Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001348.1 Hibiscus syriacus cultivar Beakdansim tig00002626_pilon, 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: 109184
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2310 original size:2 final size:2
Alignment explanation
Indices: 2303--2330 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2293 TATACCCATA
2303 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
2331 TTACAGGACC
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:8534 original size:22 final size:22
Alignment explanation
Indices: 8504--8564 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
8494 GGCATGTAAA
8504 ATTTGTCCCGAATGACCTATGT
1 ATTTGTCCCGAATGACCTATGT
* *
8526 ATTTATCCCGAATGACCTTTGT
1 ATTTGTCCCGAATGACCTATGT
*
8548 ATATGTCCCGAATGACC
1 ATTTGTCCCGAATGACC
8565 GTATAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTTGTCCCGAATGACCTATGT
Found at i:9005 original size:22 final size:22
Alignment explanation
Indices: 8949--8994 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
8939 AAAATACGGT
*
8949 ATGAACAGTATCGTGAACATTG
1 ATGAACAGTATCGCGAACATTG
8971 ATGAACAGTATCGCGAACATTG
1 ATGAACAGTATCGCGAACATTG
8993 AT
1 AT
8995 ATAGTGTATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (22 bp):
ATGAACAGTATCGCGAACATTG
Found at i:9021 original size:21 final size:21
Alignment explanation
Indices: 8988--9041 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
8978 GTATCGCGAA
* *
8988 CATTGATATAGTGTATCGATG
1 CATTGCTACAGTGTATCGATG
9009 CATTGCTACAGTGTATCGATG
1 CATTGCTACAGTGTATCGATG
9030 CATTGCTACAGT
1 CATTGCTACAGT
9042 ACTTTCATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (21 bp):
CATTGCTACAGTGTATCGATG
Found at i:9622 original size:18 final size:18
Alignment explanation
Indices: 9599--9713 Score: 122
Period size: 18 Copynumber: 5.9 Consensus size: 18
9589 ATTAAATATT
9599 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
9617 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
*
9639 TGTCCCAAAGGACCACTA
1 TGTCCCGAAGGACCACTA
9657 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCAC----TA
* *
9679 TGTCCCAAAGAACCACTA
1 TGTCCCGAAGGACCACTA
*
9697 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
9714 GTATAACCCT
Statistics
Matches: 82, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
18 49 0.60
22 33 0.40
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:9654 original size:40 final size:40
Alignment explanation
Indices: 9599--9718 Score: 213
Period size: 40 Copynumber: 3.0 Consensus size: 40
9589 ATTAAATATT
*
9599 TGTCCCGAAGGACCACTATGTCCCGAAGGACCACTGTATA
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTGTATA
9639 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTGTATA
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTGTATA
* *
9679 TGTCCCAAAGAACCACTATGTCCTGAAGGACCACTGTATA
1 TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTGTATA
9719 ACCCTTGACT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.21
Consensus pattern (40 bp):
TGTCCCAAAGGACCACTATGTCCCGAAGGACCACTGTATA
Found at i:10281 original size:20 final size:20
Alignment explanation
Indices: 10256--10327 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
10246 AATGAAGGTA
10256 TGTATCGATGCACTCTACAG
1 TGTATCGATGCACTCTACAG
*
10276 TGTATCGATGTACTCTACAG
1 TGTATCGATGCACTCTACAG
10296 TGTATCGATGCACTCTACAG
1 TGTATCGATGCACTCTACAG
*
10316 TTTATCGATGCA
1 TGTATCGATGCA
10328 TCCATTAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.33
Consensus pattern (20 bp):
TGTATCGATGCACTCTACAG
Found at i:13626 original size:11 final size:11
Alignment explanation
Indices: 13610--13634 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
13600 CAAATGATCA
13610 TTTTACCCTTC
1 TTTTACCCTTC
13621 TTTTACCCTTC
1 TTTTACCCTTC
13632 TTT
1 TTT
13635 CTTTCAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.32, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTACCCTTC
Found at i:14411 original size:18 final size:17
Alignment explanation
Indices: 14382--14420 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
14372 CTTCTAAAAT
14382 TTTTAAATTTTTATATA
1 TTTTAAATTTTTATATA
*
14399 TTTTAAATATTTTTTATA
1 TTTTAAAT-TTTTATATA
14417 TTTT
1 TTTT
14421 TATTACTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTAAATTTTTATATA
Found at i:14464 original size:25 final size:24
Alignment explanation
Indices: 14436--14500 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
14426 CTAATATACT
14436 TTTATTCCTTTAAAATTTTTATAAA
1 TTTATT-CTTTAAAATTTTTATAAA
* **
14461 TTTATTATTCTTCAATTTTTATAAA
1 TTTATTCTT-TAAAATTTTTATAAA
14486 TTTATTCTATTAAAA
1 TTTATTCT-TTAAAA
14501 AATTGCAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 2 0.06
25 29 0.91
26 1 0.03
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTATTCTTTAAAATTTTTATAAA
Found at i:17368 original size:5 final size:5
Alignment explanation
Indices: 17358--17425 Score: 54
Period size: 5 Copynumber: 13.8 Consensus size: 5
17348 GTTAGATAAA
* *
17358 AAAAT AAAAT AAGAT --AAT AAGAAA AAAAT AAAAT -AAAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
17405 AAAAT ATAAAA ACAAAT AAAA
1 AAAAT A-AAAT A-AAAT AAAA
17426 ATAAGATGGT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
3 2 0.04
4 8 0.16
5 28 0.56
6 12 0.24
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:17374 original size:18 final size:19
Alignment explanation
Indices: 17351--17432 Score: 62
Period size: 19 Copynumber: 4.2 Consensus size: 19
17341 GGAACGTGTT
17351 AGATAAAA-AAATAAAATA
1 AGATAAAACAAATAAAATA
*
17369 AGATAATAAGAAA-AAAATA
1 AGATAA-AACAAATAAAATA
* *
17388 AAATAAATA-AAATAAATAAA
1 AGATAAA-ACAAATAAA-ATA
*
17408 ATATAAAAACAAATAAAAATA
1 AGAT-AAAACAAAT-AAAATA
17429 AGAT
1 AGAT
17433 GGTGAGATAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
18 10 0.20
19 17 0.33
20 9 0.18
21 12 0.24
22 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (19 bp):
AGATAAAACAAATAAAATA
Found at i:17397 original size:9 final size:9
Alignment explanation
Indices: 17353--17425 Score: 68
Period size: 9 Copynumber: 8.7 Consensus size: 9
17343 AACGTGTTAG
17353 ATAAAA-AA
1 ATAAAATAA
17361 ATAAAATAA
1 ATAAAATAA
17370 GAT--AAT-A
1 -ATAAAATAA
*
17377 AGAAAA-AA
1 ATAAAATAA
17385 ATAAAATAA
1 ATAAAATAA
17394 ATAAAATAA
1 ATAAAATAA
*
17403 ATAAAATAT
1 ATAAAATAA
*
17412 A-AAAACAA
1 ATAAAATAA
17420 ATAAAA
1 ATAAAA
17426 ATAAGATGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
6 1 0.02
7 1 0.02
8 23 0.43
9 26 0.49
10 2 0.04
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (9 bp):
ATAAAATAA
Found at i:17413 original size:25 final size:25
Alignment explanation
Indices: 17355--17431 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 25
17345 CGTGTTAGAT
17355 AAAAAAATAAAATAAGAT--AATAAG
1 AAAAAAATAAAATAA-ATAAAATAAG
17379 AAAAAAATAAAATAAATAAAATAA-
1 AAAAAAATAAAATAAATAAAATAAG
* *
17403 ATAAAATATAAAAACAAATAAAAATAAG
1 A-AAAAAAT-AAAATAAAT-AAAATAAG
17431 A
1 A
17432 TGGTGAGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
23 2 0.04
24 16 0.36
25 11 0.24
26 8 0.18
27 7 0.16
28 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (25 bp):
AAAAAAATAAAATAAATAAAATAAG
Found at i:17567 original size:30 final size:30
Alignment explanation
Indices: 17533--17602 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
17523 ATAAAGCAAA
* *
17533 ATAAAATAAAGACG-ATAATATATTAAATAG
1 ATAAAATAAAGA-GTAAAATAAATTAAATAG
*
17563 ATAAAATCAAGAGTAAAATAAATTAAATAG
1 ATAAAATAAAGAGTAAAATAAATTAAATAG
* *
17593 AGAAATTAAA
1 ATAAAATAAA
17603 TAGATGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 1 0.03
30 32 0.97
ACGTcount: A:0.63, C:0.03, G:0.10, T:0.24
Consensus pattern (30 bp):
ATAAAATAAAGAGTAAAATAAATTAAATAG
Found at i:17600 original size:13 final size:13
Alignment explanation
Indices: 17582--17606 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17572 AGAGTAAAAT
17582 AAATTAAATAGAG
1 AAATTAAATAGAG
17595 AAATTAAATAGA
1 AAATTAAATAGA
17607 TGTAAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATTAAATAGAG
Found at i:17635 original size:16 final size:15
Alignment explanation
Indices: 17611--17640 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
17601 AATAGATGTA
17611 AAAGAAAAAAAAAGT
1 AAAGAAAAAAAAAGT
17626 AAAGATAAAAAAAAG
1 AAAGA-AAAAAAAAG
17641 CCATAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (15 bp):
AAAGAAAAAAAAAGT
Found at i:17775 original size:2 final size:2
Alignment explanation
Indices: 17768--17806 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
17758 AATATGTATG
17768 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
17807 GAATGTTAAA
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:20325 original size:37 final size:37
Alignment explanation
Indices: 20265--20513 Score: 169
Period size: 37 Copynumber: 6.8 Consensus size: 37
20255 GAAACGTTTT
* ** * * *
20265 CAAAGTTTATGTTTCAATAGAAACTGTCTCTAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTATCTCAAGCGAGA
*
20303 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
** * * *
20340 CAAAA-TTCATTTCAAGGGAAA-TGTTTTCAA---TG-
1 CAAAATTTTGTTTCAAGGGAAACT-ATCTCAAGCGAGA
* ** * *
20372 -----TTTACGTTTCAAGAAAAACTGTCTCAAGGGAGA
1 CAAAATTT-TGTTTCAAGGGAAACTATCTCAAGCGAGA
*
20405 CAAAATTTTGTTTCAAGGGAAACTATCTTAAGCGAGA
1 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
*
20442 CAAAATCTTCTGTTTCAAGGGAAACTATCTCAAGCGAAA
1 CAAAAT-TT-TGTTTCAAGGGAAACTATCTCAAGCGAGA
* *
20481 TAAAATATTTTGTTTCGAGGGAAACTATCTCAA
1 -CAAA-ATTTTGTTTCAAGGGAAACTATCTCAA
20514 AATCTTCTTT
Statistics
Matches: 167, Mismatches: 27, Indels: 33
0.74 0.12 0.15
Matches are distributed among these distances:
28 2 0.01
29 16 0.10
30 1 0.01
32 1 0.01
33 1 0.01
35 1 0.01
36 19 0.11
37 58 0.35
38 12 0.07
39 49 0.29
40 5 0.03
41 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.30
Consensus pattern (37 bp):
CAAAATTTTGTTTCAAGGGAAACTATCTCAAGCGAGA
Found at i:20368 original size:102 final size:104
Alignment explanation
Indices: 20247--20466 Score: 336
Period size: 102 Copynumber: 2.1 Consensus size: 104
20237 ATATTTTGTG
* * * *
20247 TTTCAAGGGAAACGTTTTCAAAGTTTATGTTTCAATAGAAACTGTCTCTAGGGAGACAAAATTTT
1 TTTCAAGGGAAACGTTTTCAAAGTTTACGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTT
20312 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TTC-A
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTCTA
* *
20349 TTTCAAGGGAAATGTTTTCAATGTTTACGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAACGTTTTCAAAGTTTACGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTT
* * *
20414 GTTTCAAGGGAAACTATCTTAAGCGAGACAAAATCTTCTG
66 GTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CTTCTA
20454 TTTCAAGGGAAAC
1 TTTCAAGGGAAAC
20467 TATCTCAAGC
Statistics
Matches: 105, Mismatches: 10, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
102 90 0.86
104 3 0.03
105 12 0.11
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.30
Consensus pattern (104 bp):
TTTCAAGGGAAACGTTTTCAAAGTTTACGTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTT
GTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTTCTA
Found at i:20465 original size:39 final size:37
Alignment explanation
Indices: 20377--20513 Score: 166
Period size: 39 Copynumber: 3.6 Consensus size: 37
20367 CAATGTTTAC
** * *
20377 GTTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTT
1 GTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTTT
*
20414 GTTTCAAGGGAAACTATCTTAAGCGAGACAAAATCTTCT
1 GTTTCAAGGGAAACTATCTCAAGCGAGACAAAAT-TT-T
* *
20453 GTTTCAAGGGAAACTATCTCAAGCGAAATAAAATATTTT
1 GTTTCAAGGGAAACTATCTCAAGCGAGA-CAAA-ATTTT
*
20492 GTTTCGAGGGAAACTATCTCAA
1 GTTTCAAGGGAAACTATCTCAA
20514 AATCTTCTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
37 29 0.33
38 2 0.02
39 49 0.56
40 5 0.06
41 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (37 bp):
GTTTCAAGGGAAACTATCTCAAGCGAGACAAAATTTT
Found at i:20625 original size:36 final size:36
Alignment explanation
Indices: 20583--20687 Score: 104
Period size: 36 Copynumber: 2.9 Consensus size: 36
20573 CTCAAGCGAG
* *
20583 ACAAATCTTGTTTTAAGAAAAACAATCTTGAGTGAA
1 ACAAATCTTGTTTCAAGAAAAACAATCTTAAGTGAA
* * * * ** *
20619 ATAAATCTTCTTTCGAGTAAAACTGTCTTAAGTGAG
1 ACAAATCTTGTTTCAAGAAAAACAATCTTAAGTGAA
*
20655 ACAAAGTC-TGTTTCAAGAAAAACAATCTCAAGT
1 ACAAA-TCTTGTTTCAAGAAAAACAATCTTAAGT
20688 AAGATAAATC
Statistics
Matches: 52, Mismatches: 16, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
36 50 0.96
37 2 0.04
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (36 bp):
ACAAATCTTGTTTCAAGAAAAACAATCTTAAGTGAA
Found at i:20659 original size:72 final size:75
Alignment explanation
Indices: 20524--20682 Score: 227
Period size: 72 Copynumber: 2.1 Consensus size: 75
20514 AATCTTCTTT
*
20524 AAAAACAGTCTTGAGTGAAATGAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAA-
1 AAAAACAATCTTGAGTGAAATGAAAT-CCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAAG
*
20588 TCTTGTTTTAAG
65 TC-TGTTTCAAG
* * *
20600 AAAAACAATCTTGAGTGAAAT-AAAT-CTTCTTTCGAGT-AAAACTGTCTTAAGTGAGACAAAGT
1 AAAAACAATCTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAAGT
20662 CTGTTTCAAG
66 CTGTTTCAAG
20672 AAAAACAATCT
1 AAAAACAATCT
20683 CAAGTAAGAT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
72 39 0.51
73 14 0.18
75 4 0.05
76 20 0.26
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (75 bp):
AAAAACAATCTTGAGTGAAATGAAATCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAAGT
CTGTTTCAAG
Found at i:21975 original size:94 final size:94
Alignment explanation
Indices: 21782--22037 Score: 363
Period size: 94 Copynumber: 2.7 Consensus size: 94
21772 AGCTGAATTG
* * * * * *
21782 ATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGATAGCTTAATATCATTGTA-TATATATTA
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTATA-TA
21846 TAATCACCTTTATCAGGCTAGCTGAATATTATCC
61 TAATCACCTTTATCAGGCTAGCTGAATATTATCC
* *
21880 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACATCTCAAGCTTTATTGTATATGTAATC
1 ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATATAATC
21945 ACCTTTATCAGGCTAGCTGAATATTATCC
66 ACCTTTATCAGGCTAGCTGAATATTATCC
*
21974 ATAAAG-TCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATATAAT
1 ATAAAGCT-GGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATATAAT
22038 ATTGTAATCT
Statistics
Matches: 146, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
93 1 0.01
94 96 0.66
95 7 0.05
96 2 0.01
97 2 0.01
98 38 0.26
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (94 bp):
ATAAAGCTGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATATAATC
ACCTTTATCAGGCTAGCTGAATATTATCC
Found at i:26528 original size:2 final size:2
Alignment explanation
Indices: 26521--26556 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
26511 TAACTTAGGC
*
26521 AT AT AT AT AT AT AT AC 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 AT AT
26557 GTGTATGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28163 original size:18 final size:19
Alignment explanation
Indices: 28140--28206 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
28130 AGAACATGTC
28140 AGATAA-AA-AAAGAAAATA
1 AGATAATAAGAAA-AAAATA
28158 AGATAATAAGAAAAAAATAA
1 AGATAATAAGAAAAAAAT-A
*
28178 AGAAAATATA-AAAACAAATA
1 AGATAATA-AGAAAA-AAATA
28198 A-A-AATAAGA
1 AGATAATAAGA
28207 TGGTGAGATA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
17 1 0.02
18 11 0.26
19 8 0.19
20 17 0.40
21 5 0.12
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.13
Consensus pattern (19 bp):
AGATAATAAGAAAAAAATA
Found at i:28185 original size:20 final size:20
Alignment explanation
Indices: 28147--28199 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
28137 GTCAGATAAA
*
28147 AAAAGAAAAT-AAGATAATA-
1 AAAA-AAAATAAAGAAAATAT
28166 AGAAAAAAATAAAGAAAATAT
1 A-AAAAAAATAAAGAAAATAT
28187 AAAAACAAATAAA
1 AAAAA-AAATAAA
28200 AATAAGATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 6 0.21
20 15 0.52
21 8 0.28
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.13
Consensus pattern (20 bp):
AAAAAAAATAAAGAAAATAT
Found at i:28288 original size:24 final size:23
Alignment explanation
Indices: 28261--28310 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
28251 AAAGAATATA
28261 AAAG-AAATGAAAATATAAAAAGAT
1 AAAGAAAAT-AAAATA-AAAAAGAT
*
28285 AAAGCAAAATAAAATAAAGAAGAT
1 AAAG-AAAATAAAATAAAAAAGAT
28309 AA
1 AA
28311 TATATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 13 0.57
25 6 0.26
26 4 0.17
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (23 bp):
AAAGAAAATAAAATAAAAAAGAT
Found at i:28329 original size:30 final size:30
Alignment explanation
Indices: 28293--28362 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
28283 ATAAAGCAAA
* *
28293 ATAAAATAAAGAAG-ATAATATATTAAATAG
1 ATAAAATAAAG-AGTAAAATAAATTAAATAG
*
28323 ATAAAATTAAGAGTAAAATAAATTAAATAG
1 ATAAAATAAAGAGTAAAATAAATTAAATAG
* *
28353 AGAAATTAAA
1 ATAAAATAAA
28363 TAGATGTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (30 bp):
ATAAAATAAAGAGTAAAATAAATTAAATAG
Found at i:28360 original size:13 final size:13
Alignment explanation
Indices: 28342--28366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28332 AGAGTAAAAT
28342 AAATTAAATAGAG
1 AAATTAAATAGAG
28355 AAATTAAATAGA
1 AAATTAAATAGA
28367 TGTAAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATTAAATAGAG
Found at i:31024 original size:2 final size:2
Alignment explanation
Indices: 31017--31042 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31007 TATATTTTAA
31017 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
31043 TAATAATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32030 original size:21 final size:21
Alignment explanation
Indices: 31981--32054 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
31971 ACCACCGCCG
* *
31981 CCGCCGTCTTCCTTCTTCTC-
1 CCGCCGCCTTCCTTTTTCTCT
*
32001 CC-CCACCTTCCTTTTTCTCT
1 CCGCCGCCTTCCTTTTTCTCT
*
32021 CCGCCGCCTTCTTTTTTCTCT
1 CCGCCGCCTTCCTTTTTCTCT
*
32042 CCGCCTCC-TCCTT
1 CCGCCGCCTTCCTT
32055 CCTTCTTCTC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 14 0.31
20 8 0.18
21 23 0.51
ACGTcount: A:0.01, C:0.50, G:0.07, T:0.42
Consensus pattern (21 bp):
CCGCCGCCTTCCTTTTTCTCT
Found at i:32121 original size:21 final size:21
Alignment explanation
Indices: 32096--32146 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
32086 TTTTGGTTTC
32096 TCTTTCTTCTCACCGGCGGCG
1 TCTTTCTTCTCACCGGCGGCG
*
32117 TCTTTCTTCTCACCGGCGTCG
1 TCTTTCTTCTCACCGGCGGCG
32138 TCTTTCTTC
1 TCTTTCTTC
32147 GGAGGAACCA
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:0.04, C:0.37, G:0.18, T:0.41
Consensus pattern (21 bp):
TCTTTCTTCTCACCGGCGGCG
Found at i:56912 original size:22 final size:23
Alignment explanation
Indices: 56887--56930 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
56877 AATTAAGTTT
56887 TAATCTTA-AAA-TAATTTCAAAA
1 TAATCTTATAAAGT-ATTTCAAAA
*
56909 TAATTTTATAAAGTATTTCAAA
1 TAATCTTATAAAGTATTTCAAA
56931 CCATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 11 0.58
24 1 0.05
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (23 bp):
TAATCTTATAAAGTATTTCAAAA
Found at i:58068 original size:24 final size:25
Alignment explanation
Indices: 58022--58071 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
58012 ATTTCGATTT
58022 TTTTCAGTTATCGATTTTTTGGATCGA
1 TTTTCAGTTAT--ATTTTTTGGATCGA
58049 TTTTCAGTTAT-TTTTTTGGATCG
1 TTTTCAGTTATATTTTTTGGATCG
58072 GATTGGATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 12 0.52
27 11 0.48
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (25 bp):
TTTTCAGTTATATTTTTTGGATCGA
Found at i:61563 original size:3 final size:3
Alignment explanation
Indices: 61557--61605 Score: 80
Period size: 3 Copynumber: 15.7 Consensus size: 3
61547 TTATTTTTAA
61557 ATT ATT ATT ATT ATT ATTT ATT ATTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT A-TT ATT A-TT ATT ATT ATT ATT ATT ATT ATT
61604 AT
1 AT
61606 GAAATAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 38 0.86
4 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:61574 original size:23 final size:23
Alignment explanation
Indices: 61547--61605 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
61537 ACTAATTTTT
61547 TTATTT-TTAAATTATTATTATTA
1 TTATTTATT-AATTATTATTATTA
*
61570 TTATTTATTATTTATTATTATTA
1 TTATTTATTAATTATTATTATTA
61593 TTA-TTATT-ATTAT
1 TTATTTATTAATTAT
61606 GAAATAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 22 0.67
24 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTATTTATTAATTATTATTATTA
Found at i:62996 original size:28 final size:26
Alignment explanation
Indices: 62964--63017 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
62954 ATTAGTCATA
62964 TAAATATATATATATATATATATTTTTT
1 TAAATA-ATA-ATATATATATATTTTTT
* *
62992 TAAATAATAATATTTATTTATTTTTT
1 TAAATAATAATATATATATATTTTTT
63018 AATATTAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.62
27 3 0.12
28 6 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TAAATAATAATATATATATATTTTTT
Found at i:64841 original size:21 final size:21
Alignment explanation
Indices: 64815--64859 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
64805 GATTTCTGGG
* *
64815 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
64836 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
64857 CAA
1 CAA
64860 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:66609 original size:23 final size:22
Alignment explanation
Indices: 66550--66616 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
66540 TATGGACATC
* *
66550 ATTCTACGGGAACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
66572 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
66594 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
66617 TTTATACGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
22 27 0.64
23 15 0.36
ACGTcount: A:0.21, C:0.25, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:69783 original size:21 final size:21
Alignment explanation
Indices: 69757--69801 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
69747 GATTTCTGGG
* *
69757 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
69778 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
69799 CAA
1 CAA
69802 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:71553 original size:23 final size:22
Alignment explanation
Indices: 71494--71560 Score: 116
Period size: 22 Copynumber: 3.0 Consensus size: 22
71484 TATGGACATC
*
71494 ATTCTACGGGCACTACGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
71516 ATTCTACGGGCACTTCGGTGCA
1 ATTCTACGGGCACTTCGGTGCA
71538 ATTCTACGGGGCACTTCGGTGCA
1 ATTCTAC-GGGCACTTCGGTGCA
71561 TTTATACGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 28 0.65
23 15 0.35
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
ATTCTACGGGCACTTCGGTGCA
Found at i:74456 original size:20 final size:21
Alignment explanation
Indices: 74421--74467 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
74411 ACATCCACGT
74421 TTTTGCA--TTTGCGTTTACA
1 TTTTGCATCTTTGCGTTTACA
* *
74440 -TTTGCATCTTTGTGTTTTCA
1 TTTTGCATCTTTGCGTTTACA
74460 TTTTGCAT
1 TTTTGCAT
74468 TTGTACTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.26
20 10 0.43
21 7 0.30
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.57
Consensus pattern (21 bp):
TTTTGCATCTTTGCGTTTACA
Found at i:80574 original size:54 final size:54
Alignment explanation
Indices: 80475--80686 Score: 234
Period size: 54 Copynumber: 3.9 Consensus size: 54
80465 ACCAGGAATC
80475 TGTGCAGAAACCAC-AGAAAATGATGAATGT-TTGTCAAATGTTTTACGAACATA
1 TGTGCAGAAACCACAAG-AAATGATGAATGTGTTGTCAAATGTTTTACGAACATA
* *
80528 TGTGCA-AAAGCCACAAGAAATGATGAATGTGTTGTCAAATGCTTTACAAACATA
1 TGTGCAGAAA-CCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATA
* * * * * * *
80582 TGGGCAGAAGCCACAGGAAA-GAATGAATATGTTGTCAAATGTTTTACTAGCATC
1 TGTGCAGAAACCACAAGAAATG-ATGAATGTGTTGTCAAATGTTTTACGAACATA
* * * * * *
80636 TGAGTATAAACCACATGAGATGATGAATGTATTGTCAAATGTTTTACGAAC
1 TGTGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
80687 CAGTTATTCT
Statistics
Matches: 133, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 3 0.02
53 24 0.18
54 103 0.77
55 3 0.02
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (54 bp):
TGTGCAGAAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATA
Found at i:80671 original size:108 final size:107
Alignment explanation
Indices: 80478--80682 Score: 261
Period size: 108 Copynumber: 1.9 Consensus size: 107
80468 AGGAATCTGT
* *
80478 GCAGAAACCACAGAAAATGATGAATGTTTGTCAAATGTTTTACGAACATATGTGCAAAAGCCACA
1 GCAGAAACCACAGAAAATGATGAATATTTGTCAAATGTTTTACGAACATATGAGCAAAAGCCACA
*
80543 AGAAATGATGAATGTGTTGTCAAATGCTTTACAAACATATGG
66 AGAAATGATGAATGTATTGTCAAATGCTTTACAAACATATGG
* * * * * *
80585 GCAGAAGCCACAGGAAA-GAATGAATATGTTGTCAAATGTTTTACTAGCATCTGAGTATAAA-CC
1 GCAGAAACCACAGAAAATG-ATGAATAT-TTGTCAAATGTTTTACGAACATATGAGCA-AAAGCC
* * *
80648 ACATGAGATGATGAATGTATTGTCAAATGTTTTAC
63 ACAAGAAATGATGAATGTATTGTCAAATGCTTTAC
80683 GAACCAGTTA
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
106 1 0.01
107 22 0.27
108 57 0.69
109 3 0.04
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.28
Consensus pattern (107 bp):
GCAGAAACCACAGAAAATGATGAATATTTGTCAAATGTTTTACGAACATATGAGCAAAAGCCACA
AGAAATGATGAATGTATTGTCAAATGCTTTACAAACATATGG
Found at i:81159 original size:22 final size:22
Alignment explanation
Indices: 81042--81157 Score: 139
Period size: 22 Copynumber: 5.4 Consensus size: 22
81032 ATCTACACTC
81042 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
*
81064 TCAAAGATGATATATTCTCTCT
1 TCAAAGATGATAGATTCTCTCT
* *
81086 TCAAATATGATAGATTCTTTCT
1 TCAAAGATGATAGATTCTCTCT
*
81108 TCAAAGATGATAGA--CACTCT
1 TCAAAGATGATAGATTCTCTCT
* * *
81128 CCAAAGATAATATATTCTC-CTT
1 TCAAAGATGATAGATTCTCTC-T
81150 TCAAAGAT
1 TCAAAGAT
81158 AAAAGCTTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
20 15 0.19
21 1 0.01
22 63 0.80
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTCT
Found at i:81952 original size:74 final size:74
Alignment explanation
Indices: 81822--82388 Score: 954
Period size: 74 Copynumber: 7.7 Consensus size: 74
81812 GTAAACTATT
* * * **
81822 TCCGAGTCATCTGTAAGACCTACAGTGTATGATGTTTTCAAAAATCCTTCAAGAGCTTTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
81887 TTTAAAGCC
66 TTTAAAGCC
*
81896 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
*
81961 TTTAAAGAC
66 TTTAAAGCC
** *
81970 TCCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
82035 TTTAAAGCC
66 TTTAAAGCC
* * *
82044 TCCGGGTCATCTATAAGACCTACAGTGCATGATGTTTTTAAAAAGCCTTCAGGAGCTTTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
82109 TTTAAAGCC
66 TTTAAAGCC
* *
82118 TCCAGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCATTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
82183 TTTAAAGCC
66 TTTAAAGCC
*
82192 TCCGGGTCATTTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
82257 TTTAAAGCC
66 TTTAAAGCC
*
82266 TCCAGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
82331 TTTAAAGCC
66 TTTAAAGCC
** *
82340 TCCGGGTCATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTT
82389 TGGGTCATCT
Statistics
Matches: 463, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 463 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (74 bp):
TCCGGGTCATCTGTAAGACCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATA
TTTAAAGCC
Found at i:82746 original size:16 final size:16
Alignment explanation
Indices: 82727--82759 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
82717 TTTTAAAATT
*
82727 TTTATTTTTATTATTA
1 TTTATTGTTATTATTA
82743 TTTATTGTTATTATTA
1 TTTATTGTTATTATTA
82759 T
1 T
82760 GAAATAAAAA
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:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (16 bp):
TTTATTGTTATTATTA
Found at i:84089 original size:23 final size:23
Alignment explanation
Indices: 84031--84103 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
84021 TTATTTGTAA
84031 TATTATTTTATTATTACTTT--T
1 TATTATTTTATTATTACTTTCAT
* **
84052 GATATATGTAAATTATTACTTTCAT
1 TAT-TAT-TTTATTATTACTTTCAT
* *
84077 TATTATTTTATTACTATTTTCA-
1 TATTATTTTATTATTACTTTCAT
84099 TATTA
1 TATTA
84104 GTCATATAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 7
0.73 0.15 0.13
Matches are distributed among these distances:
21 2 0.05
22 8 0.20
23 24 0.60
24 3 0.08
25 3 0.08
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (23 bp):
TATTATTTTATTATTACTTTCAT
Found at i:84237 original size:2 final size:2
Alignment explanation
Indices: 84230--84258 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84220 TTATAAAAAT
84230 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 T
84259 TATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:90350 original size:47 final size:45
Alignment explanation
Indices: 90278--90403 Score: 175
Period size: 47 Copynumber: 2.8 Consensus size: 45
90268 TATAAAATCC
90278 CTTACCATTTA-TCCTATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
90323 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
90370 CTTGCCA-TTATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
90404 GTATGCTTAC
Statistics
Matches: 74, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
44 24 0.32
45 10 0.14
46 2 0.03
47 35 0.47
48 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:90604 original size:59 final size:59
Alignment explanation
Indices: 90512--90640 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
90502 CGTAGTGCTA
* * **
90512 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
90571 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
90630 TCCCGAATATG
1 TCCCGAATATG
90641 CAGCCTGTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:100346 original size:6 final size:6
Alignment explanation
Indices: 100335--100368 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
100325 TGTTTGCATA
100335 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTG
1 TGTGGG TGTGGG TGTGGG TGTGGG TGTGGG TGTG
100369 TTATCTATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (6 bp):
TGTGGG
Found at i:101315 original size:20 final size:20
Alignment explanation
Indices: 101290--101356 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
101280 TTTTCCCAAT
101290 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCAAATAAGTAAA
* * ** *
101310 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGC-AAATAAGTAAA
101331 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCAAATAAGTAAA
101351 TCGCAA
1 TCGCAA
101357 CGCGAATTGG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAATGCAAATAAGTAAA
Found at i:101333 original size:21 final size:21
Alignment explanation
Indices: 101307--101382 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
101297 GCAAATAAGT
101307 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* * ** *
101328 AAATCGCAATGC-AAATAAGT
1 AAATCGCAACGCGAATTGGGA
101348 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
101369 AAATCGCAATGCGA
1 AAATCGCAACGCGA
101383 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:101335 original size:41 final size:41
Alignment explanation
Indices: 101290--101380 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
101280 TTTTCCCAAT
101290 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
101331 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
101372 TCGCAATGC
1 TCGCAATGC
101381 GATACTGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (41 bp):
TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:101395 original size:41 final size:41
Alignment explanation
Indices: 101309--101443 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
101299 AAATAAGTAA
* * *
101309 ATCGCAACGCGAATTGGGAAAATCGCAATGCAAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGC-GATACTG-ACT
101350 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
101391 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
101432 TTCGCAACGCGA
1 ATCGCAACGCGA
101444 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:101396 original size:20 final size:19
Alignment explanation
Indices: 101371--101485 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
101361 AATTGGGAAA
*
101371 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
101391 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
101412 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
101432 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
101452 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
101472 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
101486 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.60
21 23 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:101681 original size:22 final size:22
Alignment explanation
Indices: 101653--101696 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
101643 CACTCTCTCA
101653 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
101675 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
101697 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:102013 original size:20 final size:20
Alignment explanation
Indices: 101959--102017 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
101949 GCGATTATCT
**
101959 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
101979 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
101999 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
102018 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:103354 original size:18 final size:18
Alignment explanation
Indices: 103328--103372 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
103318 CTCCACTTCG
*
103328 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
103346 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
103364 GAGCCATCA
1 GAGCCATCA
103373 TTTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:103907 original size:14 final size:14
Alignment explanation
Indices: 103888--103945 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
103878 ATGCGAAATG
103888 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
103902 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
103918 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
103934 AAAATCGCAACG
1 AAAATCGCAACG
103946 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:103930 original size:32 final size:33
Alignment explanation
Indices: 103872--103962 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
103862 GGAAATGGCT
103872 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
103905 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
103937 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
103963 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:105232 original size:19 final size:19
Alignment explanation
Indices: 105210--105340 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
105200 GGAAATTACT
105210 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
105229 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
105243 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
105262 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
105276 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
105295 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
105309 ATAGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
105328 ATCGCAACGCGAA
1 ATCGCAATGCGAA
105341 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:105252 original size:33 final size:33
Alignment explanation
Indices: 105210--105336 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
105200 GGAAATTACT
105210 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
105243 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
105275 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
105309 ATAGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
105337 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:105317 original size:66 final size:66
Alignment explanation
Indices: 105211--105343 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
105201 GAAATTACTA
* *
105211 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
105276 T
66 T
*
105277 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
105342 T
66 T
105343 T
1 T
105344 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:105514 original size:14 final size:14
Alignment explanation
Indices: 105497--105533 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
105487 CATCAATTAA
105497 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
105511 ACAAATCACCTTTT
1 ACAAATCAACTTTT
105525 ACAAATCAA
1 ACAAATCAA
105534 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:106944 original size:21 final size:21
Alignment explanation
Indices: 106878--106944 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
106868 GTGAATCGGG
*
106878 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
106898 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
106920 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
106941 CTCT
1 CTCT
106945 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:106963 original size:42 final size:41
Alignment explanation
Indices: 106878--107000 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
106868 GTGAATCGGG
* * * *
106878 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
106920 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
106962 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
107001 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:109075 original size:32 final size:33
Alignment explanation
Indices: 109015--109113 Score: 110
Period size: 32 Copynumber: 3.0 Consensus size: 33
109005 ACGAGATAAT
* *
109015 GAGAATCGCCAACGCGGAAAGGACTATCGCAACGA
1 GAGAATCG-CAACGC-GAAATGACTATCGCAACCA
* *
109050 TAGAATCGCAACGC-AAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
109082 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
109114 GCGAAATAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 27 0.50
33 14 0.26
34 6 0.11
35 7 0.13
ACGTcount: A:0.39, C:0.27, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:109118 original size:20 final size:19
Alignment explanation
Indices: 109085--109155 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
109075 GCGACCAGAC
109085 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
109104 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
* *
109124 AATCGTAACTCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
109143 AATCGCAATGCGA
1 AATCGCAACGCGA
109156 TTTTGTGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 27 0.61
20 17 0.39
ACGTcount: A:0.46, C:0.21, G:0.18, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Done.