Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005163.1 Hibiscus syriacus cultivar Beakdansim tig00011647_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: 89611
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:2342 original size:21 final size:20
Alignment explanation
Indices: 2316--2357 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2306 ATTTCTGGGC
* *
2316 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCC-TTCA
2337 AGGGGAACCGATACCCTTCA
1 AGGGGAACCGATACCCTTCA
2357 A
1 A
2358 CGAACAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.31, C:0.26, G:0.26, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCTTCA
Found at i:3311 original size:61 final size:61
Alignment explanation
Indices: 3186--3325 Score: 212
Period size: 61 Copynumber: 2.3 Consensus size: 61
3176 GGTCGAGGGT
* * *
3186 TTACCTATGTTCTTCGG-ACATATGGACTGTTTACCTATGTTCTCGGGACATATGAACTGT
1 TTACCTATGTTCTTCGGAACATAGGGACTGTTTACCTATGTCCTCGGGACATATGAACTGA
*
3246 TTACCTATGTTCTTCGGAACATAGGGAC-GTTTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATAGGGACTGTTTACCTATGTCC-TCGGGACATATGAACTGA
*
3307 TTACCTAGGTTCTTCGGAA
1 TTACCTATGTTCTTCGGAA
3326 TCTATGGACT
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 30 0.41
61 43 0.59
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (61 bp):
TTACCTATGTTCTTCGGAACATAGGGACTGTTTACCTATGTCCTCGGGACATATGAACTGA
Found at i:3322 original size:31 final size:31
Alignment explanation
Indices: 3184--3336 Score: 206
Period size: 30 Copynumber: 5.0 Consensus size: 31
3174 AGGGTCGAGG
3184 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3214 GTTTACCTATGTTC-TCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
3244 GTTTACCTATGTTCTTCGGAACATAGGGAC-
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
3274 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
3305 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
3336 G
1 G
3337 GTCCTTCGGG
Statistics
Matches: 108, Mismatches: 11, Indels: 7
0.86 0.09 0.06
Matches are distributed among these distances:
29 2 0.02
30 67 0.62
31 38 0.35
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:6294 original size:21 final size:21
Alignment explanation
Indices: 6268--6312 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
6258 GATTTCTGGG
* *
6268 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
6289 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
6310 CAA
1 CAA
6313 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:6960 original size:23 final size:24
Alignment explanation
Indices: 6917--6963 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
6907 ATATGGCATG
*
6917 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
6941 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
6964 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:7179 original size:31 final size:31
Alignment explanation
Indices: 7141--7296 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
7131 AGGGTCAAGG
7141 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
7172 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
7203 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
7234 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
7265 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
7296 G
1 G
7297 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:9902 original size:64 final size:64
Alignment explanation
Indices: 9814--9974 Score: 164
Period size: 64 Copynumber: 2.5 Consensus size: 64
9804 CCCTTGATGG
* * * **
9814 GTGCATCGATGTACTA-TCTATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAGGG
1 GTGCATCGATGCACTACT-TGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAAAG
*
9877 C
64 A
* * ** *
9878 GTTCATCGATGCACTACTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAAGA
1 GTGCATCGATGCACTACTTGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAAGA
* * *
9942 GTGCATCGATACACTTCATGTGCATCGATACAC
1 GTGCATCGATGCACTACTTGTGCATCGATACAC
9975 CTTGAATAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
64 78 0.98
65 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
GTGCATCGATGCACTACTTGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAAGA
Found at i:15183 original size:18 final size:18
Alignment explanation
Indices: 15151--15185 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
15141 TCAAAATTAA
15151 ATATTATTTTAAATAATT
1 ATATTATTTTAAATAATT
15169 ATATT-TTTTACAATAAT
1 ATATTATTTTA-AATAAT
15186 AACGTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATTATTTTAAATAATT
Found at i:17022 original size:20 final size:20
Alignment explanation
Indices: 16997--17036 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
16987 GCAGCGCTGG
16997 TCTTATTGCCATTCTATAAA
1 TCTTATTGCCATTCTATAAA
17017 TCTTATTGCCATTCTATAAA
1 TCTTATTGCCATTCTATAAA
17037 ATTTCCCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.05, T:0.45
Consensus pattern (20 bp):
TCTTATTGCCATTCTATAAA
Found at i:17475 original size:15 final size:15
Alignment explanation
Indices: 17434--17475 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
17424 TAACCATCAC
*
17434 TAAAAAGTCATCCTCT
1 TAAAAA-TCATTCTCT
17450 TAAAAATCATTCTCT
1 TAAAAATCATTCTCT
17465 TAAAAATCATT
1 TAAAAATCATT
17476 TATTATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAAAATCATTCTCT
Found at i:17485 original size:15 final size:15
Alignment explanation
Indices: 17434--17486 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
17424 TAACCATCAC
* *
17434 TAAAAAGTCATCCTCT
1 TAAAAA-TCATTCTAT
*
17450 TAAAAATCATTCTCT
1 TAAAAATCATTCTAT
17465 TAAAAATCATT-TAT
1 TAAAAATCATTCTAT
17479 TATAAAAT
1 TA-AAAAT
17487 GTTATAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
14 4 0.12
15 24 0.71
16 6 0.18
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.38
Consensus pattern (15 bp):
TAAAAATCATTCTAT
Found at i:27740 original size:2 final size:2
Alignment explanation
Indices: 27735--27790 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
27725 AGGGTTGAGA
27735 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
27777 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
27791 GATGTCATTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28705 original size:19 final size:17
Alignment explanation
Indices: 28664--28707 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28654 AGCTAAGTCC
28664 TTTTCTCTTTACATTTT
1 TTTTCTCTTTACATTTT
* *
28681 TGTTCTCTTTTCATCTTT
1 TTTTCTCTTTACAT-TTT
28699 TATTTCTCT
1 T-TTTCTCT
28708 CTCTCTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 12 0.55
18 4 0.18
19 6 0.27
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.68
Consensus pattern (17 bp):
TTTTCTCTTTACATTTT
Found at i:28777 original size:16 final size:16
Alignment explanation
Indices: 28756--28790 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
28746 CTTTTTTCTA
*
28756 TTCGAATGGGATCCTT
1 TTCGAATCGGATCCTT
*
28772 TTCGAATCTGATCCTT
1 TTCGAATCGGATCCTT
28788 TTC
1 TTC
28791 TTTTTATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (16 bp):
TTCGAATCGGATCCTT
Found at i:29422 original size:3 final size:3
Alignment explanation
Indices: 29416--29456 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
29406 TAATAACGGA
29416 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29457 ACAATTAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33569 original size:269 final size:269
Alignment explanation
Indices: 33090--33627 Score: 1076
Period size: 269 Copynumber: 2.0 Consensus size: 269
33080 TTCTTCGCCA
33090 CACGATTAGTTCTTAATTTCGCAGGGATAGGGGGCACCACTGGGGTATCTTCCTTTAATTGAAAT
1 CACGATTAGTTCTTAATTTCGCAGGGATAGGGGGCACCACTGGGGTATCTTCCTTTAATTGAAAT
33155 GTGTCAGTAGATGAACCATGAGAAGTAATGAGACCCATCATAAGAGCATCTTCCGAGTCCCTGAG
66 GTGTCAGTAGATGAACCATGAGAAGTAATGAGACCCATCATAAGAGCATCTTCCGAGTCCCTGAG
33220 GCTAACACCATCAAAATGATCAACTGATTTATTAGCTAGATGCTCTACGATATTTAATTTTGAAT
131 GCTAACACCATCAAAATGATCAACTGATTTATTAGCTAGATGCTCTACGATATTTAATTTTGAAT
33285 GATCCACAGCCTCCATTGTGTGCAACCCCAATTTGTTACTCGGTTTCTCATCGCTTTTGACACTC
196 GATCCACAGCCTCCATTGTGTGCAACCCCAATTTGTTACTCGGTTTCTCATCGCTTTTGACACTC
33350 TTTGTGAGT
261 TTTGTGAGT
33359 CACGATTAGTTCTTAATTTCGCAGGGATAGGGGGCACCACTGGGGTATCTTCCTTTAATTGAAAT
1 CACGATTAGTTCTTAATTTCGCAGGGATAGGGGGCACCACTGGGGTATCTTCCTTTAATTGAAAT
33424 GTGTCAGTAGATGAACCATGAGAAGTAATGAGACCCATCATAAGAGCATCTTCCGAGTCCCTGAG
66 GTGTCAGTAGATGAACCATGAGAAGTAATGAGACCCATCATAAGAGCATCTTCCGAGTCCCTGAG
33489 GCTAACACCATCAAAATGATCAACTGATTTATTAGCTAGATGCTCTACGATATTTAATTTTGAAT
131 GCTAACACCATCAAAATGATCAACTGATTTATTAGCTAGATGCTCTACGATATTTAATTTTGAAT
33554 GATCCACAGCCTCCATTGTGTGCAACCCCAATTTGTTACTCGGTTTCTCATCGCTTTTGACACTC
196 GATCCACAGCCTCCATTGTGTGCAACCCCAATTTGTTACTCGGTTTCTCATCGCTTTTGACACTC
33619 TTTGTGAGT
261 TTTGTGAGT
33628 GAAACCTTTT
Statistics
Matches: 269, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
269 269 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (269 bp):
CACGATTAGTTCTTAATTTCGCAGGGATAGGGGGCACCACTGGGGTATCTTCCTTTAATTGAAAT
GTGTCAGTAGATGAACCATGAGAAGTAATGAGACCCATCATAAGAGCATCTTCCGAGTCCCTGAG
GCTAACACCATCAAAATGATCAACTGATTTATTAGCTAGATGCTCTACGATATTTAATTTTGAAT
GATCCACAGCCTCCATTGTGTGCAACCCCAATTTGTTACTCGGTTTCTCATCGCTTTTGACACTC
TTTGTGAGT
Found at i:38612 original size:2 final size:2
Alignment explanation
Indices: 38607--38634 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38597 TTTACTCTTA
38607 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
38635 GAAATAAAGG
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:39052 original size:21 final size:22
Alignment explanation
Indices: 39005--39065 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
38995 TAAATTAAGA
*
39005 TTTATGGTTTACAGG-TTATGAG
1 TTTATAGTTTA-AGGTTTATGAG
*
39027 ATTATAGTTTAAGGTTTAT-AG
1 TTTATAGTTTAAGGTTTATGAG
* *
39048 TTTATAATTTAGGGTTTA
1 TTTATAGTTTAAGGTTTA
39066 GGGTTAGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.28, C:0.02, G:0.21, T:0.49
Consensus pattern (22 bp):
TTTATAGTTTAAGGTTTATGAG
Found at i:43034 original size:21 final size:21
Alignment explanation
Indices: 43009--43054 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
42999 CTGAAAATAT
*
43009 TAAAAATATTAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
43030 TAAAAATAATAATATTTTAAA
1 TAAAAATAATAATATTTTAAA
43051 TAAA
1 TAAA
43055 TTTTTATCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TAAAAATAATAATATTTTAAA
Found at i:43743 original size:14 final size:15
Alignment explanation
Indices: 43726--43758 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
43716 AATAATTTTT
43726 TTATATAAATTAA-A
1 TTATATAAATTAATA
43740 TTAT-TAAATTAATA
1 TTATATAAATTAATA
43754 TTATA
1 TTATA
43759 AGTGGAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTATATAAATTAATA
Found at i:43957 original size:21 final size:23
Alignment explanation
Indices: 43933--43987 Score: 69
Period size: 25 Copynumber: 2.4 Consensus size: 23
43923 ATATTATTAT
43933 GTATCGATA-TAT-TTTTATAAA
1 GTATCGATATTATCTTTTATAAA
*
43954 GTATCGATACATTTTCTTTTATAAA
1 GTATCGAT--ATTATCTTTTATAAA
43979 GTATCGATA
1 GTATCGATA
43988 CTTTATAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 8 0.28
23 2 0.07
24 2 0.07
25 17 0.59
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (23 bp):
GTATCGATATTATCTTTTATAAA
Found at i:44180 original size:73 final size:74
Alignment explanation
Indices: 44073--44844 Score: 1040
Period size: 73 Copynumber: 10.5 Consensus size: 74
44063 CAACATATCT
*
44073 GGTAGGTAGTTTAATGTAATAGGTAGTGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
*
44137 AAAAAAATC
66 AAAAAAACC
* * * *
44146 GGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTTACAGTGTACATTATTAGCAACCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
44211 -AAAAAACC
66 AAAAAAACC
* * * *
44219 GGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTACCGTTTACATTATTAACAGCCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
**
44284 AAAAAAATT
66 AAAAAAACC
*
44293 GGTAGGTAGTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTT-
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
**
44357 AAAAAAAAA
66 AAAAAAACC
* * *
44366 AGTAGGTATTTTAATGTAATAGGTAGCGCCTATATTTTTTTTTTACCGTTTACATTATTAACAAC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCC--TA--TTTTTTTTACCGTTTACATTATTAGCAAC
*
44431 CTTCAAAAAAATC
62 CTTCAAAAAAACC
* ** *
44444 GGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATTATTAATAATCTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAGCAACCTT
* *
44509 TAAACAAACC
65 CAAAAAAACC
* * *
44519 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA--TTTTTTACTGTTTATATTATTAGCAACCTTA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
44582 AAAAAAACC
66 AAAAAAACC
* * * * *
44591 GATAGGTAGTTTAATGTAATAGGTAGCGCATATTTTTTTTACCGTTTACTTTATTAGTAACCCT-
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
44655 AAAAAAACC
66 AAAAAAACC
* * * ** * *
44664 GATAGATAGTTTAATATAATAGGTAAAGACTA-TTTTTTTACCGTTTACATTATTAGCAACCTTA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
44728 AAAAAAACC
66 AAAAAAACC
*
44737 GGTAGGTAGTTTAATGTAATAGGTAGCGCC--TTTTTTTTACCGTTTACATTATTAGCAACCTTA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
44800 AAAAAAACC
66 AAAAAAACC
* * *
44809 GATAGGTATTTTAATATAATAGGTAGCGCCTATTTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT
44845 ATATTTCCAG
Statistics
Matches: 619, Mismatches: 66, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
72 157 0.25
73 199 0.32
74 128 0.21
75 66 0.11
76 2 0.00
77 31 0.05
78 36 0.06
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (74 bp):
GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGCAACCTTC
AAAAAAACC
Found at i:44328 original size:147 final size:146
Alignment explanation
Indices: 44073--44844 Score: 1064
Period size: 147 Copynumber: 5.2 Consensus size: 146
44063 CAACATATCT
*
44073 GGTAGGTAGTTTAATGTAATAGGTAGTGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
* * * *
44138 AAAAAATCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTTACAGTGTACATTATTAG
66 AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
*
44203 CAACCTTCAAAAAACC
131 CAACCTTAAAAAAACC
* * * *
44219 GGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTACCGTTTACATTATTAACAGCCTTC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACCGTTTACATTATTAGCAACCTTC
* *
44284 AAAAAAATTGGTAGGTAGTTTAATGTAATAGATAGCGCCTATTTTTTTTACCGTTTACATTATTA
65 AAAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
**
44349 GCAACCTTAAAAAAAAA
130 GCAACCTTAAAAAAACC
* * *
44366 AGTAGGTATTTTAATGTAATAGGTAGCGCCTATATTTTTTTTTTACCGTTTACATTATTAACAAC
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCC--TA---TTTTTTTACCGTTTACATTATTAGCAAC
*
44431 CTTCAAAAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACAT
61 CTTCAAAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACAT
** * *
44496 TATTAATAATCTTTAAACAAACC
125 TATTAGCAA-CCTTAAAAAAACC
* * *
44519 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTA-TTTTTTACTGTTTATATTATTAGCAACCTTAA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
* * * *
44583 AAAAAACCGATAGGTAGTTTAATGTAATAGGTAGCGCATATTTTTTTTACCGTTTACTTTATTAG
66 AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
* *
44648 TAACCCTAAAAAAACC
131 CAACCTTAAAAAAACC
* * * ** * *
44664 GATAGATAGTTTAATATAATAGGTAAAGACTATTTTTTTACCGTTTACATTATTAGCAACCTTAA
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
*
44729 AAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCC--TTTTTTTTACCGTTTACATTATTAG
66 AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
44792 CAACCTTAAAAAAAACC
131 CAACCTT-AAAAAAACC
* * *
44809 GATAGGTATTTTAATATAATAGGTAGCGCCTATTTT
1 GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTT
44845 ATATTTCCAG
Statistics
Matches: 558, Mismatches: 59, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
144 29 0.05
145 76 0.14
146 117 0.21
147 199 0.36
149 2 0.00
151 76 0.14
152 22 0.04
153 37 0.07
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (146 bp):
GGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
AAAAAATCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
CAACCTTAAAAAAACC
Found at i:44647 original size:298 final size:290
Alignment explanation
Indices: 44074--44844 Score: 1078
Period size: 298 Copynumber: 2.6 Consensus size: 290
44064 AACATATCTG
*
44074 GTAGGTAGTTTAATGTAATAGGTAGTGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCAA
1 GTAGGTAGTTTAATGTAATAGGTAGAGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCAA
* * *
44139 AAAAATCGGTAGGTATTTTAATATAATAGGTAGCGCCTATTTTTTTTACAGTGTACATTATTAGC
66 AAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGC
* *
44204 AACCTTCAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGACTATTTTTTTTACCGTTTACA
131 AACCTTAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA--TTTTTTACCGTTTACA
* * ** * *
44269 TTATTAACAGCCTTCAAAAAAATTGGTAGGTAGTTTAATGTAATAGATAGCGCCTATTTTTTTTA
194 TTATTAACAACCTTAAAAAAAACCGATAGGTAGTTTAATGTAATAGATAGCGCATATTTTTTTTA
*
44334 CCGTTTACATTATTAGCAACCTTAAAAAAAAAA
259 CCGTTTACATTATTAGCAACCCT-AAAAAAAAA
* * *
44367 GTAGGTATTTTAATGTAATAGGTAGCGCCTATATTTTTTTTTTACCGTTTACATTATTAACAACC
1 GTAGGTAGTTTAATGTAATAGGTAGAGCC--TA---TTTTTTTACCGTTTACATTATTAGCAACC
44432 TTCAAAAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTATTTTACCGTTTACATT
61 TTCAAAAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATT
** * * * *
44497 ATTAATAATCTTTAAACAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCCTATTTTTTACTGT
125 ATTAGCAA-CCTTAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTACCGT
* * *
44562 TTATATTATTAGCAACCTTAAAAAAAACCGATAGGTAGTTTAATGTAATAGGTAGCGCATATTTT
189 TTACATTATTAACAACCTTAAAAAAAACCGATAGGTAGTTTAATGTAATAGATAGCGCATATTTT
* * **
44627 TTTTACCGTTTACTTTATTAGTAACCCTAAAAAAACC
254 TTTTACCGTTTACATTATTAGCAACCCTAAAAAAAAA
* * * * *
44664 GATAGATAGTTTAATATAATAGGTAAAGACTATTTTTTTACCGTTTACATTATTAGCAACCTTAA
1 G-TAGGTAGTTTAATGTAATAGGTAGAGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCA
* *
44729 AAAAAACCGGTAGGTAGTTTAATGTAATAGGTAGCGCC--TTTTTTTTACCGTTTACATTATTAG
65 AAAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAG
* *
44792 CAACCTTAAAAAAAACCGATAGGTATTTTAATATAATAGGTAGCGCCTATTTT
130 CAACCTT-AAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTT
44845 ATATTTCCAG
Statistics
Matches: 424, Mismatches: 45, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
289 3 0.01
290 63 0.15
291 4 0.01
293 94 0.22
295 2 0.00
296 2 0.00
297 8 0.02
298 188 0.44
299 20 0.05
300 40 0.09
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.39
Consensus pattern (290 bp):
GTAGGTAGTTTAATGTAATAGGTAGAGCCTATTTTTTTACCGTTTACATTATTAGCAACCTTCAA
AAAAATCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAGC
AACCTTAAAAAAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTACCGTTTACATT
ATTAACAACCTTAAAAAAAACCGATAGGTAGTTTAATGTAATAGATAGCGCATATTTTTTTTACC
GTTTACATTATTAGCAACCCTAAAAAAAAA
Found at i:45827 original size:21 final size:21
Alignment explanation
Indices: 45803--45844 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45793 TCTCCGAATC
*
45803 CGAGCATCATAATAGAATTTT
1 CGAGCAACATAATAGAATTTT
*
45824 CGAGCAACATAATCGAATTTT
1 CGAGCAACATAATAGAATTTT
45845 TTTTACCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (21 bp):
CGAGCAACATAATAGAATTTT
Found at i:47935 original size:3 final size:3
Alignment explanation
Indices: 47927--47976 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
47917 TTTTTACTCA
*
47927 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
47975 TA
1 TA
47977 AATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:49417 original size:13 final size:13
Alignment explanation
Indices: 49401--49447 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
49391 ATATAATAAA
49401 TAAATATTTATTT
1 TAAATATTTATTT
*
49414 TAAATAAATTATTT
1 TAAAT-ATTTATTT
49428 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
49441 TCAATAT
1 TAAATAT
49448 CAAAGAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:60784 original size:17 final size:16
Alignment explanation
Indices: 60764--60802 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
60754 ATGCTTGAAG
*
60764 AAAAAGTGAAGAAAAAA
1 AAAAAGAGAA-AAAAAA
*
60781 AAAAAGAGAAAAAAGA
1 AAAAAGAGAAAAAAAA
60797 AAAAAG
1 AAAAAG
60803 GGGAGTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAAGAGAAAAAAAA
Found at i:62077 original size:83 final size:83
Alignment explanation
Indices: 61938--62125 Score: 340
Period size: 83 Copynumber: 2.3 Consensus size: 83
61928 AAACATTAAC
*
61938 TAGAAGATGAATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
1 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
62003 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
62021 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAT
1 TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
62086 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
* *
62104 TGGAAGATGAATTTGCTCATAG
1 TAGAAGATGAATGTGCTCATAG
62126 TAGAAATAAG
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 101 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (83 bp):
TAGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGAC
AGAACCAATCATTGAATT
Found at i:63240 original size:116 final size:113
Alignment explanation
Indices: 62955--63828 Score: 1214
Period size: 116 Copynumber: 7.6 Consensus size: 113
62945 TTTCAGAGAA
* *
62955 AGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * * * * * *
63020 AACCTTTTACCTGAATTCATCAAATTGATGGATTAGCTTTTCCAGAGAAG
66 AATCTTTTGCTTGAATTCATC-ATTTGATGGATCAACATTGCCA-AGTAG
63070 -GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
63134 AATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
66 AATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
* *
63182 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * * * *
63247 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAG
63 TTCAATCTTTTGCTTGAATTCATC-ATTTGATGGATCAACATTGCCA-AGTAG
63300 -GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
63364 AATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
66 AATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
* * *
63412 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAAGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * * * * *
63477 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAGCTTTTCCAGAGAAG
63 TTCAATCTTTTGCTTGAATTCATC-ATTTGATGGATCAACATTGCCA-AGTAG
*
63530 -GTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
63594 AATCTTTTGCTTGAATTCATCATTTGATGGATCGACATTGCCAGGTAG
66 AATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
63642 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
63707 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
63 TTCAATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
* * *
63758 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAGTTTATAATAAGAAGAACTTG
1 AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
63823 TTCAAT
63 TTCAAT
63829 AATTCTATCA
Statistics
Matches: 679, Mismatches: 64, Indels: 31
0.88 0.08 0.04
Matches are distributed among these distances:
112 11 0.02
113 102 0.15
114 202 0.30
115 5 0.01
116 282 0.42
117 69 0.10
118 8 0.01
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AATCTTTTGCTTGAATTCATCATTTGATGGATCAACATTGCCAAGTAG
Found at i:63325 original size:230 final size:230
Alignment explanation
Indices: 62955--63828 Score: 1506
Period size: 230 Copynumber: 3.8 Consensus size: 230
62945 TTTCAGAGAA
62955 AGTTCATAATGAGAAGAA--C-TCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
*
63017 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAG
66 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAG
*
63082 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAATCTTTTGCTTG
63147 AATTCATCATTTGATGGATCAACATTGCCAAGTAG
196 AATTCATCATTTGATGGATCAACATTGCCAAGTAG
63182 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
63247 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAG
66 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAG
*
63312 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAATCTTTTGCTTG
63377 AATTCATCATTTGATGGATCAACATTGCCAAGTAG
196 AATTCATCATTTGATGGATCAACATTGCCAAGTAG
*
63412 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAAGAAGAAGAAGTTCATAATGAGAAGAATTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
*
63477 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAGCTTTTCCAGAGAAGGTTCATAATGAG
66 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAG
63542 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAATCTTTTGCTTG
131 AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAATCTTTTGCTTG
* *
63607 AATTCATCATTTGATGGATCGACATTGCCAGGTAG
196 AATTCATCATTTGATGGATCAACATTGCCAAGTAG
* *
63642 AGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
1 AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
* * * * * * * *
63707 TTCAATCTTTTGCTTGAATTCATC-ATTTGATGGATCAACATTGCCA-AGTAGAGTTCATAATGA
66 TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAG-GTTCATAATGA
* *
63770 GAAGAACTCGTCATCTGAAGAAGAAAGAAGAAGTTTATAATAAGAAGAACTTGTTCAAT
130 GAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAAT
63829 AATTCTATCA
Statistics
Matches: 620, Mismatches: 20, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
227 18 0.03
228 4 0.01
229 35 0.06
230 515 0.83
231 1 0.00
232 47 0.08
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (230 bp):
AGTTCATAATGAGAAGAACTCGTCATCTGAAAAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
TTCAACCTTTTACCTGAATTCATCAAATTGATGGATTAACTTTTCCAGAGAAGGTTCATAATGAG
AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAATCTTTTGCTTG
AATTCATCATTTGATGGATCAACATTGCCAAGTAG
Found at i:64153 original size:3 final size:3
Alignment explanation
Indices: 64145--64194 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
64135 TTTTTACCCA
*
64145 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
64193 TA
1 TA
64195 AATATATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:65625 original size:13 final size:13
Alignment explanation
Indices: 65609--65655 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
65599 ATATAATAAA
65609 TAAATATTTATTT
1 TAAATATTTATTT
*
65622 TAAATAAATTATTT
1 TAAAT-ATTTATTT
65636 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
65649 TCAATAT
1 TAAATAT
65656 CAAAGAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:72157 original size:19 final size:17
Alignment explanation
Indices: 72129--72175 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
72119 GTTTAAAAGT
72129 ATCGATACTTGTAGAAAAC
1 ATCGATACTT-TAG-AAAC
* *
72148 ATCGAAACTTTTGAAAC
1 ATCGATACTTTAGAAAC
72165 ATCGATACTTT
1 ATCGATACTTT
72176 TGCAGGAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 14 0.56
18 2 0.08
19 9 0.36
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (17 bp):
ATCGATACTTTAGAAAC
Found at i:72166 original size:17 final size:17
Alignment explanation
Indices: 72144--72177 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
72134 TACTTGTAGA
72144 AAACATCGAAACTTTTG
1 AAACATCGAAACTTTTG
*
72161 AAACATCGATACTTTTG
1 AAACATCGAAACTTTTG
72178 CAGGAGTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (17 bp):
AAACATCGAAACTTTTG
Found at i:73021 original size:15 final size:15
Alignment explanation
Indices: 73002--73047 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
72992 CTATGGTGTT
73002 ACATTTAATGGTATC
1 ACATTTAATGGTATC
*
73017 GCATTTAATGGTATC
1 ACATTTAATGGTATC
73032 ACATTTAATGGTATC
1 ACATTTAATGGTATC
73047 A
1 A
73048 AAGCGTCCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (15 bp):
ACATTTAATGGTATC
Found at i:75469 original size:45 final size:45
Alignment explanation
Indices: 75405--75687 Score: 379
Period size: 45 Copynumber: 6.0 Consensus size: 45
75395 TTAAATATGC
*
75405 AAATAAGCTTATGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
75450 AAATAAGCTTACGAGCTTATGGAATAAATGGAAAGTGTATTGGCA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
75495 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
75540 AAATAAGCTTACGAGCTTATGGAATAAATGGTAA-TATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
75584 AAATAAGCTCGTAAGCTTATGGACAAGCTTATGGAATAAATGGTAAGTATATTGGTA
1 AAATAAGCT--T-A-C-----G---AGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
75641 AAATAAGCTTACGAGCTTATGGGATTAAATGGTTAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
75687 A
1 A
75688 GAAATGTTAT
Statistics
Matches: 213, Mismatches: 11, Indels: 27
0.85 0.04 0.11
Matches are distributed among these distances:
44 18 0.08
45 124 0.58
46 25 0.12
47 1 0.00
48 2 0.01
53 2 0.01
54 1 0.00
55 1 0.00
56 21 0.10
57 18 0.08
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:75658 original size:57 final size:55
Alignment explanation
Indices: 75553--75662 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 55
75543 TAAGCTTACG
75553 AGCTTATGGAATAAATGGTAATATATTAGTAAAATAAGCTCGTAAGCTTATGGACA
1 AGCTTATGGAATAAATGGTAATATATTAGTAAAATAAGCTCG-AAGCTTATGGACA
*
75609 AGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACG-AGCTTATGG
1 AGCTTATGGAATAAATGGTAA-TATATTAGTAAAATAAGC-T-CGAAGCTTATGG
75663 GATTAAATGG
Statistics
Matches: 50, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
56 21 0.42
57 26 0.52
58 1 0.02
59 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (55 bp):
AGCTTATGGAATAAATGGTAATATATTAGTAAAATAAGCTCGAAGCTTATGGACA
Found at i:76115 original size:21 final size:21
Alignment explanation
Indices: 76089--76150 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
76079 TTGAAATTAC
*
76089 TGTAGCAGTGCATCGGTACAT
1 TGTAGCAGTGCATCGATACAT
76110 TGTAGCAGTGCATCGATACAT
1 TGTAGCAGTGCATCGATACAT
76131 TGTAGCAGTGCATCGATACA
1 TGTAGCAGTGCATCGATACA
76151 CAGTTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (21 bp):
TGTAGCAGTGCATCGATACAT
Found at i:78593 original size:26 final size:26
Alignment explanation
Indices: 78553--78603 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
78543 ATAAGACCTA
* *
78553 AAAAATATAATATAAGAAA-AAAAAGG
1 AAAAATAAAAAATAA-AAATAAAAAGG
78579 AAAAATAAAAAATAAAAATAAAAAG
1 AAAAATAAAAAATAAAAATAAAAAG
78604 ATAACGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (26 bp):
AAAAATAAAAAATAAAAATAAAAAGG
Found at i:78595 original size:13 final size:14
Alignment explanation
Indices: 78579--78607 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
78569 AAAAAAAAGG
78579 AAAAATAAAAA-AT
1 AAAAATAAAAAGAT
78592 AAAAATAAAAAGAT
1 AAAAATAAAAAGAT
78606 AA
1 AA
78608 CGAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AAAAATAAAAAGAT
Found at i:86461 original size:19 final size:19
Alignment explanation
Indices: 86437--86489 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
86427 AAAATGTTTA
86437 AAAGTATCGATACTTGTAG
1 AAAGTATCGATACTTGTAG
* * *
86456 AAAGTATCGAAACTTTTGG
1 AAAGTATCGATACTTGTAG
*
86475 AGGAGTATCGATACT
1 A-AAGTATCGATACT
86490 CTTGGGCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACTTGTAG
Found at i:86494 original size:20 final size:20
Alignment explanation
Indices: 86458--86509 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
86448 ACTTGTAGAA
* *
86458 AGTATCGAAACTTTTGGAG-G
1 AGTATCGATACTCTTGG-GCG
*
86478 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCG
86498 AGTATCGATACT
1 AGTATCGATACT
86510 TTCAGTTTGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCG
Found at i:88302 original size:36 final size:36
Alignment explanation
Indices: 88213--88293 Score: 144
Period size: 36 Copynumber: 2.2 Consensus size: 36
88203 TGACTTTTCT
* *
88213 CTTTCCTCGAATCATCAGTCACCTTCTGGTTCACCG
1 CTTTCCTCGAATCATAAGTCACCTCCTGGTTCACCG
88249 CTTTCCTCGAATCATAAGTCACCTCCTGGTTCACCG
1 CTTTCCTCGAATCATAAGTCACCTCCTGGTTCACCG
88285 CTTTCCTCG
1 CTTTCCTCG
88294 TGACATAAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.16, C:0.37, G:0.14, T:0.33
Consensus pattern (36 bp):
CTTTCCTCGAATCATAAGTCACCTCCTGGTTCACCG
Found at i:88308 original size:36 final size:36
Alignment explanation
Indices: 88213--88309 Score: 133
Period size: 36 Copynumber: 2.7 Consensus size: 36
88203 TGACTTTTCT
* * *
88213 CTTTCCTCGAATCATCAGTCACCTTCTGGTTCACCG
1 CTTTCCTCGAATCATAAGCCACCTCCTGGTTCACCG
*
88249 CTTTCCTCGAATCATAAGTCACCTCCTGGTTCACCG
1 CTTTCCTCGAATCATAAGCCACCTCCTGGTTCACCG
*
88285 CTTTCCTCGTGA-CATAAGCCACCTC
1 CTTTCCTCG-AATCATAAGCCACCTC
88310 TCTCACTCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
36 55 0.98
37 1 0.02
ACGTcount: A:0.19, C:0.37, G:0.13, T:0.31
Consensus pattern (36 bp):
CTTTCCTCGAATCATAAGCCACCTCCTGGTTCACCG
Done.