Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004899.1 Kokia drynarioides strain JFW-HI SEQ_118590, 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: 31934
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:9396 original size:29 final size:29
Alignment explanation
Indices: 9364--9560 Score: 152
Period size: 29 Copynumber: 6.7 Consensus size: 29
9354 TAGATGCCCA
9364 AGGGTAAAATGGTAATTTTGGACACTTCG
1 AGGGTAAAATGGTAATTTTGGACACTTCG
*
9393 AGGGGCAAAAATGGTAATTTTGGACACTTCG
1 A-GGG-TAAAATGGTAATTTTGGACACTTCG
* * * **
9424 AGGGTAAAATAGTATTTTTTAGA-TGTTC-
1 AGGGTAAAATGGTA-ATTTTGGACACTTCG
* * * * * *
9452 ATGGCTAAAATGGGAATTTTGAAAAGTT-T
1 A-GGGTAAAATGGTAATTTTGGACACTTCG
9481 AGGGTAAAAAATGGTAATTTTGGACACTTCG
1 AGGGT--AAAATGGTAATTTTGGACACTTCG
* *
9512 GGGGCAAAATGGTAATTTTTGGACAC-TC-
1 AGGGTAAAATGGTAA-TTTTGGACACTTCG
*
9540 AGGGGTAAAATAGTAATTTTG
1 A-GGGTAAAATGGTAATTTTG
9561 AATGTTTAGT
Statistics
Matches: 132, Mismatches: 25, Indels: 23
0.73 0.14 0.13
Matches are distributed among these distances:
28 14 0.11
29 50 0.38
30 40 0.30
31 28 0.21
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (29 bp):
AGGGTAAAATGGTAATTTTGGACACTTCG
Found at i:9549 original size:88 final size:88
Alignment explanation
Indices: 9399--9562 Score: 220
Period size: 88 Copynumber: 1.9 Consensus size: 88
9389 TTCGAGGGGC
* * *** * *
9399 AAAAATGGTAATTTTGGACACTTCGAGGGTAAAATAGTATTTTTTAGATGTTCATGGCTAAAATG
1 AAAAATGGTAATTTTGGACACTTCGAGGGCAAAATAGTAATTTTTAGACACTCAGGGCTAAAATA
9464 GGAATTTTGAAAAGTTTAGGGTA
66 GGAATTTTGAAAAGTTTAGGGTA
* * * *
9487 AAAAATGGTAATTTTGGACACTTCGGGGGCAAAATGGTAATTTTTGGACACTCAGGGGTAAAATA
1 AAAAATGGTAATTTTGGACACTTCGAGGGCAAAATAGTAATTTTTAGACACTCAGGGCTAAAATA
*
9552 GTAATTTTGAA
66 GGAATTTTGAA
9563 TGTTTAGTGT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
88 64 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.33
Consensus pattern (88 bp):
AAAAATGGTAATTTTGGACACTTCGAGGGCAAAATAGTAATTTTTAGACACTCAGGGCTAAAATA
GGAATTTTGAAAAGTTTAGGGTA
Found at i:9616 original size:29 final size:29
Alignment explanation
Indices: 9583--9741 Score: 157
Period size: 29 Copynumber: 5.6 Consensus size: 29
9573 TGAAATGTGG
9583 TTTTTGGAAGTTTAGGGGTAAAAATGTAA
1 TTTTTGGAAGTTTAGGGGTAAAAATGTAA
* * *
9612 TTTTTGAGAAGTTCA--AGTAAAAATGTGA
1 TTTTTG-GAAGTTTAGGGGTAAAAATGTAA
* *
9640 TTTTTGGAAGTTTGGGGGTAAAAATATAA
1 TTTTTGGAAGTTTAGGGGTAAAAATGTAA
* *
9669 TTTTT-AAGAGTTTAGGGGTAAAAAAGTAA
1 TTTTTGGA-AGTTTAGGGGTAAAAATGTAA
* * **
9698 -TTTTGAGAAG-TTCGAGGTAAAAATGTGG
1 TTTTTG-GAAGTTTAGGGGTAAAAATGTAA
9726 TTTTTGGAAGTTTAGG
1 TTTTTGGAAGTTTAGG
9742 TACCTTCTAG
Statistics
Matches: 102, Mismatches: 20, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
27 6 0.06
28 39 0.38
29 49 0.48
30 8 0.08
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (29 bp):
TTTTTGGAAGTTTAGGGGTAAAAATGTAA
Found at i:9702 original size:57 final size:57
Alignment explanation
Indices: 9584--9709 Score: 148
Period size: 57 Copynumber: 2.2 Consensus size: 57
9574 GAAATGTGGT
* * * *
9584 TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAGAAGTTCAAGTAAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATATAATTTTTAAGAAGTTCAAGTAAAAAAGTGAA
* * *
9641 TTTTGGAAGTTTGGGGGTAAAAATATAATTTTTAAG-AGTTTAGGGGTAAAAAAGT-AA
1 TTTTGGAAGTTTAGGGGTAAAAATATAATTTTTAAGAAGTTCA--AGTAAAAAAGTGAA
9698 TTTTGAGAAGTT
1 TTTTG-GAAGTT
9710 CGAGGTAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
56 5 0.08
57 39 0.66
58 15 0.25
ACGTcount: A:0.37, C:0.01, G:0.25, T:0.37
Consensus pattern (57 bp):
TTTTGGAAGTTTAGGGGTAAAAATATAATTTTTAAGAAGTTCAAGTAAAAAAGTGAA
Found at i:11490 original size:11 final size:12
Alignment explanation
Indices: 11466--11556 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 12
11456 TTTTAAACTC
11466 AATTTAAAATTA
1 AATTTAAAATTA
11478 AATTTAGAATAAATTTA
1 AATTT---A-AAA-TTA
*
11495 AATTTAAAA-CA
1 AATTTAAAATTA
*
11506 AATTTAAATTTA
1 AATTTAAAATTA
*
11518 AATTTAAAA-CA
1 AATTTAAAATTA
*
11529 AATTTAAATTTA
1 AATTTAAAATTA
*
11541 AACTTAAAA-TA
1 AATTTAAAATTA
11552 AATTT
1 AATTT
11557 TAATTTCAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 15
0.71 0.11 0.17
Matches are distributed among these distances:
11 24 0.39
12 22 0.35
13 3 0.05
14 1 0.02
15 1 0.02
16 3 0.05
17 8 0.13
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (12 bp):
AATTTAAAATTA
Found at i:11490 original size:17 final size:17
Alignment explanation
Indices: 11470--11581 Score: 76
Period size: 17 Copynumber: 6.9 Consensus size: 17
11460 AAACTCAATT
* *
11470 TAAAATTAAATTTAGAA
1 TAAATTTAAATTTAAAA
11487 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
11504 CAAATTTAAA-TT----
1 TAAATTTAAATTTAAAA
** *
11516 TAAATTTAAA-ACAAATT
1 TAAATTTAAATTTAAA-A
*
11533 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
* *
11550 TAAATTTTAATTTCAAA
1 TAAATTTAAATTTAAAA
*
11567 T-AATTTAAAATTAAA
1 TAAATTTAAATTTAAA
11582 GATTGAGCTT
Statistics
Matches: 74, Mismatches: 15, Indels: 13
0.73 0.15 0.13
Matches are distributed among these distances:
12 9 0.12
16 13 0.18
17 49 0.66
18 3 0.04
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:11492 original size:23 final size:23
Alignment explanation
Indices: 11487--11567 Score: 126
Period size: 23 Copynumber: 3.5 Consensus size: 23
11477 AAATTTAGAA
11487 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTAAAACAAATT
11510 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTAAAACAAATT
* *
11533 TAAATTTAAACTTAAAATAAATT
1 TAAATTTAAATTTAAAACAAATT
*
11556 TTAATTTCAAAT
1 TAAATTT-AAAT
11568 AATTTAAAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 50 0.94
24 3 0.06
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (23 bp):
TAAATTTAAATTTAAAACAAATT
Found at i:11554 original size:40 final size:38
Alignment explanation
Indices: 11470--11581 Score: 109
Period size: 40 Copynumber: 2.8 Consensus size: 38
11460 AAACTCAATT
* * *
11470 TAAAATTAAATTTAGAATAAATTTAAATTTAAAACAAATT
1 TAAATTTAAATTTA-AAAAAATTTAAATTT-AAACAAATA
11510 TAAATTTAAATTTAAAACAAATTTAAATTTAAACTTAAA-A
1 TAAATTTAAATTTAAAA-AAATTTAAATTTAAAC--AAATA
* * * *
11550 TAAATTTTAATTTCAAATAATTTAAAATTAAA
1 TAAATTTAAATTTAAAAAAATTTAAATTTAAA
11582 GATTGAGCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
39 19 0.31
40 40 0.65
41 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (38 bp):
TAAATTTAAATTTAAAAAAATTTAAATTTAAACAAATA
Found at i:12440 original size:209 final size:209
Alignment explanation
Indices: 12080--12582 Score: 738
Period size: 209 Copynumber: 2.4 Consensus size: 209
12070 TCAATCGCAT
* *
12080 TTGATTTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCACTT
1 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
* * * * ** * *
12145 CTCTGTATCTTATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTTATCAGGAAGACGACCAT
66 CTCTGTATCTCATCAAGAAGACAGATTTGATCCACTTCTCTGTATCTCATCAAAAAGACAACCAC
* * * *
12210 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTAGCTCACAT
131 TTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGATTCAAAGTTTAGCTCACAT
12275 TGAGCCTT-GTTTCA
196 TGAG-CTTGGTTTCA
* * * * *
12289 TTGATTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACTGCATCACTTGTTTTAATCCATTT
1 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
* *
12354 CTCTGTATCTCATCAGGAAGACAGATTTGATCCACTTCTTTGTATCTCATCAAAAAGACAACCAC
66 CTCTGTATCTCATCAAGAAGACAGATTTGATCCACTTCTCTGTATCTCATCAAAAAGACAACCAC
* *
12419 TTTATTTCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGATTCAAAGTTTCGCTCACAT
131 TTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGATTCAAAGTTTAGCTCACAT
12484 TGAGCTTGGTTTCA
196 TGAGCTTGGTTTCA
* * *
12498 TTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCTT
1 TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
* *
12563 CTCTATATCTCACCAAGAAG
66 CTCTGTATCTCATCAAGAAG
12583 CTGACCATTT
Statistics
Matches: 259, Mismatches: 34, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
208 3 0.01
209 256 0.99
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (209 bp):
TTGATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTT
CTCTGTATCTCATCAAGAAGACAGATTTGATCCACTTCTCTGTATCTCATCAAAAAGACAACCAC
TTTATTACTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGATTCAAAGTTTAGCTCACAT
TGAGCTTGGTTTCA
Found at i:12687 original size:172 final size:172
Alignment explanation
Indices: 12414--12744 Score: 475
Period size: 172 Copynumber: 1.9 Consensus size: 172
12404 CAAAAAGACA
* * *
12414 ACCACTTTATTTCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGGATTCAAAGTTTCGCT
1 ACCACTTTATTGCTTCGACCTACTTCTCAATATCTCATCAAGAAGCTAGGATTCAAAGTTTCGCT
* *
12479 CACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATAACCGCAT
66 CACATTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATAACCGCAT
12544 CACTTGTTTT-AATCCGCTTCTCTATATCTCACCAAGAAGCTG
131 CACTT-TTTTCAATCCGCTTCTCTATATCTCACCAAGAAGCTG
* * * * * * * *
12586 ACCATTTTATTGCTTCGACCTACTTCTTAGTATCTCATTAAGAAGTTGGGGTTCGAAGTTTCGCT
1 ACCACTTTATTGCTTCGACCTACTTCTCAATATCTCATCAAGAAGCTAGGATTCAAAGTTTCGCT
* * * * *
12651 CGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCT
66 CACATTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATAACCGCAT
*
12716 CACTTTTTTCAATCCGCTTCTCTGTATCT
131 CACTTTTTTCAATCCGCTTCTCTATATCT
12745 TATTAGGAAG
Statistics
Matches: 139, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
171 4 0.03
172 135 0.97
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (172 bp):
ACCACTTTATTGCTTCGACCTACTTCTCAATATCTCATCAAGAAGCTAGGATTCAAAGTTTCGCT
CACATTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAGATAACCGCAT
CACTTTTTTCAATCCGCTTCTCTATATCTCACCAAGAAGCTG
Found at i:12896 original size:381 final size:381
Alignment explanation
Indices: 12204--12955 Score: 1022
Period size: 381 Copynumber: 2.0 Consensus size: 381
12194 TCAGGAAGAC
* *
12204 GACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTAGC
1 GACCATTTTATTACTTCGACCTACTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGTTTAGC
* * *
12269 TCACATTGAGCCTTGTTTCATTGATTTGGTATTCTTCTCTGTATCTCATCAAGAAGATGACTGCA
66 TCACATTGAGCCTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCA
* **
12334 TCACTTGTTTTAATCCATTTCTCTGTATCTCATCAGGAAGACAGATTTGATCCACTTCTTTGTAT
131 TCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGATCCACTTCTCAGTAT
* * * *
12399 CTCATCAAAAAGACAACCACTTTATTTCTTCGACCTGCTTCTCAATATCTCATCAGGAAGCTAGG
196 CTCATCAAAAAGACAACCACTTTACTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGATAGG
* *
12464 ATTCAAAGTTTCGCTCACATTGAGCTTGGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCA
261 ATTCAAAGTTTCGCTCACATTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCAGTATCTCATCA
* *
12529 GGAAGATAACCGCATCACTTGTTTTAATCCGCTTCTCTATATCTCACCAAGAAGCT
326 GGAAGATAACCACATCACTTGTTTCAATCCGCTTCTCTATATCTCACCAAGAAGCT
* * * * *
12585 GACCATTTTATTGCTTCGACCTACTTCTTAGTATCTCATTAAGAAGTTGGGGTTCGAAGTTTCGC
1 GACCATTTTATTACTTCGACCTACTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGTTTAGC
* * * *
12650 TCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCC
66 TCACATTGAGCCTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCA
* * * * *
12715 TCACTT-TTTTCAATCCGCTTCTCTGTATCTTATTAGGAAGA-TGAATTTGGTCCACTTCTCAGT
131 TCACTTGTTTT-AATCCACTTCTCTGTATCTCATCAGGAAGACAG-ATTTGATCCACTTCTCAGT
* *** * * * *
12778 ATCTCATCAAGAAGTTGACCATTTTACTGCTTCGACCTGCTTCTCAGTATCTCATCAATAAGATG
194 ATCTCATCAAAAAGACAACCACTTTACTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGATA
* ** * * * * *
12843 GGGTTTGAAGTTTCGCTCGCTTTGAGCTTTGTTTTATTGAGTTGGTATACTTCTCTGTATCTCAT
259 GGATTCAAAGTTTCGCTCACATTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCAGTATCTCAT
* * * *
12908 CAGGAATATGACCACCTCACTTGTTTCAATCTGCTTCTCTATATCTCA
324 CAGGAAGATAACCACATCACTTGTTTCAATCCGCTTCTCTATATCTCA
12956 TCAGAAAGAC
Statistics
Matches: 319, Mismatches: 50, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
380 5 0.02
381 314 0.98
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (381 bp):
GACCATTTTATTACTTCGACCTACTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGTTTAGC
TCACATTGAGCCTTGTTTCATTGAGTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCA
TCACTTGTTTTAATCCACTTCTCTGTATCTCATCAGGAAGACAGATTTGATCCACTTCTCAGTAT
CTCATCAAAAAGACAACCACTTTACTGCTTCGACCTGCTTCTCAATATCTCATCAAGAAGATAGG
ATTCAAAGTTTCGCTCACATTGAGCTTGGTTTCATTGAGTTGGTATACTTCTCAGTATCTCATCA
GGAAGATAACCACATCACTTGTTTCAATCCGCTTCTCTATATCTCACCAAGAAGCT
Found at i:12928 original size:209 final size:209
Alignment explanation
Indices: 12560--13343 Score: 982
Period size: 209 Copynumber: 3.8 Consensus size: 209
12550 TTTTAATCCG
* * * * *
12560 CTTCTCTA-TATCTCACCAAGAAGCTGACCATTTTATTGCTTCGACCTACTTCTTAGTATCTCAT
1 CTTCTC-AGTATCTCATCAAGAAGGTAACCACTTTATTGCTTCGACCTACTTCTCAGTATCTCAT
* * * *
12624 TAAGAAGTTGGGGTTCGAAGTTTCGCTCGCATTGAGCTTTGTTTCATTGAGTTGGTATACTTCTC
65 CAAGAAGCTGGGGTTCGAAGTTTCGCTCACTTTGAGCTTTGTTTCATTGAGTTGGTATACTTCTC
* * * *
12689 TGTATCTCATCAGGAAGATGACCGCCTCACTTTTTTCAATCCGCTTCTCTGTATCTTATTAGGAA
130 AGTATCTCATCAGGAAGATGACCGCCTCACTTTTTTCAATCCGCTTCTCTATATCTCATCAGGAA
*
12754 GATGAATTTGGTCCA
195 GACGAATTTGGTCCA
* * * * *
12769 CTTCTCAGTATCTCATCAAGAAGTTGACCATTTTACTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAAGAAGGTAACCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* * * * * *
12834 AATAAGATGGGGTTTGAAGTTTCGCTCGCTTTGAGCTTTGTTTTATTGAGTTGGTATACTTCTCT
66 AAGAAGCTGGGGTTCGAAGTTTCGCTCACTTTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCA
* * * * *
12899 GTATCTCATCAGGAATATGACCACCTCACTTGTTTCAATCTGCTTCTCTATATCTCATCAGAAAG
131 GTATCTCATCAGGAAGATGACCGCCTCACTTTTTTCAATCCGCTTCTCTATATCTCATCAGGAAG
*
12964 ACGAATTTGGTTCA
196 ACGAATTTGGTCCA
* *
12978 CTTCTCTGTATCTCATCAAGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
1 CTTCTCAGTATCTCATCAAGAAGGTAACCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* * * * * * *
13043 AGGAAGCTGGGGTTCGAAGATTAGCTCACTTTGAGCCTGGTTTCATTGACTTGGTCTACTTCTCA
66 AAGAAGCTGGGGTTCGAAGTTTCGCTCACTTTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCA
* * * * * *
13108 GTATCTCATCAAGAAAATGACCGCATCA-TTTATTTTAATCCACTTCTCTATATCCCATCAGGAA
131 GTATCTCATCAGGAAGATGACCGCCTCACTTT-TTTCAATCCGCTTCTCTATATCTCATCAGGAA
*
13172 GACAAATTTGGTCCA
195 GACGAATTTGGTCCA
* * * * * *
13187 CTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACATTCTTCTTAGTATCTCATC
1 CTTCTCAGTATCTCATCAAGAAGGTAACCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
* * * * *
13252 AGGAAGCTGGGGTTTGAAGATTT-GCTCACTTTGAG-TCTGATTTCATTGATTTGGTCTACTTCT
66 AAGAAGCTGGGGTTCGAAG-TTTCGCTCACTTTGAGCTTTG-TTTCATTGAGTTGGTATACTTCT
13315 CAGTATCTCATCAGGAAGATGACCGCCTC
129 CAGTATCTCATCAGGAAGATGACCGCCTC
13344 GCTGTTTTGG
Statistics
Matches: 505, Mismatches: 66, Indels: 8
0.87 0.11 0.01
Matches are distributed among these distances:
208 4 0.01
209 499 0.99
210 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (209 bp):
CTTCTCAGTATCTCATCAAGAAGGTAACCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATC
AAGAAGCTGGGGTTCGAAGTTTCGCTCACTTTGAGCTTTGTTTCATTGAGTTGGTATACTTCTCA
GTATCTCATCAGGAAGATGACCGCCTCACTTTTTTCAATCCGCTTCTCTATATCTCATCAGGAAG
ACGAATTTGGTCCA
Found at i:24901 original size:29 final size:29
Alignment explanation
Indices: 24869--25063 Score: 157
Period size: 29 Copynumber: 6.7 Consensus size: 29
24859 TGGATGCCTA
24869 AGGGCAAAATGGTAATTTTGGACACTTCG
1 AGGGCAAAATGGTAATTTTGGACACTTCG
* *
24898 AGGGGGCAAAACTGGTAATATTGGACACTTTG
1 A--GGGCAAAA-TGGTAATTTTGGACACTTCG
** **
24930 -GGGGTAAATGGTAATTTTTGGA-TGTTCG
1 AGGGCAAAATGGTAA-TTTTGGACACTTCG
* * * * * *
24958 AGGGTAACATGATAATTTTAGAAAGTTCG
1 AGGGCAAAATGGTAATTTTGGACACTTCG
24987 -GGGTCAAAATGGTAATTTTGGACACTTC-
1 AGGG-CAAAATGGTAATTTTGGACACTTCG
* *
25015 AGGGGCAAAATGGTAATTTTTGGACA-ATCA
1 A-GGGCAAAATGGTAA-TTTTGGACACTTCG
*
25045 AGGGCAAAAAGGTAATTTT
1 AGGGCAAAATGGTAATTTT
25064 TTGATGTTCG
Statistics
Matches: 133, Mismatches: 22, Indels: 23
0.75 0.12 0.13
Matches are distributed among these distances:
28 22 0.17
29 72 0.54
30 13 0.10
31 8 0.06
32 18 0.14
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (29 bp):
AGGGCAAAATGGTAATTTTGGACACTTCG
Found at i:25061 original size:87 final size:86
Alignment explanation
Indices: 24868--25120 Score: 217
Period size: 87 Copynumber: 2.9 Consensus size: 86
24858 TTGGATGCCT
* * * * * *
24868 AAGGGCAAAATGGTAATTTTGGACACTTCGAGGGGGCAAAACTGGTAATATTGGACACTTTGGGG
1 AAGGGCAAAATGGTAATTTTAGAAAGTTC--GGGGTCAAAA-TGGTAATTTTGGACACTTAGGGG
** ***
24933 GTAAATGGTAATTTTTGGATGTTC
63 CAAAATGGTAATTTTTGGACAATC
* * * *
24957 GAGGGTAACATGATAATTTTAGAAAGTTCGGGGTCAAAATGGTAATTTTGGACACTTCAGGGGCA
1 AAGGGCAAAATGGTAATTTTAGAAAGTTCGGGGTCAAAATGGTAATTTTGGACACTT-AGGGGCA
25022 AAATGGTAATTTTTGGACAATC
65 AAATGGTAATTTTTGGACAATC
* * * * * *
25044 AAGGGCAAAAAGGTAATTTTTTG-ATGTTCGAGGTCAAAAT-GTGATTTTTGGA-AGTTTAGGGG
1 AAGGGCAAAATGGTAA-TTTTAGAAAGTTCGGGGTCAAAATGGT-AATTTTGGACA-CTTAGGGG
*
25106 TAAAAT-GTAATTTTT
63 CAAAATGGTAATTTTT
25121 TAGAAGTTTG
Statistics
Matches: 134, Mismatches: 26, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
85 9 0.07
86 30 0.22
87 68 0.51
88 5 0.04
89 22 0.16
ACGTcount: A:0.32, C:0.08, G:0.28, T:0.32
Consensus pattern (86 bp):
AAGGGCAAAATGGTAATTTTAGAAAGTTCGGGGTCAAAATGGTAATTTTGGACACTTAGGGGCAA
AATGGTAATTTTTGGACAATC
Found at i:25090 original size:28 final size:27
Alignment explanation
Indices: 25059--25235 Score: 124
Period size: 28 Copynumber: 6.2 Consensus size: 27
25049 CAAAAAGGTA
*
25059 ATTTTTTGATGTTCGAGGTCAAAATGTG
1 ATTTTTTGAAGTTCGAGGT-AAAATGTG
* * * *
25087 ATTTTTGGAAGTTTAGGGGTAAAATGTA
1 ATTTTTTGAAG-TTCGAGGTAAAATGTG
*
25115 ATTTTTTAGAAGTTTG-GGTAAAAATGTG
1 ATTTTTT-GAAGTTCGAGGT-AAAATGTG
* *
25143 ATTTTTGGAAGTTCGGGGGTAAAAT-TG
1 ATTTTTTGAAGTTC-GAGGTAAAATGTG
25170 TATTTTTTGAGAAGTTCGAGGTAAAAAATTGTG
1 -ATTTTTT--GAAGTTCGAGGT--AAAA-TGTG
* * * * *
25203 ATTTTTGGAAGTTTGGGGTAAAAAGTA
1 ATTTTTTGAAGTTCGAGGTAAAATGTG
25230 ATTTTT
1 ATTTTT
25236 GAGAGTTTTG
Statistics
Matches: 120, Mismatches: 17, Indels: 25
0.74 0.10 0.15
Matches are distributed among these distances:
27 19 0.16
28 54 0.45
29 17 0.14
30 17 0.14
31 4 0.03
32 7 0.06
33 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.27, T:0.41
Consensus pattern (27 bp):
ATTTTTTGAAGTTCGAGGTAAAATGTG
Found at i:25121 original size:56 final size:56
Alignment explanation
Indices: 25051--25352 Score: 272
Period size: 56 Copynumber: 5.2 Consensus size: 56
25041 ATCAAGGGCA
* * *
25051 AAAAGGTAATTTTTT-GATGTTCGAGGTCAAAATGTGATTTTTGGAAGTTTAGGGGT
1 AAAATGTAATTTTTTAGAAGTTCG-GGTAAAAATGTGATTTTTGGAAGTTTAGGGGT
* **
25107 AAAATGTAATTTTTTAGAAGTTTGGGTAAAAATGTGATTTTTGGAAGTTCGGGGGT
1 AAAATGTAATTTTTTAGAAGTTCGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGT
25163 AAAATTGT-ATTTTTTGAGAAGTTCGAGGTAAAAAATTGTGATTTTTGGAAGTTT-GGGGT
1 AAAA-TGTAATTTTTT-AGAAGTTCG-GGT-AAAAA-TGTGATTTTTGGAAGTTTAGGGGT
* * * * *
25222 AAAAAGTAATTTTTGAG-AGTTTTGGGTAAAAATGTAATTTTTGGAAAGTTTGAGGGTT
1 AAAATGTAATTTTTTAGAAG-TTCGGGTAAAAATGTGATTTTTGG-AAGTTT-AGGGGT
* * * * * * *
25280 AAAATATAA-TTTCTAGACAATTTAGGGGTTAAAATGTAATTTTTGGAAGTTTAAGGGT
1 AAAATGTAATTTTTTAG--AAGTT-CGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGT
* *
25338 CAAAATATGATTTTT
1 -AAAATGTAATTTTT
25353 GGATAATTTA
Statistics
Matches: 205, Mismatches: 24, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
55 11 0.05
56 65 0.32
57 27 0.13
58 25 0.12
59 36 0.18
60 41 0.20
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (56 bp):
AAAATGTAATTTTTTAGAAGTTCGGGTAAAAATGTGATTTTTGGAAGTTTAGGGGT
Found at i:25245 original size:28 final size:28
Alignment explanation
Indices: 24935--25355 Score: 244
Period size: 29 Copynumber: 14.6 Consensus size: 28
24925 CTTTGGGGGT
* *
24935 AAATGGTAATTTTTGGATGTTCGAGGGT-A
1 AAAT-GTAATTTTTGGAAGTTTG-GGGTAA
* * * * *
24964 ACATGATAATTTTAGAAAGTTCGGGGTCA
1 AAATG-TAATTTTTGGAAGTTTGGGGTAA
* * *
24993 AAATGGTAA-TTTTGGACACTTCAGGGG-CA
1 AAAT-GTAATTTTTGGA-AGTT-TGGGGTAA
* *** *
25022 AAATGGTAATTTTTGGACAATCAAGGGCAA
1 AAAT-GTAATTTTTGGA-AGTTTGGGGTAA
* * * * * *
25052 AAAGGTAATTTTTTGATGTTCGAGGTCA
1 AAATGTAATTTTTGGAAGTTTGGGGTAA
*
25080 AAATGTGATTTTTGGAAGTTTAGGGGT-A
1 AAATGTAATTTTTGGAAGTTT-GGGGTAA
*
25108 AAATGTAATTTTTTAGAAGTTT-GGGTAA
1 AAATGTAA-TTTTTGGAAGTTTGGGGTAA
* *
25136 AAATGTGATTTTTGGAAGTTCGGGGGTAA
1 AAATGTAATTTTTGGAAGTT-TGGGGTAA
* * * *
25165 AATTGTATTTTTTGAGAAGTTCGAGGTAAA
1 AAATGTAATTTTTG-GAAGTTTGGGGT-AA
*
25195 AAATTGTGATTTTTGGAAGTTTGGGGTAA
1 AAA-TGTAATTTTTGGAAGTTTGGGGTAA
*
25224 AAA-GTAATTTTT-GAGAGTTTTGGGTAA
1 AAATGTAATTTTTGGA-AGTTTGGGGTAA
*
25251 AAATGTAATTTTTGGAAAGTTTGAGGGTTA
1 AAATGTAATTTTTGG-AAGTTTG-GGGTAA
* * * * *
25281 AAATATAATTTCTAGACAATTTAGGGGTTA
1 AAATGTAATTTTTGGA-AGTTT-GGGGTAA
* *
25311 AAATGTAATTTTTGGAAGTTTAAGGGTCA
1 AAATGTAATTTTTGGAAGTTT-GGGGTAA
* *
25340 AAATATGATTTTTGGA
1 AAATGTAATTTTTGGA
25356 TAATTTAGAG
Statistics
Matches: 310, Mismatches: 60, Indels: 44
0.75 0.14 0.11
Matches are distributed among these distances:
26 2 0.01
27 37 0.12
28 55 0.18
29 126 0.41
30 80 0.26
31 10 0.03
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (28 bp):
AAATGTAATTTTTGGAAGTTTGGGGTAA
Found at i:25290 original size:30 final size:29
Alignment explanation
Indices: 25087--25363 Score: 130
Period size: 28 Copynumber: 9.6 Consensus size: 29
25077 TCAAAATGTG
* *
25087 ATTTTTGG-AAGTTTAGGGGTAAAATGTA
1 ATTTTTGGAAAGTTTAGGGTTAAAATATA
* * * *
25115 ATTTTT-TAGAAGTTT-GGGTAAAAATGTG
1 ATTTTTGGA-AAGTTTAGGGTTAAAATATA
** * *
25143 ATTTTTGG-AAGTTCGGGGGTAAAAT-TGT
1 ATTTTTGGAAAGTTTAGGGTTAAAATAT-A
* * * * *
25171 ATTTTTTGAGAAG-TTCGAGGTAAAAAATTGTG
1 ATTTTTGGA-AAGTTTAG-GGT-TAAAA-TATA
*
25203 ATTTTTGG-AAGTTT-GGGGTAAAA-AGTA
1 ATTTTTGGAAAGTTTAGGGTTAAAATA-TA
* * * *
25230 ATTTTT-GAGAGTTTTGGGTAAAAATGTA
1 ATTTTTGGAAAGTTTAGGGTTAAAATATA
25258 ATTTTTGGAAAGTTTGAGGGTTAAAATATA
1 ATTTTTGGAAAGTTT-AGGGTTAAAATATA
* * *
25288 ATTTCTAGACAA-TTTAGGGGTTAAAATGTA
1 ATTTTTGGA-AAGTTTA-GGGTTAAAATATA
* *
25318 ATTTTTGG-AAGTTTAAGGGTCAAAATATG
1 ATTTTTGGAAAGTTT-AGGGTTAAAATATA
25347 ATTTTTGGATAA-TTTAG
1 ATTTTTGGA-AAGTTTAG
25364 AGACCTTCTG
Statistics
Matches: 189, Mismatches: 36, Indels: 47
0.69 0.13 0.17
Matches are distributed among these distances:
26 1 0.01
27 18 0.10
28 58 0.31
29 41 0.22
30 52 0.28
31 10 0.05
32 8 0.04
33 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (29 bp):
ATTTTTGGAAAGTTTAGGGTTAAAATATA
Found at i:25322 original size:115 final size:115
Alignment explanation
Indices: 25079--25342 Score: 311
Period size: 115 Copynumber: 2.3 Consensus size: 115
25069 GTTCGAGGTC
* * *
25079 AAAATGTGATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTTAGAAGTTTGGGTAAAAATGTGA
1 AAAATGTGATTTTTGGAAGTTTAGGGGTAAAAAGTAATTTTTGAGAAGTTTGGGTAAAAATGTAA
* * * * *
25144 TTTTTGGAAGTTCGGGGGTAAAATTGTATTTTTTGAGAAGTTCGAGGTAA
66 TTTTTGGAAGTTCGGGGGTAAAATTGAATTTCTAGACAAGTTAGAGGTAA
25194 AAAATTGTGATTTTTGGAAGTTT-GGGGTAAAAAGTAATTTTTGAG-AGTTTTGGGTAAAAATGT
1 AAAA-TGTGATTTTTGGAAGTTTAGGGGTAAAAAGTAATTTTTGAGAAG-TTTGGGTAAAAATGT
* * * * *
25257 AATTTTTGGAAAGTTTGAGGGTTAAAATAT-AATTTCTAGACAATTTAGGGGT-T
64 AATTTTTGG-AAGTTCG-GGGGTAAAAT-TGAATTTCTAGACAAGTTAGAGGTAA
* * *
25310 AAAATGTAATTTTTGGAAGTTTAAGGGTCAAAA
1 AAAATGTGATTTTTGGAAGTTTAGGGGTAAAAA
25343 TATGATTTTT
Statistics
Matches: 127, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
114 2 0.02
115 64 0.50
116 36 0.28
117 24 0.19
118 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.39
Consensus pattern (115 bp):
AAAATGTGATTTTTGGAAGTTTAGGGGTAAAAAGTAATTTTTGAGAAGTTTGGGTAAAAATGTAA
TTTTTGGAAGTTCGGGGGTAAAATTGAATTTCTAGACAAGTTAGAGGTAA
Found at i:27136 original size:11 final size:12
Alignment explanation
Indices: 27112--27177 Score: 55
Period size: 12 Copynumber: 5.7 Consensus size: 12
27102 TTTTAAACTC
27112 AATTTAAAATTA
1 AATTTAAAATTA
*
27124 AATTTAGAA-TA
1 AATTTAAAATTA
**
27135 AATTTAATTTTA
1 AATTTAAAATTA
*
27147 AACTTAAAA-TA
1 AATTTAAAATTA
* *
27158 AATTTTAATTTA
1 AATTTAAAATTA
*
27170 AAATTAAA
1 AATTTAAA
27178 GATTGGGCTT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
11 16 0.40
12 24 0.60
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (12 bp):
AATTTAAAATTA
Found at i:27138 original size:23 final size:23
Alignment explanation
Indices: 27112--27177 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
27102 TTTTAAACTC
* * *
27112 AATTTAAAATTAAATTTAGAATA
1 AATTTAAATTTAAACTTAAAATA
*
27135 AATTTAATTTTAAACTTAAAATA
1 AATTTAAATTTAAACTTAAAATA
* *
27158 AATTTTAATTTAAAATTAAA
1 AATTTAAATTTAAACTTAAA
27178 GATTGGGCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
AATTTAAATTTAAACTTAAAATA
Found at i:29114 original size:9 final size:8
Alignment explanation
Indices: 29080--29136 Score: 64
Period size: 8 Copynumber: 7.0 Consensus size: 8
29070 TCATAAATTT
29080 TATTTTTA
1 TATTTTTA
29088 TA-TTTTA
1 TATTTTTA
29095 TATTTTTA
1 TATTTTTA
29103 TATTTTTA
1 TATTTTTA
29111 -ATATTTTA
1 TAT-TTTTA
29119 TAGTTTTTTA
1 TA--TTTTTA
*
29129 CATTTTTA
1 TATTTTTA
29137 ATAATTTTAG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
7 9 0.21
8 26 0.60
9 1 0.02
10 6 0.14
11 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (8 bp):
TATTTTTA
Done.