Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018454.1 Corchorus olitorius cultivar O-4 contig18487, 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: 125494
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:153 original size:14 final size:14
Alignment explanation
Indices: 134--163 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
124 AATTGTTGGG
*
134 TTTTTTTCGTTTTT
1 TTTTTTTAGTTTTT
148 TTTTTTTAGTTTTT
1 TTTTTTTAGTTTTT
162 TT
1 TT
164 CGTTCTTTTG
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:0.03, C:0.03, G:0.07, T:0.87
Consensus pattern (14 bp):
TTTTTTTAGTTTTT
Found at i:1256 original size:23 final size:22
Alignment explanation
Indices: 1225--1278 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
1215 TTTTCACCTC
*
1225 ACCACAGGGAAAAACACAGAGTT
1 ACCAAAGGG-AAAACACAGAGTT
** *
1248 ACCAAAGGG-AGCCTCAGAGTT
1 ACCAAAGGGAAAACACAGAGTT
1269 ACCAAAGGGA
1 ACCAAAGGGA
1279 GACTATCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 18 0.69
23 8 0.31
ACGTcount: A:0.43, C:0.22, G:0.26, T:0.09
Consensus pattern (22 bp):
ACCAAAGGGAAAACACAGAGTT
Found at i:2516 original size:22 final size:22
Alignment explanation
Indices: 2482--2679 Score: 154
Period size: 22 Copynumber: 9.1 Consensus size: 22
2472 AGTTTCATTC
* * *
2482 TCATAGGGAGGTTATCGAAATT
1 TCATAGTGTGGTTATCAAAATT
2504 TCAT-GATGTGGTTATCAAAATTT
1 TCATAG-TGTGGTTATCAAAA-TT
* *
2527 TCATAGTGCGGTTA-C-CAATT
1 TCATAGTGTGGTTATCAAAATT
* * *
2547 TTATTGTGTGATTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* * *
2569 TCACATTGAGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
*
2591 TCATAGTATGGTTATCAAAATT
1 TCATAGTGTGGTTATCAAAATT
* *
2613 TCACAGTGTGGTTATCAAATTT
1 TCATAGTGTGGTTATCAAAATT
**
2635 TCATA-T-TAGGTTATTGAAATT
1 TCATAGTGT-GGTTATCAAAATT
** * *
2656 TCATAACGAGGTTATCAATATT
1 TCATAGTGTGGTTATCAAAATT
2678 TC
1 TC
2680 TACGTTAGCA
Statistics
Matches: 136, Mismatches: 32, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
20 13 0.10
21 20 0.15
22 89 0.65
23 13 0.10
24 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (22 bp):
TCATAGTGTGGTTATCAAAATT
Found at i:2633 original size:65 final size:64
Alignment explanation
Indices: 2491--2660 Score: 164
Period size: 65 Copynumber: 2.6 Consensus size: 64
2481 CTCATAGGGA
* * * * * * **
2491 GGTTATCGAAATTTCATGA-TGTGGTTATCAAAATTTTCATAGTGCGGTTACCAATTTTATTGTG
1 GGTTATCAAAATTTCA-CATTGAGGTTATCAAAA-TTTCATAGTACGGTTACAAATTTCACAGTG
2555 T
64 T
* *
2556 GATTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCACAGTG
1 GGTTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTACGGTTA-C-AAATTTCACAGTG
2621 T
64 T
* * **
2622 GGTTATCAAATTTTCATATT-AGGTTATTGAAATTTCATA
1 GGTTATCAAAATTTCACATTGAGGTTATCAAAATTTCATA
2661 ACGAGGTTAT
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
64 15 0.17
65 45 0.52
66 27 0.31
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (64 bp):
GGTTATCAAAATTTCACATTGAGGTTATCAAAATTTCATAGTACGGTTACAAATTTCACAGTGT
Found at i:2655 original size:87 final size:87
Alignment explanation
Indices: 2489--2679 Score: 203
Period size: 87 Copynumber: 2.2 Consensus size: 87
2479 TTCTCATAGG
* * * *
2489 GAGGTTATCGAAATTTCATGATGTGGTTATCAAAATTTTCATAGTGCGGTTACCAATTTTATTGT
1 GAGGTTATCAAAATTTCATGATATGGTTATCAAAATTTTCACAGTGCGGTTACAAATTTTATTGT
**
2554 GTGATTATCAAAATTTCACATT
66 GTGATTATCAAAATTTCACAAC
*
2576 GAGGTTATCAAAATTTCAT-AGTATGGTTATCAAAA-TTTCACAGTGTGGTTATCAAATTTTCAT
1 GAGGTTATCAAAATTTCATGA-TATGGTTATCAAAATTTTCACAGTGCGGTTA-CAAATTTT-AT
** *
2639 AT-TAG-G-TTATTGAAATTTCATAAC
63 -TGT-GTGATTATCAAAATTTCACAAC
*
2663 GAGGTTATCAATATTTC
1 GAGGTTATCAAAATTTC
2680 TACGTTAGCA
Statistics
Matches: 88, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
86 15 0.17
87 67 0.76
88 4 0.05
89 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (87 bp):
GAGGTTATCAAAATTTCATGATATGGTTATCAAAATTTTCACAGTGCGGTTACAAATTTTATTGT
GTGATTATCAAAATTTCACAAC
Found at i:2679 original size:65 final size:66
Alignment explanation
Indices: 2513--2660 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 66
2503 TTCATGATGT
** * * **
2513 GGTTATCAAAATTTTCATAGTGCGGTTA-C-CAATTTTATTGTGTGATTATCAAAATTTCACATT
1 GGTTATCAAAA-TTTCATAGTATGGTTATCAAAATTTCACAGTGTGATTATCAAAATTTCACATT
2576 GA
65 GA
* * *
2578 GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCACAGTGTGGTTATCAAATTTTCATATT-
1 GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCACAGTGTGATTATCAAAATTTCACATTG
2642 A
66 A
**
2643 GGTTATTGAAATTTCATA
1 GGTTATCAAAATTTCATA
2661 ACGAGGTTAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 14 0.20
65 29 0.41
66 27 0.39
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (66 bp):
GGTTATCAAAATTTCATAGTATGGTTATCAAAATTTCACAGTGTGATTATCAAAATTTCACATTG
A
Found at i:8584 original size:20 final size:20
Alignment explanation
Indices: 8543--8585 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
8533 TTCTCACAAG
* *
8543 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
8563 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
8583 TTT
1 TTT
8586 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:14137 original size:20 final size:20
Alignment explanation
Indices: 14096--14138 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14086 CTCTCACAAG
* *
14096 TTTCTAGCCGTTGGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
14116 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
14136 TTT
1 TTT
14139 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:19094 original size:20 final size:20
Alignment explanation
Indices: 19055--19094 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
19045 GTTGTTTAAT
* *
19055 ATCTAACACAACGACTTAAG
1 ATCTAACACAACAACCTAAG
*
19075 ATCTAACGCAACAACCTAAG
1 ATCTAACACAACAACCTAAG
19095 TGTCCGCTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.28, G:0.10, T:0.17
Consensus pattern (20 bp):
ATCTAACACAACAACCTAAG
Found at i:19759 original size:201 final size:200
Alignment explanation
Indices: 19232--19803 Score: 892
Period size: 202 Copynumber: 2.8 Consensus size: 200
19222 TGCGAAAAGT
* *
19232 TTTTTACAACCACTTTAATTGGTTACGTATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAAC
1 TTTTTGCAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAAC
* ** *
19297 ACTTACGTAACGACCTCTAGGTAGTTATCAAAATAATTTAAAAACGATTAAATGTCGTTACGAAA
66 ACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTT-GGAAA
* * *
19362 ACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGTAGCATTTGATTGGTTGTG
130 ACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCG
19427 TAATAA
195 TAATAA
** * *
19433 TTTTTGCAGTCACTTTTAATTGGTTACGAATAACTTTTAAAAATAATTAAAAGTCGTTTCCAAAA
1 TTTTTGCAACCAC-TTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAA
* *
19498 CACTTACATAACGACCTCTAGCTAGTTGCCAAAATAATTTAAAAACGACTAAATGTCGTTGTGAA
65 CACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTG-GAA
*
19563 AACCCTTATGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGC
129 AACCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGC
19628 GTAATAA
194 GTAATAA
* *
19635 TTTTTGCAACCACTTTAATTGGTTATGAATAACTTTTAGAAATGATTAAATGTCGTTTCCAAAAC
1 TTTTTGCAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAAC
* * * * * *
19700 ACTTACATTACGACCTATGGGTAGTTGCCAAAATGATTTAAAAACGATTATATGTCGTTGCAAAA
66 ACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGGAAAA
*
19765 CCCTTACGCAATGACGTTGTTTTGGTTGTGAAATCTTTT
131 CCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTT
19804 GAATGGCTTT
Statistics
Matches: 337, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
200 41 0.12
201 111 0.33
202 185 0.55
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (200 bp):
TTTTTGCAACCACTTTAATTGGTTACGAATAACTTTTAAAAATGATTAAATGTCGTTTCCAAAAC
ACTTACATAACGACCTCTAGGTAGTTGCCAAAATAATTTAAAAACGATTAAATGTCGTTGGAAAA
CCCTTACGCAACGACGTTGTTTTGGTTGTGAAATCTTTTACGTAGCAACATTTGATTGGTTGCGT
AATAA
Found at i:27744 original size:23 final size:21
Alignment explanation
Indices: 27718--27777 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 21
27708 ATGGATGTGA
27718 CAGAGATGAAGAATATGGCAGAG
1 CAGA-ATGAAGAATA-GGCAGAG
*
27741 CAGAATTAATGAAGTAGGCAGAG
1 CAGAATGAA-GAA-TAGGCAGAG
*
27764 GAGAATAGAAGAAT
1 CAGAAT-GAAGAAT
27778 GAATGGCAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 5 0.16
23 22 0.71
24 4 0.13
ACGTcount: A:0.47, C:0.07, G:0.32, T:0.15
Consensus pattern (21 bp):
CAGAATGAAGAATAGGCAGAG
Found at i:30787 original size:15 final size:15
Alignment explanation
Indices: 30767--30796 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30757 TATTAAAATT
*
30767 ATATTTTTTTTATAA
1 ATATTTTATTTATAA
30782 ATATTTTATTTATAA
1 ATATTTTATTTATAA
30797 TTTAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATATTTTATTTATAA
Found at i:30923 original size:52 final size:52
Alignment explanation
Indices: 30841--30947 Score: 187
Period size: 52 Copynumber: 2.1 Consensus size: 52
30831 TGATTTGCGG
*
30841 TAACGATATATTAGGTTACGTTTTAGTTTTCCTCAAGATCTGTCCAAGGAGC
1 TAACGATATATTAAGTTACGTTTTAGTTTTCCTCAAGATCTGTCCAAGGAGC
* *
30893 TAACGATATATTAAGTTAGGTTTTATTTTTCCTCAAGATCTGTCCAAGGAGC
1 TAACGATATATTAAGTTACGTTTTAGTTTTCCTCAAGATCTGTCCAAGGAGC
30945 TAA
1 TAA
30948 TTAACCAAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (52 bp):
TAACGATATATTAAGTTACGTTTTAGTTTTCCTCAAGATCTGTCCAAGGAGC
Found at i:37422 original size:2 final size:2
Alignment explanation
Indices: 37415--37453 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
37405 GATTTACTCC
37415 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
37454 GTTTGATTCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37753 original size:26 final size:26
Alignment explanation
Indices: 37723--37777 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
37713 TTACATTTAG
37723 TATCATGAAAATCATATTAGTTAGCA
1 TATCATGAAAATCATATTAGTTAGCA
37749 TATCATGAAAATCATATTAGTTAGCA
1 TATCATGAAAATCATATTAGTTAGCA
37775 TAT
1 TAT
37778 TTGGCTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (26 bp):
TATCATGAAAATCATATTAGTTAGCA
Found at i:41572 original size:131 final size:132
Alignment explanation
Indices: 41383--41648 Score: 410
Period size: 131 Copynumber: 2.0 Consensus size: 132
41373 TGCCGTTGCA
* * *
41383 ACTTAATTTGTGGCTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTTGCTGCGAAAAT
1 ACTTAATTTGTGACTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAAC
* * *
41448 CAATTAGT-AACATATATTAAGCAACGACTAACAATAGTCGTTGCGAAAAGAGTAAGATTTCACA
66 CAATTAGTGAA-ATATATCAAGCAACAACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACA
*
41512 GCG
130 ACG
41515 ACTTAATTTGTGACTTCAAAAGTAATTATG-TTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAAC
1 ACTTAATTTGTGACTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAAC
* * **
41579 CAATTTGTGAAATATATCAAGCAACAACTAACAAAAGTCGTTGTGAAAAGTTTAAGATTTCACAA
66 CAATTAGTGAAATATATCAAGCAACAACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAA
41644 CG
131 CG
41646 ACT
1 ACT
41649 AACAAAAGTC
Statistics
Matches: 122, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
131 91 0.75
132 31 0.25
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.32
Consensus pattern (132 bp):
ACTTAATTTGTGACTTCAAAAGTAATTATGTTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAAC
CAATTAGTGAAATATATCAAGCAACAACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAA
CG
Found at i:41656 original size:41 final size:41
Alignment explanation
Indices: 41600--41689 Score: 135
Period size: 41 Copynumber: 2.2 Consensus size: 41
41590 ATATATCAAG
* *
41600 CAACAACTAACAAAAGTCGTTGTGAAAAGTTTAAGATTTCA
1 CAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCA
* **
41641 CAACGACTAACAAAAGTCGTTGCGGAAAGTTTAAGATTTTG
1 CAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCA
41682 CAACGACT
1 CAACGACT
41690 TAATCTGTCG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.26
Consensus pattern (41 bp):
CAACGACTAACAAAAGTCGTTGCGAAAAGTTTAAGATTTCA
Found at i:41689 original size:131 final size:129
Alignment explanation
Indices: 41423--41690 Score: 281
Period size: 131 Copynumber: 2.0 Consensus size: 129
41413 TTTTTTGTAG
* * * * *
41423 CGACTTTCAAGGTTGCTGCGAAAATCAATTAGTAACATATATTAAGCAACGACTAACAATAGTCG
1 CGACTTTCAAGGTCGCTGCGAAAACCAATTAGTAACATATATCAAGCAACAACTAACAAAAGTCG
* * *** * * *
41488 TTGCGAAAAGAGTAAGATTTCACAGCGACTTAATTTGTGACTTCAAAAGTAATTATGTTTTTGTA
66 TTGCGAAAAGAGTAAGATTTCACAACGACTAAAAAAGTGA-TTCAAAAGT-ATTAAGATTTTGCA
*
41553 G
129 A
*
41554 CGACTTTCAAGGTCGCTGCGAAAACCAATTTGTGAA-ATATATCAAGCAACAACTAACAAAAGTC
1 CGACTTTCAAGGTCGCTGCGAAAACCAATTAGT-AACATATATCAAGCAACAACTAACAAAAGTC
* ** *
41618 GTTGTGAAAAGTTTAAGATTTCACAACGACTAACAAAAGTCG-TTGCGGAAAGT-TTAAGATTTT
65 GTTGCGAAAAGAGTAAGATTTCACAACGACTAA-AAAAGT-GATT-C-AAAAGTATTAAGATTTT
41681 GCAA
126 GCAA
41685 CGACTT
1 CGACTT
41691 AATCTGTCGT
Statistics
Matches: 113, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
131 101 0.89
132 6 0.05
133 6 0.05
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (129 bp):
CGACTTTCAAGGTCGCTGCGAAAACCAATTAGTAACATATATCAAGCAACAACTAACAAAAGTCG
TTGCGAAAAGAGTAAGATTTCACAACGACTAAAAAAGTGATTCAAAAGTATTAAGATTTTGCAA
Found at i:41820 original size:173 final size:172
Alignment explanation
Indices: 41468--41834 Score: 477
Period size: 173 Copynumber: 2.1 Consensus size: 172
41458 CATATATTAA
* * *
41468 GCAACGACTAACAATAGTCGTTGCGAAAAGAGTAAGATTTCACAGCGACTTAATTTGTGACTTCA
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAACGACTTAATCTGTGACTTCA
* *
41533 AAAGTAATTATGTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAACCAATTTGTGAAATATATCA
66 AAAGTAATCATGTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAACCAATTTGTAAAATATATCA
* * ** *
41598 AGCAACAACTAACAAAAGTCGTTGTGAAAAGTTTAAGATTTC
131 AACAACAACTAACAAAAGTCGTTGCGAAAAGACTAAGAATTC
* * ** ** *
41640 ACAACGACTAACAAAAGTCGTTGCGGAAAGTTTAAGATTTTGCAACGACTTAATCTGTCG-TTTC
1 GCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAACGACTTAATCTGT-GACTTC
* *
41704 AAAAGTAATCATGTTTTTTGTAGCGACTTTCAAGGTCGCTTC-AAATATCAATTTGTAAAATATA
65 AAAAGTAATCATG-TTTTTGTAGCGACTTTCAAGGTCGCTGCGAAA-ACCAATTTGTAAAATATA
* * *
41768 TTAAACAACGACTAACAAAAGTCGTTGCGAAAAGACTATGAATTC
128 TCAAACAACAACTAACAAAAGTCGTTGCGAAAAGACTAAGAATTC
* *
41813 GCAACGACTAATAGAAGTCGTT
1 GCAACGACTAACAAAAGTCGTT
41835 CTAAAACTGG
Statistics
Matches: 167, Mismatches: 25, Indels: 5
0.85 0.13 0.03
Matches are distributed among these distances:
172 67 0.40
173 100 0.60
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (172 bp):
GCAACGACTAACAAAAGTCGTTGCGAAAAGAGTAAGATTTCACAACGACTTAATCTGTGACTTCA
AAAGTAATCATGTTTTTGTAGCGACTTTCAAGGTCGCTGCGAAAACCAATTTGTAAAATATATCA
AACAACAACTAACAAAAGTCGTTGCGAAAAGACTAAGAATTC
Found at i:58553 original size:202 final size:202
Alignment explanation
Indices: 58185--58594 Score: 723
Period size: 202 Copynumber: 2.0 Consensus size: 202
58175 TTCCTTAATA
58185 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
* *
58250 ATTTAATAAATCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATAATAGT
66 ATTTAATAAATCAACCAC-AATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAAT
*
58315 AATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
130 AATATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
*
58380 CACCATTG
195 CAACATTG
*
58388 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAATTTTTGTTTGACATTGATCTAATTT
1 ATAAATAAATCGGATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTT
* *
58453 AATTTAATAAATCAACCA-ATTGTTCAACTACTTTTTTTTGGTATAGTTATATATATATAATAAT
65 AATTTAATAAATCAACCACAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAAT
*
58517 AATATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAATTTAATAACATT
130 AATATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATT
58582 CAACATTG
195 CAACATTG
58590 ATAAA
1 ATAAA
58595 GTTATTAAGC
Statistics
Matches: 198, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
202 117 0.59
203 16 0.08
204 65 0.33
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (202 bp):
ATAAATAAATCGGATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
ATTTAATAAATCAACCACAATGTTCAACTAATTTTTTTTGGTATAGTTATATATATATAATAATA
ATATGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
AACATTG
Found at i:59146 original size:36 final size:36
Alignment explanation
Indices: 59106--59175 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
59096 GAGATTCTGG
* *
59106 AGAAATATGATAATCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
59142 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
59176 GGTTATTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:60551 original size:57 final size:58
Alignment explanation
Indices: 60448--60556 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
60438 ATCATGCCTC
*
60448 GGTCCTAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
1 GGTCCGAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
* *
60506 GGTCCGAAAACG-CTTTTTTTATG-CATCTAAT-AAAGAACATGTCACTTGATA
1 GGTCCGAAAACGTC-TTTTTTA-GCCATCTAATAAAAAAACATGTCACTCGATA
60557 TTTGATTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
57 19 0.41
58 26 0.57
59 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (58 bp):
GGTCCGAAAACGTCTTTTTTAGCCATCTAATAAAAAAACATGTCACTCGATAAGTCTT
Found at i:64876 original size:13 final size:13
Alignment explanation
Indices: 64858--64883 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64848 GTACTTAAGA
64858 TGTCCCTAAATAC
1 TGTCCCTAAATAC
64871 TGTCCCTAAATAC
1 TGTCCCTAAATAC
64884 CCAAATGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
TGTCCCTAAATAC
Found at i:75934 original size:29 final size:29
Alignment explanation
Indices: 75890--75950 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
75880 AGTGCAAGAC
75890 GATAATTATTTCATGAATTTTATTTGGAT
1 GATAATTATTTCATGAATTTTATTTGGAT
*
75919 GATAATTATTTTATGAATTTTATTTGGAT
1 GATAATTATTTCATGAATTTTATTTGGAT
75948 GAT
1 GAT
75951 GGATTTGATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.31, C:0.02, G:0.15, T:0.52
Consensus pattern (29 bp):
GATAATTATTTCATGAATTTTATTTGGAT
Found at i:84465 original size:14 final size:14
Alignment explanation
Indices: 84455--84484 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
84445 TAATAAATTT
84455 TACTAAATAAATAA
1 TACTAAATAAATAA
84469 TACTAAATAAATAA
1 TACTAAATAAATAA
84483 TA
1 TA
84485 TATAAATACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
TACTAAATAAATAA
Found at i:84492 original size:15 final size:15
Alignment explanation
Indices: 84458--84511 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
84448 TAAATTTTAC
*
84458 TAAATAAATAATA-C
1 TAAATAAATAATATA
84472 TAAATAAATAATATA
1 TAAATAAATAATATA
*
84487 TAAATACATAGA-ATA
1 TAAATAAATA-ATATA
*
84502 AAAATAAATA
1 TAAATAAATA
84512 TTTATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 13 0.38
15 20 0.59
16 1 0.03
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (15 bp):
TAAATAAATAATATA
Found at i:85946 original size:78 final size:78
Alignment explanation
Indices: 85857--86009 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
85847 AGATTTATAG
* *
85857 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTTATTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
85922 TACCATTTTACTA
66 TACCATTTTACTA
*
85935 TTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
86000 TACCATTTTA
66 TACCATTTTA
86010 TTACTTTAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.50
Consensus pattern (78 bp):
TTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTTACTA
Found at i:95578 original size:36 final size:34
Alignment explanation
Indices: 95509--95580 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 34
95499 TAATGTGTAG
**
95509 ACATTTCTCTTCAATCTTTTTTTTTTTGGGTAAGA
1 ACATTTCTCTTCAATCTTTTTTTAGTT-GGTAAGA
95544 ACATTTCTCTTCAATTCTTTTATTATAGTT-GTAAGA
1 ACATTTCTCTTCAA-TCTTTT-TT-TAGTTGGTAAGA
95580 A
1 A
95581 GTGGAGCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 14 0.44
36 13 0.41
37 2 0.06
38 3 0.09
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.51
Consensus pattern (34 bp):
ACATTTCTCTTCAATCTTTTTTTAGTTGGTAAGA
Found at i:95660 original size:2 final size:2
Alignment explanation
Indices: 95611--95647 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
95601 TTGGGCATGC
95611 TA TA TA TA TA 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 TA TA TA TA TA T
95648 GTACAAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:100005 original size:3 final size:3
Alignment explanation
Indices: 99997--100022 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
99987 GAGTATCTTT
99997 GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GA
100023 TGATGATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:100027 original size:3 final size:3
Alignment explanation
Indices: 100021--100047 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
100011 AGAAGAAGAA
100021 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
100048 TACTGTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:101666 original size:7 final size:7
Alignment explanation
Indices: 101654--101684 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
101644 AACTGGGTAT
101654 TTTGTTC
1 TTTGTTC
101661 TTTGTTC
1 TTTGTTC
101668 TTTGTTC
1 TTTGTTC
101675 TTTGGTTC
1 TTT-GTTC
101683 TT
1 TT
101685 GTACAGATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.74
8 6 0.26
ACGTcount: A:0.00, C:0.13, G:0.16, T:0.71
Consensus pattern (7 bp):
TTTGTTC
Found at i:105840 original size:2 final size:2
Alignment explanation
Indices: 105828--105859 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
105818 ATTATGTACC
*
105828 AT AT AT TT 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 AT AT
105860 GGCAAATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:113561 original size:14 final size:14
Alignment explanation
Indices: 113542--113568 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
113532 TTGGTAGAAA
113542 AATATTCTATTTTG
1 AATATTCTATTTTG
113556 AATATTCTATTTT
1 AATATTCTATTTT
113569 TTTAGCTGCA
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:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (14 bp):
AATATTCTATTTTG
Found at i:114795 original size:6 final size:6
Alignment explanation
Indices: 114787--114819 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
114777 AAACGAAAAC
*
114787 TCTTCC TCTTCA TCTTCA TCTTCA TCTTCA TCT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCT
114820 ACCTCTTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.12, C:0.36, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:114826 original size:18 final size:18
Alignment explanation
Indices: 114786--114827 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
114776 CAAACGAAAA
* *
114786 CTCTTCCTCTTCATCTTC
1 CTCTTCATCTTCATCTAC
*
114804 ATCTTCATCTTCATCTAC
1 CTCTTCATCTTCATCTAC
114822 CTCTTC
1 CTCTTC
114828 GTTTTCCTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.12, C:0.40, G:0.00, T:0.48
Consensus pattern (18 bp):
CTCTTCATCTTCATCTAC
Found at i:115355 original size:24 final size:24
Alignment explanation
Indices: 115327--115375 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
115317 TGAAATTGTT
115327 GGGAATTGAATTTGATTTTTCGGA
1 GGGAATTGAATTTGATTTTTCGGA
115351 GGGAATTGAATTTGATTTTTCGGA
1 GGGAATTGAATTTGATTTTTCGGA
115375 G
1 G
115376 CTATAAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.04, G:0.31, T:0.41
Consensus pattern (24 bp):
GGGAATTGAATTTGATTTTTCGGA
Found at i:125410 original size:25 final size:25
Alignment explanation
Indices: 125363--125410 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
125353 AATAATAAAA
*
125363 AAAAGAAATATATATTTATTTTTTT
1 AAAAGAAATATATATTTACTTTTTT
*
125388 AAAAGAAATATATATTTCCTTTT
1 AAAAGAAATATATATTTACTTTT
125411 ATGATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (25 bp):
AAAAGAAATATATATTTACTTTTTT
Done.