Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001048.1 Hibiscus syriacus cultivar Beakdansim tig00002078_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: 99501
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1590 original size:3 final size:3
Alignment explanation
Indices: 1579--1623 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
1569 ATAATAATAA
* *
1579 TAT TA- TAT TAT TAT TAT TAT TAT TAT CAT CAT TAT TAT TA- TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1624 ACATATAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:3500 original size:19 final size:19
Alignment explanation
Indices: 3478--3516 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
3468 AAATTCAGAG
*
3478 TAAATTAATTAAATTTTAA
1 TAAATTAATCAAATTTTAA
*
3497 TAAATTAATCATATTTTAA
1 TAAATTAATCAAATTTTAA
3516 T
1 T
3517 TTTATATTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTAATCAAATTTTAA
Found at i:8318 original size:24 final size:24
Alignment explanation
Indices: 8264--8310 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
8254 TTTCTATCAA
* * *
8264 AGTCAACGATCAACAGTCAACGGC
1 AGTCAACGGTCAAAAGTCAACAGC
8288 AGTCAACGGTCAAAAGTCAACAG
1 AGTCAACGGTCAAAAGTCAACAG
8311 TGGTCAACAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.13
Consensus pattern (24 bp):
AGTCAACGGTCAAAAGTCAACAGC
Found at i:9739 original size:28 final size:28
Alignment explanation
Indices: 9707--9763 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
9697 TGACTTTTTT
*
9707 ATATTATATTGTCGAGTTAATGCTTGAA
1 ATATTATATTATCGAGTTAATGCTTGAA
* *
9735 ATATTATATTATCGAGTTAGTGTTTGAA
1 ATATTATATTATCGAGTTAATGCTTGAA
9763 A
1 A
9764 ATAGAGATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (28 bp):
ATATTATATTATCGAGTTAATGCTTGAA
Found at i:10545 original size:2 final size:2
Alignment explanation
Indices: 10538--10581 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
10528 GAATTGGCGC
10538 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
10580 AT
1 AT
10582 TGTGTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13457 original size:18 final size:17
Alignment explanation
Indices: 13413--13460 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 17
13403 AATTATTCTA
13413 ATTTTTTAAATAATAAT
1 ATTTTTTAAATAATAAT
13430 ATTAAGTTTTATAATAATAAT
1 ATT---TTTTA-AATAATAAT
13451 ATTTTTTAAA
1 ATTTTTTAAA
13461 AATTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 5 0.19
18 5 0.19
20 5 0.19
21 12 0.44
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTTTAAATAATAAT
Found at i:13575 original size:14 final size:14
Alignment explanation
Indices: 13558--13584 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13548 TTCATTTTAC
13558 GGAAAATATTTTCT
1 GGAAAATATTTTCT
13572 GGAAAATATTTTC
1 GGAAAATATTTTC
13585 AGTGAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (14 bp):
GGAAAATATTTTCT
Found at i:15763 original size:3 final size:3
Alignment explanation
Indices: 15755--15892 Score: 172
Period size: 3 Copynumber: 44.0 Consensus size: 3
15745 CGGGTCTTTT
15755 TTA TTA TTA TTTA TTTA TTA TTA TTA TT- TTAA TTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
* *
15802 TTA TTA TTA TTA TATA TTA CATA TT- TTGC TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA TTA -TTA TTA TT-A TTA -TTA TTA TTA TTA TTA
15850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
15893 CATATTTTAC
Statistics
Matches: 123, Mismatches: 3, Indels: 18
0.85 0.02 0.12
Matches are distributed among these distances:
2 4 0.03
3 97 0.79
4 22 0.18
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17389 original size:30 final size:30
Alignment explanation
Indices: 17350--17483 Score: 116
Period size: 30 Copynumber: 4.5 Consensus size: 30
17340 TGCTAATATC
*
17350 ATTTGAGTCCCTTAATTTTCTATTTTTACT
1 ATTTTAGTCCCTTAATTTTCTATTTTTACT
* * * *
17380 ATTTTAGTCCTTTAAATGTCTGCATTTGT--T
1 ATTTTAGTCCCTTAATTTTCT--ATTTTTACT
* *
17410 A-TTTAGCCCCTTAAGTTTCTATTTTTACT
1 ATTTTAGTCCCTTAATTTTCTATTTTTACT
*
17439 ATTTTAG-CCCTTTAAGTTTT-TATTTTTGCT
1 ATTTTAGTCCC-TTAA-TTTTCTATTTTTACT
*
17469 ATTTTAGTCCTTTAA
1 ATTTTAGTCCCTTAA
17484 ATTCTTGTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
27 5 0.06
29 20 0.24
30 48 0.58
31 5 0.06
32 5 0.06
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (30 bp):
ATTTTAGTCCCTTAATTTTCTATTTTTACT
Found at i:17501 original size:30 final size:30
Alignment explanation
Indices: 17376--17511 Score: 86
Period size: 30 Copynumber: 4.6 Consensus size: 30
17366 TTTCTATTTT
17376 TACTATTTTAGTCCTTTAAATGTC-TGCATTTG
1 TACTATTTTAGTCCTTTAAAT-TCTTG--TTTG
* * *
17408 T--TA-TTTAGCCCCTTAAGTTTCTAT-TTT-
1 TACTATTTTAGTCCTTTAA-ATTCT-TGTTTG
* * * * *
17435 TACTATTTTAGCCCTTTAAGTTTTTATTTT
1 TACTATTTTAGTCCTTTAAATTCTTGTTTG
*
17465 TGCTATTTTAGTCCTTTAAATTCTTGTTTG
1 TACTATTTTAGTCCTTTAAATTCTTGTTTG
**
17495 TACTATTTCGGTCCTTT
1 TACTATTTTAGTCCTTT
17512 GAGTGTATGT
Statistics
Matches: 81, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.01
28 4 0.05
29 21 0.26
30 53 0.65
31 1 0.01
32 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.10, T:0.55
Consensus pattern (30 bp):
TACTATTTTAGTCCTTTAAATTCTTGTTTG
Found at i:23754 original size:36 final size:36
Alignment explanation
Indices: 23711--23949 Score: 392
Period size: 36 Copynumber: 6.7 Consensus size: 36
23701 TCTTAAAATG
*
23711 AATTTTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
* *
23747 AATTTTGTCTCACTTGAGACAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
23783 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
23819 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
*
23855 AATTGTGTCTCGCTTGAGATAGTTTTCTTAAAAACA
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
* **
23891 AATTGTGTATCGCTTGAGACAGTTTTCTTAAAAATG
1 AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
*
23927 AATTTTGTCT--CTTGAGACAGTTT
1 AATTGTGTCTCGCTTGAGACAGTTT
23950 CTAATTAAAA
Statistics
Matches: 193, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
34 13 0.07
36 180 0.93
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (36 bp):
AATTGTGTCTCGCTTGAGACAGTTTTCTTAAAAACA
Found at i:24311 original size:28 final size:28
Alignment explanation
Indices: 24236--24333 Score: 108
Period size: 28 Copynumber: 3.4 Consensus size: 28
24226 GAGACAGTTG
*
24236 CTTTTGAAACACATCATCTTTGAGTTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTCTGTTT
*
24267 TTTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
*
24296 CTTTTGAAACAAATCTTTTAGTC-GATTT
1 CTTTTGAAACAAATCTTTGAGTCTG-TTT
*
24324 CTCTTGAAAC
1 CTTTTGAAAC
24334 CATAATCCCT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
27 1 0.02
28 31 0.52
29 17 0.28
31 3 0.05
32 8 0.13
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:24842 original size:18 final size:18
Alignment explanation
Indices: 24798--24850 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
24788 TAGATATTTT
*
24798 TTATTATTTATT-TATTTA
1 TTATTAATTATTATA-TTA
24816 TTATT-ATTATTATATTA
1 TTATTAATTATTATATTA
*
24833 TTATTAATTAATATATTA
1 TTATTAATTATTATATTA
24851 CATATTTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTAATTATTATATTA
Found at i:24842 original size:21 final size:21
Alignment explanation
Indices: 24798--24838 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
24788 TAGATATTTT
24798 TTATTATTTATTTATTTATTA
1 TTATTATTTATTTATTTATTA
24819 TTATTA-TTATATTA-TTATTA
1 TTATTATTTAT-TTATTTATTA
24839 ATTAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTATTTATTTATTTATTA
Found at i:29284 original size:20 final size:21
Alignment explanation
Indices: 29259--29307 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
29249 TTACCCTAAA
*
29259 TTTTAACAT-AAAAT-ATATAT
1 TTTTAA-ATGAAAATAAAATAT
29279 TTTTAAATGAAAATAAAATAT
1 TTTTAAATGAAAATAAAATAT
29300 TTTTAAAT
1 TTTTAAAT
29308 TAAGTTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 11 0.42
21 13 0.50
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTTTAAATGAAAATAAAATAT
Found at i:29324 original size:27 final size:26
Alignment explanation
Indices: 29291--29373 Score: 100
Period size: 25 Copynumber: 3.3 Consensus size: 26
29281 TTAAATGAAA
29291 ATAAAATATTTTTAAATTAAGTTTAT
1 ATAAAATATTTTTAAATTAAGTTTAT
* *
29317 AATAAAATATATTT-AA-TAAGTTAAT
1 -ATAAAATATTTTTAAATTAAGTTTAT
* *
29342 ATAAAATATTTTTAAGTTAA-TATAT
1 ATAAAATATTTTTAAATTAAGTTTAT
29367 ATAAAAT
1 ATAAAAT
29374 TATATTATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 12 0.25
25 19 0.40
26 5 0.10
27 12 0.25
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
ATAAAATATTTTTAAATTAAGTTTAT
Found at i:29350 original size:24 final size:23
Alignment explanation
Indices: 29291--29365 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 23
29281 TTAAATGAAA
*
29291 ATAAAATATTTTTAAATTAAGTTTAT
1 ATAAAATA-TTTT-AA-TAAGTTAAT
29317 AATAAAATATATTTAATAAGTTAAT
1 -ATAAAATAT-TTTAATAAGTTAAT
29342 ATAAAATATTTT--TAAGTTAAT
1 ATAAAATATTTTAATAAGTTAAT
29363 ATA
1 ATA
29366 TATAAAATTA
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
21 12 0.26
23 3 0.07
24 9 0.20
25 8 0.17
26 3 0.07
27 11 0.24
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
ATAAAATATTTTAATAAGTTAAT
Found at i:29667 original size:39 final size:39
Alignment explanation
Indices: 29622--29740 Score: 138
Period size: 39 Copynumber: 3.1 Consensus size: 39
29612 TTTAAAAAAC
29622 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
* *
29661 AATTTAGAATGTT-ATGGTGTCAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTAAT-GTG-AAATAATTTAAGAAATTAAG
* * *
29700 ATTTTAGAATGTTAGA-GTGAAATAATTTGAG-AATTATG
1 AATTTAGAATGTTA-ATGTGAAATAATTTAAGAAATTAAG
29738 AAT
1 AAT
29741 AAAAATTTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 12 0.18
39 53 0.78
40 2 0.03
41 1 0.01
ACGTcount: A:0.44, C:0.01, G:0.18, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAATGTGAAATAATTTAAGAAATTAAG
Found at i:31802 original size:27 final size:26
Alignment explanation
Indices: 31755--31836 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 26
31745 TAAGTTGAAT
*
31755 TAATATTCATCACATTCATTCAAATA
1 TAATATTAATCACATTCATTCAAATA
* * * *
31781 TGGATATTAATCATATTAATTCAACTA
1 T-AATATTAATCACATTCATTCAAATA
*
31808 CTAATATTAATCACATTCATTAAAATA
1 -TAATATTAATCACATTCATTCAAATA
31835 TA
1 TA
31837 GCGTCAACAA
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
26 3 0.07
27 40 0.91
28 1 0.02
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (26 bp):
TAATATTAATCACATTCATTCAAATA
Found at i:31960 original size:25 final size:25
Alignment explanation
Indices: 31932--31979 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
31922 TAATGGTGTC
*
31932 ATTATTTTTTATCATTATAATAAGT
1 ATTATTTTTCATCATTATAATAAGT
*
31957 ATTATTTTTCGTCATTATAATAA
1 ATTATTTTTCATCATTATAATAA
31980 AAAATGTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (25 bp):
ATTATTTTTCATCATTATAATAAGT
Found at i:33164 original size:20 final size:20
Alignment explanation
Indices: 33139--33178 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
33129 TTCCAACTAT
33139 CTCCTTAATAGTATTAATAA
1 CTCCTTAATAGTATTAATAA
33159 CTCCTTAATAGTATTAATAA
1 CTCCTTAATAGTATTAATAA
33179 TGTCTTCGTC
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:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (20 bp):
CTCCTTAATAGTATTAATAA
Found at i:34076 original size:18 final size:19
Alignment explanation
Indices: 34041--34077 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
34031 CACGGAATGT
34041 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
34061 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
34078 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:34613 original size:15 final size:15
Alignment explanation
Indices: 34590--34623 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34580 TAAAATATTA
*
34590 CCGGGAATGACATTC
1 CCGGAAATGACATTC
34605 CCGGAAATGACATTC
1 CCGGAAATGACATTC
34620 CCGG
1 CCGG
34624 TAAAACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.26, T:0.18
Consensus pattern (15 bp):
CCGGAAATGACATTC
Found at i:35359 original size:228 final size:225
Alignment explanation
Indices: 34718--35372 Score: 622
Period size: 228 Copynumber: 2.9 Consensus size: 225
34708 CACCCTTGAG
* * *
34718 GTCGAAAGCTCAGATACAATTGATAATGTCAAGGCC-AAGATCCAAGACAAAGAAGGG-ATCCCT
1 GTCGAGAGCTCAGATACAATTGATAATGTCAAGGCCTAAGATCCAAGA-AAAGGAGGGTATCCCA
* * * * * *
34781 CCGGACCAACAGAGGCTTATCTTTGCCGGTAAACAGCTAGTGGATGGCAGAACCCTTGCCGACTA
65 CCGGACCAGCAGAGG-TTATCTTTGCTGG-AAACAGCTTGAGGATGGCAGGACCCTTGCAGACTA
* * * * * * * *
34846 CAATATCCAAAAAGAGTCCACCCTGCACCTTGTCCTTCACC-TCGGGGTGGTATGCAGATATTTG
128 CAACATCCAAAAGGAGTCAACCCTGCA-CTAGT-CTTCGCCTTCGAGGTGGCATGCAAATATTTG
* * * * *
34910 TGAAA-ACACTTACTGGCAAGACCATAACCTTAGAG
191 T-AAAGACACTCACAGGAAAGACCATAACATTAGAA
* * * * * *
34945 GTCTAGAGTTCCGATACAATTGATAATGACAAGG-CTAAGATCCAAGACAAGGAGGGTATTCCAC
1 GTCGAGAGCTCAGATACAATTGATAATGTCAAGGCCTAAGATCCAAGAAAAGGAGGGTATCCCAC
* * *
35009 CGGACCAGCAGAGGTTAATTTTTGCTGGGAAACAGCTTGAAGATGGTC-GGACCCTTGTAGACTA
66 CGGACCAGCAGAGGTT-ATCTTTGCT-GGAAACAGCTTGAGGATGG-CAGGACCCTTGCAGACTA
* * * * * * * * * *
35073 TAACATTCAAAAGGAGTCTACCCTTCACTTGGTGTTACGTCTCCGTGGTGGCATGCAAATTTTTG
128 CAACATCCAAAAGGAGTCAACCCTGCAC-TAGTCTT-CGCCTTCGAGGTGGCATGCAAATATTTG
* * *
35138 TAAAGACTCTCACAGGAAAGACTATTACATTAGAA
191 TAAAGACACTCACAGGAAAGACCATAACATTAGAA
* * * *
35173 GTCGAGAGCTCTGATACAATTGACAATGTGAAGGCCTAA-ATCCAAGATAAGGAGGGTATCCCAC
1 GTCGAGAGCTCAGATACAATTGATAATGTCAAGGCCTAAGATCCAAGAAAAGGAGGGTATCCCAC
* * * *
35237 CTGACCAGCAGAGGTTGATCTTTGCTGGAAAGCAGCTTGAGGATGGGAGGACTCTCGCAGACTAC
66 CGGACCAGCAGAGGTT-ATCTTTGCTGGAAA-CAGCTTGAGGATGGCAGGACCCTTGCAGACTAC
* * *
35302 AACATCCAAAAGGAATCAACCCTGCATCTAGTCTTGCGCCTTCGAGGAGGGATGCAAATATTTGT
129 AACATCCAAAAGGAGTCAACCCTGCA-CTAGTCTT-CGCCTTCGAGGTGGCATGCAAATATTTGT
*
35367 GAAGAC
192 AAAGAC
35373 CTTGACGGGA
Statistics
Matches: 343, Mismatches: 72, Indels: 25
0.78 0.16 0.06
Matches are distributed among these distances:
226 13 0.04
227 126 0.37
228 199 0.58
229 5 0.01
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (225 bp):
GTCGAGAGCTCAGATACAATTGATAATGTCAAGGCCTAAGATCCAAGAAAAGGAGGGTATCCCAC
CGGACCAGCAGAGGTTATCTTTGCTGGAAACAGCTTGAGGATGGCAGGACCCTTGCAGACTACAA
CATCCAAAAGGAGTCAACCCTGCACTAGTCTTCGCCTTCGAGGTGGCATGCAAATATTTGTAAAG
ACACTCACAGGAAAGACCATAACATTAGAA
Found at i:39748 original size:22 final size:22
Alignment explanation
Indices: 39720--39764 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
39710 ATGTTTCCTT
39720 AATAAAAAATGCAATCTGTAGA
1 AATAAAAAATGCAATCTGTAGA
39742 AATAAAAAATGCAATCTGTAGA
1 AATAAAAAATGCAATCTGTAGA
39764 A
1 A
39765 CCTTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (22 bp):
AATAAAAAATGCAATCTGTAGA
Found at i:40138 original size:20 final size:20
Alignment explanation
Indices: 40115--40175 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
40105 CCTTTCATAT
40115 TTATCTCTACCCTTTGGTAA
1 TTATCTCTACCCTTTGGTAA
* ** *
40135 TTAT-T-T-TCCTTTCATAT
1 TTATCTCTACCCTTTGGTAA
40152 TTATCTCTACCCTTTGGTAA
1 TTATCTCTACCCTTTGGTAA
40172 TTAT
1 TTAT
40176 TACCTTCCCA
Statistics
Matches: 30, Mismatches: 8, Indels: 6
0.68 0.18 0.14
Matches are distributed among these distances:
17 11 0.37
18 2 0.07
19 2 0.07
20 15 0.50
ACGTcount: A:0.20, C:0.21, G:0.07, T:0.52
Consensus pattern (20 bp):
TTATCTCTACCCTTTGGTAA
Found at i:40142 original size:37 final size:37
Alignment explanation
Indices: 40088--40176 Score: 169
Period size: 37 Copynumber: 2.4 Consensus size: 37
40078 ATTCCTTCTG
*
40088 CCTTTGGTAATTGTTTTCCTTTCATATTTATCTCTAC
1 CCTTTGGTAATTATTTTCCTTTCATATTTATCTCTAC
40125 CCTTTGGTAATTATTTTCCTTTCATATTTATCTCTAC
1 CCTTTGGTAATTATTTTCCTTTCATATTTATCTCTAC
40162 CCTTTGGTAATTATT
1 CCTTTGGTAATTATT
40177 ACCTTCCCAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.18, C:0.20, G:0.08, T:0.54
Consensus pattern (37 bp):
CCTTTGGTAATTATTTTCCTTTCATATTTATCTCTAC
Found at i:44498 original size:102 final size:101
Alignment explanation
Indices: 44262--44515 Score: 240
Period size: 102 Copynumber: 2.5 Consensus size: 101
44252 TCAGATTTTC
* * * ** ** *
44262 AAGTCAAACAAGTTGGCAAATGAATGCCTTCTTCTTGAACTTGAAGAAATTGTGTCATATGGGTT
1 AAGTCAAAAAAGTTGGCAAATGAATGCCTT-TCCTTGAACTTGAAGACACAGTGTCATATGAATA
* * *
44327 TTGAATAGACTATTGTGTCGAAGGCATCTCCATATTA
65 TTGAACAGAATATTGTGTAGAAGGCATCTCCATATTA
* * * * * * *
44364 AAGTCCAAGAAGTTGGTAGATAAATTCATTTCCTTGGAACTTGAAGACACAGTGTCATATGAATA
1 AAGTCAAAAAAGTTGGCAAATGAATGCCTTTCCTT-GAACTTGAAGACACAGTGTCATATGAATA
* * * * * *
44429 TTGAACAGAATGTTGTGTAGATGGTATTTCCATGTTG
65 TTGAACAGAATATTGTGTAGAAGGCATCTCCATATTA
*
44466 AGGTCAAAAAAGTTGGCAAATGAATGCCTTTCCCTTGAA-TTGGAAGACAC
1 AAGTCAAAAAAGTTGGCAAATGAATGCCTTT-CCTTGAACTT-GAAGACAC
44516 GTTGCCATAT
Statistics
Matches: 118, Mismatches: 31, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
101 6 0.05
102 108 0.92
103 4 0.03
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (101 bp):
AAGTCAAAAAAGTTGGCAAATGAATGCCTTTCCTTGAACTTGAAGACACAGTGTCATATGAATAT
TGAACAGAATATTGTGTAGAAGGCATCTCCATATTA
Found at i:45461 original size:173 final size:172
Alignment explanation
Indices: 45141--46047 Score: 425
Period size: 173 Copynumber: 5.3 Consensus size: 172
45131 GTTCCCAGTC
* *
45141 GGGGAACTATTCACATCAACCACCCTTATGTTTGATGGGATTAGACACTATGACATGATATAGAT
1 GGGGAACTATTCACATAAACCACCCTTATGTTTGATGGGA-TAGACACTATGACATGATAAAGAT
* * * * * * *
45206 TCTATGAAAATGGTGAAAGCGCTTGTTGTGGAACGAGACTTCCTTTTTATTGTCATAGATTCTTT
65 TCTATAAAAATGATGAAAGCGCTTGTAGTGGAACGAGACTTACTTTTTATTATCAAAGATTCTCT
*
45271 GTATTTGTCAATCAATTATATGAAAATATAATGTCCCTATTTT
130 GCATTTGTCAATCAATTATATGAAAATATAATGTCCCTATTTT
* *
45314 GGGGAACTATTCATATAAACC-CTCTTTATGTTTGATGGGCA-AGACACTATGACATGATAAAGA
1 GGGGAACTATTCACATAAACCAC-CCTTATGTTTGATGGG-ATAGACACTATGACATGATAAAGA
* * **
45377 TTCTTTTAAAAAAT-ATGAAAGCGCTTGTAGT-GAGACGA-ACCTTACTTTTTTTTATCAAATTT
64 TTC-TAT-AAAAATGATGAAAGCGCTTGTAGTGGA-ACGAGA-CTTACTTTTTATTATCAAAGAT
* * * * * ** * *
45439 TCTCTGCATTTTTTAGTCAATTATATGTAGATATAAT-TTTCTCA-GTC
125 TCTCTGCATTTGTCAATCAATTATATGAAAATATAATGTCCCT-ATTTT
* * * ** * * * * *
45486 GAGAAACTGTTCATGTCAACC-TCCTTATGTTTGAT-GGATGAGACATTATGACATTATAGAGAT
1 GGGGAACTATTCACATAAACCACCCTTATGTTTGATGGGAT-AGACACTATGACATGATAAAGAT
* ** * * * * * * * * * ***
45549 TCTCTGAAAAATG-TGAAAATGGTTATTGTGGGATGAGCCTTCCATTTTATTGTTGTAGATTCTC
65 TCTAT-AAAAATGATGAAAGCGCTTGTAGTGGAACGAGACTTACTTTTTATTATCAAAGATTCTC
* * * * * *
45613 TACATTTGTCAACCCAATTATATGTAGATATAATGTTCCC-ATGTC
129 TGCATTTGTCAA-TCAATTATATGAAAATATAATG-TCCCTATTTT
** * * * * * * *
45658 AAGGAACTATTCACATCAACCTCCCTTATGTTAGATGGGACAAGACACTATGACATGACACAGAC
1 GGGGAACTATTCACATAAACCACCCTTATGTTTGATGGGA-TAGACACTATGACATGATAAAGAT
* * * * * * ** * **
45723 TCTCTGAAAAA-GGTGAAAGCTCTTGTTGTGGGACGAGTCTT-CCCTTT-TTGTCAAATTTTCTC
65 TCTAT-AAAAATGATGAAAGCGCTTGTAGTGGAACGAGACTTACTTTTTATTATCAAAGATTCTC
* * * * * *
45785 TACATTTTTCAGTGAATTATAT-ACAGATATAATGTTCCC-ATTTC
129 TGCATTTGTCAATCAATTATATGA-AAATATAATG-TCCCTATTTT
** ** * ** * * * * *
45829 GGGGAGTTATTCATGTCAACCTTCTTTATGTTTGATGGGATGAGACACTATGATATGACAAAAAC
1 GGGGAACTATTCACATAAACCACCCTTATGTTTGATGGGAT-AGACACTATGACATGATAAAGAT
* * * * * * * * * *** *
45894 TCTCTAAAAAAGGTGAAAGTTGCTTGTTGTGGGACGAGTCTTCCTTTTT-TTGTCAATTTTTCTA
65 TCTATAAAAATGATGAAAG-CGCTTGTAGTGGAACGAGACTTACTTTTTATTATCAAAGATTCTC
* * * * * * * * *
45958 TGTATTTTTTAGTCAATTATAAGCAGATATAATGTTCC-A-ATT
129 TGCATTTGTCAATCAATTATATGAAAATATAATGTCCCTATTTT
* * *
46000 CGGAAACTATTCACATCAA-C-CCCTTATGTTTGATGGGATAAGACACTA
1 GGGGAACTATTCACATAAACCACCCTTATGTTTGATGGGAT-AGACACTA
46048 ATAGATGGCA
Statistics
Matches: 577, Mismatches: 131, Indels: 56
0.76 0.17 0.07
Matches are distributed among these distances:
169 26 0.05
170 55 0.10
171 161 0.28
172 111 0.19
173 165 0.29
174 59 0.10
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (172 bp):
GGGGAACTATTCACATAAACCACCCTTATGTTTGATGGGATAGACACTATGACATGATAAAGATT
CTATAAAAATGATGAAAGCGCTTGTAGTGGAACGAGACTTACTTTTTATTATCAAAGATTCTCTG
CATTTGTCAATCAATTATATGAAAATATAATGTCCCTATTTT
Found at i:45805 original size:171 final size:173
Alignment explanation
Indices: 45124--46138 Score: 862
Period size: 171 Copynumber: 5.9 Consensus size: 173
45114 AAAATGAAAA
* *
45124 ATATAATGTTCCCA-GTCGGGGAACTATTCACATCAACCACCCTTATGTTTGATGGGATTAGACA
1 ATATAATGTTCCCATGTCGGGGAACTATTCACATCAACCTCCCTTATGTTTGATGGGATAAGACA
* * * * * *
45188 CTATGACATGATATAGATTCTATGAAAATGGTGAAAGC-GCTTGTTGTGGAACGAGACTTCCTTT
66 CTATGACATGACAAAGATTCTCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTTCCTTT
* ** * * * * * *
45252 TTATTGTCATAGATTCTTTGTATTTGTCAATCAATTATATGAAA
131 TT-TTGTCAAATTTTCTCTGCATTTTTCAGTCAATTATATGCAG
* * * * * *
45296 ATATAATG-TCCCTATTTTGGGGAACTATTCATATAAACC-CTCTTTATGTTTGATGGG-CAAGA
1 ATATAATGTTCCC-ATGTCGGGGAACTATTCACATCAACCTC-CCTTATGTTTGATGGGATAAGA
* * * ** * * *
45358 CACTATGACATGATAAAGATTCTTTTAAAAAATATGAAAGC-GCTTGTAGTGAGACGAACCTTAC
64 CACTATGACATGACAAAGATTC-TCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTT-C
* * * *
45422 TTTTTTTTATCAAATTTTCTCTGCATTTTTTAGTCAATTATATGTAG
127 CTTTTTTTGTCAAATTTTCTCTGCATTTTTCAGTCAATTATATGCAG
* * * * * ** *
45469 ATATAATTTTCTCA-GTCGAGAAACTGTTCATGTCAACCT-CCTTATGTTTGAT-GGATGAGACA
1 ATATAATGTTCCCATGTCGGGGAACTATTCACATCAACCTCCCTTATGTTTGATGGGATAAGACA
* * * * * * * * *
45531 TTATGACATTATAGAGATTCTCTGAAAAATGTGAAA-ATGGTTATTGTGGGATGAGCCTTCCATT
66 CTATGACATGACAAAGATTCTCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTTCC-TT
* *** ** * * ** *
45595 TTATTGTTGTAGATTCTCTACATTTGTCAACCCAATTATATGTAG
130 TTTTTGTCAAATTTTCTCTGCATTTTTC-AGTCAATTATATGCAG
** * *
45640 ATATAATGTTCCCATGTCAAGGAACTATTCACATCAACCTCCCTTATGTTAGATGGGACAAGACA
1 ATATAATGTTCCCATGTCGGGGAACTATTCACATCAACCTCCCTTATGTTTGATGGGATAAGACA
* * * *
45705 CTATGACATGACACAGACTCTCTGAAAAAGGTGAAAGCT-CTTGTTGTGGGACGAGTCTTCC-CT
66 CTATGACATGACAAAGATTCTCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTTCCTTT
* * *
45768 TTTTGTCAAATTTTCTCTACATTTTTCAGTGAATTATATACAG
131 TTTTGTCAAATTTTCTCTGCATTTTTCAGTCAATTATATGCAG
* ** ** * * *
45811 ATATAATGTTCCCATTTCGGGGAGTTATTCATGTCAACCTTCTTTATGTTTGATGGGATGAGACA
1 ATATAATGTTCCCATGTCGGGGAACTATTCACATCAACCTCCCTTATGTTTGATGGGATAAGACA
* * * * * *
45876 CTATGATATGACAAAAACTCTCTAAAAAAGGTGAAAGTTGCTTGTTGTGGGACGAGTCTTCCTTT
66 CTATGACATGACAAAGATTCTCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTTCCTTT
* * * * *
45941 TTTTGTCAATTTTTCTATGTATTTTTTAGTCAATTATAAGCAG
131 TTTTGTCAAATTTTCTCTGCATTTTTCAGTCAATTATATGCAG
* *
45984 ATATAATGTTCCAAT-TC-GGAAACTATTCACATCAA-C-CCCTTATGTTTGATGGGATAAGACA
1 ATATAATGTTCCCATGTCGGGGAACTATTCACATCAACCTCCCTTATGTTTGATGGGATAAGACA
* * * * * *
46045 CTAAT-AGATGGCATAGATTCTCTG-AAAAGGTGAAAG-TGCTTCTTGTGGGATGAACCTTCCCT
66 CT-ATGACATGACAAAGATTCTCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTT-CCT
* * ** *
46107 TTTATTGTCATAGATTCTCTGCATTTGTCAGT
129 TTTTTTGTCAAATTTTCTCTGCATTTTTCAGT
46139 ATGCAAATAT
Statistics
Matches: 668, Mismatches: 156, Indels: 42
0.77 0.18 0.05
Matches are distributed among these distances:
167 18 0.03
168 38 0.06
169 38 0.06
170 53 0.08
171 175 0.26
172 116 0.17
173 164 0.25
174 65 0.10
175 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (173 bp):
ATATAATGTTCCCATGTCGGGGAACTATTCACATCAACCTCCCTTATGTTTGATGGGATAAGACA
CTATGACATGACAAAGATTCTCTGAAAAAGGTGAAAGCTGCTTGTTGTGGGACGAGCCTTCCTTT
TTTTGTCAAATTTTCTCTGCATTTTTCAGTCAATTATATGCAG
Found at i:45977 original size:344 final size:338
Alignment explanation
Indices: 45124--46109 Score: 925
Period size: 344 Copynumber: 2.9 Consensus size: 338
45114 AAAATGAAAA
** * *
45124 ATATAATGTTCCCAGTCGGGGAACTATTCACATCAACCACCCTTATGTTTGATGGGATTAGACAC
1 ATATAATGTTCCCAGTCGGGGAACTATTCATGTCAACC-TCCTTATGTTTGATGGGATGAGACAC
* * * * *
45189 TATGACATGATATAGATTCTATGAAAATGGTGAAAGCGCTTGTTGTGGAACGAGACTTCCTTTTT
65 TATGACATGATAAAGATTCTCTGAAAAAGGTGAAAGTGCTTGTTGTGGGACGAGACTTCCTTTTT
** * * * * *
45254 ATTGTC-ATAGATTCTTTGTATTTGTCAATCAATTATATGAAAATATAATG-TCCCTATTTTGGG
130 ATTGTCAAT-TTTTCTATGTATTTTTAAATCAATTATATGAAGATATAATGTTCCC-A--TT-CG
* * * *
45317 GAACTATTCATATAAACCCTCTTTATGTTTGATGGG-CAAGACACTATGACATGATAAAGATTCT
190 GAACTATTCACATCAACCC-CCTTATGTTTGATGGGACAAGACACTATGACATGACAAAGATTC-
* * ** * * * ** *
45381 TTTAAAAAATATGAAAGCGCTTGTAGTGAGACGAACCTTACTTTTTTTTATCAAATTTTCTCTGC
253 TCTGAAAAAGGTGAAAGCTCTTGTTGTGGGACGAACCTT-C-CCTTTTTATCAAATTTTCTCTAC
* **
45446 ATTTTTTAGTCAATTATATGTAG
316 ATTTTTCAGTCAATTATATACAG
* * * * * *
45469 ATATAATTTTCTCAGTCGAGAAACTGTTCATGTCAACCTCCTTATGTTTGAT-GGATGAGACATT
1 ATATAATGTTCCCAGTCGGGGAACTATTCATGTCAACCTCCTTATGTTTGATGGGATGAGACACT
* * * * * * * * *
45533 ATGACATTATAGAGATTCTCTGAAAAATGTGAAAATGGTTATTGTGGGATGAGCCTTCCATTTTA
66 ATGACATGATAAAGATTCTCTGAAAAAGGTGAAAGTGCTTGTTGTGGGACGAGACTTCCTTTTTA
* * * * ** *
45598 TTGTTGTAGA-TTCTCTA--CATTTGTCAACCCAATTATATGTAGATATAATGTTCCCATGTCAA
131 TTG-T-CA-ATTTTTCTATGTATTT-TTAAATCAATTATATGAAGATATAATGTTCCCAT-TC--
* * *
45660 GGAACTATTCACATCAACCTCCCTTATGTTAGATGGGACAAGACACTATGACATGACACAGACTC
189 GGAACTATTCACATCAACC-CCCTTATGTTTGATGGGACAAGACACTATGACATGACAAAGATTC
** *
45725 TCTGAAAAAGGTGAAAGCTCTTGTTGTGGGACGAGTCTTCCCTTTTTGTCAAATTTTCTCTACAT
253 TCTGAAAAAGGTGAAAGCTCTTGTTGTGGGACGAACCTTCCCTTTTTATCAAATTTTCTCTACAT
*
45790 TTTTCAGTGAATTATATACAG
318 TTTTCAGTCAATTATATACAG
* ** *
45811 ATATAATGTTCCCATTTCGGGGAGTTATTCATGTCAACCTTCTTTATGTTTGATGGGATGAGACA
1 ATATAATGTTCCCA-GTCGGGGAACTATTCATGTCAACC-TCCTTATGTTTGATGGGATGAGACA
* * * * * *
45876 CTATGATATGACAAAAACTCTCTAAAAAAGGTGAAAGTTGCTTGTTGTGGGACGAGTCTTCCTTT
64 CTATGACATGATAAAGATTCTCTGAAAAAGGTGAAAG-TGCTTGTTGTGGGACGAGACTTCCTTT
* * * * *
45941 TT-TTGTCAATTTTTCTATGTATTTTTTAGTCAATTATAAGCAGATATAATGTTCCAATTCGGAA
128 TTATTGTCAATTTTTCTATGTATTTTTAAATCAATTATATGAAGATATAATGTTCCCATTCGG-A
* * * *
46005 ACTATTCACATCAA-CCCCTTATGTTTGATGGGATAAGACACTAAT-AGATGGCATAGATTCTCT
192 ACTATTCACATCAACCCCCTTATGTTTGATGGGACAAGACACT-ATGACATGACAAAGATTCTCT
* *
46068 G-AAAAGGTGAAAG-TGCTTCTTGTGGGATGAACCTTCCCTTTT
256 GAAAAAGGTGAAAGCT-CTTGTTGTGGGACGAACCTTCCCTTTT
46110 ATTGTCATAG
Statistics
Matches: 515, Mismatches: 105, Indels: 48
0.77 0.16 0.07
Matches are distributed among these distances:
338 1 0.00
339 35 0.07
340 40 0.08
341 5 0.01
342 67 0.13
343 98 0.19
344 137 0.27
345 107 0.21
346 24 0.05
347 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (338 bp):
ATATAATGTTCCCAGTCGGGGAACTATTCATGTCAACCTCCTTATGTTTGATGGGATGAGACACT
ATGACATGATAAAGATTCTCTGAAAAAGGTGAAAGTGCTTGTTGTGGGACGAGACTTCCTTTTTA
TTGTCAATTTTTCTATGTATTTTTAAATCAATTATATGAAGATATAATGTTCCCATTCGGAACTA
TTCACATCAACCCCCTTATGTTTGATGGGACAAGACACTATGACATGACAAAGATTCTCTGAAAA
AGGTGAAAGCTCTTGTTGTGGGACGAACCTTCCCTTTTTATCAAATTTTCTCTACATTTTTCAGT
CAATTATATACAG
Found at i:47838 original size:19 final size:19
Alignment explanation
Indices: 47814--47887 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 19
47804 ATGTATTTTA
47814 TGCATCGATGCACAGGCAG
1 TGCATCGATGCACAGGCAG
* *
47833 TGCATCGATGCACCGATAGGGAA
1 TGCATCGATGCA-C---AGGCAG
* *
47856 TGCATCGATACACTGTGCAG
1 TGCATCGATGCACAG-GCAG
47876 TGCATCGATGCA
1 TGCATCGATGCA
47888 TACCTTCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 13 0.30
20 14 0.33
22 1 0.02
23 15 0.35
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.20
Consensus pattern (19 bp):
TGCATCGATGCACAGGCAG
Found at i:48857 original size:103 final size:103
Alignment explanation
Indices: 48631--48849 Score: 370
Period size: 103 Copynumber: 2.1 Consensus size: 103
48621 AGTCGAGGGT
*
48631 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
48696 CTTGATCCTAGGCATATGTATATGATTTTTAAGGAATG
66 CTTGATCCTAGGCATATGTATATGATTTTTAAGGAATG
*
48734 ATATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
1 ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
*
48799 CTTGATCCTTA-GTATATGTATATG-TTTCTTAAGGAATG
66 CTTGATCC-TAGGCATATGTATATGATTT-TTAAGGAATG
*
48837 ATATGTGCTCCTT
1 ATATGTGGTCCTT
48850 ATGGACATTA
Statistics
Matches: 109, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
102 3 0.03
103 104 0.95
104 2 0.02
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
ATATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATA
CTTGATCCTAGGCATATGTATATGATTTTTAAGGAATG
Found at i:48900 original size:23 final size:23
Alignment explanation
Indices: 48874--48931 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
48864 ATGGCACTAT
*
48874 GGTGCAATTCTACGCGACACTCC
1 GGTGCAATTATACGCGACACTCC
* * *
48897 GGTGCAATTATACGTGGCACTTC
1 GGTGCAATTATACGCGACACTCC
48920 GGTGCAATTATA
1 GGTGCAATTATA
48932 TGAGCTGTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
GGTGCAATTATACGCGACACTCC
Found at i:54216 original size:23 final size:23
Alignment explanation
Indices: 54184--54242 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
54174 TATGGTTCTA
*
54184 CGGTGCAATTGTACGCGGCACTC
1 CGGTGCAATTATACGCGGCACTC
* * *
54207 CTGTGCAATTATACGTGGCACTT
1 CGGTGCAATTATACGCGGCACTC
54230 CGGTGCAATTATA
1 CGGTGCAATTATA
54243 TGAGTTGTGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (23 bp):
CGGTGCAATTATACGCGGCACTC
Found at i:56433 original size:8 final size:8
Alignment explanation
Indices: 56420--56445 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
56410 ATGTATTGAA
56420 ATTTCAAG
1 ATTTCAAG
56428 ATTTCAAG
1 ATTTCAAG
56436 ATTTCAAG
1 ATTTCAAG
56444 AT
1 AT
56446 ATGGTAGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (8 bp):
ATTTCAAG
Found at i:59826 original size:103 final size:103
Alignment explanation
Indices: 59644--59869 Score: 373
Period size: 103 Copynumber: 2.2 Consensus size: 103
59634 GTCGAGGGTC
*
59644 TATGTGGTTCTTCAGGACATATATGTATTCTTTGGAACATGTATGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTATGAAGTATGGTGAGACACATAC
* * *
59709 TTGATCCTTGGTATATGTATATGATTCTTATGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
* * *
59747 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTATGAAGTATGGTGAGACACATAC
59812 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
59850 TATGTGGTCCTT-ATGGACAT
1 TATGTGGTCCTTCA-GGACAT
59870 TATTATATAG
Statistics
Matches: 114, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
103 114 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTATGAAGTATGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:59905 original size:23 final size:23
Alignment explanation
Indices: 59879--59945 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
59869 TTATTATATA
* *
59879 GCACTACGGTGGAATTCTATGCG
1 GCACTACGGTGCAATTATATGCG
* * * *
59902 GCACTCCGGTGTAATTATACGTG
1 GCACTACGGTGCAATTATATGCG
*
59925 GCACTTCGGTGCAATTATATG
1 GCACTACGGTGCAATTATATG
59946 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (23 bp):
GCACTACGGTGCAATTATATGCG
Found at i:61895 original size:13 final size:13
Alignment explanation
Indices: 61877--61902 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61867 AAAGAAATAT
61877 TAAAAACATTACA
1 TAAAAACATTACA
61890 TAAAAACATTACA
1 TAAAAACATTACA
61903 ATTAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAACATTACA
Found at i:76260 original size:20 final size:20
Alignment explanation
Indices: 76231--76269 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
76221 AAAGCTCATA
*
76231 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
76251 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
76270 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:88266 original size:20 final size:20
Alignment explanation
Indices: 88237--88275 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
88227 TTTCCACCAC
88237 ATGCAACTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
*
88257 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
88276 TATGAGCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:88278 original size:10 final size:10
Alignment explanation
Indices: 88243--88280 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
88233 CCACATGCAA
88243 CTATATGATC
1 CTATATGATC
*
88253 CTAAATGCAT-
1 CTATATG-ATC
88263 CTATATGATC
1 CTATATGATC
88273 CTATATGA
1 CTATATGA
88281 GCTTTTAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 2 0.08
10 20 0.83
11 2 0.08
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (10 bp):
CTATATGATC
Done.