Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014558.1 Kokia drynarioides strain JFW-HI SEQ_129597, 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: 41481
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 86 characters in sequence are not A, C, G, or T
Found at i:2092 original size:14 final size:14
Alignment explanation
Indices: 2073--2106 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2063 TTTCAATAAT
* *
2073 TTTAAAGAAAAGTC
1 TTTAAAAAAAAGTA
2087 TTTAAAAAAAAGTA
1 TTTAAAAAAAAGTA
2101 TTTAAA
1 TTTAAA
2107 CATAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.56, C:0.03, G:0.09, T:0.32
Consensus pattern (14 bp):
TTTAAAAAAAAGTA
Found at i:9362 original size:30 final size:29
Alignment explanation
Indices: 9294--9994 Score: 550
Period size: 30 Copynumber: 23.8 Consensus size: 29
9284 TTTGAAGTCG
*
9294 AAAATGGGATTTTTGGAAG-TTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* ** *
9322 AAAATAGAATTTTTAAAAGTTTCAGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
*
9352 AAAATGGAATTTTTGCAAG-TTCGAGGGTAA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGT-A
* *
9382 AAAATGGAATTTTTTTGAAAG-TACGAGGGTA
1 AAAATGGAA--TTTTTGGAAGTTTCG-GGGTA
*
9413 AAAATAGGATTTTTTGGAAG-TTCGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTCG-GGGTA
* * *
9443 AAAAGGGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGAAG-TTTCGGGGTA
* *
9473 AAGATGGTATTTTTGGAAG-TTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* ** *
9502 AAAACT-AAATTTTTAAAAGTTTCGGAGTCA
1 AAAA-TGGAATTTTTGGAAGTTTCGGGGT-A
*
9532 AAAATGGGATTTTTGGAAG-TTCGGGGGT-
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* ** *
9560 AAAATGGAATTTTTAGAAGTTTTAGGGTT
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* * * *
9589 AAAATGGGATTTTAGGTAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
9618 AAAATGAAATTTTTAGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
*
9648 AAAATGGGATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTA
* *
9677 AAAATGGAATTTTTAGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
9707 AAAATGGGAATTTTT-GAAG-TTCGAGGGTA
1 AAAAT-GGAATTTTTGGAAGTTTCG-GGGTA
* * *
9736 AAAACT-AAATTTTTAGAAGTTTTGGGGTCA
1 AAAA-TGGAATTTTTGGAAGTTTCGGGGT-A
* * *
9766 AATATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* *
9795 AAAATGGAATTTTTAGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
* **
9825 AAAATGGGATTTTTGGAAG-TTCAAAGGTA
1 AAAATGGAATTTTTGGAAGTTTC-GGGGTA
* * *
9854 AAAATAGAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGT-A
* *
9884 AAAATGGGATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTA
* * * *
9913 AAAATAGAATTTTTAGAAGTTTTGGGGACA
1 AAAATGGAATTTTTGGAAGTTTCGGGG-TA
* *
9943 AAAATGGGATTTTTGAAAG-TTCGGGAGTA
1 AAAATGGAATTTTTGGAAGTTTCGGG-GTA
* *
9972 AAAACGAAATTTTTGGATAGTTT
1 AAAATGGAATTTTTGGA-AGTTT
9995 AGGGATCTCC
Statistics
Matches: 537, Mismatches: 100, Indels: 69
0.76 0.14 0.10
Matches are distributed among these distances:
28 49 0.09
29 223 0.42
30 225 0.42
31 20 0.04
32 20 0.04
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTA
Found at i:9489 original size:59 final size:59
Alignment explanation
Indices: 9255--9994 Score: 827
Period size: 59 Copynumber: 12.5 Consensus size: 59
9245 TTTTTAAACA
* * * ** *
9255 TTCGGGGGT-AAAAGGGTAATTTTGAG-AGTTTTGAAGTCGAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGG-AATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * ** * *
9313 TTCGAGGGT-AAAATAGAATTTTTAAAAGTTTCAGGGTCAAAAATGGAATTTTTGCAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* ** *
9371 TTCGAGGGTAAAAAATGGAATTTTTTTGAAAG-TACGAGGGT-AAAAATAGGATTTTTTGGAAG
1 TTCGAGGGT-AAAAATGGAA-TTTTTAG-AAGTTTTG-GGGTCAAAAATGGGA-TTTTTGGAAG
* * * * * *
9433 TTCGAGGGTAAAAAGGGAATTTTTGGAAGTTTTAGGGTTAAAGATGGTATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * * * *
9492 TTCGGGGGTAAAAACT-AAATTTTTAAAAGTTTCGGAGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAA-TGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * * * *
9551 TTCGGGGGT-AAAATGGAATTTTTAGAAGTTTTAGGGT-TAAAATGGGATTTTAGGTAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
9608 TTTGGGGGTAAAAATGAAATTTTTAGAAGTTTCGGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
*
9667 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGGAATTTTT-GAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGG-ATTTTTGGAAG
* *
9726 TTCGAGGGTAAAAACT-AAATTTTTAGAAGTTTTGGGGTCAAATATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAA-TGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * *
9785 TTTGGGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * *
9844 TTCAAAGGTAAAAATAGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * * * *
9903 TTTGGGGGTAAAAATAGAATTTTTAGAAGTTTTGGGGACAAAAATGGGATTTTTGAAAG
1 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
* * *
9962 TTCG-GGAGTAAAAACGAAATTTTTGGATAGTTT
1 TTCGAGG-GTAAAAATGGAATTTTTAGA-AGTTT
9995 AGGGATCTCC
Statistics
Matches: 579, Mismatches: 84, Indels: 36
0.83 0.12 0.05
Matches are distributed among these distances:
57 33 0.06
58 102 0.18
59 361 0.62
60 34 0.06
61 24 0.04
62 25 0.04
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (59 bp):
TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:11766 original size:17 final size:17
Alignment explanation
Indices: 11744--11816 Score: 51
Period size: 17 Copynumber: 4.2 Consensus size: 17
11734 TTTTATGAAG
**
11744 TTTTAAATCCATTTAAA
1 TTTTAAATAAATTTAAA
*
11761 TTTTAATTAAATTTAAA
1 TTTTAAATAAATTTAAA
*
11778 -TTTAAAGCAGAA-TTAAA
1 TTTTAAA-TA-AATTTAAA
*
11795 TTTAAAAGATAAATTTAAA
1 TTT-TAA-ATAAATTTAAA
11814 TTT
1 TTT
11817 AAAAAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
16 5 0.12
17 20 0.47
18 6 0.14
19 11 0.26
20 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTTAAATAAATTTAAA
Found at i:20479 original size:7 final size:7
Alignment explanation
Indices: 20461--20489 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
20451 CATATCATCA
20461 ATAATA-
1 ATAATAT
20467 ATAATAT
1 ATAATAT
20474 ATAATAT
1 ATAATAT
20481 ATAATAT
1 ATAATAT
20488 AT
1 AT
20490 GTAATTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATAATAT
Found at i:25366 original size:6 final size:6
Alignment explanation
Indices: 25355--25418 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
25345 CCGGATCTTT
* * * *
25355 TTTTAA TTTTAA ATTTAGA -TTT-A TTTTAA ATTTAA -GTTAA TCTTAA
1 TTTTAA TTTTAA TTTTA-A TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
*
25401 ATTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA
25419 AATTAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
4 1 0.02
5 7 0.15
6 38 0.81
7 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (6 bp):
TTTTAA
Found at i:25382 original size:17 final size:17
Alignment explanation
Indices: 25360--25424 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
25350 TCTTTTTTTA
25360 ATTTTAAATTT-AGATTT
1 ATTTTAAATTTAAG-TTT
*
25377 ATTTTAAATTTAAGTTA
1 ATTTTAAATTTAAGTTT
* *
25394 ATCTTAAATTTAATTTT
1 ATTTTAAATTTAAGTTT
*
25411 AATTTTAAAATTAA
1 -ATTTTAAATTTAA
25425 AAAAGTTCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
17 27 0.68
18 13 0.32
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAGTTT
Found at i:26208 original size:3 final size:3
Alignment explanation
Indices: 26202--26232 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
26192 AGATCTTTTG
26202 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
26233 ATAAAAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27249 original size:29 final size:29
Alignment explanation
Indices: 27200--27476 Score: 196
Period size: 30 Copynumber: 9.7 Consensus size: 29
27190 GAGGTCCCAA
* *
27200 AACTTCCAAAAATTTCGTTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * *
27229 AATTTCCAAAAATTCCATTTTTAACCCTG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
*
27258 AAACTTCCAAAAATT-CA---GT----CCG
1 -AACTTCCAAAAATTCCATTTTTACCCCCG
* ***
27280 AATTTCCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
* * **
27310 AACTTCCATAAATTTCATTTTTACCCTTG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
*
27339 AACTTCCAAAAATCCCA-TTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* ***
27367 AACTTCCAAAAATCCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
* ***
27397 AACTTCCAAAATTTCCATTTTTACATTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* **
27426 AAGTTCCAAAAA-TCTCATTTTTGACCCCAA
1 AACTTCCAAAAATTC-CATTTTT-ACCCCCG
*
27456 AACTTCCAAAAAATCCATTTT
1 AACTTCCAAAAATTCCATTTT
27477 GTCCTTAACC
Statistics
Matches: 193, Mismatches: 40, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
21 13 0.07
22 4 0.02
25 1 0.01
26 1 0.01
28 28 0.15
29 69 0.36
30 75 0.39
31 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:27268 original size:30 final size:29
Alignment explanation
Indices: 27200--27476 Score: 200
Period size: 29 Copynumber: 9.7 Consensus size: 29
27190 GAGGTCCCAA
* * * *
27200 AACTTCCAAAAATTTCGTTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTAACCCTG
*
27229 AATTTCCAAAAATTCCATTTTTAACCCTG
1 AACTTCCAAAAATTCCATTTTTAACCCTG
*
27258 AAACTTCCAAAAATT-CA---GT---CC-G
1 -AACTTCCAAAAATTCCATTTTTAACCCTG
* *
27280 AATTTCCAAAAATTCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTTAACCCT-G
* *
27310 AACTTCCATAAATTTCATTTTT-ACCCTTG
1 AACTTCCAAAAATTCCATTTTTAACCC-TG
* * *
27339 AACTTCCAAAAATCCCA-TTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTAACCCTG
* *
27367 AACTTCCAAAAATCCCATTTTTAACCCTAA
1 AACTTCCAAAAATTCCATTTTTAACCCT-G
* **
27397 AACTTCCAAAATTTCCATTTTT-ACATTCG
1 AACTTCCAAAAATTCCATTTTTAACCCT-G
* * **
27426 AAGTTCCAAAAA-TCTCATTTTTGACCCCAA
1 AACTTCCAAAAATTC-CATTTTT-AACCCTG
*
27456 AACTTCCAAAAAATCCATTTT
1 AACTTCCAAAAATTCCATTTT
27477 GTCCTTAACC
Statistics
Matches: 194, Mismatches: 36, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
21 13 0.07
22 3 0.02
23 2 0.01
25 1 0.01
26 1 0.01
28 26 0.13
29 75 0.39
30 70 0.36
31 3 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTAACCCTG
Found at i:27302 original size:51 final size:51
Alignment explanation
Indices: 27226--27323 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
27216 GTTTTTACCC
*
27226 CCGAATTTCCAAAAATTCCATTTTTAACCCTGAAACTTCCAAAAATTCAGT
1 CCGAATTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCAGT
*
27277 CCGAATTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCATAAATT
1 CCGAATTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATT
27324 TCATTTTTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (51 bp):
CCGAATTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTCAGT
Found at i:27385 original size:87 final size:88
Alignment explanation
Indices: 27277--27476 Score: 273
Period size: 87 Copynumber: 2.3 Consensus size: 88
27267 AAAATTCAGT
* *
27277 CCGAATTTCCAAAAATTCCATTTTTAACCCTAAAACTTCCATAAATTT-CATTTTTACCCTT-GA
1 CCGAACTTCCAAAAA-TCCATTTTTAACCCTAAAACTTCCA-AAATTTCCATTTTTA-CATTCGA
27340 ACTTCCAAAAATCCCA-TTTT-ACCC
63 ACTTCCAAAAATCCCATTTTTGACCC
*
27364 CCGAACTTCCAAAAATCCCATTTTTAACCCTAAAACTTCCAAAATTTCCATTTTTACATTCGAAG
1 CCGAACTTCCAAAAAT-CCATTTTTAACCCTAAAACTTCCAAAATTTCCATTTTTACATTCGAAC
*
27429 TTCCAAAAATCTCATTTTTGACCC
65 TTCCAAAAATCCCATTTTTGACCC
**
27453 CAAAACTTCCAAAAAATCCATTTT
1 CCGAACTTCC-AAAAATCCATTTT
27477 GTCCTTAACC
Statistics
Matches: 101, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
86 10 0.10
87 62 0.61
88 4 0.04
89 19 0.19
90 6 0.06
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (88 bp):
CCGAACTTCCAAAAATCCATTTTTAACCCTAAAACTTCCAAAATTTCCATTTTTACATTCGAACT
TCCAAAAATCCCATTTTTGACCC
Found at i:27446 original size:59 final size:58
Alignment explanation
Indices: 27283--27476 Score: 212
Period size: 59 Copynumber: 3.3 Consensus size: 58
27273 CAGTCCGAAT
* * * **
27283 TTCCAAAAATTCCATTTTTA-ACCCTAAAACTTCCATAAATTTCATTTTTACCCTTGAAC
1 TTCCAAAAATTCCATTTTTACACCC--GAACTTCCAAAAATCTCATTTTTACCCTAAAAC
* * *
27342 TTCCAAAAATCCCA-TTTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCCTAAAAC
1 TTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATCTCATTTTT-ACCCTAAAAC
* ** * *
27400 TTCCAAAATTTCCATTTTTACATTCGAAGTTCCAAAAATCTCATTTTTGACCCCAAAAC
1 TTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATCTCATTTTT-ACCCTAAAAC
*
27459 TTCCAAAAAATCCATTTT
1 TTCCAAAAATTCCATTTT
27477 GTCCTTAACC
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
57 19 0.17
58 25 0.22
59 69 0.61
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.35
Consensus pattern (58 bp):
TTCCAAAAATTCCATTTTTACACCCGAACTTCCAAAAATCTCATTTTTACCCTAAAAC
Found at i:33444 original size:130 final size:130
Alignment explanation
Indices: 33279--33522 Score: 434
Period size: 130 Copynumber: 1.9 Consensus size: 130
33269 CTAAAAATCA
* *
33279 AAAAGTTCCATACAAAATTGATTGTCGATCAATTAGATACCACAATTTATAGAGATCATTGACTA
1 AAAAGTTCCATACAAAATTGATTGTCGATCAATTAGATACAACAATTTATAGAGATCATTAACTA
* * *
33344 CAAGTCTATGGACTTAGCCGCCACCACTTAATTCTATGTATAGCCACTCAAAAGCCTAGCTACCT
66 CAAATCTATGAACTTAGCCACCACCACTTAATTCTATGTATAGCCACTCAAAAGCCTAGCTACCT
33409 AAAAGTTCCATACAAAATTGATTGTCGATCAATTAGATACAACAATTTATAGAGATCATTAACTA
1 AAAAGTTCCATACAAAATTGATTGTCGATCAATTAGATACAACAATTTATAGAGATCATTAACTA
*
33474 CAAATCTATGAACTTAGCCACCTCCACTTAATTCTATGTATAGCCACTC
66 CAAATCTATGAACTTAGCCACCACCACTTAATTCTATGTATAGCCACTC
33523 TAATAGATTT
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (130 bp):
AAAAGTTCCATACAAAATTGATTGTCGATCAATTAGATACAACAATTTATAGAGATCATTAACTA
CAAATCTATGAACTTAGCCACCACCACTTAATTCTATGTATAGCCACTCAAAAGCCTAGCTACCT
Found at i:37266 original size:2 final size:2
Alignment explanation
Indices: 37259--37292 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
37249 ACTCTGAATT
37259 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
37293 TTATCGGCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:37604 original size:51 final size:51
Alignment explanation
Indices: 37543--37642 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
37533 AATAACAAAT
** * *
37543 TTAACCCTCAACTTTTACATATTAT-ATCGATTTAATCATAATTTTAAATAA
1 TTAACCCTCAAAATTTACA-AATATCATCAATTTAATCATAATTTTAAATAA
* * *
37594 TTAACTCTCAAAATTTACAAATATCCTCAATTTAATCCTAATTTTAAAT
1 TTAACCCTCAAAATTTACAAATATCATCAATTTAATCATAATTTTAAAT
37643 TTATTTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
50 4 0.10
51 37 0.90
ACGTcount: A:0.40, C:0.17, G:0.01, T:0.42
Consensus pattern (51 bp):
TTAACCCTCAAAATTTACAAATATCATCAATTTAATCATAATTTTAAATAA
Found at i:41461 original size:15 final size:15
Alignment explanation
Indices: 41441--41471 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41431 TCTAGTAAAT
41441 ACCAAAATATAATAA
1 ACCAAAATATAATAA
41456 ACCAAAATATAATAA
1 ACCAAAATATAATAA
41471 A
1 A
41472 AAAGCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.68, C:0.13, G:0.00, T:0.19
Consensus pattern (15 bp):
ACCAAAATATAATAA
Done.