATCTTCT
196 AGTACCAGGAAAGTGCCAAGGATGATAAAGCCGGTGAAGAAGTTGCAGAGCTTTCTGCATCTTCT
* *
48371 AAAGAACATAACATAAATGTATCAGAAAAGTTACTGATGGTTGAGGATGCTGATGAAGG-TGATG
261 AAAGAACATAACATAAATGCATCAGAAAAGTTACTGATGGTTGAGGATGCTGATGAAGGCAG-TG
* * * * * * * *
48435 TCGGTGAATTGAAGCTGACCTCCCCTTTGTCTGAGGCTGAGTCGATTCTCAATG
325 TCGGTAAAGTGAAGCTGAACTCCACATCGTCCGAGGCTGAGTCAATTCTCAATG
* * *
48489 TTGGTGAAGTTAAGCTG-AATGCCACTTTGTCTGAGGTTGAGTCAG-TTCTCAATGAGGCAACAG
1 TTGGTGAAATTAAGCTGAAAT-CCACTTTGTCTGAGGCT-AATCAGATTCTCAATGAGGCAACAG
* * *
48552 AGCATCAGACAGTAGATGAATCTGTTGATAATGACATTGTGGCACCTTTTGAAGTTAATATCGAA
64 AGCATCAGACAGTAGATGAATCTGTTGATAATGACATAGTGGCACCTTCTGAAGTTAAAATCGAA
* * * * *
48617 ACTGAAATTACTACTGAAACTACGTCTTTAGGGGGCAGCTCTGGAGAGGATGTGCCTCATAGTCT
129 ACTGAAATTACTACTGAAACTACGTCTTCAGGGGGCAGCTCTGAAAAGGATGTGCCTCACACTCT
* *
48682 AAAGTTCCAGGAAAGTGCCAAGGATGATAAAGCCGGTGAAGAAGTTGCAGAGCTTTCTGCATGTT
194 AAAGTACCAGGAAAGTGCCAAGGATGATAAAGCCGGTGAAGAAGTTGCAGAGCTTTCTGCATCTT
* *
48747 CTGAAGAACATAGCATAAATGCATCAGAAAAGTTACTGATGGTTGAGGATGCTGATGAAGGCAGT
259 CTAAAGAACATAACATAAATGCATCAGAAAAGTTACTGATGGTTGAGGATGCTGATGAAGGCAGT
* *
48812 GTTGGTAAAGTGAAGCTGAATTCCACATCGTCCGAGGCTGAGTCAATTCTCAATG
324 GTCGGTAAAGTGAAGCTGAACTCCACATCGTCCGAGGCTGAGTCAATTCTCAATG
48867 AGGCAACATC
Statistics
Matches: 330, Mismatches: 45, Indels: 6
0.87 0.12 0.02
Matches are distributed among these distances:
377 3 0.01
378 323 0.98
379 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (378 bp):
TTGGTGAAATTAAGCTGAAATCCACTTTGTCTGAGGCTAATCAGATTCTCAATGAGGCAACAGAG
CATCAGACAGTAGATGAATCTGTTGATAATGACATAGTGGCACCTTCTGAAGTTAAAATCGAAAC
TGAAATTACTACTGAAACTACGTCTTCAGGGGGCAGCTCTGAAAAGGATGTGCCTCACACTCTAA
AGTACCAGGAAAGTGCCAAGGATGATAAAGCCGGTGAAGAAGTTGCAGAGCTTTCTGCATCTTCT
AAAGAACATAACATAAATGCATCAGAAAAGTTACTGATGGTTGAGGATGCTGATGAAGGCAGTGT
CGGTAAAGTGAAGCTGAACTCCACATCGTCCGAGGCTGAGTCAATTCTCAATG
Found at i:54185 original size:15 final size:14
Alignment explanation
Indices: 54165--54195 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
54155 TACTACTAAT
54165 AAAAAAGAAAAGTAA
1 AAAAAAGAAAAG-AA
54180 AAAAAAGAAAAGAA
1 AAAAAAGAAAAGAA
54194 AA
1 AA
54196 GTTAAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAGAAAAGAA
Found at i:54210 original size:20 final size:19
Alignment explanation
Indices: 54165--54203 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 19
54155 TACTACTAAT
54165 AAAAAAGAAAAGTAAAAAA
1 AAAAAAGAAAAGTAAAAAA
54184 AAGAAAAGAAAAGTTAAAAA
1 AA-AAAAGAAAAG-TAAAAA
54204 TTAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.11
20 10 0.56
21 6 0.33
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (19 bp):
AAAAAAGAAAAGTAAAAAA
Found at i:55922 original size:21 final size:21
Alignment explanation
Indices: 55898--55941 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
55888 ATAAACTGGA
55898 TTGCTAAAT-ACCGCCCCATTT
1 TTGCT-AATCACCGCCCCATTT
* *
55919 TTGCTATTCACCGCCTCATTT
1 TTGCTAATCACCGCCCCATTT
55940 TT
1 TT
55942 TACCTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAATCACCGCCCCATTT
Done.