Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005869.1 Hibiscus syriacus cultivar Beakdansim tig00013797_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: 79244
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2735 original size:16 final size:16
Alignment explanation
Indices: 2714--2748 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2704 TTCACATCTT
2714 TGCATAGCACATTCAA
1 TGCATAGCACATTCAA
2730 TGCATAGCACATTCAA
1 TGCATAGCACATTCAA
2746 TGC
1 TGC
2749 TTATGCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (16 bp):
TGCATAGCACATTCAA
Found at i:6285 original size:54 final size:54
Alignment explanation
Indices: 6220--6846 Score: 631
Period size: 54 Copynumber: 11.7 Consensus size: 54
6210 AAATAGGCAT
* *
6220 TAAGTGTGCAAATCACGGAATTAATCATATGTTGATGAACAACCATTTCGACAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * * *
6274 TAAGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAATCGTTTCGACAG
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * *
6328 TATGTGTACAAATCACAGAATTCATCATATGTTGATGAATAACCATTTCGACAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * *
6382 TAAGTGTGCAAATCACGGAATTCATCACATGTTGATGAATAA-C---TGGGCAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
** * * *
6432 TAAGTGTGCAAATCACATAATTCATTATATGTTGATGAATAACCGTTTCGGCAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* * *
6486 TAAGTGTGCAAATCACAGAATTCATCATATGTTG-TGAATAA-CAGTTTTGGA-AT
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCA--TTTCGACAC
* *** * *
6539 TAAGTGTGTAAATCATATAATTCATCATATATTGATGGATAACCATTTC-AGCAC
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* ** *
6593 TAAGTGTGAAAAGT-ACGGAATTCATCATATGTTGATGAATAACTGTTTCGGCAC
1 TAAGTGTGCAAA-TCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
* **
6647 TAAGTGTACAAAGTACAC--AATTCATCATATGTTGATGAATAACTGTTTC-AGCAC
1 TAAGTGTGCAAA-T-CACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* * * *
6701 GAAGTGCGCAAAGT-ACGAAATTCATCATATGTTGATGAATAATCATTTC-AGCAC
1 TAAGTGTGCAAA-TCACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* * *
6755 TAAGTGTGCAAAGT-ACGGAATTCATCATAGGTT-ATGTATAATCATTTC-AGCAC
1 TAAGTGTGCAAA-TCACGGAATTCATCATATGTTGATGAATAACCATTTCGA-CAC
* * * * *
6808 TATGTGTGCAAAACACGAAATTCATAATATGTTTATGAA
1 TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAA
6847 AAGATCGTAT
Statistics
Matches: 488, Mismatches: 66, Indels: 38
0.82 0.11 0.06
Matches are distributed among these distances:
50 43 0.09
51 1 0.00
52 4 0.01
53 88 0.18
54 347 0.71
55 3 0.01
56 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.31
Consensus pattern (54 bp):
TAAGTGTGCAAATCACGGAATTCATCATATGTTGATGAATAACCATTTCGACAC
Found at i:13528 original size:7 final size:7
Alignment explanation
Indices: 13518--13558 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
13508 GAAATTTTGG
13518 GTTTTTT
1 GTTTTTT
13525 GTTTTTT
1 GTTTTTT
13532 -TTCTTTT
1 GTT-TTTT
*
13539 TTTTTTT
1 GTTTTTT
13546 GTTTTTT
1 GTTTTTT
13553 GTTTTT
1 GTTTTT
13559 GAAAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 2 0.06
7 27 0.87
8 2 0.06
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (7 bp):
GTTTTTT
Found at i:17442 original size:18 final size:18
Alignment explanation
Indices: 17419--17454 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17409 TTGCTCGCGA
*
17419 GCTTTTCGAGTTGAGTAT
1 GCTTTTCAAGTTGAGTAT
17437 GCTTTTCAAGTTGAGTAT
1 GCTTTTCAAGTTGAGTAT
17455 CAAATAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.25, T:0.44
Consensus pattern (18 bp):
GCTTTTCAAGTTGAGTAT
Found at i:23106 original size:17 final size:16
Alignment explanation
Indices: 23064--23106 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
23054 TTCAATTGCA
23064 TGTTTAATTTTCAATT
1 TGTTTAATTTTCAATT
* *
23080 TATTTCAATTTATCCATT
1 TGTTT-AATTT-TCAATT
23098 TGTTTAATT
1 TGTTTAATT
23107 CACATAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 9 0.41
18 9 0.41
ACGTcount: A:0.26, C:0.09, G:0.05, T:0.60
Consensus pattern (16 bp):
TGTTTAATTTTCAATT
Found at i:32115 original size:12 final size:13
Alignment explanation
Indices: 32091--32119 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
32081 AAATGAAAAA
32091 AAATGCAAAATGT
1 AAATGCAAAATGT
32104 AAATGC-AAATGT
1 AAATGCAAAATGT
32116 AAAT
1 AAAT
32120 ATGTGAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.24
Consensus pattern (13 bp):
AAATGCAAAATGT
Found at i:33153 original size:15 final size:15
Alignment explanation
Indices: 33133--33180 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
33123 ATCTTAACCT
33133 CATGCTTTCTAGTTC
1 CATGCTTTCTAGTTC
33148 CATGC-TT-T-GTT-
1 CATGCTTTCTAGTTC
33159 -ATGCTTTCTAGTTC
1 CATGCTTTCTAGTTC
33173 CATGCTTT
1 CATGCTTT
33181 GTTTAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
10 4 0.14
11 2 0.07
12 4 0.14
13 4 0.14
14 2 0.07
15 12 0.43
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (15 bp):
CATGCTTTCTAGTTC
Found at i:33168 original size:25 final size:25
Alignment explanation
Indices: 33134--33183 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
33124 TCTTAACCTC
33134 ATGCTTTCTAGTTCCATGCTTTGTT
1 ATGCTTTCTAGTTCCATGCTTTGTT
33159 ATGCTTTCTAGTTCCATGCTTTGTT
1 ATGCTTTCTAGTTCCATGCTTTGTT
33184 TAGAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.12, C:0.20, G:0.16, T:0.52
Consensus pattern (25 bp):
ATGCTTTCTAGTTCCATGCTTTGTT
Found at i:34683 original size:16 final size:16
Alignment explanation
Indices: 34659--34689 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34649 ATAGTAATAC
*
34659 TAATGATAAATATATA
1 TAATCATAAATATATA
34675 TAATCATAAATATAT
1 TAATCATAAATATAT
34690 GAAAGTAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (16 bp):
TAATCATAAATATATA
Found at i:36099 original size:3 final size:3
Alignment explanation
Indices: 36091--36150 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
36081 AGCTTGTTTG
**
36091 TAA TAA TAA TAA TTT TAA TAA TAA TAA TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
36136 TTA TAA TAA CAA TAA
1 TAA TAA TAA TAA TAA
36151 AAAATGGGTA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39706 original size:29 final size:29
Alignment explanation
Indices: 39674--39733 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
39664 TGGTAATAAT
* * *
39674 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
39703 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
39732 AA
1 AA
39734 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:41307 original size:3 final size:3
Alignment explanation
Indices: 41301--41376 Score: 102
Period size: 3 Copynumber: 25.3 Consensus size: 3
41291 GCAAAAAAAA
* *
41301 AAT AAT -AT AAT ATGT AAT ATT AAT AAT -AT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
41346 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41377 TAAGACCCGG
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
2 4 0.06
3 56 0.86
4 5 0.08
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:41674 original size:43 final size:44
Alignment explanation
Indices: 41567--41850 Score: 200
Period size: 46 Copynumber: 6.6 Consensus size: 44
41557 GATATGGGGA
* * ** ** *
41567 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT
* *
41612 GATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 -ATGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGT
*
41657 -TGACACGGCTCCTACGTGATGAGGAGATCTGG---TC--TGGT
1 ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGT
* * ** ** *
41695 GATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 -ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCT-ATGGT
* *
41741 GATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT
1 -ATGACACGGCTCCTACGTGATGAGGA-GAGCTGGTTATCTATGGT
*
41786 -TGACACGGCTCCTACGTGATGAGGAGATCTGG---TC--TGGT
1 ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGT
* *
41824 GATGACACGGTTCCTACATGATGAGGA
1 -ATGACACGGCTCCTACGTGATGAGGA
41851 CGGCTGGCCA
Statistics
Matches: 196, Mismatches: 28, Indels: 34
0.76 0.11 0.13
Matches are distributed among these distances:
38 8 0.04
40 56 0.29
42 2 0.01
43 56 0.29
45 8 0.04
46 64 0.33
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (44 bp):
ATGACACGGCTCCTACGTGATGAGGAGAGCTGGTTATCTATGGT
Found at i:41848 original size:83 final size:85
Alignment explanation
Indices: 41697--41857 Score: 227
Period size: 83 Copynumber: 1.9 Consensus size: 85
41687 GGTCTGGTGA
* *
41697 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG-C-TCT--AGGTGATAACACGGTTCCTACATGA
41762 TGAGGACGGCTGGTTATCTATGGT
62 TGAGGACGGCTGGTTATCTATGGT
* * *
41786 TGACACGGCTCCTACGTGATGAGGAGATCTGG-TCT-GGTGATGACACGGTTCCTACATGATGAG
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGTGATAACACGGTTCCTACATGATGAG
41849 GACGGCTGG
66 GACGGCTGG
41858 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 35 0.52
86 3 0.04
89 29 0.43
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (85 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCTCTAGGTGATAACACGGTTCCTACATGATGAG
GACGGCTGGTTATCTATGGT
Found at i:41863 original size:129 final size:129
Alignment explanation
Indices: 41528--41847 Score: 541
Period size: 129 Copynumber: 2.5 Consensus size: 129
41518 TGTTGGGGAC
* * * * * * *
41528 GACACTGCTCATACGTGATGAAGAGTTCTGATATGGGGAATGACACGGCTCATACGTGATGAAGA
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTG-ATGACACGGCTCATACGTGATGAAGA
41593 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
65 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
41658 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGCTCATACGTGATGAAGAG
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGCTCATACGTGATGAAGAG
41723 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
66 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
* * *
41787 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGTTCCTACATGATGA
1 GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGCTCATACGTGATGA
41848 GGACGGCTGG
Statistics
Matches: 180, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
129 149 0.83
130 31 0.17
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (129 bp):
GACACGGCTCCTACGTGATGAGGAGATCTGGTCTGGTGATGACACGGCTCATACGTGATGAAGAG
TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTT
Found at i:41916 original size:28 final size:28
Alignment explanation
Indices: 41876--41938 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
41866 AGGAGTTATG
* *
41876 GTTTCAAGAGAAACCA-AATTAAAGATTT
1 GTTTCAAAAGAAA-CAGAATCAAAGATTT
*
41904 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGAATCAAAGATTT
41932 GTTTCAA
1 GTTTCAA
41939 GAAAACAAGC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 2 0.06
28 29 0.94
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGAATCAAAGATTT
Found at i:41967 original size:30 final size:28
Alignment explanation
Indices: 41896--41971 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 28
41886 AAACCAAATT
41896 AAAGATTTGTTTCAAAAGAAACAGACTC
1 AAAGATTTGTTTCAAAAGAAACAGACTC
*
41924 AAAGATTTGTTTCAAGA-AAACA-AGCTC
1 AAAGATTTGTTTCAAAAGAAACAGA-CTC
41951 AAAGATAATGTGTTTCAAAAG
1 AAAGAT--T-TGTTTCAAAAG
41972 CAACTGTCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 1 0.02
27 14 0.34
28 16 0.39
29 1 0.02
30 9 0.22
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAGACTC
Found at i:42162 original size:66 final size:65
Alignment explanation
Indices: 41973--42162 Score: 154
Period size: 66 Copynumber: 2.9 Consensus size: 65
41963 TTTCAAAAGC
** * *
41973 AACTGTCTCGAAAGAGACAAAATTCATTTCAAATGAAACAA-CTCAAAAGATG-ACGTTTAAAGG
1 AACTGTCTC-AAAGAGACAAAATTCATTTCAAGGGAAACAATTTC-AAAGATGTATGTTTAAAGG
42036 GA
64 GA
* * ** * * * * * * *
42038 AATTGTCTCAAGCGAGACAAAATTTGTTTTTAAGGG-AAC-GTTCTCAAATATCTGTGTTTCATG
1 AACTGTCTCAA-AGAGACAAAA-TTCATTTCAAGGGAAACAATT-TCAAAGATGTATGTTTAAAG
42101 GGA
63 GGA
*
42104 AACTGTCTCAAATGAGACAAAATTCATTTCAAGGGAAACAATTTCAAAGATGTTTGTTT
1 AACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACAATTTCAAAGATGTATGTTT
42163 TGTTTCATGG
Statistics
Matches: 93, Mismatches: 24, Indels: 15
0.70 0.18 0.11
Matches are distributed among these distances:
64 2 0.02
65 35 0.38
66 54 0.58
67 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (65 bp):
AACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACAATTTCAAAGATGTATGTTTAAAGGGA
Found at i:42402 original size:15 final size:15
Alignment explanation
Indices: 42359--42402 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
42349 AAGATGATCT
* *
42359 TGTTTTAAGAAAAAA
1 TGTTTCAAGAGAAAA
42374 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
42389 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
42403 CGACTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:42558 original size:40 final size:40
Alignment explanation
Indices: 42498--42577 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
42488 GTTTTAATAA
42498 AAACAATCTCAAAGGTGGGTAGTTTT-AAAAGAAATTGTCT
1 AAACAATCTCAAAGGTGGGTA-TTTTCAAAAGAAATTGTCT
* * *
42538 AAACGATCTCAAATGTGGGTATTTTCAAAAGAAGTTGTCT
1 AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
42578 CGAGAGACAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.31
Consensus pattern (40 bp):
AAACAATCTCAAAGGTGGGTATTTTCAAAAGAAATTGTCT
Found at i:42631 original size:63 final size:63
Alignment explanation
Indices: 42559--42683 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 63
42549 AATGTGGGTA
* * * *
42559 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAGCAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
* * *
42621 TTTTCCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCAAAAGAAACAGACTCAAAGAT
1 TTTT-CAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
42684 GGATCTCATC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 4 0.07
63 13 0.24
64 37 0.69
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.30
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
Found at i:42955 original size:63 final size:64
Alignment explanation
Indices: 42851--43073 Score: 247
Period size: 67 Copynumber: 3.5 Consensus size: 64
42841 ATGAACATAT
* * * * * * *
42851 TCAAAGATTTACTTCAAGAGAAACTGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGA
1 TCAAAGATTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAAA
*
42914 T
64 C
* *
42915 TCAAAGATTT-TTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTGTTTCCAAAGAAACAAAC
1 TCAAAGATTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAAAC
* *
42979 TCAAAGATTTTTGTTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAA
1 TCAAAGA--TTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTT-CAAAGAAACAA
43044 AC
63 AC
*
43046 TCAAAGATTT-TTTCAAAAGAAACAATCT
1 TCAAAGATTTATTTCAAAAGAAACTATCT
43074 CAAAGATTTT
Statistics
Matches: 138, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
62 1 0.01
63 30 0.22
64 41 0.30
65 5 0.04
66 3 0.02
67 58 0.42
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (64 bp):
TCAAAGATTTATTTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCAAAGAAACAAAC
Found at i:42971 original size:37 final size:37
Alignment explanation
Indices: 42925--43041 Score: 104
Period size: 37 Copynumber: 3.4 Consensus size: 37
42915 TCAAAGATTT
*
42925 TTTCAAAAGAAATTATCTTAAAAGAGACAAAATTTTG
1 TTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTG
* * * * *
42962 TTTCCAAAGAAACAAAC-T-CAA-AG----ATTTTTG
1 TTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTG
* *
42992 TTTTAAAAGAAACTATCTTAAGAGAGACAAAATTTTG
1 TTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTG
*
43029 TTTCCAAAGAAAC
1 TTTCAAAAGAAAC
43042 AAACTCAAAG
Statistics
Matches: 58, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
30 19 0.33
31 1 0.02
32 1 0.02
33 2 0.03
34 2 0.03
35 2 0.03
36 1 0.02
37 30 0.52
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (37 bp):
TTTCAAAAGAAACTATCTTAAAAGAGACAAAATTTTG
Found at i:43083 original size:26 final size:27
Alignment explanation
Indices: 43029--43085 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
43019 CAAAATTTTG
*
43029 TTTCCAAAGAAACAAACTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
*
43056 TTTCAAAAGAAACAATCTCAAAGATTT
1 TTTCAAAAGAAACAAACTCAAAGATTT
43083 TTT
1 TTT
43086 TTCAAAATTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAAACTCAAAGATTT
Found at i:43146 original size:52 final size:53
Alignment explanation
Indices: 43072--43174 Score: 163
Period size: 52 Copynumber: 2.0 Consensus size: 53
43062 AAGAAACAAT
**
43072 CTCAAAGATTTTTTTTCAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
* *
43125 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACATAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
43175 AAATAAATAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
52 38 0.83
53 8 0.17
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:43247 original size:29 final size:27
Alignment explanation
Indices: 43170--43262 Score: 95
Period size: 26 Copynumber: 3.4 Consensus size: 27
43160 CATAACTTTG
*
43170 TTTCAAAATAAATAGACTCAAAG--ATT
1 TTTCAAAAGAAATA-ACTCAAAGATATT
43196 TTTCAAAAGAAATAACTCAAAGATATT
1 TTTCAAAAGAAATAACTCAAAGATATT
*
43223 TATTCAAAAGGAACA-AACTCCAAGAT-TT
1 T-TTCAAAA-GAA-ATAACTCAAAGATATT
*
43251 TTTCAAGAGAAA
1 TTTCAAAAGAAA
43263 CTGTCTCAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
25 9 0.15
26 16 0.27
27 10 0.17
28 10 0.17
29 13 0.22
30 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (27 bp):
TTTCAAAAGAAATAACTCAAAGATATT
Found at i:43755 original size:105 final size:104
Alignment explanation
Indices: 43576--43814 Score: 317
Period size: 105 Copynumber: 2.3 Consensus size: 104
43566 TAGAGAAATT
*
43576 GTCTCAAGCGAGACAAAGTTTGTTTT--GAG-AAAACGATCTCAAGTGAGATCAACTTTGTTTAA
1 GTCTCAAGCGAGACAAAGTTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTAA
* *
43638 TGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
66 TGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * * *
43677 GTCTCAAGCGAGACAAAATTTGTTTTAAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAGTTTGTTTTAAGAGAAA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
43741 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
63 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
43782 GTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAA
1 GTCTCAAGCGAGACAAAGTTTGTTTTAAGAGAA
43815 TTTGTCTCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
101 25 0.21
103 2 0.02
104 4 0.03
105 83 0.70
106 5 0.04
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (104 bp):
GTCTCAAGCGAGACAAAGTTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTAA
TGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:43821 original size:36 final size:36
Alignment explanation
Indices: 43781--43915 Score: 168
Period size: 35 Copynumber: 3.8 Consensus size: 36
43771 AAAGGAAAAA
* * *
43781 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * **
43817 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
*
43852 TGTCTCAAGCGAGAC-AAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
43887 TGTCTCAAGCGAGACAAAATTTGTTTTAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTAA
43916 AATTCTCAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
34 8 0.10
35 42 0.50
36 34 0.40
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:43865 original size:35 final size:34
Alignment explanation
Indices: 43781--43915 Score: 164
Period size: 36 Copynumber: 3.9 Consensus size: 34
43771 AAAGGAAAAA
* *
43781 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGA-AA-T
* * *
43817 TGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAAA-T
*
43852 TGTCTCAAGCGAGAC-AAATTTGCTTTGAAAGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTT-TAAGAAAT
43887 TGTCTCAAGCGAGACAAAATTTGTTTTAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTAA
43916 AATTCTCAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
34 9 0.11
35 37 0.44
36 39 0.46
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (34 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAAAT
Found at i:43901 original size:70 final size:71
Alignment explanation
Indices: 43781--43913 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 71
43771 AAAGGAAAAA
* * *
43781 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGACAAAATTTGTTTTTA
1 TGTCTCAAGCGAGACGAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTA
43846 GAAAGC
66 GAAAGC
*
43852 TGTCTCAAGCGAGAC-AAATTTGCTTTGAA-AGAAATTGTCTCAAGCGAGACAAAATTTGTTTT
1 TGTCTCAAGCGAGACGAAATTTG-TTTGAAGAGAAATTGTCTCAAACGAGACAAAATTTGTTTT
43914 AAAATTCTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
70 37 0.65
71 20 0.35
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (71 bp):
TGTCTCAAGCGAGACGAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTA
GAAAGC
Found at i:44290 original size:12 final size:12
Alignment explanation
Indices: 44273--44320 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
44263 TGTAACATGC
44273 ATGTATGTGTTG
1 ATGTATGTGTTG
*
44285 ATGTATGTATATATG
1 ATGTATG--TGT-TG
44300 TATGTATGTGTTG
1 -ATGTATGTGTTG
44313 ATGTATGT
1 ATGTATGT
44321 TTCTCAATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 15 0.50
13 2 0.07
14 4 0.13
15 2 0.07
16 7 0.23
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (12 bp):
ATGTATGTGTTG
Found at i:44294 original size:16 final size:16
Alignment explanation
Indices: 44273--44320 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
44263 TGTAACATGC
44273 ATGTATGTGTTGATGT
1 ATGTATGTGTTGATGT
*
44289 ATGTA--T-AT-ATGT
1 ATGTATGTGTTGATGT
44301 ATGTATGTGTTGATGT
1 ATGTATGTGTTGATGT
44317 ATGT
1 ATGT
44321 TTCTCAATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 9 0.35
13 1 0.04
14 2 0.08
15 1 0.04
16 13 0.50
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (16 bp):
ATGTATGTGTTGATGT
Found at i:46210 original size:20 final size:20
Alignment explanation
Indices: 46141--46211 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 20
46131 TTCAAAGTGG
46141 AAAGAATATTTCAAGGTCTC
1 AAAGAATATTTCAAGGTCTC
* **
46161 AAAGAGAGGGAATGTTTCAAGGTCGA
1 --A-A-A--GAATATTTCAAGGTCTC
46187 AAAGAATATTTCAAGGTCTC
1 AAAGAATATTTCAAGGTCTC
46207 AAAGA
1 AAAGA
46212 GATAGAATGT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
20 19 0.49
22 2 0.05
23 2 0.05
24 2 0.05
26 14 0.36
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (20 bp):
AAAGAATATTTCAAGGTCTC
Found at i:46218 original size:26 final size:26
Alignment explanation
Indices: 46140--46219 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 26
46130 TTTCAAAGTG
46140 GAAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
** *
46166 GAGGGAATGTTTCAAGG--TC---GA
1 GAAAGAATATTTCAAGGTCTCAAAGA
46187 -AAAGAATATTTCAAGGTCTCAAAGA
1 GAAAGAATATTTCAAGGTCTCAAAGA
*
46212 GATAGAAT
1 GAAAGAAT
46220 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 2 0.05
26 20 0.49
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.24
Consensus pattern (26 bp):
GAAAGAATATTTCAAGGTCTCAAAGA
Found at i:46220 original size:46 final size:45
Alignment explanation
Indices: 46128--46221 Score: 143
Period size: 46 Copynumber: 2.1 Consensus size: 45
46118 ATAAATACAG
* *
46128 TGTTTCAAAGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGGAA
1 TGTTTCAAAGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
* *
46173 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAAGT-GAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
46219 TGT
1 TGT
46222 CAAAAATTGG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 10 0.23
46 34 0.77
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (45 bp):
TGTTTCAAAGTGAAAAGAATATTTCAAGGTCTCAAAGAGAGAGAA
Found at i:50457 original size:29 final size:29
Alignment explanation
Indices: 50425--50484 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
50415 TGGTAATAAT
* * *
50425 AAATTAAAGGGCTAAAACAGAAAAATAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
* *
50454 AAATTAAAAGACTAAAATAGCAAAACAGA
1 AAATTAAAAGACTAAAACAGAAAAACAGA
50483 AA
1 AA
50485 CGTAGGGACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.13, T:0.13
Consensus pattern (29 bp):
AAATTAAAAGACTAAAACAGAAAAACAGA
Found at i:52077 original size:3 final size:3
Alignment explanation
Indices: 52065--52131 Score: 100
Period size: 3 Copynumber: 22.0 Consensus size: 3
52055 AATATATATG
*
52065 TAA TAT TAA TAA T-A TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
52110 TAA TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TA-A TAA
52132 ATAAGACCCG
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 2 0.03
3 51 0.86
4 6 0.10
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:54196 original size:35 final size:33
Alignment explanation
Indices: 54152--54224 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 33
54142 GACCAAATCC
* * *
54152 AAAACAAAAATGAATCATTCAGTTTCTTCTTCA
1 AAAACAAAAATAAATCATGCAATTTCTTCTTCA
*
54185 ACAAACAAAAAATAAATCATGCAATTTGTTCTTCA
1 A-AAAC-AAAAATAAATCATGCAATTTCTTCTTCA
54220 AAAAC
1 AAAAC
54225 TGAATCGTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
33 1 0.03
34 8 0.24
35 25 0.74
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.29
Consensus pattern (33 bp):
AAAACAAAAATAAATCATGCAATTTCTTCTTCA
Found at i:54987 original size:63 final size:63
Alignment explanation
Indices: 54869--54993 Score: 146
Period size: 65 Copynumber: 2.0 Consensus size: 63
54859 GTTTGCTGTT
* * *
54869 TTAGTGTAAGTTTTTACAATTTAATATATTGCTTCTATAATAGCAGTATTGATATATTATATA
1 TTAGTGTAAGTTTTTACAATTTAATACATTGCTTCAATAATAGCAGTATTGATATAATATATA
* * * **
54932 TTAGTGTAAGAATTTTTACGATTTAATACATTGTTTCAATTATAGTTGT-TT-ATATAATATAT
1 TTAGTGTAAG--TTTTTACAATTTAATACATTGCTTCAATAATAGCAGTATTGATATAATATAT
54994 TGTTTCTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
63 20 0.38
64 2 0.04
65 30 0.58
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (63 bp):
TTAGTGTAAGTTTTTACAATTTAATACATTGCTTCAATAATAGCAGTATTGATATAATATATA
Found at i:54998 original size:16 final size:16
Alignment explanation
Indices: 54972--55015 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
54962 TTGTTTCAAT
54972 TATAGTTGTTTATATAA
1 TATA-TTGTTTATATAA
*
54989 TATATTGTTTCTATAA
1 TATATTGTTTATATAA
*
55005 CATATTGTTTA
1 TATATTGTTTA
55016 GTTTAAGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.55
Consensus pattern (16 bp):
TATATTGTTTATATAA
Found at i:55721 original size:21 final size:21
Alignment explanation
Indices: 55692--55735 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
55682 TTGTGAATAA
* *
55692 GTTACTAAGGTTGTTGAGGGT
1 GTTAATAAGATTGTTGAGGGT
*
55713 GTTAATAAGATTGTTGATGGT
1 GTTAATAAGATTGTTGAGGGT
55734 GT
1 GT
55736 GATAATTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.41
Consensus pattern (21 bp):
GTTAATAAGATTGTTGAGGGT
Found at i:56371 original size:15 final size:15
Alignment explanation
Indices: 56351--56385 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
56341 TATTGGAGAG
56351 GATGTTGTGGAAGAA
1 GATGTTGTGGAAGAA
56366 GATGTTGTGGAAGAA
1 GATGTTGTGGAAGAA
56381 GATGT
1 GATGT
56386 AGTAAACGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.40, T:0.29
Consensus pattern (15 bp):
GATGTTGTGGAAGAA
Found at i:58396 original size:54 final size:54
Alignment explanation
Indices: 58273--58727 Score: 597
Period size: 54 Copynumber: 8.4 Consensus size: 54
58263 TGGTTTTCGT
* * ** * * * **
58273 ACACGTAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTTGGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTC-TTAAGTTGC
* *
58328 ACACATAGTGCCAATACAAAAATTCATAAACTTATTATGAACTTCTTAAGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* * * *
58382 ACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTTC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
*
58436 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAACTTCTTAAGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* * * * * * *
58490 ACACACAGTTCCAGTAGGGAAATTCATAACCTTATTATGAATTTCTTAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
*
58544 ACACATAGTGCTAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* * *
58598 ACACACATTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
* *
58652 ACACATAGTGCCAATACGAAAATTCATAAAATTATTTTGAATTTCTTAAGGTTGC
1 ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAA-GTTGC
**
58707 AC-CATAACGCCAATACTGAAA
1 ACACATAGTGCCAATAC-GAAA
58728 CTCATTATGA
Statistics
Matches: 349, Mismatches: 49, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 302 0.87
55 47 0.13
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (54 bp):
ACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGC
Found at i:58469 original size:108 final size:108
Alignment explanation
Indices: 58279--58708 Score: 671
Period size: 108 Copynumber: 4.0 Consensus size: 108
58269 TCGTACACGT
* * * * * *
58279 AGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTTGGGTTGCACACATAGTGCCAATA
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATA
*
58344 CAAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
65 CGAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
*
58388 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTTCACACATAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
58453 GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
66 GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
* * * * *
58496 AGTTCCAGTAGGGAAATTCATAACCTTATTATGAATTTCTTAGGTTGCACACATAGTGCTAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
*
58561 GAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
66 GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
* *
58604 ATTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
1 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
* * *
58669 GAAAATTCATAAAATTATTTTGAATTTCTTAAGGTTGCAC
66 GAAAATTCATAAACTTATTATGAACTTCTTAA-GTTGCAC
58709 CATAACGCCA
Statistics
Matches: 296, Mismatches: 24, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
108 255 0.86
109 41 0.14
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (108 bp):
AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATAC
GAAAATTCATAAACTTATTATGAACTTCTTAAGTTGCACACAC
Found at i:63192 original size:18 final size:19
Alignment explanation
Indices: 63169--63216 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
63159 GATGCAGTTA
* *
63169 GTATCGATAC-TGATGTGG
1 GTATCGATACATGAGGTAG
63187 GTATCGATACTATGAGGTAG
1 GTATCGATAC-ATGAGGTAG
63207 GTATCGATAC
1 GTATCGATAC
63217 CGTGGATTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (19 bp):
GTATCGATACATGAGGTAG
Found at i:63284 original size:22 final size:22
Alignment explanation
Indices: 63258--63319 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
63248 ACTGCAAGGG
* *
63258 AGTATCGGTACCATATTATAGA
1 AGTATCGATACCATAGTATAGA
63280 AGTATCGATACCATAGTATAGA
1 AGTATCGATACCATAGTATAGA
*
63302 AGTATCGATACCACAGTA
1 AGTATCGATACCATAGTA
63320 GAGGTACCGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGA
Found at i:63969 original size:61 final size:60
Alignment explanation
Indices: 63728--64032 Score: 346
Period size: 60 Copynumber: 5.1 Consensus size: 60
63718 ATGCTCTAAA
* * * *
63728 ATGA-AAGTTAAATGCCTGACGGTGCATTTTGGCAGAAATGTGTCACTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAAAGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* * *
63787 ATGATAAGATAAATGGCTAACA-TTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAA-AGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* * * * *
63847 ATGATAAGTTAAATGTCTAATGGTGCATTTTGGCAGAAAAGTGTCATTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAAAGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* *
63907 ATGATAAGTTAAATGACTAAAGGTGCATTTTTGACAGAAAGGTGCCACTAATGCAAGTTAG
1 ATGATAAGTTAAATGCCTAAAGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
* * * * * * ** *
63968 ATTAAAAATTTAAATGCCT-AATGAGAATTTTTGGCATTAAGGTGCCACTAATGCTAGTTAG
1 A-TGATAAGTTAAATGCCTAAAGGTGCA-TTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
64029 ATGA
1 ATGA
64033 AAAAACAATG
Statistics
Matches: 209, Mismatches: 32, Indels: 9
0.84 0.13 0.04
Matches are distributed among these distances:
59 4 0.02
60 126 0.60
61 66 0.32
62 13 0.06
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.30
Consensus pattern (60 bp):
ATGATAAGTTAAATGCCTAAAGGTGCATTTTGGCAGAAAGGTGCCACTAATGCAAGTTAG
Found at i:67594 original size:54 final size:54
Alignment explanation
Indices: 67510--67852 Score: 474
Period size: 54 Copynumber: 6.3 Consensus size: 54
67500 ATCACGTGGG
* * *
67510 GTTGCACCCATAGTGCCAATACAGAAATTCATAAACTTATTATGAACTTCTTAA
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* * *
67564 GTTTCACACACAGTGCCAATACGGAAATTCATAAAATTATTATGAATTTCTT-A
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* **
67617 GTTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAGCTTCTTAA
1 G-TTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* * * *
67672 GTTGCACACACAGTTCCAATAGGGAAATTCATAAACTTATTATGAATTTCTTAG
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
*
67726 GTTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAA
1 GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
* * * *
67780 GGTTGTACACATAGTTCCAATACAGAAATTCATAAACTCATTATGAATTT-TGTAA
1 -GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCT-TAA
67835 GGTTGCACACATAGTGCC
1 -GTTGCACACATAGTGCC
67853 CTTTCGGTAA
Statistics
Matches: 254, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
53 2 0.01
54 187 0.74
55 65 0.26
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (54 bp):
GTTGCACACATAGTGCCAATACGGAAATTCATAAACTTATTATGAATTTCTTAA
Found at i:67668 original size:108 final size:108
Alignment explanation
Indices: 67473--67852 Score: 523
Period size: 108 Copynumber: 3.5 Consensus size: 108
67463 TATTATGCCG
* * * ** ** *
67473 ATACGGTAATTCACAAACTCATTATGAATCACGTGGGGTTGCACCCATAGTGCCAATAC-AGAAA
1 ATACGGAAATTCATAAACTTATTATGAATTTC-TTAGGTTGCACACATAGTGCCAATACGA-AAA
*
67537 TTCATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTGCCA
64 TTCATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTTCCA
* *
67582 ATACGGAAATTCATAAAATTATTATGAATTTCTTAGTTTGCACACATAGTGCCAATACGAAAATT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
* *
67647 CATAAACTTATTATGAGCTTCTTAAGTTGCACACACAGTTCCA
66 CATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTTCCA
*
67690 ATAGGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
1 ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
* *
67755 CATAAACTTATTATGAATTTCTTAAGGTTGT-ACACATAGTTCCA
66 CATAAACTTATTATGAACTTCTTAA-GTT-TCACACACAGTTCCA
* *
67799 ATACAGAAATTCATAAACTCATTATGAATTT-TGTAAGGTTGCACACATAGTGCC
1 ATACGGAAATTCATAAACTTATTATGAATTTCT-T-AGGTTGCACACATAGTGCC
67853 CTTTCGGTAA
Statistics
Matches: 243, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
108 153 0.63
109 71 0.29
110 19 0.08
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (108 bp):
ATACGGAAATTCATAAACTTATTATGAATTTCTTAGGTTGCACACATAGTGCCAATACGAAAATT
CATAAACTTATTATGAACTTCTTAAGTTTCACACACAGTTCCA
Found at i:69987 original size:18 final size:19
Alignment explanation
Indices: 69964--69999 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
69954 ATGACAAGCC
69964 TATTGGAAATG-TTGAAAA
1 TATTGGAAATGTTTGAAAA
69982 TATTGGAAATGTTTGAAA
1 TATTGGAAATGTTTGAAA
70000 TAATCCAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.22, T:0.36
Consensus pattern (19 bp):
TATTGGAAATGTTTGAAAA
Found at i:70694 original size:27 final size:27
Alignment explanation
Indices: 70654--70709 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
70644 TTTTGTATTT
* *
70654 TGGTCTTTTGTTTTGTATGCAACAAGC
1 TGGTCTTTTATTTTGTATGAAACAAGC
70681 TGGTCTTTTATTTTGTATGAAACAAGC
1 TGGTCTTTTATTTTGTATGAAACAAGC
70708 TG
1 TG
70710 ATTGATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.45
Consensus pattern (27 bp):
TGGTCTTTTATTTTGTATGAAACAAGC
Found at i:73662 original size:14 final size:14
Alignment explanation
Indices: 73643--73692 Score: 68
Period size: 14 Copynumber: 3.6 Consensus size: 14
73633 AAGTCAATGG
73643 GTTGACTCAGAAGA
1 GTTGACTCAGAAGA
73657 GTTGACTCAGACA-A
1 GTTGACTCAGA-AGA
73671 GTTGACTCA-AACGA
1 GTTGACTCAGAA-GA
73685 GTTGACTC
1 GTTGACTC
73693 GATTTAGACC
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.03
13 1 0.03
14 30 0.91
15 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGAAGA
Done.