Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006464.1 Hibiscus syriacus cultivar Beakdansim tig00015664_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: 97065
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:12294 original size:2 final size:2
Alignment explanation
Indices: 12287--12313 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12277 CATATTTAAA
12287 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
12314 CTCTATACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16657 original size:39 final size:39
Alignment explanation
Indices: 16592--16698 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
16582 AATTAAAAGA
* *
16592 AATAATTTAGATTGCTAAGGTAAAATAATGTAAAAAATT
1 AATAATTTAGAATGTTAAGGTAAAATAATGTAAAAAATT
* * *
16631 AATAATTTAGAATGTTACAGG-GAAATAATTTAAGAAATT
1 AATAATTTAGAATGTTA-AGGTAAAATAATGTAAAAAATT
* * *
16670 AA-AATTTTAGAAGGTTAGGGTGAAATAAT
1 AATAA-TTTAGAATGTTAAGGTAAAATAAT
16699 TTGATAATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
38 4 0.07
39 51 0.88
40 3 0.05
ACGTcount: A:0.49, C:0.02, G:0.17, T:0.33
Consensus pattern (39 bp):
AATAATTTAGAATGTTAAGGTAAAATAATGTAAAAAATT
Found at i:18301 original size:35 final size:36
Alignment explanation
Indices: 18254--18348 Score: 122
Period size: 36 Copynumber: 2.7 Consensus size: 36
18244 CACATACATT
* *
18254 AATTACATTCTAAACCCCAAATTTC-AAAATACTTC
1 AATTACAATCTAAACCCCAAATTCCAAAAATACTTC
*
18289 AATTACAATCTAAACCTCAAATTCCAAAAATACTTC
1 AATTACAATCTAAACCCCAAATTCCAAAAATACTTC
**
18325 AATTAC-ATGCCCAACCCCAAATTC
1 AATTACAAT-CTAAACCCCAAATTC
18349 ATAATCCATT
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
35 24 0.46
36 28 0.54
ACGTcount: A:0.43, C:0.28, G:0.01, T:0.27
Consensus pattern (36 bp):
AATTACAATCTAAACCCCAAATTCCAAAAATACTTC
Found at i:18997 original size:105 final size:107
Alignment explanation
Indices: 18832--19040 Score: 332
Period size: 105 Copynumber: 1.9 Consensus size: 107
18822 AAACTATTTA
* * *
18832 AATTAGAATCATATAATATTATAGTATTATAAATATTTATAATTAAATTTAAACAAAAACTC-AA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAAA
18896 A-AATTCAATTCGACTTGATTTAAATTTTATAAACTGAACTG
66 ATAATTCAATTCGACTTGATTTAAATTTTATAAACTGAACTG
*
18937 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACATAAACTCGAA
1 AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTC-AA
*
19002 AATTCAATTCAATTCGACTTTATTTAAATTTTATAAACT
65 AA-T-AATTCAATTCGACTTGATTTAAATTTTATAAACT
19041 CAAATCGAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
105 58 0.62
107 3 0.03
110 33 0.35
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (107 bp):
AATTAGAATCAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAAAAACTCAAA
ATAATTCAATTCGACTTGATTTAAATTTTATAAACTGAACTG
Found at i:19276 original size:35 final size:34
Alignment explanation
Indices: 19253--19332 Score: 115
Period size: 35 Copynumber: 2.3 Consensus size: 34
19243 AGGGTTGGGT
*
19253 ATGTAATTGAAGTATTTTGGAATTTGTGGTTCAGA
1 ATGTAATTGAAGCATTTTGGAATTTG-GGTTCAGA
* *
19288 ATGTAATTGAAGCATTTTGGATTTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTGGAATTT-GGGTTCAGA
19323 ATGTAATTGA
1 ATGTAATTGA
19333 TGATTGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 40 0.98
36 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.42
Consensus pattern (34 bp):
ATGTAATTGAAGCATTTTGGAATTTGGGTTCAGA
Found at i:22545 original size:81 final size:81
Alignment explanation
Indices: 21735--22510 Score: 1219
Period size: 81 Copynumber: 9.6 Consensus size: 81
21725 CCTCCGTTGG
* * *
21735 TGATTTTGAACCGAGGCCAAGCACAACGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
*
21800 AGAAATCATTCGTTAA
66 AGAAATCATTCGCTAA
* * * *
21816 TGATTTTGAACCGAGGCCAAGCACAACGGCCTACGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
*
21881 AGAAATCATTCGTTAA
66 AGAAATCATTCGCTAA
* * * * *
21897 TGATTTTGAACCGAGGCCAAGCACAACGGCCTACGGAGACAATGATGTTGGCTTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
21962 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
* * *
21978 TGATTTTGAACCGAGACCAAGCGTATCGGCCTACGAAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
22043 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
* * *
22059 TGATTTTGAATCAAGACCAAGCGTATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
22124 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
22140 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
22205 AGAAATCATTCGCTAA
66 AGAAATCATTCGCTAA
*
22221 TAATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
* *
22286 AGAAATTATTCACTAA
66 AGAAATCATTCGCTAA
* * *
22302 TGATTTTGAACCGAGACCAAGCGTATCGGCCTATGGAGACAATGATGTTGGTCTTAAAGAAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
* *
22367 AGAAATCGTTCACTAA
66 AGAAATCATTCGCTAA
* *
22383 TGATTTTGAACCGAGACCAAACGTATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
* *
22448 AGAAATTATTCACTAA
66 AGAAATCATTCGCTAA
* * * * *
22464 TGATTTTGAACCGAGACCAAGCACAACAGCCTAGGGAGACGATGATG
1 TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATG
22511 CTGATCTTAA
Statistics
Matches: 658, Mismatches: 37, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 658 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (81 bp):
TGATTTTGAACCGAGACCAAGCATATCGGCCTATGGAGACAATGATGTTGGCCTTAAAGGAAAAA
AGAAATCATTCGCTAA
Found at i:23376 original size:29 final size:31
Alignment explanation
Indices: 23315--23390 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
23305 TAAATTCTAT
*
23315 AAAATAATAT--TATAAT-TTATAAATATTA
1 AAAATAATATAATATAATATTATAAACATTA
*
23343 AAAAT-CTATAAT-TAATATTATAAACA-TA
1 AAAATAATATAATATAATATTATAAACATTA
23371 ACAAATAATATAATATAATA
1 A-AAATAATATAATATAATA
23391 ATATTATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 3 0.08
28 12 0.31
29 13 0.33
30 6 0.15
31 5 0.13
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (31 bp):
AAAATAATATAATATAATATTATAAACATTA
Found at i:23746 original size:150 final size:145
Alignment explanation
Indices: 23535--23816 Score: 429
Period size: 150 Copynumber: 1.9 Consensus size: 145
23525 GTTTATTGAA
* * * *
23535 TTCGAGATATTTTTAGTGAAACGGACACGATATGCGTTCAGAGGCCAAAAGAGGGTGATTTAAAA
1 TTCGAGATATTTTTAGTAAAACAGACACGATACGCGTTCAGAGGCCAAAAGAGGGCGATTTAAAA
* *
23600 ATTTTAGGGTCTAACAGTCGTTGATGACAGTGATCGATGATAATCGACGATGACAGTGGTGAGTG
66 ATTTTAAGGTCCAACAGTCGTTGATGACAGTGATCGATGATAATCGACGATGACAGTGGTGAGTG
23665 ACAGTGATCAATGAT
131 ACAGTGATCAATGAT
*
23680 TTCGAGATATTTTCCTAGTAAAATAGACACCAGATACGCGTTCAGGAGGCCAAAAGAGGGCGATT
1 TTCGAGATATTTT--TAGTAAAACAGACA-C-GATACGCGTTCA-GAGGCCAAAAGAGGGCGATT
* * *
23745 TAAAAATTTTAAGGTCCAACGGTCGTTGATGACAGTGATCGATGATAATCGACGGTGACATTGGT
61 TAAAAATTTTAAGGTCCAACAGTCGTTGATGACAGTGATCGATGATAATCGACGATGACAGTGGT
23810 GAGTGAC
126 GAGTGAC
23817 TAGGGATGGC
Statistics
Matches: 122, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
145 13 0.11
147 11 0.09
148 1 0.01
149 11 0.09
150 86 0.70
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.27
Consensus pattern (145 bp):
TTCGAGATATTTTTAGTAAAACAGACACGATACGCGTTCAGAGGCCAAAAGAGGGCGATTTAAAA
ATTTTAAGGTCCAACAGTCGTTGATGACAGTGATCGATGATAATCGACGATGACAGTGGTGAGTG
ACAGTGATCAATGAT
Found at i:24437 original size:255 final size:255
Alignment explanation
Indices: 23986--24497 Score: 925
Period size: 255 Copynumber: 2.0 Consensus size: 255
23976 AGCAAGCAAT
*
23986 TGGGATGTTGGAGTTGGTTCCCAAACAGTTCATGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
1 TGGGATGTTGGAGTTGGTTCCCAAACAGATCATGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
24051 GAGGAGTGGCTCTACGAATGTTATGGAGACAGATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
66 GAGGAGTGGCTCTACGAATGTTATGGAGACAGATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
*
24116 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGTGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
131 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
*
24181 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTTCCAAACAGTAAACCAA
196 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAGTAAACCAA
* *
24241 TGGGATGTTGGAGTTGGTTCCCAGACAGATCGTGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
1 TGGGATGTTGGAGTTGGTTCCCAAACAGATCATGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
* *
24306 GAGGAGTGGCTCTACGAATGTTATGGAGACATATTGTAGGGAGCATGTAGTCGTAGAGCTGGATT
66 GAGGAGTGGCTCTACGAATGTTATGGAGACAGATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
* *
24371 GTTGTGTTGCTTTCGATGTTAATTCTCATAGTGCGCCTAATATGGGTTTTGGGGGGCTAAAGAAC
131 GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
* *
24436 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAGACAGTAAACTAA
196 ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAGTAAACCAA
24496 TG
1 TG
24498 TTAGGAAAAT
Statistics
Matches: 246, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
255 246 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.31
Consensus pattern (255 bp):
TGGGATGTTGGAGTTGGTTCCCAAACAGATCATGATGGGGTAGCAGCGCATGCTTCAATTTGTCA
GAGGAGTGGCTCTACGAATGTTATGGAGACAGATTGTAGGGAGCATGTAGTCGCAGAGCTGGATT
GTTGTGTTGCTTTCGATGTTAATGCTCATAGTGCGCCTAATATGGGTTTTGAGGGGCTAAAGAAC
ATGGAAACTGCTGCTTTTGATGTTAATGCTTATAGTACGGGTTCCCAAACAGTAAACCAA
Found at i:28993 original size:16 final size:16
Alignment explanation
Indices: 28969--29002 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28959 TATCGCCGAC
*
28969 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
28985 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
29001 CG
1 CG
29003 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:30026 original size:12 final size:12
Alignment explanation
Indices: 30005--30034 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
29995 TTAGCTGGGC
30005 GGGC-GGATGTG
1 GGGCGGGATGTG
30016 GGGCGGGATGTG
1 GGGCGGGATGTG
30028 GGGCGGG
1 GGGCGGG
30035 TAATGTCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.22
12 14 0.78
ACGTcount: A:0.07, C:0.10, G:0.70, T:0.13
Consensus pattern (12 bp):
GGGCGGGATGTG
Found at i:31224 original size:22 final size:22
Alignment explanation
Indices: 31199--31245 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
31189 ATGACATGTA
*
31199 TTTCTCTATTTTATAGCACGTT
1 TTTCTCTATTTTATAACACGTT
* * *
31221 TTTCTTTGTTTTCTAACACGTT
1 TTTCTCTATTTTATAACACGTT
31243 TTT
1 TTT
31246 TTATCTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.60
Consensus pattern (22 bp):
TTTCTCTATTTTATAACACGTT
Found at i:31254 original size:22 final size:22
Alignment explanation
Indices: 31215--31257 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31205 TATTTTATAG
*
31215 CACGTTTTTCTTTGTTTTCTAA
1 CACGTTTTTCTTTCTTTTCTAA
31237 CACGTTTTT-TTATCTTTTCTA
1 CACGTTTTTCTT-TCTTTTCTA
31258 TCAGTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.14, C:0.19, G:0.07, T:0.60
Consensus pattern (22 bp):
CACGTTTTTCTTTCTTTTCTAA
Found at i:42377 original size:27 final size:27
Alignment explanation
Indices: 42317--42377 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
42307 AAGGAAGCAT
* *
42317 AAGAAAGAAAGGGAGAAGAGTGTCGAG
1 AAGAAAGAAAGGAAGAAGAGTGACGAG
*
42344 -AGAAAAGAAAGGAAGAAGAG-GAGGAAG
1 AAG-AAAGAAAGGAAGAAGAGTGACG-AG
42371 AAGAAAG
1 AAGAAAG
42378 GGAGTCCGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.14
27 22 0.79
28 2 0.07
ACGTcount: A:0.56, C:0.02, G:0.39, T:0.03
Consensus pattern (27 bp):
AAGAAAGAAAGGAAGAAGAGTGACGAG
Found at i:42479 original size:17 final size:17
Alignment explanation
Indices: 42457--42492 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
42447 TTATTAGTTT
42457 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
42474 GTTAGTTTAGGGTTAGG
1 GTTAGTTTAGGGTTAGG
42491 GT
1 GT
42493 AAAAAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.42, T:0.42
Consensus pattern (17 bp):
GTTAGTTTAGGGTTAGG
Found at i:42699 original size:30 final size:30
Alignment explanation
Indices: 42636--42735 Score: 141
Period size: 30 Copynumber: 3.4 Consensus size: 30
42626 TAATTAATTT
* * *
42636 TTTAGTAG-TGAA-TTATAATTAAAAAATAT
1 TTTATTAGTTGAAGTTAT-ATTAAAGAATAG
*
42665 TTTATTAGTTTAAGTTATATTAAAGAATAG
1 TTTATTAGTTGAAGTTATATTAAAGAATAG
42695 TTTATTAGTTGAAGTTATATTAAAGAATAG
1 TTTATTAGTTGAAGTTATATTAAAGAATAG
42725 TTTATTAGTTG
1 TTTATTAGTTG
42736 TTTAAAGAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
29 7 0.11
30 53 0.83
31 4 0.06
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (30 bp):
TTTATTAGTTGAAGTTATATTAAAGAATAG
Found at i:42730 original size:15 final size:16
Alignment explanation
Indices: 42677--42731 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
42667 TATTAGTTTA
42677 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
42693 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
42707 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
42723 AGTT-TATTA
1 AGTTATATTA
42732 GTTGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:42816 original size:15 final size:16
Alignment explanation
Indices: 42788--42821 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
42778 GTTTGTTACT
42788 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
42804 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
42819 TTA
1 TTA
42822 AATTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:43459 original size:49 final size:49
Alignment explanation
Indices: 43393--43726 Score: 398
Period size: 49 Copynumber: 6.3 Consensus size: 49
43383 CACAACTTTC
* *
43393 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
* *
43452 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAAT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
*
43512 CATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
43563 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
43612 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
43661 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCAAT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
43710 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
43727 AATTATTACT
Statistics
Matches: 269, Mismatches: 5, Indels: 11
0.94 0.02 0.04
Matches are distributed among these distances:
49 154 0.57
50 6 0.02
51 1 0.00
53 1 0.00
54 1 0.00
60 106 0.39
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:43462 original size:60 final size:60
Alignment explanation
Indices: 43391--43579 Score: 369
Period size: 60 Copynumber: 3.1 Consensus size: 60
43381 GGCACAACTT
43391 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
1 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
43451 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
1 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
*
43511 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATTATTACTAA
1 TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
43571 TCATTACTA
1 TCATTACTA
43580 TCAAATCATT
Statistics
Matches: 128, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
60 128 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (60 bp):
TCATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAA
Found at i:43548 original size:21 final size:20
Alignment explanation
Indices: 43398--43548 Score: 80
Period size: 21 Copynumber: 7.5 Consensus size: 20
43388 CTTTCATTAC
43398 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
* *
43420 TAAATATTAATAACAAT--T
1 TAAATATTACTATCAATCAT
* * * *
43438 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
43458 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
* *
43480 TAAATATTAATAACAAT--T
1 TAAATATTACTATCAATCAT
* * * *
43498 TCATTATTACTAATC-ATTAC
1 TAAATATTACT-ATCAATCAT
43518 TAAATCATTACTATCAAATCAT
1 TAAAT-ATTACTATC-AATCAT
43540 TAAATATTA
1 TAAATATTA
43549 ATAATAATTT
Statistics
Matches: 95, Mismatches: 22, Indels: 25
0.67 0.15 0.18
Matches are distributed among these distances:
18 22 0.23
19 4 0.04
20 18 0.19
21 30 0.32
22 21 0.22
ACGTcount: A:0.46, C:0.15, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATTACTATCAATCAT
Found at i:43626 original size:98 final size:103
Alignment explanation
Indices: 43453--43783 Score: 447
Period size: 109 Copynumber: 3.1 Consensus size: 103
43443 ATTACTAATC
* * *
43453 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAACAATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAAGTTC---A--ACT-ATCATTAC
43518 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
59 TAAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
43563 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTC-A-T-T-ATTACT-AATCA
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTCAACTATCATTACTAAATCA
*
43623 TTACTATCAAATCATTAAAAATTAATAATAATTTCATT
66 TTACTATCAAATCATTAAATATTAATAATAATTTCATT
*
43661 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCAATATTACTAATCATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTC---A--ACT-ATCATTACT
* *
43726 AAATTATTACTATCAAATCATTAAATATTAATAATAATTTCATC
60 AAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
43770 ATTACTAATCATTA
1 ATTACTAATCATTA
43784 TTAAATCTTA
Statistics
Matches: 202, Mismatches: 8, Indels: 23
0.87 0.03 0.10
Matches are distributed among these distances:
98 87 0.43
99 6 0.03
100 1 0.00
102 1 0.00
103 1 0.00
104 1 0.00
105 1 0.00
107 1 0.00
108 6 0.03
109 91 0.45
110 6 0.03
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.40
Consensus pattern (103 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAAGTTCAACTATCATTACTAAATCA
TTACTATCAAATCATTAAATATTAATAATAATTTCATT
Found at i:43738 original size:60 final size:60
Alignment explanation
Indices: 43661--43790 Score: 210
Period size: 60 Copynumber: 2.2 Consensus size: 60
43651 TAATTTCATT
43661 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCAAT-ATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTC-ATCATTACTAATC
* *
43720 ATTACTAAATTATTACTATCAAATCATTAAATATTAATAATAATTTCATCATTACTAATC
1 ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATC
*
43780 ATTATTAAATC
1 ATTACTAAATC
43791 TTATAAATAC
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
59 8 0.12
60 57 0.88
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATCATTACTAATC
Found at i:43754 original size:21 final size:20
Alignment explanation
Indices: 43671--43755 Score: 52
Period size: 21 Copynumber: 4.2 Consensus size: 20
43661 ATTACTAATC
*
43671 ATTACTATCAAATCATTAAAA
1 ATTACTATC-AATCATTAAAT
* *
43692 ATTA--AT-AATAATTTCAAT
1 ATTACTATCAATCA-TTAAAT
* *
43710 ATTACTAATC-ATTACTAAATT
1 ATTACT-ATCAATCATTAAA-T
43731 ATTACTATCAAATCATTAAAT
1 ATTACTATC-AATCATTAAAT
43752 ATTA
1 ATTA
43756 ATAATAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
17 4 0.08
18 8 0.17
19 2 0.04
20 6 0.12
21 21 0.44
22 7 0.15
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTACTATCAATCATTAAAT
Found at i:46984 original size:21 final size:21
Alignment explanation
Indices: 46959--47003 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
46949 ACATATAATA
*
46959 TAAATTAA-ACAAAATATTTT
1 TAAAATAACACAAAATATTTT
*
46979 TAAAATAACACTAAATATTTT
1 TAAAATAACACAAAATATTTT
47000 TAAA
1 TAAA
47004 CACAATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATAACACAAAATATTTT
Found at i:47337 original size:28 final size:30
Alignment explanation
Indices: 47296--47357 Score: 110
Period size: 28 Copynumber: 2.1 Consensus size: 30
47286 ATTTTTTATA
47296 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
47326 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
47354 TAAT
1 TAAT
47358 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 25 0.78
29 1 0.03
30 6 0.19
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:47814 original size:23 final size:23
Alignment explanation
Indices: 47781--47824 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
47771 GCTTGGCTAC
*
47781 AATCTCTCAGCTATGGATGCAGG
1 AATCTCCCAGCTATGGATGCAGG
47804 AATCTCCCAGCTATGGATGCA
1 AATCTCCCAGCTATGGATGCA
47825 ACCCATGCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (23 bp):
AATCTCCCAGCTATGGATGCAGG
Found at i:47839 original size:32 final size:32
Alignment explanation
Indices: 47797--47900 Score: 136
Period size: 32 Copynumber: 3.2 Consensus size: 32
47787 TCAGCTATGG
*
47797 ATGCAGGAATCTCCCAGCTATGGATGCAACCC
1 ATGCACGAATCTCCCAGCTATGGATGCAACCC
*
47829 ATGCACGAATCTCCTAGCTATGGATGCAACCC
1 ATGCACGAATCTCCCAGCTATGGATGCAACCC
* *****
47861 ATGAACGAGGGAGCCAGCTATGGATGCAACCC
1 ATGCACGAATCTCCCAGCTATGGATGCAACCC
47893 ATGCACGA
1 ATGCACGA
47901 GGGAGCAGGC
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.30, C:0.29, G:0.24, T:0.17
Consensus pattern (32 bp):
ATGCACGAATCTCCCAGCTATGGATGCAACCC
Found at i:50009 original size:2 final size:2
Alignment explanation
Indices: 50002--50039 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
49992 ATAATTTTTA
*
50002 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50040 GCTTATCATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50010 original size:16 final size:15
Alignment explanation
Indices: 49975--50008 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49965 ATATTCATGA
49975 ATATAATTTTTACAT
1 ATATAATTTTTACAT
*
49990 GTATAATTTTTA-AT
1 ATATAATTTTTACAT
50004 ATATA
1 ATATA
50009 TATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATAATTTTTACAT
Found at i:50102 original size:2 final size:2
Alignment explanation
Indices: 50091--50134 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
50081 AACAATTTGT
50091 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50132 TA T
1 TA T
50135 GAGGATTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:53639 original size:31 final size:32
Alignment explanation
Indices: 53585--53644 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
53575 TTGGTTCGAA
* *
53585 AAAATTGAAATTTTAGATGCTAAA-ACATACC
1 AAAATTGAAAGTTTAGATACTAAATACATACC
* *
53616 AAAATTGATAGTTTAGGTACTAAATACAT
1 AAAATTGAAAGTTTAGATACTAAATACAT
53645 TAAGCTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.32
Consensus pattern (32 bp):
AAAATTGAAAGTTTAGATACTAAATACATACC
Found at i:53694 original size:121 final size:121
Alignment explanation
Indices: 53501--53731 Score: 293
Period size: 121 Copynumber: 1.9 Consensus size: 121
53491 TTCCAAAACA
* * * * *
53501 GATAGTTTAGGTACTAAACGCGTTAAGTTTTTAAGGCGGGGTACTAAAATGAAATAAAAACTAAA
1 GATAGTTTAGGTACTAAACACATTAAGCTTTTAACGCGGGATACTAAAATGAAATAAAAACTAAA
*** * * * *
53566 TGTTAGGTATTG-GTTCGAAAAAATTGAAATTTTAGATGCTAAAACATACCAAAATT
66 CACTAGGTA-TGAGTTCGAAAAAATTAAAAATTTAAATACTAAAACATACCAAAATT
* * *
53622 GATAGTTTAGGTACTAAATACATTAAGCTTTTAACGTGGGATACTAAAATGAAATGAAAACTAAA
1 GATAGTTTAGGTACTAAACACATTAAGCTTTTAACGCGGGATACTAAAATGAAATAAAAACTAAA
* *
53687 CACTAGGTATGATTTTGAAAAAATTAAAAATTTAAATACTAAAAC
66 CACTAGGTATGAGTTCGAAAAAATTAAAAATTTAAATACTAAAAC
53732 TAATTAAAAC
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
120 2 0.02
121 90 0.98
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (121 bp):
GATAGTTTAGGTACTAAACACATTAAGCTTTTAACGCGGGATACTAAAATGAAATAAAAACTAAA
CACTAGGTATGAGTTCGAAAAAATTAAAAATTTAAATACTAAAACATACCAAAATT
Found at i:55493 original size:16 final size:16
Alignment explanation
Indices: 55469--55512 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
55459 TTGACTAGTT
* *
55469 CATAGATATCTATATA
1 CATACATATATATATA
55485 CATACATATATATATA
1 CATACATATATATATA
* *
55501 TATATATATATA
1 CATACATATATA
55513 CACACATTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (16 bp):
CATACATATATATATA
Found at i:55528 original size:2 final size:2
Alignment explanation
Indices: 55474--55512 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
55464 TAGTTCATAG
* * *
55474 AT AT CT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55513 CACACATTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:56924 original size:63 final size:64
Alignment explanation
Indices: 56822--56944 Score: 171
Period size: 63 Copynumber: 1.9 Consensus size: 64
56812 CTTCTTCTTC
** *
56822 TTGAATTTGAATGAATTGAATTGTGAGTATGGT-AAAAAAATGAATAATAT-AAGAATATTTTTT
1 TTGAATTTGAATGAAGCGAATTGTGAGTATGGTAAAAAAAAGGAATAAT-TGAAGAATATTTTTT
*
56885 TTGAATTTGAATGAAGCGAATTGT-AGGTATGGTATAAAAAAGGAATAATTGAAGAATATT
1 TTGAATTTGAATGAAGCGAATTGTGA-GTATGGTAAAAAAAAGGAATAATTGAAGAATATT
56945 AAATTAGGGA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
62 1 0.02
63 30 0.57
64 22 0.42
ACGTcount: A:0.43, C:0.01, G:0.20, T:0.36
Consensus pattern (64 bp):
TTGAATTTGAATGAAGCGAATTGTGAGTATGGTAAAAAAAAGGAATAATTGAAGAATATTTTTT
Found at i:57795 original size:20 final size:20
Alignment explanation
Indices: 57770--57824 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
57760 ATTTTCCTCG
*
57770 AGGGATCAATCCTTTTGTCA
1 AGGGATCGATCCTTTTGTCA
* *
57790 AGGGATCGATCATTTTGTTA
1 AGGGATCGATCCTTTTGTCA
57810 AGGGATCGATCCTTT
1 AGGGATCGATCCTTT
57825 GAGCCAGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (20 bp):
AGGGATCGATCCTTTTGTCA
Found at i:57885 original size:21 final size:21
Alignment explanation
Indices: 57861--57901 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
57851 TTTAAAGCGC
*
57861 GAAAACGATCGAGTAAGTTTT
1 GAAAACGATCGACTAAGTTTT
* *
57882 GAAAAGGTTCGACTAAGTTT
1 GAAAACGATCGACTAAGTTT
57902 AAAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (21 bp):
GAAAACGATCGACTAAGTTTT
Found at i:63789 original size:4 final size:4
Alignment explanation
Indices: 63782--63814 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
63772 ATTGACACAC
63782 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
63815 ACTCTTTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:63797 original size:106 final size:110
Alignment explanation
Indices: 63512--63897 Score: 392
Period size: 115 Copynumber: 3.4 Consensus size: 110
63502 CATACATACA
*
63512 TGAGGGTGCTCTTGGTAGACAAAGGGAGCTTCAAAAATTCATTGACACACACACACATACATACA
1 TGAGGGTGCTCTTGGTAAACAAAGGGAGCTTCAAAAATTCATTG----ACACACACATACATACA
* *
63577 TGCATGCATAACTCTTTTGTTTGCCATCTATCTTTCCATATGCAGGCACT
62 TACATGCATAACTCTTTTGTTTGCCATC-ATCTTTCCACATGCAGGCACT
* **
63627 TGAGGGTGCTCTTGGTAAACAAAGGGAGTTTCAAAAATTCATTG--ACATTCATACATACATTAC
1 TGAGGGTGCTCTTGGTAAACAAAGGGAGCTTCAAAAATTCATTGACACACACATACATACA-TAC
63690 ATGCATAACTCTTTTGTTTGCCATC-T-TTT-CACATGCAGGCACT
65 ATGCATAACTCTTTTGTTTGCCATCATCTTTCCACATGCAGGCACT
** * *
63733 TGAGGGTGCTCTTTTTAAACAAA-GAAGCTTCAAAATTTCATTGACACACACATACATACATACA
1 TGAGGGTGCTCTTGGTAAACAAAGGGAGCTTCAAAAATTCATTGACACACACATACATACATACA
* * * * *
63797 TACATACATACATACATAACTCT-TTTG-CTTGCTATCTTTCCATATGTAGGCACT
66 TGCAT--A-AC-T-C-T---TTTGTTTGCCAT-C-ATCTTTCCACATGCAGGCACT
* * * *
63851 TAAGGATGCTCTTGGTAAACAAAGGGAGCTTCAGAAATTCATCGACA
1 TGAGGGTGCTCTTGGTAAACAAAGGGAGCTTCAAAAATTCATTGACA
63898 GGAAAGAGAT
Statistics
Matches: 227, Mismatches: 26, Indels: 32
0.80 0.09 0.11
Matches are distributed among these distances:
105 17 0.07
106 42 0.19
107 16 0.07
108 2 0.01
109 15 0.07
110 28 0.12
111 1 0.00
112 1 0.00
113 2 0.01
114 5 0.02
115 44 0.19
116 1 0.00
117 3 0.01
118 31 0.14
119 19 0.08
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (110 bp):
TGAGGGTGCTCTTGGTAAACAAAGGGAGCTTCAAAAATTCATTGACACACACATACATACATACA
TGCATAACTCTTTTGTTTGCCATCATCTTTCCACATGCAGGCACT
Found at i:63820 original size:118 final size:120
Alignment explanation
Indices: 63671--63897 Score: 307
Period size: 118 Copynumber: 1.9 Consensus size: 120
63661 AAATTCATTG
* * * * *
63671 ACATTCATACATACATTACATGCATAACTCTTTTGTTTGCCATCTTTTCACATGCAGGCACTTGA
1 ACATACATACATACATTACATACATAACTCTTTTGCTTGCCATCTTTCCACATGCAGGCACTTAA
* ** *
63736 GGGTGCTCTTTTTAAACAAA-GAAGCTTCA-AAATTTCATTGACACACACATACAT
66 GGATGCTCTTGGTAAACAAAGGAAGCTTCAGAAA-TTCATCGACACACACATACAT
* * *
63790 ACATACATACATACA-TACATACATAACTCTTTTGCTTGCTATCTTTCCATATGTAGGCACTTAA
1 ACATACATACATACATTACATACATAACTCTTTTGCTTGCCATCTTTCCACATGCAGGCACTTAA
*
63854 GGATGCTCTTGGTAAACAAAGGGAGCTTCAGAAATTCATCGACA
66 GGATGCTCTTGGTAAACAAAGGAAGCTTCAGAAATTCATCGACA
63898 GGAAAGAGAT
Statistics
Matches: 93, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
118 59 0.63
119 31 0.33
120 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (120 bp):
ACATACATACATACATTACATACATAACTCTTTTGCTTGCCATCTTTCCACATGCAGGCACTTAA
GGATGCTCTTGGTAAACAAAGGAAGCTTCAGAAATTCATCGACACACACATACAT
Found at i:67237 original size:12 final size:12
Alignment explanation
Indices: 67220--67245 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
67210 CATCAAGTGC
67220 GTGCGTGCGTGT
1 GTGCGTGCGTGT
67232 GTGCGTGCGTGT
1 GTGCGTGCGTGT
67244 GT
1 GT
67246 TGCAGTATCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (12 bp):
GTGCGTGCGTGT
Found at i:69563 original size:21 final size:21
Alignment explanation
Indices: 69537--69585 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
69527 CACATCAAAT
69537 CGTCCCCAAATAAACTTTGAC
1 CGTCCCCAAATAAACTTTGAC
*
69558 CGTCCCCAAGTAAACTTTGAC
1 CGTCCCCAAATAAACTTTGAC
*
69579 CATCCCC
1 CGTCCCC
69586 GAATTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.39, G:0.10, T:0.22
Consensus pattern (21 bp):
CGTCCCCAAATAAACTTTGAC
Found at i:72865 original size:41 final size:41
Alignment explanation
Indices: 72798--72912 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 41
72788 GCTAAAACTC
* *
72798 GTACTTTAGTGGCGTTTATACGACAAACGCCGCTAAAG-ATAA
1 GTACTTTAGTGGCGTTTATA-AACAAACGCCGCCAAAGAAT-A
* * * * *
72840 GTACTTTAGTAGCGTTTGTAAACAAACGCCACCATAGAATC
1 GTACTTTAGTGGCGTTTATAAACAAACGCCGCCAAAGAATA
* *
72881 GTTCTTTAGTGGCGTTTTTAAACAAACGCCGC
1 GTACTTTAGTGGCGTTTATAAACAAACGCCGC
72913 AATAGGGTAC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 41 0.67
42 20 0.33
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (41 bp):
GTACTTTAGTGGCGTTTATAAACAAACGCCGCCAAAGAATA
Found at i:72979 original size:42 final size:41
Alignment explanation
Indices: 72933--73059 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 41
72923 ATATATCGTT
* *
72933 GCGTTTTTTAAATAAACGCCGCTAAACCCAAATACTTTAGTG
1 GCGTTTTTTAAA-AAACGCCGCTAAAACCTAATACTTTAGTG
* *
72975 GCGTTTTATTCAAAAACGCCGCTAAATA-CTCATACTTTAGTG
1 GCGTTTT-TTAAAAAACGCCGCTAAA-ACCTAATACTTTAGTG
* * * * *
73017 ACG-ATTTTAGACAAACGCCGCTAAAACCTAGTACTTTATTG
1 GCGTTTTTTA-AAAAACGCCGCTAAAACCTAATACTTTAGTG
73058 GC
1 GC
73060 ATTTACCCAT
Statistics
Matches: 69, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
40 3 0.04
41 28 0.41
42 34 0.49
43 4 0.06
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (41 bp):
GCGTTTTTTAAAAAACGCCGCTAAAACCTAATACTTTAGTG
Found at i:75624 original size:43 final size:43
Alignment explanation
Indices: 75571--75858 Score: 382
Period size: 43 Copynumber: 6.7 Consensus size: 43
75561 GTTTGTATAG
* *
75571 AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
75614 AAAAACGCCGCTATAGATCT-AACCTTTTGCGGCATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
75656 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
75699 AAAAACGCCGCTATAGATCT-GACCTTTTACGGCATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* ** * *
75741 AAAAACGCCACTATAAATCTTTACCTTTAGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* * ** *
75784 AAAAGCGCCGCTATAGATCTCGACCTTTTGCGGTGTTTGTTCA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* *
75827 AAAAACGCCGCTATATATCTCGACTTTTTGCG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCG
75859 TTTTTGTTCT
Statistics
Matches: 214, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
42 75 0.35
43 139 0.65
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (43 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
Found at i:75706 original size:85 final size:85
Alignment explanation
Indices: 75571--75880 Score: 412
Period size: 85 Copynumber: 3.7 Consensus size: 85
75561 GTTTGTATAG
* * *
75571 AAAAACGCCGCTATAAATCTCGACCTTTTGC-AGCATTTGTTCAAAAAACGCCGCTATAGATCTA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGA-CTTTTGTTCCAAAAACGCCGCTATAGATCTG
75635 ACCTTTTGCGGCATTTGTTCC
65 ACCTTTTGCGGCATTTGTTCC
75656 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTGA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTGA
*
75721 CCTTTTACGGCATTTGTTCC
66 CCTTTTGCGGCATTTGTTCC
* ** * * * *
75741 AAAAACGCCACTATAAATCTTTACCTTTAGCGGCGTTTGTTCCAAAAGCGCCGCTATAGATCTCG
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCT-G
** *
75806 ACCTTTTGCGGTGTTTGTTCA
65 ACCTTTTGCGGCATTTGTTCC
* * *
75827 AAAAACGCCGCTATATATCTCGACTTTTTGCG-TTTTTGTTCTC--AAACGCCGCTA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTC-CAAAAACGCCGCTA
75881 ACTTTAGCGG
Statistics
Matches: 198, Mismatches: 24, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
84 10 0.05
85 142 0.72
86 46 0.23
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (85 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCCAAAAACGCCGCTATAGATCTGA
CCTTTTGCGGCATTTGTTCC
Found at i:75867 original size:128 final size:128
Alignment explanation
Indices: 75571--75857 Score: 407
Period size: 128 Copynumber: 2.2 Consensus size: 128
75561 GTTTGTATAG
* * *
75571 AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCAAAAAACGCCGCTATAGATCTAA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCCAAAAACGCCACTATAAATCTAA
* *
75636 CCTTTTGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCC
66 CCTTTAGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCA
* * * *
75699 AAAAACGCCGCTATAGATCT-GACCTTTTACGGCATTTGTTCCAAAAACGCCACTATAAATCTTT
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCCAAAAACGCCACTATAAATC-TA
* * * *
75763 ACCTTTAGCGGCGTTTGTTCCAAAAGCGCCGCTATAGATCTCGACCTTTTGCG-GTGTTTGTTCA
65 ACCTTTAGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGACT-TTTGTTCA
* *
75827 AAAAACGCCGCTATATATCTCGACTTTTTGC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGC
75858 GTTTTTGTTC
Statistics
Matches: 140, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
127 37 0.26
128 95 0.68
129 8 0.06
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (128 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCAGCATTTGTTCCAAAAACGCCACTATAAATCTAA
CCTTTAGCGGCATTTGTTCCAAAAACGCCGCTATAAATCTCGACCTTTTGCGACTTTTGTTCA
Found at i:80665 original size:6 final size:6
Alignment explanation
Indices: 80654--80711 Score: 98
Period size: 6 Copynumber: 9.7 Consensus size: 6
80644 TTTTTATATC
*
80654 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTCTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
*
80702 ATTTAA TTTT
1 TTTTAA TTTT
80712 TAAATATCCA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTAA
Found at i:82294 original size:15 final size:15
Alignment explanation
Indices: 82274--82310 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
82264 ATATTTAGCT
*
82274 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
82289 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
82304 GGGCGGG
1 GGGCGGG
82311 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:83695 original size:30 final size:31
Alignment explanation
Indices: 83651--83734 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 31
83641 GTACTGAAAT
* *
83651 AAAATAA-AAATTAAACATT-AAATATGATTTA
1 AAAATAATAATTTAAATATTAAAATA-GA-TTA
83682 AAAA-AAT-ATTTAAATATTAAAATAGATTA
1 AAAATAATAATTTAAATATTAAAATAGATTA
83711 AAAATTAATAATTTAAATATTAAA
1 AAAA-TAATAATTTAAATATTAAA
83735 GTTATATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
29 7 0.15
30 13 0.28
31 12 0.26
32 14 0.30
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (31 bp):
AAAATAATAATTTAAATATTAAAATAGATTA
Found at i:84827 original size:2 final size:2
Alignment explanation
Indices: 84820--84881 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
84810 ACAATGAATG
84820 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
84862 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
84882 CAATGTATGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85554 original size:27 final size:28
Alignment explanation
Indices: 85524--85579 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
85514 TTTTAGTATC
* *
85524 TAGTATTTAA-ATTTTAGTCTAAAATTT
1 TAGTATGTAATATTTTAATCTAAAATTT
*
85551 TAGTATGTAATATTTTAATCTAAATTTT
1 TAGTATGTAATATTTTAATCTAAAATTT
85579 T
1 T
85580 GGTTTGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.36, C:0.04, G:0.07, T:0.54
Consensus pattern (28 bp):
TAGTATGTAATATTTTAATCTAAAATTT
Found at i:86914 original size:24 final size:23
Alignment explanation
Indices: 86886--86932 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
86876 TGGAATGATT
86886 ATTTATTTATTTAT-TATATCTTAA
1 ATTTATTT-TTTATATATAT-TTAA
86910 ATTTATTTTTTATATATATTTAA
1 ATTTATTTTTTATATATATTTAA
86933 CGATCGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (23 bp):
ATTTATTTTTTATATATATTTAA
Done.