Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009585.1 Hibiscus syriacus cultivar Beakdansim tig00116962_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: 8285662
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 35
Found at i:2682704 original size:20 final size:20
Alignment explanation
Indices: 2682679--2682722 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2682669 ATATATATAT
2682679 ATATATATATATGGATGGATGG
1 ATATAT-TA-ATGGATGGATGG
*
2682701 ATATATTAATGGGTGGATGG
1 ATATATTAATGGATGGATGG
2682721 AT
1 AT
2682723 GCTGCGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (20 bp):
ATATATTAATGGATGGATGG
Found at i:2682706 original size:2 final size:2
Alignment explanation
Indices: 2682661--2682690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2682651 CGTTTTTTTA
2682661 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
2682691 GGATGGATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2683105 original size:33 final size:33
Alignment explanation
Indices: 2683058--2683120 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
2683048 TTGGTTTTTG
*
2683058 CTGCCTAGATCTAGACCCTTGTGTTAGTTTCTA
1 CTGCCTAGACCTAGACCCTTGTGTTAGTTTCTA
*
2683091 CTGCCTAGACCTAGACCTTTGTGTTAGTTT
1 CTGCCTAGACCTAGACCCTTGTGTTAGTTT
2683121 TTTTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (33 bp):
CTGCCTAGACCTAGACCCTTGTGTTAGTTTCTA
Found at i:2688517 original size:11 final size:12
Alignment explanation
Indices: 2688501--2688542 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
2688491 TTCATGTAAT
2688501 TAAAATAAA-AA
1 TAAAATAAAGAA
2688512 TAAAATAAAGAA
1 TAAAATAAAGAA
2688524 TAATAATTAAAGTAA
1 TAA-AA-TAAAG-AA
2688539 TAAA
1 TAAA
2688543 TTTAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 5 0.19
13 2 0.07
14 6 0.22
15 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (12 bp):
TAAAATAAAGAA
Found at i:2690108 original size:3 final size:3
Alignment explanation
Indices: 2690102--2690147 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2690092 AATTATTATT
2690102 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2690148 GTATGTGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2690552 original size:137 final size:137
Alignment explanation
Indices: 2690299--2690683 Score: 486
Period size: 137 Copynumber: 2.8 Consensus size: 137
2690289 AAATCAAACT
* * * * * * * *
2690299 GGTGTATGACACTGTTCCTTCGTGATGAGGATATTTGGTCATTTTTAGAAATAAATAGTGATAAC
1 GGTGAATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATATTTA-AAAT-ATTTGAGATAAC
* *
2690364 ACAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGAAG-CGACTCCTTCGTGATGAGAA
64 ACAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTTGACTCCTTCGTGATGAGAA
2690428 GTTCTGATC
129 GTTCTGATC
*
2690437 GGTGGATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATATTTAAAGATATTTGAGATAACA
1 GGTGAATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATATTTAAA-ATATTTGAGATAACA
* ** * *
2690502 CAGTTCCTTCGTGATGAGGACATCTGACTATCTAAGAATGATGTTG-CTCCTTCGTGATGAGGAG
65 CAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTTGACTCCTTCGTGATGAGAAG
2690566 TTCTGATC
130 TTCTGATC
** * * * *
2690574 AATGAATGACATTGTTCCTTCGTGATGTGGACGTCTGGCCATCTTTAAATATATTTGAGATAACA
1 GGTGAATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATATTTAAA-ATATTTGAGATAACA
* * * *
2690639 CAATTCTTTCGTGATGATGACGTCTGGTTATATAAGGATGATGTT
65 CAGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTT
2690684 TCCTAAAGTA
Statistics
Matches: 214, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
137 169 0.79
138 45 0.21
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (137 bp):
GGTGAATGACATTGTTCCTTCGTGATGAGGACATCTGGTCATATTTAAAATATTTGAGATAACAC
AGTTCCTTCGTGATGAGGACGTCTGGTTATCTAAGGATGATGTTGACTCCTTCGTGATGAGAAGT
TCTGATC
Found at i:2690593 original size:40 final size:41
Alignment explanation
Indices: 2690504--2690610 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 41
2690494 AGATAACACA
**
2690504 GTTCCTTCGTGATGAGGACATCTGACTATCTAAGAATGATGTT
1 GTTCCTTCGTGATGAGGACATCTGA--ATCTAAGAATGACATT
* **
2690547 GCTCCTTCGTGATGAGGAGTTCTG-ATC-AATGAATGACATT
1 GTTCCTTCGTGATGAGGACATCTGAATCTAA-GAATGACATT
* *
2690587 GTTCCTTCGTGATGTGGACGTCTG
1 GTTCCTTCGTGATGAGGACATCTG
2690611 GCCATCTTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
39 2 0.04
40 31 0.57
43 21 0.39
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (41 bp):
GTTCCTTCGTGATGAGGACATCTGAATCTAAGAATGACATT
Found at i:2694041 original size:21 final size:21
Alignment explanation
Indices: 2694015--2694059 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2694005 GATTTCTGGG
* *
2694015 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
2694036 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
2694057 CAA
1 CAA
2694060 ACGAACAAAA
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:2695828 original size:103 final size:103
Alignment explanation
Indices: 2695649--2695861 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
2695639 GGGTCTACGC
2695649 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
2695714 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
2695752 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
2695817 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
2695855 AGTCCTT
1 GGTCCTT
2695862 ATGGACATTA
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:2695911 original size:23 final size:23
Alignment explanation
Indices: 2695878--2695940 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2695868 ATTATTATAT
2695878 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
2695901 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
2695924 GGCACTTCGGTACAATT
1 GGCACTACGGTGCAATT
2695941 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:2700787 original size:11 final size:12
Alignment explanation
Indices: 2700771--2700812 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 12
2700761 TTCATGTAAT
2700771 TAAAATAAA-AA
1 TAAAATAAAGAA
2700782 TAAAATAAAGAA
1 TAAAATAAAGAA
2700794 TAATAATTAAAGTAA
1 TAA-AA-TAAAG-AA
2700809 TAAA
1 TAAA
2700813 TTTAAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.33
12 5 0.19
13 2 0.07
14 6 0.22
15 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (12 bp):
TAAAATAAAGAA
Found at i:2704365 original size:17 final size:18
Alignment explanation
Indices: 2704343--2704382 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2704333 CCCATGTATA
2704343 TATGTGAGAAC-TTAAGG
1 TATGTGAGAACATTAAGG
*
2704360 TATGTGAGTACATTAAGG
1 TATGTGAGAACATTAAGG
2704378 T-TGTG
1 TATGTG
2704383 CACTATTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (18 bp):
TATGTGAGAACATTAAGG
Found at i:2705629 original size:9 final size:9
Alignment explanation
Indices: 2705615--2705640 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2705605 ATCCCATGTC
2705615 CATATAACT
1 CATATAACT
2705624 CATATAACT
1 CATATAACT
2705633 CATATAAC
1 CATATAAC
2705641 ATTTTTCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (9 bp):
CATATAACT
Found at i:2707118 original size:24 final size:24
Alignment explanation
Indices: 2707091--2707199 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
2707081 AATTTTTTTA
* * *
2707091 TCTGATTTCCGATTTGAATTATGT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
2707115 TCTGATTTATGATTTGAATTCTTT
1 TCTGATTTCTGATCTGAATTCTGT
* * *
2707139 TTTGATTTCTGACCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2707163 TCTGATATCTGATCTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
*
2707187 TTTGATTTCTGAT
1 TCTGATTTCTGAT
2707200 ATCTCCGTTT
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.18, C:0.13, G:0.17, T:0.52
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2723136 original size:147 final size:147
Alignment explanation
Indices: 2722869--2723167 Score: 544
Period size: 147 Copynumber: 2.0 Consensus size: 147
2722859 GTTTTACTTG
* *
2722869 CTGATGAAATGGGGATTGGAAAAACTGTATCTGCTGTTGCCTTTATTTTGTCACTTTATTTTGAG
1 CTGATGAAATGGGGATTGGAAAAACTGTATCTGCTGTCGCCTTTATTTCGTCACTTTATTTTGAG
* *
2722934 TTTAAAGCTACTCTGCCATGTTTAGTGCTGCTTCCACTTTCTACTATTCCTAACTAGCTTGTTGA
66 TTTAAAGCTACTCTGCCATGTTTAGTGCTGCTTCCACTTTCTACTATGCCTAACTAGCTTGCTGA
2722999 GTTCTCATTATGGGCCC
131 GTTCTCATTATGGGCCC
* *
2723016 CTGATGAAATGGGGCTTGGAAAAACTGTATGTGCTGTCGCCTTTATTTCGTCACTTTATTTTGAG
1 CTGATGAAATGGGGATTGGAAAAACTGTATCTGCTGTCGCCTTTATTTCGTCACTTTATTTTGAG
2723081 TTTAAAGCTACTCTGCCATGTTTAGTGCTGCTTCCACTTTCTACTATGCCTAACTAGCTTGCTGA
66 TTTAAAGCTACTCTGCCATGTTTAGTGCTGCTTCCACTTTCTACTATGCCTAACTAGCTTGCTGA
2723146 GTTCTCATTATGGGCCC
131 GTTCTCATTATGGGCCC
2723163 CTGAT
1 CTGAT
2723168 TTAAATGTTG
Statistics
Matches: 146, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
147 146 1.00
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.39
Consensus pattern (147 bp):
CTGATGAAATGGGGATTGGAAAAACTGTATCTGCTGTCGCCTTTATTTCGTCACTTTATTTTGAG
TTTAAAGCTACTCTGCCATGTTTAGTGCTGCTTCCACTTTCTACTATGCCTAACTAGCTTGCTGA
GTTCTCATTATGGGCCC
Found at i:2725688 original size:31 final size:31
Alignment explanation
Indices: 2725650--2725805 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
2725640 CCCGAAGGAC
* * *
2725650 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
2725681 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
2725712 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2725743 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2725774 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
2725805 C
1 C
2725806 CCTCGACCCT
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2726510 original size:21 final size:21
Alignment explanation
Indices: 2726480--2726524 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2726470 ATTCTGCCGT
* *
2726480 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2726501 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2726522 TTG
1 TTG
2726525 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2728826 original size:19 final size:19
Alignment explanation
Indices: 2728804--2728859 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 19
2728794 GTCTGTTTCC
*
2728804 TACAGTATGTTTTCTACAA
1 TACAGTCTGTTTTCTACAA
*
2728823 TACAGTCTGTTTTCTTTC--
1 TACAGTCTGTTTTC-TACAA
2728841 TACAGTCTGTTTTCTACAA
1 TACAGTCTGTTTTCTACAA
2728860 GGTATCAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 2 0.06
18 14 0.45
19 13 0.42
20 2 0.06
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACAA
Found at i:2734756 original size:19 final size:19
Alignment explanation
Indices: 2734732--2734789 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2734722 GTATGTTTCC
*
2734732 TACAGTATGTTTTCTACAA
1 TACAGTCTGTTTTCTACAA
* *
2734751 TACAGTCTGTTGTCTTTC--
1 TACAGTCTGTTTTC-TACAA
2734769 TACAGTCTGTTTTCTACAA
1 TACAGTCTGTTTTCTACAA
2734788 TA
1 TA
2734790 ATAAGTTCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.06
18 13 0.42
19 14 0.45
20 2 0.06
ACGTcount: A:0.24, C:0.19, G:0.12, T:0.45
Consensus pattern (19 bp):
TACAGTCTGTTTTCTACAA
Found at i:2735525 original size:18 final size:18
Alignment explanation
Indices: 2735502--2735544 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
2735492 GGAGGTTGTT
2735502 AGGGAAGGTTGATTTCTC
1 AGGGAAGGTTGATTTCTC
2735520 AGGGAAGGTTGATTTCTC
1 AGGGAAGGTTGATTTCTC
*
2735538 GGGGAAG
1 AGGGAAG
2735545 ATTAAGGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.23, C:0.09, G:0.40, T:0.28
Consensus pattern (18 bp):
AGGGAAGGTTGATTTCTC
Found at i:2741126 original size:18 final size:18
Alignment explanation
Indices: 2741103--2741141 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
2741093 ACATGCAGTT
2741103 GAACTTTTGTTAAAGAAC
1 GAACTTTTGTTAAAGAAC
2741121 GAACTTTTGTTAAAGAAC
1 GAACTTTTGTTAAAGAAC
2741139 GAA
1 GAA
2741142 AGTGGAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (18 bp):
GAACTTTTGTTAAAGAAC
Found at i:2748933 original size:3 final size:3
Alignment explanation
Indices: 2748925--2748950 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2748915 TATAGGCGGT
2748925 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
2748951 TTGATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2750695 original size:29 final size:29
Alignment explanation
Indices: 2750651--2750724 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 29
2750641 CAGAAATTAA
* *
2750651 TTACGAAACTAACACCCTTTTAAAAATAC
1 TTACAAAACTAGCACCCTTTTAAAAATAC
*
2750680 TTACAAAACTAGCACCCTTTTAAAAATAT
1 TTACAAAACTAGCACCCTTTTAAAAATAC
*
2750709 TTACAAAAATAGCACC
1 TTACAAAACTAGCACC
2750725 GAACAGAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.46, C:0.23, G:0.04, T:0.27
Consensus pattern (29 bp):
TTACAAAACTAGCACCCTTTTAAAAATAC
Found at i:2751256 original size:10 final size:10
Alignment explanation
Indices: 2751241--2751267 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2751231 AAGCTAGCTT
2751241 AAATGAGGAA
1 AAATGAGGAA
2751251 AAATGAGGAA
1 AAATGAGGAA
2751261 AAATGAG
1 AAATGAG
2751268 TTTAACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.30, T:0.11
Consensus pattern (10 bp):
AAATGAGGAA
Found at i:2754072 original size:31 final size:31
Alignment explanation
Indices: 2754034--2754097 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
2754024 TTGGTCCATA
*
2754034 AGGAATTACCAATC-G-GTACTGAACCTGTCAG
1 AGGAATTACCAA-CAGCG-ACTGAACCTGCCAG
2754065 AGGAATTACCAACAGCGACTGAACCTGCCAG
1 AGGAATTACCAACAGCGACTGAACCTGCCAG
2754096 AG
1 AG
2754098 TCTTCATACC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 1 0.03
31 28 0.93
32 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.17
Consensus pattern (31 bp):
AGGAATTACCAACAGCGACTGAACCTGCCAG
Found at i:2754933 original size:29 final size:29
Alignment explanation
Indices: 2754900--2754961 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
2754890 CATAAATTAA
2754900 TTACGAAACTAACACCCTTTTAAAAATAC
1 TTACGAAACTAACACCCTTTTAAAAATAC
*
2754929 TTACGAAACTAACACCCTTTTAAAAATAG
1 TTACGAAACTAACACCCTTTTAAAAATAC
2754958 TTAC
1 TTAC
2754962 AAAAATAGCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.29
Consensus pattern (29 bp):
TTACGAAACTAACACCCTTTTAAAAATAC
Found at i:2754973 original size:29 final size:29
Alignment explanation
Indices: 2754900--2754973 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
2754890 CATAAATTAA
* *
2754900 TTACGAAACTAACACCCTTTTAAAAATAC
1 TTACAAAAATAACACCCTTTTAAAAATAC
* * *
2754929 TTACGAAACTAACACCCTTTTAAAAATAG
1 TTACAAAAATAACACCCTTTTAAAAATAC
*
2754958 TTACAAAAATAGCACC
1 TTACAAAAATAACACC
2754974 GAACAGAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.46, C:0.23, G:0.05, T:0.26
Consensus pattern (29 bp):
TTACAAAAATAACACCCTTTTAAAAATAC
Found at i:2755670 original size:53 final size:53
Alignment explanation
Indices: 2755601--2755703 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 53
2755591 TACATTATGG
* * * * * *
2755601 CATGGTGATTCATCCATTGT-TTGCCACTAACATTTTTTTTAATGTTTAAATCC
1 CATGATGATTAATCCATTATCTT-CCACCAACATTTTTTTAAATATTTAAATCC
2755654 CATGATGATTAATCCATTATCTTCCACCAACATTTTTTTAAATATTTAAA
1 CATGATGATTAATCCATTATCTTCCACCAACATTTTTTTAAATATTTAAA
2755704 ACCCCATGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
53 41 0.95
54 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.08, T:0.44
Consensus pattern (53 bp):
CATGATGATTAATCCATTATCTTCCACCAACATTTTTTTAAATATTTAAATCC
Found at i:2755882 original size:20 final size:21
Alignment explanation
Indices: 2755858--2756037 Score: 179
Period size: 20 Copynumber: 9.0 Consensus size: 21
2755848 AGTTTCCAAT
2755858 TTCGCAACGCGAATATGT-AAA
1 TTCGCAACGCGAATA-GTCAAA
*
2755879 -TCGCAACAC-AGA-AGTCAAA
1 TTCGCAACGCGA-ATAGTCAAA
*
2755898 TTCGCAACAC-AA-AGTCAAA
1 TTCGCAACGCGAATAGTCAAA
*
2755917 TTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCGAA-TAGTCAAA
* *
2755938 -TCGCAACAC-AAAAGTCAAA
1 TTCGCAACGCGAATAGTCAAA
2755957 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAATAGTCAAA
* *
2755977 TTCACAACGCG-ATAGTGAAA
1 TTCGCAACGCGAATAGTCAAA
2755997 TTCGCAACGCG-ATAGTCAAA
1 TTCGCAACGCGAATAGTCAAA
2756017 TTCGCAACGCGAA-AGTCAAA
1 TTCGCAACGCGAATAGTCAAA
2756037 T
1 T
2756038 GTTTTTACGC
Statistics
Matches: 137, Mismatches: 12, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.03
19 27 0.20
20 100 0.73
21 4 0.03
22 2 0.01
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (21 bp):
TTCGCAACGCGAATAGTCAAA
Found at i:2755902 original size:40 final size:40
Alignment explanation
Indices: 2755858--2756037 Score: 201
Period size: 40 Copynumber: 4.5 Consensus size: 40
2755848 AGTTTCCAAT
*
2755858 TTCGCAACGCGAATATGT-AAA-TCGCAACACAGA-AGTCAAA
1 TTCGCAACGCGAA-A-GTCAAATTCGCAACGC-GATAGTCAAA
* *
2755898 TTCGCAACAC-AAAGTCAAATTCGCAACGCGAATTTGT-AAA
1 TTCGCAACGCGAAAGTCAAATTCGCAACGCG-A-TAGTCAAA
* *
2755938 -TCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTCAAA
* * *
2755977 TTCACAACGCGATAGTGAAATTCGCAACGCGATAGTCAAA
1 TTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTCAAA
2756017 TTCGCAACGCGAAAGTCAAAT
1 TTCGCAACGCGAAAGTCAAAT
2756038 GTTTTTACGC
Statistics
Matches: 120, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
37 2 0.02
38 8 0.07
39 24 0.20
40 84 0.70
41 2 0.02
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (40 bp):
TTCGCAACGCGAAAGTCAAATTCGCAACGCGATAGTCAAA
Found at i:2756003 original size:60 final size:59
Alignment explanation
Indices: 2755862--2756037 Score: 230
Period size: 60 Copynumber: 2.9 Consensus size: 59
2755852 TCCAATTTCG
* * *
2755862 CAACGCGAATATGTAAATCGCAACACAGAAGTCAAATTCGCAACAC-AAAGTCAAATTCG
1 CAACGCG-ATATGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCA
* *
2755921 CAACGCGAATTTGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGATAGTCAAATTCA
1 CAACGCG-ATATGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCA
* * *
2755981 CAACGCGATA-GTGAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGTCAAAT
1 CAACGCGATATGT-AAA-TCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAAT
2756038 GTTTTTACGC
Statistics
Matches: 104, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
58 2 0.02
59 48 0.46
60 54 0.52
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.18
Consensus pattern (59 bp):
CAACGCGATATGTAAATCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAATTCA
Found at i:2758526 original size:12 final size:12
Alignment explanation
Indices: 2758509--2758550 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2758499 TTTTTCGGCA
*
2758509 TTATTTATTTAT
1 TTATTTATTAAT
*
2758521 TTATTTACTAAT
1 TTATTTATTAAT
*
2758533 TTATGTATTAAT
1 TTATTTATTAAT
2758545 TTATTT
1 TTATTT
2758551 TCAGTGGCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (12 bp):
TTATTTATTAAT
Found at i:2758774 original size:21 final size:21
Alignment explanation
Indices: 2758701--2758792 Score: 60
Period size: 21 Copynumber: 4.4 Consensus size: 21
2758691 CTATCATTAA
* * *
2758701 TCAAGAGGCACCTCCTATCGT
1 TCAAGAGGCCCCTCCCATCAT
* *
2758722 TCAAGAGGCGCCTCTCATCA-
1 TCAAGAGGCCCCTCCCATCAT
* * *
2758742 TCGAATAAGCCCCTCCCACCAT
1 TC-AAGAGGCCCCTCCCATCAT
* ** *
2758764 TCAAGAGGCCCTTGTCATCGT
1 TCAAGAGGCCCCTCCCATCAT
2758785 TCAAGAGG
1 TCAAGAGG
2758793 TCCCGCCCGC
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 2 0.04
21 49 0.92
22 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
TCAAGAGGCCCCTCCCATCAT
Found at i:2760380 original size:20 final size:20
Alignment explanation
Indices: 2760352--2760390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2760342 GATTTTCGGT
*
2760352 TTGCAAATTTGGTTATCGCG
1 TTGCAAATTTGGCTATCGCG
*
2760372 TTGCGAATTTGGCTATCGC
1 TTGCAAATTTGGCTATCGC
2760391 AACGTTTATT
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:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (20 bp):
TTGCAAATTTGGCTATCGCG
Found at i:2760658 original size:39 final size:39
Alignment explanation
Indices: 2760604--2760690 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
2760594 TCAAGTTGTT
*
2760604 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGAATTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGAATTG
**
2760643 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGAACCATATGAGAATTG
2760682 GATTTTGAT
1 GATTTTGAT
2760691 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.20, C:0.14, G:0.21, T:0.46
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGAACCATATGAGAATTG
Found at i:2761533 original size:34 final size:34
Alignment explanation
Indices: 2761495--2761566 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
2761485 AAAGTCAAAT
2761495 TCGCAACGC-GATTTTCG-GTTTGCGAATTTGACTA
1 TCGCAACGCTGATTTT-GTGTTT-CGAATTTGACTA
* *
2761529 TCGCAACGCTTATTTTGTGTTTCGAATTTGACTT
1 TCGCAACGCTGATTTTGTGTTTCGAATTTGACTA
2761563 TCGC
1 TCGC
2761567 GTTGATCGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 25 0.74
35 9 0.26
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (34 bp):
TCGCAACGCTGATTTTGTGTTTCGAATTTGACTA
Found at i:2761870 original size:18 final size:18
Alignment explanation
Indices: 2761847--2761882 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2761837 AAGCCGGTTG
*
2761847 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
2761865 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
2761883 CCTTTTGCTT
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:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:2764323 original size:12 final size:12
Alignment explanation
Indices: 2764302--2764335 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2764292 GGTTTTGGGT
*
2764302 TTTGAGATTGTG
1 TTTGATATTGTG
2764314 TTTGATATTGTG
1 TTTGATATTGTG
*
2764326 TTTGGTATTG
1 TTTGATATTG
2764336 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2764924 original size:14 final size:15
Alignment explanation
Indices: 2764888--2764925 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2764878 GAAATCATTG
2764888 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
2764903 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
2764918 AAAAATTA
1 AAAAATTA
2764926 GAGACGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2765106 original size:19 final size:20
Alignment explanation
Indices: 2765082--2765128 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2765072 ACTAAAACCT
2765082 GTTGCGAAATTAAAT-TCGC
1 GTTGCGAAATTAAATATCGC
* * *
2765101 GTTGCGAATTTGACTATCGC
1 GTTGCGAAATTAAATATCGC
2765121 GTTGCGAA
1 GTTGCGAA
2765129 TTTGACTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGAAATTAAATATCGC
Found at i:2765122 original size:20 final size:20
Alignment explanation
Indices: 2765097--2765155 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
2765087 GAAATTAAAT
2765097 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
2765117 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
***
2765137 TATTGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
2765156 TCTGTGTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:2765163 original size:20 final size:21
Alignment explanation
Indices: 2765101--2765163 Score: 87
Period size: 20 Copynumber: 3.1 Consensus size: 21
2765091 TTAAATTCGC
*
2765101 GTTGCGAATTTGACTATC-GC
1 GTTGCGAATTTGACTATCTGT
*
2765121 GTTGCGAATTTGACTATAT-T
1 GTTGCGAATTTGACTATCTGT
2765141 GTTGCGAATTTGACT-TCTGT
1 GTTGCGAATTTGACTATCTGT
2765161 GTT
1 GTT
2765164 ACGATTTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.95
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (21 bp):
GTTGCGAATTTGACTATCTGT
Found at i:2765185 original size:40 final size:43
Alignment explanation
Indices: 2765092--2765187 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 43
2765082 GTTGCGAAAT
*
2765092 TAAATTCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGAC
1 TAAATTCGCGTTGCGAATTTGACTATCGCGTTACGAATTTGAC
* *
2765135 TATATT---GTTGCGAATTTGACT-TCTGTGTTACG-ATTT-AC
1 TAAATTCGCGTTGCGAATTTGACTATC-GCGTTACGAATTTGAC
2765173 -AAATTCGCGTTGCGA
1 TAAATTCGCGTTGCGA
2765188 TTTACATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
37 4 0.09
38 2 0.04
39 6 0.13
40 28 0.62
43 5 0.11
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.39
Consensus pattern (43 bp):
TAAATTCGCGTTGCGAATTTGACTATCGCGTTACGAATTTGAC
Found at i:2765204 original size:20 final size:20
Alignment explanation
Indices: 2765160--2765207 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2765150 TTGACTTCTG
* *
2765160 TGTTACGATTTACAAATTCG
1 TGTTGCGATTTACAAATTCA
* *
2765180 CGTTGCGATTTACATATTCA
1 TGTTGCGATTTACAAATTCA
2765200 TGTTGCGA
1 TGTTGCGA
2765208 AATTGGAAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (20 bp):
TGTTGCGATTTACAAATTCA
Found at i:2770031 original size:21 final size:22
Alignment explanation
Indices: 2770005--2770045 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2769995 GTATTCACAT
2770005 GAATCAAATAA-CATATATATC
1 GAATCAAATAATCATATATATC
* *
2770026 GAATCATATAATCATGTATA
1 GAATCAAATAATCATATATA
2770046 ACTCATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (22 bp):
GAATCAAATAATCATATATATC
Found at i:2776764 original size:55 final size:55
Alignment explanation
Indices: 2776705--2777191 Score: 282
Period size: 51 Copynumber: 9.1 Consensus size: 55
2776695 GTCAGGATAA
* *
2776705 ATAAGACTTGAAAAATCTTCAA-ATGACGAGCCTGCTCCCTATTCCTTCAGGAAGT
1 ATAAGACTTGAAAAATCTTCAACA-AACGTGCCTGCTCCCTATTCCTTCAGGAAGT
* * ** * * * * *
2776760 ATAAGACTCGAACAATCCTT-TGCAAGCGTGTCTTCTCCCTATTCATTCAGGGAGT
1 ATAAGACTTGAAAAAT-CTTCAACAAACGTGCCTGCTCCCTATTCCTTCAGGAAGT
* * * *
2776815 ATAAGAC-TCAAACAATCTTCAACAAACGTGTCTGCTCCCTATTCGTTCAGGGAGT
1 ATAAGACTTGAAA-AATCTTCAACAAACGTGCCTGCTCCCTATTCCTTCAGGAAGT
* *
2776870 ATAAGACTTGAATAATCTTCAACAAACGGGTCC-GCTCCCTATTCCTTCA-GAGAGT
1 ATAAGACTTGAAAAATCTTCAACAAACGTG-CCTGCTCCCTATTCCTTCAGGA-AGT
* *
2776925 ATAAGACTCG----ATCTTCAATAAACGTGTCC-GCTCCCTATTCCTTCA-GAGAGT
1 ATAAGACTTGAAAAATCTTCAACAAACGTG-CCTGCTCCCTATTCCTTCAGGA-AGT
* * * * *
2776976 ATAGGAC-TCAAACAATCTTCAACGAACTTGTCC-GCTCCCTATTCCTTCA-TAGAGT
1 ATAAGACTTGAAA-AATCTTCAACAAACGTG-CCTGCTCCCTATTCCTTCAGGA-AGT
* * * *
2777031 ATAGGAC-T---CAATCTTCAACGAACTTGTCC-GCTCCCTATTCCTTCA-GAGAGT
1 ATAAGACTTGAAAAATCTTCAACAAACGTG-CCTGCTCCCTATTCCTTCAGGA-AGT
* * *
2777082 ATAGGACTT----AATCTTCAACGAACTTGTCC-GCTCCCTATTCCTTCA-GAGAGT
1 ATAAGACTTGAAAAATCTTCAACAAACGTG-CCTGCTCCCTATTCCTTCAGGA-AGT
* * * *
2777133 ATAGGAC-T---CAATCTTCAACGAACTTGTCC-GCTCCCTATTCCTTCA-GAGAGT
1 ATAAGACTTGAAAAATCTTCAACAAACGTG-CCTGCTCCCTATTCCTTCAGGA-AGT
*
2777184 ATAGGACT
1 ATAAGACT
2777192 CAATCTTCAA
Statistics
Matches: 380, Mismatches: 37, Indels: 33
0.84 0.08 0.07
Matches are distributed among these distances:
50 1 0.00
51 191 0.50
52 1 0.00
54 6 0.02
55 173 0.46
56 8 0.02
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (55 bp):
ATAAGACTTGAAAAATCTTCAACAAACGTGCCTGCTCCCTATTCCTTCAGGAAGT
Found at i:2776960 original size:51 final size:51
Alignment explanation
Indices: 2776794--2777404 Score: 889
Period size: 51 Copynumber: 11.7 Consensus size: 51
2776784 AGCGTGTCTT
* * * * * *
2776794 CTCCCTATTCATTCAGGGAGTATAAGACTCAAACAATCTTCAACAAACGTGTCTG
1 CTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCG
* * * * * **
2776849 CTCCCTATTCGTTCAGGGAGTATAAGACTTGAATAATCTTCAACAAACGGGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAACGAACTTGTCCG
* * ** *
2776904 CTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACGTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
2776955 CTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACT----CAATCTTCAACGAACTTGTCCG
*
2777010 CTCCCTATTCCTTCATAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
*
2777061 CTCCCTATTCCTTCAGAGAGTATAGGACTTAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
2777112 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
2777163 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
* *
2777214 CCCCCTATTCCTTCAGAGAGTATAGGACTCAATATTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
* *
2777265 CTCCCTATTCCTTCAGAGAGTATATGACTCAATCTTCAACGAACTTGTCCA
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
*
2777316 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATATTCAACGAACTTGTCCG
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
2777367 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCA
1 CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCA
2777405 TAAAATAAGT
Statistics
Matches: 521, Mismatches: 30, Indels: 14
0.92 0.05 0.02
Matches are distributed among these distances:
51 399 0.77
54 1 0.00
55 120 0.23
56 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.29
Consensus pattern (51 bp):
CTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCG
Found at i:2777456 original size:37 final size:37
Alignment explanation
Indices: 2777415--2777487 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2777405 TAAAATAAGT
2777415 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
*
2777452 TTGCTTCACTACTCTTTCGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
2777488 ACTATTTTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:2778794 original size:16 final size:16
Alignment explanation
Indices: 2778762--2778898 Score: 73
Period size: 16 Copynumber: 8.1 Consensus size: 16
2778752 TGAACCCTCC
* *
2778762 TTTT-ATTTCTCTTTT
1 TTTTCATTTTTCTCTT
2778777 TTTTCATTTTTCTCTT
1 TTTTCATTTTTCTCTT
*
2778793 TTTTCATTTTTCATTTT
1 TTTTCATTTTTC-TCTT
* *
2778810 TTCTTCCATTTTCCATTTT
1 TT-TT-CATTTTTC-TCTT
* *
2778829 TTCTTC-TTTTTTTC-C
1 TT-TTCATTTTTCTCTT
* *
2778844 TTTTCGTTTTTTCCATCAT
1 TTTTC-ATTTTT-C-TCTT
*
2778863 TTTTCTTTTTTCTCATT
1 TTTTCATTTTTCTC-TT
2778880 TTTTCATTTTTTCTCTT
1 TTTTCA-TTTTTCTCTT
2778897 TT
1 TT
2778899 ATTTCTTCTT
Statistics
Matches: 99, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
14 3 0.03
15 6 0.06
16 29 0.29
17 20 0.20
18 19 0.19
19 22 0.22
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTTCATTTTTCTCTT
Found at i:2778821 original size:19 final size:17
Alignment explanation
Indices: 2778773--2778839 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 17
2778763 TTTATTTCTC
2778773 TTTTTTTTCATTTTTC-
1 TTTTTTTTCATTTTTCA
*
2778789 TCTTTTTTCATTTTTCA
1 TTTTTTTTCATTTTTCA
*
2778806 TTTTTTCTTCCATTTTCCA
1 TTTTTT-TT-CATTTTTCA
2778825 TTTTTTCTTC-TTTTT
1 TTTTTT-TTCATTTTT
2778840 TTCCTTTTCG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
16 15 0.34
17 9 0.20
18 3 0.07
19 17 0.39
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTTTCATTTTTCA
Found at i:2778839 original size:61 final size:58
Alignment explanation
Indices: 2778767--2778903 Score: 145
Period size: 61 Copynumber: 2.2 Consensus size: 58
2778757 CCTCCTTTTA
*
2778767 TTTCTCTTTTTTTTCATTTTTC-TCTTTTT-TCATTTTTCATTTTTTCTTCCA-TTTTCCATTT
1 TTTCTC-TTTTTTTC-CTTTTCGT-TTTTTCTCATTTTTC-TTTTTTC-T-CATTTTTCCATTT
*
2778828 TTTCTTCTTTTTTTCCTTTTCGTTTTTTCCATCATTTTTCTTTTTTCTCATTTTTTCATTT
1 TTTC-TCTTTTTTTCCTTTTCGTTTTTT-C-TCATTTTTCTTTTTTCTCATTTTTCCATTT
2778889 TTTCTCTTTTATTTC
1 TTTCTCTTTT-TTTC
2778904 TTCTTCAAGC
Statistics
Matches: 67, Mismatches: 2, Indels: 14
0.81 0.02 0.17
Matches are distributed among these distances:
60 18 0.27
61 31 0.46
62 9 0.13
63 9 0.13
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.72
Consensus pattern (58 bp):
TTTCTCTTTTTTTCCTTTTCGTTTTTTCTCATTTTTCTTTTTTCTCATTTTTCCATTT
Found at i:2778840 original size:19 final size:19
Alignment explanation
Indices: 2778799--2778884 Score: 60
Period size: 19 Copynumber: 4.8 Consensus size: 19
2778789 TCTTTTTTCA
*
2778799 TTTTT-CATTTTTTCTTCC
1 TTTTTCCATTTTTTCTTCT
*
2778817 ATTTTCCATTTTTTCTTCTT
1 TTTTTCCATTTTTTCTTC-T
*
2778837 TTTTTCC---TTTTC--GT
1 TTTTTCCATTTTTTCTTCT
**
2778851 TTTTTCCATCATTT-TTCT
1 TTTTTCCATTTTTTCTTCT
2778869 TTTTTCTCATTTTTTC
1 TTTTTC-CATTTTTTC
2778885 ATTTTTTCTC
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
14 8 0.16
17 8 0.16
18 11 0.22
19 18 0.35
20 6 0.12
ACGTcount: A:0.07, C:0.21, G:0.01, T:0.71
Consensus pattern (19 bp):
TTTTTCCATTTTTTCTTCT
Found at i:2778892 original size:44 final size:42
Alignment explanation
Indices: 2778776--2778890 Score: 126
Period size: 44 Copynumber: 2.7 Consensus size: 42
2778766 ATTTCTCTTT
* *
2778776 TTTTTCATTTTTCTCTTTTTTCATTTTTCATTTTTTCTTCCA
1 TTTTTCTTTTTTCTCTTTTTTCATTTTTCATTTTTTCATCCA
* * *
2778818 TTTTCCATTTTTTCTTCTTTTTTTC-CTTTTCGTTTTTTCCAT-CA
1 TTTTTC-TTTTTTC-TC-TTTTTTCATTTTTCATTTTTT-CATCCA
2778862 TTTTTCTTTTTTCTCATTTTTTCATTTTT
1 TTTTTCTTTTTTCTC-TTTTTTCATTTTT
2778891 TCTCTTTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
42 14 0.23
43 17 0.28
44 20 0.33
45 9 0.15
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (42 bp):
TTTTTCTTTTTTCTCTTTTTTCATTTTTCATTTTTTCATCCA
Found at i:2788592 original size:51 final size:50
Alignment explanation
Indices: 2788537--2788642 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 50
2788527 TATCTACCCC
* *
2788537 CATGCTTTGTTATCCAAAAAAAGA-AATCCTAACCGCATAATATCTAATTCG
1 CATGC-TT-TTATCCAAAAAAAAATAAACCTAACCGCATAATATCTAATTCG
* * *
2788588 CATGC--TTATTCAAAAAAAAATAAACCTAACCGCATGATATCTAGTTCG
1 CATGCTTTTATCCAAAAAAAAATAAACCTAACCGCATAATATCTAATTCG
2788636 CATGCTT
1 CATGCTT
2788643 GTTCGAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
47 13 0.28
48 29 0.62
51 5 0.11
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (50 bp):
CATGCTTTTATCCAAAAAAAAATAAACCTAACCGCATAATATCTAATTCG
Found at i:2788618 original size:48 final size:50
Alignment explanation
Indices: 2788552--2788663 Score: 156
Period size: 48 Copynumber: 2.2 Consensus size: 50
2788542 TTTGTTATCC
*
2788552 AAAAAAAGAAATCCTAACCGCATAATATCTAATTCGCATGCTTATTC-AA
1 AAAAAAATAAATCCTAACCGCATAATATCTAATTCGCATGCTTATTCGAA
* * *
2788601 AAAAAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCTTGTTCGAA
1 AAAAAAATAAATCCTAACCGCATAATATCTAATTCGCATGCTTATTCGAA
2788650 AAATGAAAATAAAT
1 AAA--AAAATAAAT
2788664 GACTCAAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
48 32 0.58
49 15 0.27
51 8 0.15
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.26
Consensus pattern (50 bp):
AAAAAAATAAATCCTAACCGCATAATATCTAATTCGCATGCTTATTCGAA
Found at i:2793228 original size:24 final size:22
Alignment explanation
Indices: 2793154--2793240 Score: 86
Period size: 22 Copynumber: 3.9 Consensus size: 22
2793144 CATAATTGTC
* *
2793154 CCAAAGGATCACATAGTTTGCA
1 CCAAAGTACCACATAGTTTGCA
* *
2793176 CTAAAGGACCACATAGTTTGCA
1 CCAAAGTACCACATAGTTTGCA
* *
2793198 TCAAAGTGCCACATAGGTTTTGCA
1 CCAAAGTACCACATA-G-TTTGCA
*
2793222 CCGAAGTACCACATA-TTTG
1 CCAAAGTACCACATAGTTTG
2793241 TCATGGATGA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
21 4 0.07
22 31 0.57
23 1 0.02
24 18 0.33
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (22 bp):
CCAAAGTACCACATAGTTTGCA
Found at i:2793961 original size:20 final size:20
Alignment explanation
Indices: 2793936--2793987 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2793926 AAGTTTTAAG
*
2793936 GGTATCGATACCATCCTACA
1 GGTATCGATACCACCCTACA
* **
2793956 GGTATCGATACTACCCTTGA
1 GGTATCGATACCACCCTACA
2793976 GGTATCGATACC
1 GGTATCGATACC
2793988 TCTATCAGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (20 bp):
GGTATCGATACCACCCTACA
Found at i:2810680 original size:23 final size:22
Alignment explanation
Indices: 2810615--2810682 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
2810605 TTATTTTTAT
*
2810615 TTTTA-TTTTAAAAAAGTAATT
1 TTTTATTTTTAAAAAAGTAATA
***
2810636 TTTTATGTGCAAAAAAAAGTAATA
1 TTTTAT-T-TTTAAAAAAGTAATA
2810660 TTTTATTTTTAATAAAAGTAATA
1 TTTTATTTTTAA-AAAAGTAATA
2810683 GCGCATCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
21 5 0.14
22 2 0.06
23 12 0.33
24 17 0.47
ACGTcount: A:0.46, C:0.01, G:0.07, T:0.46
Consensus pattern (22 bp):
TTTTATTTTTAAAAAAGTAATA
Found at i:2811332 original size:2 final size:2
Alignment explanation
Indices: 2811304--2811389 Score: 138
Period size: 2 Copynumber: 43.5 Consensus size: 2
2811294 CCCCTTTGCT
* * *
2811304 TA TA TT TA TA TA TT TA TA CA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2811345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2811387 TA T
1 TA T
2811390 TGTACATGAG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
1 1 0.01
2 76 0.99
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2813805 original size:90 final size:90
Alignment explanation
Indices: 2813652--2813835 Score: 359
Period size: 90 Copynumber: 2.0 Consensus size: 90
2813642 TCAAAATAAG
*
2813652 AAATTCAAAATGTTAGAAACGAATTTAGAACATGTTGATAAATTGGTAAGATTATTGGTTTCCAA
1 AAATTCAAAATGTTAGAAACGAATTTAGAACATGTTGATAAATTGGTAAGATTATTAGTTTCCAA
2813717 ATTTAAGATAGAATATTGGATATTA
66 ATTTAAGATAGAATATTGGATATTA
2813742 AAATTCAAAATGTTAGAAACGAATTTAGAACATGTTGATAAATTGGTAAGATTATTAGTTTCCAA
1 AAATTCAAAATGTTAGAAACGAATTTAGAACATGTTGATAAATTGGTAAGATTATTAGTTTCCAA
2813807 ATTTAAGATAGAATATTGGATATTA
66 ATTTAAGATAGAATATTGGATATTA
2813832 AAAT
1 AAAT
2813836 GTGTTAAAGT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 93 1.00
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.35
Consensus pattern (90 bp):
AAATTCAAAATGTTAGAAACGAATTTAGAACATGTTGATAAATTGGTAAGATTATTAGTTTCCAA
ATTTAAGATAGAATATTGGATATTA
Found at i:2814959 original size:18 final size:18
Alignment explanation
Indices: 2814936--2814970 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2814926 AGGGTTCTAT
2814936 GTGGTCCTTTGGGACATA
1 GTGGTCCTTTGGGACATA
2814954 GTGGTCCTTTGGGACAT
1 GTGGTCCTTTGGGACAT
2814971 TTCTACGCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (18 bp):
GTGGTCCTTTGGGACATA
Found at i:2816497 original size:32 final size:31
Alignment explanation
Indices: 2816461--2816559 Score: 91
Period size: 32 Copynumber: 3.2 Consensus size: 31
2816451 TTGTGATTTT
2816461 TATTTGAACTTGTTGTAAATAATTTATTTATG
1 TATTTGAA-TTGTTGTAAATAATTTATTTATG
* *
2816493 TATTTTG-ATT-TT-CAAACAAATTGTGATTT-T-
1 TA-TTTGAATTGTTGTAAA-TAATT-T-ATTTATG
2816523 TATTTGAATTTGTTGTAAATAATTTATTTATG
1 TATTTGAA-TTGTTGTAAATAATTTATTTATG
2816555 TATTT
1 TATTT
2816560 TGATTTTCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
29 7 0.13
30 13 0.25
31 8 0.15
32 18 0.34
33 7 0.13
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (31 bp):
TATTTGAATTGTTGTAAATAATTTATTTATG
Found at i:2816500 original size:33 final size:32
Alignment explanation
Indices: 2816463--2816562 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 32
2816453 GTGATTTTTA
2816463 TTTGAACTTGTTGTAAATAATTTATTTATGTAT
1 TTTGAA-TTGTTGTAAATAATTTATTTATGTAT
* *
2816496 TTTG-ATT-TT-CAAACAAATTGTGATTT-T-TA-
1 TTTGAATTGTTGTAAA-TAATT-T-ATTTATGTAT
2816525 TTTGAATTTGTTGTAAATAATTTATTTATGTAT
1 TTTGAA-TTGTTGTAAATAATTTATTTATGTAT
2816558 TTTGA
1 TTTGA
2816563 TTTTCAAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
29 7 0.13
30 13 0.25
31 8 0.15
32 13 0.25
33 12 0.23
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.55
Consensus pattern (32 bp):
TTTGAATTGTTGTAAATAATTTATTTATGTAT
Found at i:2816522 original size:62 final size:62
Alignment explanation
Indices: 2816448--2816570 Score: 237
Period size: 62 Copynumber: 2.0 Consensus size: 62
2816438 AAACATGTAG
2816448 AAATTGTGATTTTTATTTGAACTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAAC
1 AAATTGTGATTTTTATTTGAACTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAAC
*
2816510 AAATTGTGATTTTTATTTGAATTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAA
1 AAATTGTGATTTTTATTTGAACTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAA
2816571 TAAAGGAGTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (62 bp):
AAATTGTGATTTTTATTTGAACTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAAC
Found at i:2816542 original size:29 final size:29
Alignment explanation
Indices: 2816448--2816542 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
2816438 AAACATGTAG
*
2816448 AAATTGTGATTTTTATTTGAACTTGTTGT
1 AAATTGTGATTTTTATTTGAATTTGTTGT
* * *****
2816477 AAATAAT-TTATTTATGTATTTTGATTTTCAAAC
1 AAAT--TGTGATTT-T-TA-TTTGAATTTGTTGT
2816510 AAATTGTGATTTTTATTTGAATTTGTTGT
1 AAATTGTGATTTTTATTTGAATTTGTTGT
2816539 AAAT
1 AAAT
2816543 AATTTATTTA
Statistics
Matches: 45, Mismatches: 15, Indels: 12
0.62 0.21 0.17
Matches are distributed among these distances:
29 16 0.36
30 7 0.16
31 4 0.09
32 7 0.16
33 11 0.24
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (29 bp):
AAATTGTGATTTTTATTTGAATTTGTTGT
Found at i:2816573 original size:29 final size:29
Alignment explanation
Indices: 2816477--2816573 Score: 92
Period size: 29 Copynumber: 3.2 Consensus size: 29
2816467 AACTTGTTGT
2816477 AAATAATTTATTTATGTATTTTGATTTTC
1 AAATAATTTATTTATGTATTTTGATTTTC
* *
2816506 AAACAAATTGTGATTT-T-TA-TTTGAATTTGTTGT
1 AAA-TAATT-T-ATTTATGTATTTTG-A-TT-TT-C
2816539 AAATAATTTATTTATGTATTTTGATTTTC
1 AAATAATTTATTTATGTATTTTGATTTTC
2816568 AAATAA
1 AAATAA
2816574 AGGAGTTCAA
Statistics
Matches: 54, Mismatches: 4, Indels: 20
0.69 0.05 0.26
Matches are distributed among these distances:
29 13 0.24
30 13 0.24
31 8 0.15
32 13 0.24
33 7 0.13
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (29 bp):
AAATAATTTATTTATGTATTTTGATTTTC
Found at i:2816595 original size:62 final size:61
Alignment explanation
Indices: 2816462--2816583 Score: 176
Period size: 62 Copynumber: 2.0 Consensus size: 61
2816452 TGTGATTTTT
* * **
2816462 ATTTGAACTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAACAAATTGTGATTTTT
1 ATTTGAATTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAACAAA-TGTGAGTTCA
*
2816524 ATTTGAATTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAATAAA-G-GAGTTCA
1 ATTTGAATTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAACAAATGTGAGTTCA
2816583 A
1 A
2816584 CTTTTGTAAT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
59 5 0.09
60 1 0.02
62 49 0.89
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (61 bp):
ATTTGAATTTGTTGTAAATAATTTATTTATGTATTTTGATTTTCAAACAAATGTGAGTTCA
Found at i:2819936 original size:22 final size:22
Alignment explanation
Indices: 2819893--2819938 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2819883 AAAAAATTAT
*
2819893 TTTTATTAAATATTTTTGATAA
1 TTTTATTAAATATTTTTAATAA
*
2819915 TTTTATTTAAT-TTTTTAAATAA
1 TTTTATTAAATATTTTT-AATAA
2819937 TT
1 TT
2819939 ATGATGTCGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTTTATTAAATATTTTTAATAA
Found at i:2822309 original size:31 final size:30
Alignment explanation
Indices: 2822252--2822309 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
2822242 CCATTTTTAT
*
2822252 TTTTATTATTATTATTCTTTATATTATCTA
1 TTTTATTATTATTATTCTGTATATTATCTA
*
2822282 TTTTATTTTTATTTATTCATGTA-ATTAT
1 TTTTATTATTA-TTATTC-TGTATATTAT
2822310 ATATATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.42
31 11 0.46
32 3 0.12
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (30 bp):
TTTTATTATTATTATTCTGTATATTATCTA
Found at i:2824033 original size:10 final size:10
Alignment explanation
Indices: 2824018--2824051 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
2824008 TTCATTTACC
2824018 ATTTATTTTT
1 ATTTATTTTT
2824028 ATTTATTTTT
1 ATTTATTTTT
* *
2824038 ATCTATTTCT
1 ATTTATTTTT
2824048 ATTT
1 ATTT
2824052 TACTAACATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:2834086 original size:14 final size:14
Alignment explanation
Indices: 2834067--2834094 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2834057 GGAGCATCTC
2834067 TAAAAATAAAAAAA
1 TAAAAATAAAAAAA
2834081 TAAAAATAAAAAAA
1 TAAAAATAAAAAAA
2834095 CCAGAGTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:2834493 original size:105 final size:105
Alignment explanation
Indices: 2834311--2834944 Score: 1142
Period size: 105 Copynumber: 6.0 Consensus size: 105
2834301 AGGTTTTACC
2834311 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2834376 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
2834416 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
2834481 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
2834521 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
2834586 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
2834626 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
2834691 ACGAAGGGACCGCTGGTTGTCTACAAGCATTTCTCAAATC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
2834731 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAGCTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
2834796 ATGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAGATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * *
2834836 CAGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
2834901 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATT
2834942 CAG
1 CAG
2834945 CTTCACAACG
Statistics
Matches: 508, Mismatches: 20, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 496 0.98
106 12 0.02
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:2835027 original size:20 final size:20
Alignment explanation
Indices: 2835002--2835043 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
2834992 CCAGAACTCT
2835002 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
*
2835022 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
2835042 GA
1 GA
2835044 CGAAGGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:2835290 original size:21 final size:23
Alignment explanation
Indices: 2835266--2835315 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 23
2835256 TTTTGTATTA
*
2835266 ATATTATTATATTA-TAC-AATT
1 ATATTATTATATAATTACTAATT
2835287 ATA-TA-TATATAATTACTAATT
1 ATATTATTATATAATTACTAATT
*
2835308 TTATTATT
1 ATATTATT
2835316 TAAATGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
19 6 0.26
20 5 0.22
21 9 0.39
22 2 0.09
23 1 0.04
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTATTATATAATTACTAATT
Found at i:2836510 original size:18 final size:18
Alignment explanation
Indices: 2836480--2836546 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
2836470 TTTACCATTT
*
2836480 TTATTTTTATTATTATTA
1 TTATTTATATTATTATTA
* **
2836498 TTCTTTATATTATCCTTA
1 TTATTTATATTATTATTA
* *
2836516 TTATTTCTATTATTACTA
1 TTATTTATATTATTATTA
*
2836534 TTTTTTAT-TTATT
1 TTATTTATATTATT
2836547 CATGTAATTA
Statistics
Matches: 38, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
17 5 0.13
18 33 0.87
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:2837728 original size:5 final size:5
Alignment explanation
Indices: 2837718--2837742 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2837708 GTTACCATTC
2837718 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
2837743 AAAGTTGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:2838750 original size:30 final size:31
Alignment explanation
Indices: 2838716--2838774 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
2838706 CTTTTGTGCT
2838716 AATTATATTAAAAAACT-T-AAAATATTACTG
1 AATTATATTAAAAAA-TATAAAAATATTACTG
*
2838746 AATTATTTTAAAAAATATAAAAATATTAC
1 AATTATATTAAAAAATATAAAAATATTAC
2838775 AAAATTATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 15 0.58
31 10 0.38
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (31 bp):
AATTATATTAAAAAATATAAAAATATTACTG
Found at i:2838769 original size:31 final size:30
Alignment explanation
Indices: 2838716--2838814 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 30
2838706 CTTTTGTGCT
* **
2838716 AATTATATTAAAAAACTTAAAATATTACTG
1 AATTATTTTAAAAAACTTAAAATATTACAA
2838746 AATTATTTTAAAAAA-TATAAAAATATTACAA
1 AATTATTTTAAAAAACT-T-AAAATATTACAA
* * *
2838777 AATTATTCTAAAATA-TTAAACA-ATTAAAA
1 AATTATTTTAAAAAACTTAAA-ATATTACAA
*
2838806 AAATATTTT
1 AATTATTTT
2838815 TTTTAAAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
29 17 0.29
30 17 0.29
31 24 0.41
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.37
Consensus pattern (30 bp):
AATTATTTTAAAAAACTTAAAATATTACAA
Found at i:2838802 original size:29 final size:31
Alignment explanation
Indices: 2838746--2838872 Score: 93
Period size: 31 Copynumber: 4.1 Consensus size: 31
2838736 AATATTACTG
* *
2838746 AATTATTTTAAAAAATATAAAAATATTACAA
1 AATTATTCTAAAAAATATAAAAATATTAAAA
* *
2838777 AATTATTCTAAAATAT-TAAACAAT-TAAAAA
1 AATTATTCTAAAAAATATAAA-AATATTAAAA
* * **
2838807 AATATTTTTTTTAAAATATATAAAATATT-AAA
1 AAT-TATTCTAAAAAATATA-AAAATATTAAAA
*
2838839 GATTA--CTAAAAAACTATAAAAATATTTAAAA
1 AATTATTCTAAAAAA-TATAAAAATA-TTAAAA
2838870 AAT
1 AAT
2838873 ATTTGTGTGA
Statistics
Matches: 72, Mismatches: 16, Indels: 16
0.69 0.15 0.15
Matches are distributed among these distances:
29 11 0.15
30 17 0.24
31 31 0.43
32 10 0.14
33 3 0.04
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (31 bp):
AATTATTCTAAAAAATATAAAAATATTAAAA
Found at i:2851734 original size:24 final size:24
Alignment explanation
Indices: 2851682--2851737 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2851672 GGTTATGTTG
* *
2851682 TTTATGTTCATTTATGTTCGTTCG
1 TTTATGTTCATTTATGTTCATTCA
* *
2851706 GTTATGTTCGTTTATGTTCATTCA
1 TTTATGTTCATTTATGTTCATTCA
2851730 TTTATGTT
1 TTTATGTT
2851738 TAACCCAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.14, C:0.11, G:0.16, T:0.59
Consensus pattern (24 bp):
TTTATGTTCATTTATGTTCATTCA
Found at i:2851890 original size:7 final size:7
Alignment explanation
Indices: 2851872--2851981 Score: 66
Period size: 7 Copynumber: 15.6 Consensus size: 7
2851862 ATCTGATTAT
2851872 TAAAATCC
1 TAAAA-CC
2851880 TAAAACC
1 TAAAACC
2851887 TAAAACC
1 TAAAACC
*
2851894 T-AAACT
1 TAAAACC
* *
2851900 TTAAATC
1 TAAAACC
*
2851907 TTAAACC
1 TAAAACC
2851914 TTAAAACC
1 -TAAAACC
2851922 T-AAACC
1 TAAAACC
* *
2851928 TTAAATCT
1 -TAAAACC
* *
2851936 TATATCC
1 TAAAACC
2851943 T-AAACC
1 TAAAACC
2851949 ATAAAACC
1 -TAAAACC
2851957 TAAAACC
1 TAAAACC
*
2851964 T-AACCC
1 TAAAACC
2851970 ATAAAACC
1 -TAAAACC
2851978 TAAA
1 TAAA
2851982 CCCTTAATCT
Statistics
Matches: 81, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
6 17 0.21
7 41 0.51
8 23 0.28
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAAACC
Found at i:2851911 original size:28 final size:28
Alignment explanation
Indices: 2851874--2851988 Score: 94
Period size: 28 Copynumber: 4.1 Consensus size: 28
2851864 CTGATTATTA
* *
2851874 AAATCCTAAAACCTAAAACCTAAACTTT
1 AAATCTTAAAACCTAAAACCTAAACCTT
2851902 AAATCTT-AAACCTTAAAACCTAAACCTT
1 AAATCTTAAAACC-TAAAACCTAAACCTT
* *
2851930 AAATCTTATATCCT-AAACCATAAAACC-T
1 AAATCTTAAAACCTAAAACC-T-AAACCTT
* * *
2851958 AAAACCT-AACCCATAAAACCTAAACCCTT
1 AAATCTTAAAACC-TAAAACCTAAA-CCTT
2851987 AA
1 AA
2851989 TCTGATTATG
Statistics
Matches: 71, Mismatches: 8, Indels: 15
0.76 0.09 0.16
Matches are distributed among these distances:
27 16 0.23
28 39 0.55
29 16 0.23
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (28 bp):
AAATCTTAAAACCTAAAACCTAAACCTT
Found at i:2851919 original size:35 final size:35
Alignment explanation
Indices: 2851880--2851966 Score: 115
Period size: 35 Copynumber: 2.5 Consensus size: 35
2851870 ATTAAAATCC
* *
2851880 TAAAACCTAAAACCTAAA-CTTTAAATCTTAAACCT
1 TAAAACCTAAAACCTAAATC-TTAAATCCTAAACCA
*
2851915 TAAAACCT-AAACCTTAAATCTTATATCCTAAACCA
1 TAAAACCTAAAACC-TAAATCTTAAATCCTAAACCA
2851950 TAAAACCTAAAACCTAA
1 TAAAACCTAAAACCTAA
2851967 CCCATAAAAC
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
34 5 0.11
35 35 0.76
36 6 0.13
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.26
Consensus pattern (35 bp):
TAAAACCTAAAACCTAAATCTTAAATCCTAAACCA
Found at i:2851971 original size:21 final size:21
Alignment explanation
Indices: 2851909--2851981 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
2851899 TTTAAATCTT
*
2851909 AAACCTTAAAACCTAAACCTTA
1 AAACC-TAAAACCTAAACCATA
* * * *
2851931 AATCTTATATCCTAAACCATA
1 AAACCTAAAACCTAAACCATA
*
2851952 AAACCTAAAACCTAACCCATA
1 AAACCTAAAACCTAAACCATA
2851973 AAACCTAAA
1 AAACCTAAA
2851982 CCCTTAATCT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 38 0.93
22 3 0.07
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCTAAAACCTAAACCATA
Found at i:2853288 original size:16 final size:16
Alignment explanation
Indices: 2853263--2853293 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2853253 CTGATGATTT
*
2853263 TTTTTTGAGTTCGAGC
1 TTTTTCGAGTTCGAGC
2853279 TTTTTCGAGTTCGAG
1 TTTTTCGAGTTCGAG
2853294 TCGAGTTTTA
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:0.13, C:0.13, G:0.26, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCGAGC
Found at i:2854246 original size:32 final size:33
Alignment explanation
Indices: 2854210--2854275 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 33
2854200 TAAATAATTT
2854210 AACTAAAGACG-CAGGGTAAT-CCTAGGAGCAAA
1 AACTAAAGACGTC-GGGTAATCCCTAGGAGCAAA
*
2854242 AACTAAAGACGTCGGGTAATCCCTTGGAGCAAA
1 AACTAAAGACGTCGGGTAATCCCTAGGAGCAAA
2854275 A
1 A
2854276 TTTTAGCCTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
AACTAAAGACGTCGGGTAATCCCTAGGAGCAAA
Found at i:2854465 original size:27 final size:27
Alignment explanation
Indices: 2854435--2854489 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2854425 CACCATTGCT
* *
2854435 TTCAAGCACTAGTTCATCAACATAATG
1 TTCAAGCACTAGCTCAACAACATAATG
*
2854462 TTCAAGCACTAGCTCAACGACATAATG
1 TTCAAGCACTAGCTCAACAACATAATG
2854489 T
1 T
2854490 AAAAGGAGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (27 bp):
TTCAAGCACTAGCTCAACAACATAATG
Found at i:2854886 original size:31 final size:31
Alignment explanation
Indices: 2854851--2854912 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2854841 TGTGTTTAAT
2854851 TGATGACAT-AAATATGTCATGTCACTCAAAA
1 TGATGACATGAAATATGTCATGTCA-TCAAAA
** *
2854882 TGATGATGTGACATATGTCATGTCATCAAAA
1 TGATGACATGAAATATGTCATGTCATCAAAA
2854913 ATAATAGTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (31 bp):
TGATGACATGAAATATGTCATGTCATCAAAA
Found at i:2855535 original size:11 final size:12
Alignment explanation
Indices: 2855506--2855534 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
2855496 TAAATATTAG
2855506 AAAAAAGGGTTA
1 AAAAAAGGGTTA
2855518 AAAAAAGGGTTA
1 AAAAAAGGGTTA
2855530 AAAAA
1 AAAAA
2855535 GAAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (12 bp):
AAAAAAGGGTTA
Found at i:2856836 original size:12 final size:12
Alignment explanation
Indices: 2856814--2856861 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
2856804 AATGGACCAT
2856814 AAAGAAAAATAAA
1 AAAG-AAAATAAA
2856827 AAAGAAAAT--A
1 AAAGAAAATAAA
2856837 AAAGAATAA-AAA
1 AAAGAA-AATAAA
2856849 AAAG-AAATAAA
1 AAAGAAAATAAA
2856860 AA
1 AA
2856862 TGTAAATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 9 0.29
11 8 0.26
12 10 0.32
13 4 0.13
ACGTcount: A:0.83, C:0.00, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAGAAAATAAA
Found at i:2856861 original size:22 final size:23
Alignment explanation
Indices: 2856814--2856860 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
2856804 AATGGACCAT
2856814 AAAGAAAAATAAAAAAGAAAATA
1 AAAGAAAAATAAAAAAGAAAATA
*
2856837 AAAGAATAA-AAAAAAG-AAATA
1 AAAGAAAAATAAAAAAGAAAATA
2856858 AAA
1 AAA
2856861 ATGTAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 7 0.30
23 8 0.35
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (23 bp):
AAAGAAAAATAAAAAAGAAAATA
Found at i:2856884 original size:2 final size:2
Alignment explanation
Indices: 2856877--2856916 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2856867 ATGAAAACAT
2856877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2856917 ATGTTTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2856979 original size:36 final size:36
Alignment explanation
Indices: 2856916--2857191 Score: 179
Period size: 35 Copynumber: 7.8 Consensus size: 36
2856906 ATATATATAT
*
2856916 AATGTTTTCAAAATCATATTTTATATATATATTTTTTAAA
1 AATGTTTTCAAAA-C-TA-TAT-TATATATATTTTTTAAA
* * *
2856956 AATGTTTTTAAAACTATATTATATATA-CTTTCAAA
1 AATGTTTTCAAAACTATATTATATATATTTTTTAAA
* * * * *
2856991 AACGTTTTCAAAAATATATTA-A-AAATGTTTT-CA
1 AATGTTTTCAAAACTATATTATATATATTTTTTAAA
* * *
2857024 AA-G-----AACTA-TATATTATATATATGTTTTCAA
1 AATGTTTTCAA-AACTATATTATATATATTTTTTAAA
*
2857054 AATGTTTTCAAAGCTATA-TATTATATATATTTTTAAA
1 AATGTTTTCAAAACTATATTA-TATATAT-TTTTTAAA
2857091 AATGTTTTCAAAAACTATA-TAT-TATA-TTTTT-AA
1 AATGTTTTC-AAAACTATATTATATATATTTTTTAAA
*
2857124 AATATTTTCAAAAACTATATATTATATATATTTTTTCAAA
1 AATGTTTTC-AAAAC--TATATTATATATATTTTTT-AAA
* *
2857164 AATCATTTTCAAAACTATAATATATATA
1 AAT-GTTTTCAAAACTATATTATATATA
2857192 ACATTTTCAA
Statistics
Matches: 192, Mismatches: 21, Indels: 48
0.74 0.08 0.18
Matches are distributed among these distances:
27 9 0.05
28 2 0.01
29 8 0.04
30 3 0.02
31 1 0.01
32 1 0.01
33 21 0.11
34 9 0.05
35 30 0.16
36 28 0.15
37 22 0.11
38 29 0.15
39 1 0.01
40 22 0.11
41 6 0.03
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
AATGTTTTCAAAACTATATTATATATATTTTTTAAA
Found at i:2857015 original size:23 final size:25
Alignment explanation
Indices: 2856988--2857034 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
2856978 ATATACTTTC
2856988 AAAAACGTTTTCAAA-AA-TATATT
1 AAAAACGTTTTCAAAGAACTATATT
*
2857011 AAAAATGTTTTCAAAGAACTATAT
1 AAAAACGTTTTCAAAGAACTATAT
2857035 ATTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.67
24 2 0.10
25 5 0.24
ACGTcount: A:0.51, C:0.09, G:0.06, T:0.34
Consensus pattern (25 bp):
AAAAACGTTTTCAAAGAACTATATT
Found at i:2857020 original size:98 final size:100
Alignment explanation
Indices: 2856939--2857191 Score: 271
Period size: 109 Copynumber: 2.5 Consensus size: 100
2856929 TCATATTTTA
* *
2856939 TATATATATTTTTTAAAAATGTTTTTAAAAC-TATATTATATATACTTTCAAAAACGTTTTCAAA
1 TATATATATGTTTTAAAAATGTTTTCAAAACATATATTATATATACTTTCAAAAACGTTTTCAAA
2857003 AA-TATATTAAAAATGTTTTCAAAGAACTATATAT
66 AACTATATTAAAAATGTTTTCAAAGAACTATATAT
* * * * *
2857037 TATATATATGTTTTCAAAATGTTTTCAAAGCTATATATTATATATATTTTTAAAAATGTTTTCAA
1 TATATATATGTTTTAAAAATGTTTTCAAAAC-ATATATTATATATACTTTCAAAAACGTTTTCAA
*
2857102 AAACTATATATTATATTTTTAAAATATTTTCAAA-AACTATATAT
65 AAAC--TATA-T-TA-----AAAATGTTTTCAAAGAACTATATAT
* * *
2857146 TATATATATTTTTTCAAAAATCATTTTCAAAAC-TATAATATATATA
1 TATATATATGTTTT-AAAAAT-GTTTTCAAAACATATATTATATATA
2857192 ACATTTTCAA
Statistics
Matches: 128, Mismatches: 13, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
98 27 0.21
100 32 0.25
103 4 0.03
104 1 0.01
105 2 0.02
109 35 0.27
110 18 0.14
111 9 0.07
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (100 bp):
TATATATATGTTTTAAAAATGTTTTCAAAACATATATTATATATACTTTCAAAAACGTTTTCAAA
AACTATATTAAAAATGTTTTCAAAGAACTATATAT
Found at i:2857057 original size:40 final size:38
Alignment explanation
Indices: 2857012--2857191 Score: 216
Period size: 38 Copynumber: 4.8 Consensus size: 38
2857002 AAATATATTA
2857012 AAAATGTTTTCAAAGAACTATATATTATATATATGTTTTC
1 AAAATGTTTTCAAA-AACTATATATTATATATAT-TTTTC
* *
2857052 AAAATGTTTTC-AAAGCTATATATTATATATATTTTTA
1 AAAATGTTTTCAAAAACTATATATTATATATATTTTTC
2857089 AAAATGTTTTCAAAAAC--TATA-TAT-TATATTTTT-
1 AAAATGTTTTCAAAAACTATATATTATATATATTTTTC
*
2857122 AAAATATTTTCAAAAACTATATATTATATATATTTTTTC
1 AAAATGTTTTCAAAAACTATATATTATATATA-TTTTTC
*
2857161 AAAAATCATTTTC-AAAACTATA-A-TATATATA
1 -AAAAT-GTTTTCAAAAACTATATATTATATATA
2857192 ACATTTTCAA
Statistics
Matches: 127, Mismatches: 4, Indels: 20
0.84 0.03 0.13
Matches are distributed among these distances:
33 16 0.13
34 9 0.07
35 7 0.06
36 7 0.06
37 19 0.15
38 35 0.28
39 3 0.02
40 25 0.20
41 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (38 bp):
AAAATGTTTTCAAAAACTATATATTATATATATTTTTC
Found at i:2857229 original size:26 final size:26
Alignment explanation
Indices: 2857167--2857223 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
2857157 TTTCAAAAAT
2857167 CATTTTCAAAACTATAATATATATAA
1 CATTTTCAAAACTATAATATATATAA
2857193 CATTTTCAAAACTAT-ATA-ATATATA
1 CATTTTCAAAACTATAATATATATA-A
2857218 CATTTT
1 CATTTT
2857224 TTAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 5 0.17
25 10 0.33
26 15 0.50
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (26 bp):
CATTTTCAAAACTATAATATATATAA
Found at i:2857296 original size:16 final size:16
Alignment explanation
Indices: 2857277--2857309 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2857267 ACCGATTTTT
2857277 TAAAAACTA-TATATTA
1 TAAAAA-TACTATATTA
2857293 TAAAAATACTATATTA
1 TAAAAATACTATATTA
2857309 T
1 T
2857310 CATATATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 14 0.88
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAAAATACTATATTA
Found at i:2858296 original size:86 final size:85
Alignment explanation
Indices: 2858064--2858380 Score: 386
Period size: 85 Copynumber: 3.7 Consensus size: 85
2858054 ATACGCCATC
* * ** * * *
2858064 GAGCTGAATGGAATCAAACTCGGAA-GTCTTCATTGACAAATAACCCTTCTCGCCTTGAGATATG
1 GAGCTGAATAGAATCAAACTC-GAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATG
*
2858128 CTGTAAATTTGATATGCCCTC
65 CTGTAAATTTGATATGCCCTT
* * *
2858149 GAGCTGAATAGAATCGAACTCGAAGGTTTTTTTGTTGGCAGATAGCCATTCTCGCCTTGAGCTAT
1 GAGCTGAATAGAATCAAACTCGAAGG--TTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTAT
* * **
2858214 GTTGTAAATTTGATACGCAGTTT
64 GCTGTAAATTTGATATGC-CCTT
*
2858237 GAGCTGAATAGAATCAAACTCGAAGGTTTTTGTTGACAGATAGTCCTTCTCGCCTTGAGCTATGC
1 GAGCTGAATAGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
*
2858302 TGCAAATTTGATATGCCCTT
66 TGTAAATTTGATATGCCCTT
* * * *
2858322 GAGTTGAATGGAAT-AGAACTCGACGGTTTTTGTTGACAGATAGCCCTTATCGCCTTGAG
1 GAGCTGAATAGAATCA-AACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAG
2858381 ATATACTGCG
Statistics
Matches: 198, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
84 4 0.02
85 74 0.37
86 49 0.25
87 45 0.23
88 26 0.13
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (85 bp):
GAGCTGAATAGAATCAAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGC
TGTAAATTTGATATGCCCTT
Found at i:2862745 original size:20 final size:22
Alignment explanation
Indices: 2862720--2862759 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
2862710 TGTTGTATAT
2862720 AACCG-TTGGGGATG-TTTTGG
1 AACCGTTTGGGGATGATTTTGG
2862740 AACCGTTTGGGGATGATTTT
1 AACCGTTTGGGGATGATTTT
2862760 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.17, C:0.10, G:0.35, T:0.38
Consensus pattern (22 bp):
AACCGTTTGGGGATGATTTTGG
Found at i:2865962 original size:22 final size:22
Alignment explanation
Indices: 2865931--2865979 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
2865921 TGTAAATGAT
2865931 AAAAATAAAATAAAAGAAAA-G
1 AAAAATAAAATAAAAGAAAAGG
*
2865952 AAAAATAAAAATAAAATAAAAGG
1 AAAAAT-AAAATAAAAGAAAAGG
2865975 AAAAA
1 AAAAA
2865980 AAGTTAGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 6 0.24
22 13 0.52
23 6 0.24
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (22 bp):
AAAAATAAAATAAAAGAAAAGG
Found at i:2867097 original size:24 final size:24
Alignment explanation
Indices: 2867070--2867177 Score: 108
Period size: 24 Copynumber: 4.5 Consensus size: 24
2867060 AAACAGAAAT
*
2867070 ATCAGAAATCAAAATAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
2867094 ATCATATATCAGAATAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* *
2867118 ATCAGAAATCAGAACAAAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
2867142 AACAGAAATCAAAACAGAATGCAA
1 ATCAGAAATCAAAACAGAATTCAG
*
2867166 ATCGGAAATCAA
1 ATCAGAAATCAA
2867178 CTAAAATATG
Statistics
Matches: 68, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 68 1.00
ACGTcount: A:0.54, C:0.16, G:0.13, T:0.18
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:2867157 original size:12 final size:12
Alignment explanation
Indices: 2867072--2867160 Score: 65
Period size: 12 Copynumber: 7.4 Consensus size: 12
2867062 ACAGAAATAT
*
2867072 CAGAAATCAAAA
1 CAGAAATCAGAA
* * *
2867084 TAGAATTCAGAT
1 CAGAAATCAGAA
* *
2867096 CATATATCAGAA
1 CAGAAATCAGAA
* *
2867108 TAG-AATCCAGAT
1 CAGAAAT-CAGAA
2867120 CAGAAATCAGAA
1 CAGAAATCAGAA
2867132 CA-AAATTCAGAA
1 CAGAAA-TCAGAA
*
2867144 CAGAAATCAAAA
1 CAGAAATCAGAA
2867156 CAGAA
1 CAGAA
2867161 TGCAAATCGG
Statistics
Matches: 57, Mismatches: 16, Indels: 8
0.70 0.20 0.10
Matches are distributed among these distances:
11 5 0.09
12 46 0.81
13 6 0.11
ACGTcount: A:0.55, C:0.16, G:0.12, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:2872787 original size:23 final size:24
Alignment explanation
Indices: 2872747--2872791 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
2872737 TAAATTCTGT
*
2872747 TATGATACCTGACCTGGATTCTAA
1 TATGATACCTGACATGGATTCTAA
*
2872771 TATGATA-TTGACATGGATTCT
1 TATGATACCTGACATGGATTCT
2872792 GTCTGATACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
TATGATACCTGACATGGATTCTAA
Found at i:2872953 original size:35 final size:35
Alignment explanation
Indices: 2872905--2872974 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
2872895 TTGAAGAAAG
* *
2872905 ATTACTTGGAGGCTCCTCGGCTTTGTGCTCAGGGC
1 ATTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGC
*
2872940 ATTACTTGCAGGCTCATCGGCTTTGTTCTCAGGGC
1 ATTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGC
2872975 CTTATTGTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.13, C:0.26, G:0.29, T:0.33
Consensus pattern (35 bp):
ATTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGC
Found at i:2877452 original size:24 final size:24
Alignment explanation
Indices: 2877432--2877515 Score: 98
Period size: 24 Copynumber: 3.5 Consensus size: 24
2877422 TAAATTCTGT
* *
2877432 TATGATACCTGACCTAGATTCTAA
1 TATGATACTTGACCTGGATTCTAA
* *
2877456 TCTGATA-TTGACATGGATTCTAA
1 TATGATACTTGACCTGGATTCTAA
* * *
2877479 TATGATACATGACCTGGATTATGA
1 TATGATACTTGACCTGGATTCTAA
2877503 TATGATACTTGAC
1 TATGATACTTGAC
2877516 TTGAATTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
23 19 0.39
24 30 0.61
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (24 bp):
TATGATACTTGACCTGGATTCTAA
Found at i:2877532 original size:24 final size:24
Alignment explanation
Indices: 2877478--2877525 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
2877468 ATGGATTCTA
*
2877478 ATATGATACATGACCTGGATTATG
1 ATATGATACATGACCTGAATTATG
* *
2877502 ATATGATACTTGACTTGAATTATG
1 ATATGATACATGACCTGAATTATG
2877526 TTTTGATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (24 bp):
ATATGATACATGACCTGAATTATG
Found at i:2877639 original size:35 final size:35
Alignment explanation
Indices: 2877592--2877666 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
2877582 TAAAGGAAGA
* * *
2877592 TTACTTGGAGGCTCCTCGTCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
*
2877627 TTACTTGCAGGCTCATCGGCTTTGTTCTCAGGGCC
1 TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
2877662 TTACT
1 TTACT
2877667 GTTCGTGACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.11, C:0.28, G:0.25, T:0.36
Consensus pattern (35 bp):
TTACTTGCAGGCTCATCGGCTTTGTGCTCAGGGCC
Found at i:2877735 original size:2 final size:2
Alignment explanation
Indices: 2877728--2877778 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2877718 CATATGGGGG
2877728 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2877770 TA TA TA TA T
1 TA TA TA TA T
2877779 GTTTTAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2880351 original size:24 final size:24
Alignment explanation
Indices: 2880312--2880418 Score: 108
Period size: 24 Copynumber: 4.5 Consensus size: 24
2880302 AAATGGAAAT
* *
2880312 ATCAGAAATCCA-AACAGAATTCAT
1 ATCAGAAAT-CAGAACATAATTCAA
* * *
2880336 ATCATATATCAGAACATAATCCAA
1 ATCAGAAATCAGAACATAATTCAA
* * *
2880360 ATCAGAAATCAGAATAAAATTCAT
1 ATCAGAAATCAGAACATAATTCAA
*
2880384 ATAAGAAATCAGAACATAATTCAA
1 ATCAGAAATCAGAACATAATTCAA
*
2880408 ATCAAAAATCA
1 ATCAGAAATCA
2880419 AATAAAACAT
Statistics
Matches: 65, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
23 2 0.03
24 63 0.97
ACGTcount: A:0.54, C:0.17, G:0.07, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAGAACATAATTCAA
Found at i:2880383 original size:48 final size:47
Alignment explanation
Indices: 2880312--2880425 Score: 147
Period size: 48 Copynumber: 2.4 Consensus size: 47
2880302 AAATGGAAAT
* * * * *
2880312 ATCAGAAATCCAAACAGAATTCATATCATATATCAGAACATAATCCAA
1 ATCAGAAAT-CAAATAAAATTCATATAAGAAATCAGAACATAATCCAA
*
2880360 ATCAGAAATCAGAATAAAATTCATATAAGAAATCAGAACATAATTCAA
1 ATCAGAAATCA-AATAAAATTCATATAAGAAATCAGAACATAATCCAA
*
2880408 ATCAAAAATCAAATAAAA
1 ATCAGAAATCAAATAAAA
2880426 CATTCATGTA
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
47 9 0.16
48 49 0.84
ACGTcount: A:0.56, C:0.16, G:0.06, T:0.22
Consensus pattern (47 bp):
ATCAGAAATCAAATAAAATTCATATAAGAAATCAGAACATAATCCAA
Found at i:2888966 original size:20 final size:21
Alignment explanation
Indices: 2888912--2888974 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
2888902 GATTCCCCTG
2888912 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
2888936 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
2888956 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
2888975 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:2893057 original size:117 final size:117
Alignment explanation
Indices: 2892835--2893058 Score: 283
Period size: 117 Copynumber: 1.9 Consensus size: 117
2892825 AACTTTCAAA
* *
2892835 TTGAAATTTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAAGAT
1 TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACAT
* *
2892900 TTCATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAAT
66 TTCATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAAT
* * * * *
2892952 TTGAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCCTT-TCTCAAC
1 TTGAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCT-TCAAC
* * **
2893015 ATTTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAAG
64 ATTTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAAG
2893059 ATCATTTTTA
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
116 2 0.02
117 85 0.93
118 4 0.04
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (117 bp):
TTGAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCATTCTTCAACAT
TTCATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAAT
Found at i:2897312 original size:297 final size:297
Alignment explanation
Indices: 2896757--2897352 Score: 782
Period size: 297 Copynumber: 2.0 Consensus size: 297
2896747 TTTTCAATGG
* * * * * ***
2896757 CGGAGAGCTCGATTCTGAAACATCGAAAACTTTTACTTCCTCACCCCTCTATGCACCGGGGACGA
1 CGGAGAGCTAGATTCAGAAACATCGAAAACTTTGACTTCCTCACCCCTCCACGCACCGACAACGA
* * * *
2896822 CGGAGACACGGAGAACACCGTTGGACTTGAAACGAAGCAAGGAACACGATGGTGCGGGAGGTATT
66 CGGAGACACGGAGAACACCGGTGGACTAGAAACGAAGCAAGCAACACGATGGTGCGGGAGGTATC
* * *
2896887 GAAAATGGATGGCCGGATCGACGTGAATCGACGGAAAACCAACAGAAATTGAGTTAAAACCGACA
131 AAAAACGGATGGCCAGATCGACGTGAATCGACGGAAAACCAACAGAAATTGAGTTAAAACCGACA
* * * * * * * *
2896952 ATACTTCCTACTGAAATTGACGGCGAATGGTGCCGATTAACGACGGGATGTCTGAGGGGTTTTGT
196 ACACTTCCAACTGAAATTGACGACGAACGGCGCCGATTAACGACGAGAGGTCTGAGAGGTTTTGT
* * *
2897017 TTATCGGTCGACAATGAACACGATAGTGGTTTTGGTT
261 TCATCGGTCGACAACGAACACGATAGTGATTTTGGTT
* *
2897054 CGGAGAGCTAGATTCAGAAACATCGAAAACTTTGACTTCTTCACCCCTCCACGCGCCGACAACGA
1 CGGAGAGCTAGATTCAGAAACATCGAAAACTTTGACTTCCTCACCCCTCCACGCACCGACAACGA
* * * *
2897119 CGGAGACACGGAGGACACCGGTGGACTCAG-AACGATGCAAGCAACACGATGGTGTGGGAGGTGT
66 CGGAGACACGGAGAACACCGGTGGACT-AGAAACGAAGCAAGCAACACGATGGTGCGGGAGGTAT
* * *
2897183 CAAAAACGGATGGCTAGATCGACGTGAATCGACGGAAAACCAACGGAAATTGAGTTAAAACCGAT
130 CAAAAACGGATGGCCAGATCGACGTGAATCGACGGAAAACCAACAGAAATTGAGTTAAAACCGAC
* * * * *
2897248 GACACTTCCAAGTGAAATTGACGATGAACGGCGCCGATTCACGACGAGAGGT-TTACGAGGTTTT
195 AACACTTCCAACTGAAATTGACGACGAACGGCGCCGATTAACGACGAGAGGTCTGA-GAGGTTTT
* *
2897312 GTTCATTGGTCGACAACGAACACGATGGTGATTTTGGTT
259 GTTCATCGGTCGACAACGAACACGATAGTGATTTTGGTT
2897351 CG
1 CG
2897353 TCAAACGGTG
Statistics
Matches: 255, Mismatches: 42, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
296 2 0.01
297 252 0.99
298 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (297 bp):
CGGAGAGCTAGATTCAGAAACATCGAAAACTTTGACTTCCTCACCCCTCCACGCACCGACAACGA
CGGAGACACGGAGAACACCGGTGGACTAGAAACGAAGCAAGCAACACGATGGTGCGGGAGGTATC
AAAAACGGATGGCCAGATCGACGTGAATCGACGGAAAACCAACAGAAATTGAGTTAAAACCGACA
ACACTTCCAACTGAAATTGACGACGAACGGCGCCGATTAACGACGAGAGGTCTGAGAGGTTTTGT
TCATCGGTCGACAACGAACACGATAGTGATTTTGGTT
Found at i:2897979 original size:4 final size:4
Alignment explanation
Indices: 2897970--2897999 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2897960 TTTAATCTTA
*
2897970 AAAT AAAT AAAT AAAT AAAC AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2898000 TAATAAAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (4 bp):
AAAT
Found at i:2898721 original size:2 final size:2
Alignment explanation
Indices: 2898714--2898744 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2898704 GCACTTTCTT
2898714 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2898745 GGTTTATGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2900927 original size:18 final size:18
Alignment explanation
Indices: 2900904--2900956 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
2900894 GAGGGTTCTA
*
2900904 AGTGGTCATTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
2900922 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCGGGACAT
2900940 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
2900957 AGTTTAAGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:2908551 original size:12 final size:12
Alignment explanation
Indices: 2908534--2908577 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2908524 TTATATATAC
2908534 TTTCAAAAATGT
1 TTTCAAAAATGT
* *
2908546 TTTCAAAACTAT
1 TTTCAAAAATGT
*
2908558 ATT-AAAAATGT
1 TTTCAAAAATGT
2908569 TTTCAAAAA
1 TTTCAAAAA
2908578 CTATGTATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.39
Consensus pattern (12 bp):
TTTCAAAAATGT
Found at i:2908564 original size:23 final size:23
Alignment explanation
Indices: 2908538--2908610 Score: 92
Period size: 23 Copynumber: 3.0 Consensus size: 23
2908528 ATATACTTTC
2908538 AAAAATGTTTTCAAAACTATATT
1 AAAAATGTTTTCAAAACTATATT
2908561 AAAAATGTTTTCAAAAACTATGTATT
1 AAAAATGTTTTC-AAAACTA--TATT
*
2908587 ATATATATGTTTTCAAAACTATAT
1 A-A-AAATGTTTTCAAAACTATAT
2908611 ATTATATATA
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
23 12 0.27
24 7 0.16
25 3 0.07
26 5 0.11
27 8 0.18
28 9 0.20
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (23 bp):
AAAAATGTTTTCAAAACTATATT
Found at i:2908573 original size:35 final size:35
Alignment explanation
Indices: 2908498--2908577 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
2908488 TTACAATATT
* * * *
2908498 TTTTTAAAAATGTTTTTAAAACTATATTATATATA
1 TTTTCAAAAATGTTTTCAAAACTATATTAAAAATA
* *
2908533 CTTTCAAAAATGTTTTCAAAACTATATTAAAAATG
1 TTTTCAAAAATGTTTTCAAAACTATATTAAAAATA
2908568 TTTTCAAAAA
1 TTTTCAAAAA
2908578 CTATGTATTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTTCAAAAATGTTTTCAAAACTATATTAAAAATA
Done.