Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 10 of 310
Found at i:2526645 original size:22 final size:22
Alignment explanation
Indices: 2526620--2526664 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2526610 TTTAATAAAG
2526620 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
2526642 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
2526664 A
1 A
2526665 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:2530421 original size:22 final size:22
Alignment explanation
Indices: 2530396--2530440 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2530386 TTTAATAAAG
2530396 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
2530418 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
2530440 A
1 A
2530441 CACTACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:2534731 original size:24 final size:22
Alignment explanation
Indices: 2534684--2534760 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 22
2534674 TAAATACAAT
*
2534684 TTAATAAAA--TAATAT-ATAA
1 TTAATAAAATTTAATATAATTA
2534703 TTTAATAAAATTCTTAATATAATTA
1 -TTAATAAAA-T-TTAATATAATTA
*
2534728 TTAATAATATTTAATATAAAATTA
1 TTAATAAAATTTAATAT--AATTA
*
2534752 TTATTAAAA
1 TTAATAAAA
2534761 ATATTTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
20 9 0.20
22 7 0.15
23 1 0.02
24 26 0.57
25 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (22 bp):
TTAATAAAATTTAATATAATTA
Found at i:2534759 original size:12 final size:12
Alignment explanation
Indices: 2534704--2534765 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
2534694 AATATATAAT
*
2534704 TTAATAAAATTC
1 TTAATAAAATTA
*
2534716 TTAATATAATTA
1 TTAATAAAATTA
*
2534728 TTAATAATATT-
1 TTAATAAAATTA
*
2534739 TAATATAAAATTA
1 TTA-ATAAAATTA
* *
2534752 TTATTAAAAATA
1 TTAATAAAATTA
2534764 TT
1 TT
2534766 TCAATTCCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (12 bp):
TTAATAAAATTA
Found at i:2534899 original size:23 final size:23
Alignment explanation
Indices: 2534865--2534911 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2534855 TACGGTATGA
*
2534865 TAATCCTCTAATAATATTTTATT
1 TAATCCTCTAATAACATTTTATT
*
2534888 TAATCCTTTAATAACATTTTATT
1 TAATCCTCTAATAACATTTTATT
2534911 T
1 T
2534912 TAATAGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.00, T:0.53
Consensus pattern (23 bp):
TAATCCTCTAATAACATTTTATT
Found at i:2536450 original size:62 final size:62
Alignment explanation
Indices: 2536373--2536492 Score: 188
Period size: 62 Copynumber: 1.9 Consensus size: 62
2536363 CACACAATGA
* *
2536373 ACCATTAATCACAAATCTTT-AAAACTCAGTTCAAATGCAATAGCATCTTAAGTACCATCACT
1 ACCATTAATCACAAAT-TTTCAAAACTCAATTCAAATGCAATAGCATCTTAAGAACCATCACT
* *
2536435 ACCATTAATCTCAAATTTTCATAACTCAATTCAAATGCAATAGCATCTTAAGAACCAT
1 ACCATTAATCACAAATTTTCAAAACTCAATTCAAATGCAATAGCATCTTAAGAACCAT
2536493 AACGCAATGA
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
61 3 0.06
62 50 0.94
ACGTcount: A:0.41, C:0.23, G:0.06, T:0.30
Consensus pattern (62 bp):
ACCATTAATCACAAATTTTCAAAACTCAATTCAAATGCAATAGCATCTTAAGAACCATCACT
Found at i:2537475 original size:89 final size:89
Alignment explanation
Indices: 2537368--2537546 Score: 349
Period size: 89 Copynumber: 2.0 Consensus size: 89
2537358 TTGATTAAAC
2537368 TATCTTCATGTGACATACTATATAATTGATGGAAAATGAATATGTTAAGTTGACAAATTTTAACA
1 TATCTTCATGTGACATACTATATAATTGATGGAAAATGAATATGTTAAGTTGACAAATTTTAACA
2537433 GAATCTACCAATGATGATAATGAT
66 GAATCTACCAATGATGATAATGAT
*
2537457 TATCTTCATGTGACATACTATATGATTGATGGAAAATGAATATGTTAAGTTGACAAATTTTAACA
1 TATCTTCATGTGACATACTATATAATTGATGGAAAATGAATATGTTAAGTTGACAAATTTTAACA
2537522 GAATCTACCAATGATGATAATGAT
66 GAATCTACCAATGATGATAATGAT
2537546 T
1 T
2537547 GGATTAGGAT
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 89 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (89 bp):
TATCTTCATGTGACATACTATATAATTGATGGAAAATGAATATGTTAAGTTGACAAATTTTAACA
GAATCTACCAATGATGATAATGAT
Found at i:2537736 original size:17 final size:17
Alignment explanation
Indices: 2537714--2537747 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2537704 AGTTAAAAGT
2537714 ATATTGACAAATTTAGC
1 ATATTGACAAATTTAGC
2537731 ATATTGACAAATTTAGC
1 ATATTGACAAATTTAGC
2537748 CCTTAGCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
ATATTGACAAATTTAGC
Found at i:2540426 original size:126 final size:128
Alignment explanation
Indices: 2540121--2540428 Score: 352
Period size: 130 Copynumber: 2.4 Consensus size: 128
2540111 AACGGTAAAT
* * * * *
2540121 CGAAACCCAGCACGATTGGGCACGATTTATCGAATTTCCAAATACGAAACATTGCCTCATTTTAA
1 CGAAACCCAGCACGATTGGGCACGATTTCTCAAATTTCCAAACACGAAATATCGCCTCATTTTAA
* * *
2540186 TTTAAGGAAACATAGATGAAATTTCAAAAGGATATTCTATATTCTAGTCAATTGAGAAAAAAAAA
66 TTTAAGAAAACATAGATGAAATCTCAAAAGGATATTCCATA-TCTA-TCAATTGAGAAAAAAAAA
* * * * *
2540251 CGAAACCCAGCACGATTGGGCACGATCTCTCAAACTCCCAAACATGAAATATCGCCTCGTTTTAA
1 CGAAACCCAGCACGATTGGGCACGATTTCTCAAATTTCCAAACACGAAATATCGCCTCATTTTAA
* * * * * **
2540316 TTTAAGAAAACATGGATGAGATCTCACAAGGATATTCCATA-GT-TCAATTGA-ATGAAAAAGT
66 TTTAAGAAAACATAGATGAAATCTCAAAAGGATATTCCATATCTATCAATTGAGA-AAAAAAAA
* * * *
2540377 CGTAACCGAGCACGATTGAGCATGATTTCTCAAATTTCCAAACACGAAATAT
1 CGAAACCCAGCACGATTGGGCACGATTTCTCAAATTTCCAAACACGAAATAT
2540429 TTCCTTATGC
Statistics
Matches: 149, Mismatches: 28, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
125 1 0.01
126 57 0.38
128 1 0.01
130 90 0.60
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (128 bp):
CGAAACCCAGCACGATTGGGCACGATTTCTCAAATTTCCAAACACGAAATATCGCCTCATTTTAA
TTTAAGAAAACATAGATGAAATCTCAAAAGGATATTCCATATCTATCAATTGAGAAAAAAAAA
Found at i:2542614 original size:133 final size:133
Alignment explanation
Indices: 2542416--2542691 Score: 464
Period size: 133 Copynumber: 2.1 Consensus size: 133
2542406 TCGATACATG
* * * **
2542416 GAGATAAGACTCGCCATTTTCGATTTGCTCTATAGCTGATACATGGAGATAAGATCTGCAATTTT
1 GAGATAAGGCTCGCCATTTTCGATCTGCTCCATAGCCAATACATGGAGATAAGATCTGCAATTTT
* *
2542481 CAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTTCAACCTGCTCTCTTGCTA-CTT
66 CAGCCTGTTACACTACTGCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTT
2542545 CAAA
131 -AAA
2542549 GAGATAAGGCTCGCCATTTTCGATCTGCTCCATAGCCAATACATGGAGATAAGATCTGCAATTTT
1 GAGATAAGGCTCGCCATTTTCGATCTGCTCCATAGCCAATACATGGAGATAAGATCTGCAATTTT
2542614 CAGCCTGTTACACTACTGCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTT
66 CAGCCTGTTACACTACTGCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTT
*
2542679 AGA
131 AAA
2542682 GAGATAAGGC
1 GAGATAAGGC
2542692 GGTTGGTTTA
Statistics
Matches: 134, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
133 131 0.98
134 3 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (133 bp):
GAGATAAGGCTCGCCATTTTCGATCTGCTCCATAGCCAATACATGGAGATAAGATCTGCAATTTT
CAGCCTGTTACACTACTGCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTT
AAA
Found at i:2542831 original size:310 final size:310
Alignment explanation
Indices: 2542256--2543132 Score: 1355
Period size: 310 Copynumber: 2.8 Consensus size: 310
2542246 AGATTTGCCC
* * *
2542256 TTTCTGATTTGCT-CATAGCCGGTACATGGAGATAAGATCTGTAATTTTCATCCTGTTACCCTAC
1 TTTC-GATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTAC
* * * * *
2542320 TGCCTAGGGGGTTAAGGCTCGTATGTTCAACCTACTATCTTGCTACCTCAGAGAGATAAGGTCGG
65 TGCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGG
* * * *
2542385 TGGCTTAAATCTGCTCCATAGTCGATACATGGAGATAAGACTCGCCATTTTCGATTTGCTCTATA
130 TGGCTTAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTCGATCTGCTCCATA
* *
2542450 GCTGATACATGGAGATAAGATCTGCAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
195 GCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
*
2542515 TCGTATCTTCAACCTGCTCTCTTGCTA-CTTCAAAGAGATAAGGCTCGCCAT
260 TCGTATCTCCAACCTGCTCTCTTGCTACCTT-AAAGAGATAAGGCTCGCCAT
* * *
2542566 TTTCGATCTGCTCCATAGCCAATACATGGAGATAAGATCTGCAATTTTCAGCCTGTTACACTACT
1 TTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACT
*
2542631 GCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTTAGAGAGATAAGG-CGGT
66 GCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGG-
* * * * **
2542695 TGGTTTAAATATGCTCCATAGCCGATATATGAAGATAAGACTTTCCATCTTCGATCTGCTCCATA
130 TGGCTTAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTCGATCTGCTCCATA
*
2542760 GCCGATACATGGAGATAAGATCTATAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
195 GCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGC
* *
2542825 TCGTATCTCCAACCTGCTCTCTTGCTACCTTAGAGAGATAAGGCTTGCCAT
260 TCGTATCTCCAACCTGCTCTCTTGCTACCTTAAAGAGATAAGGCTCGCCAT
*
2542876 TTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGTTACCCTACT
1 TTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACT
* * *
2542941 GCTTAGGGGGTTAAAACTTGTATCTTCAACCTGCTCTCTTGCTACCTCAGGGAGATAAGGTCGGT
66 GCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGT
* * **
2543006 GGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCAATCTTTAATCTGCTCCATAG
131 GGCTTAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTCGATCTGCTCCATAG
* * *
2543071 CCAATACATGGAGATAAGATCTGTAATTTTCAACCTGTTACCCTACTGCTTAGAGGGTTAAG
196 CCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAG
2543133 ACTTGTGGCT
Statistics
Matches: 513, Mismatches: 50, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
309 10 0.02
310 497 0.97
311 6 0.01
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (310 bp):
TTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACT
GCTTAGGGGGTTAAGACTCGTATCTTCAACCTGCTCTCTTGCTACCTCAGAGAGATAAGGTCGGT
GGCTTAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATCTTCGATCTGCTCCATAG
CCGATACATGGAGATAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCT
CGTATCTCCAACCTGCTCTCTTGCTACCTTAAAGAGATAAGGCTCGCCAT
Found at i:2542903 original size:133 final size:132
Alignment explanation
Indices: 2542727--2543044 Score: 451
Period size: 133 Copynumber: 2.4 Consensus size: 132
2542717 CGATATATGA
* *
2542727 AGATAAGACTTTCCATCTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTC
1 AGATAAGGCTTGCCAT-TTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTC
** *
2542792 AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCGTATCTCCAACCTGCTCTCTTGCTACCTTA
65 AGCCTGTTACCCTACTGCTTAGGGGGTTAAAACTCGTATCTCCAACCTGCTCTCTTGCTACCTCA
2542857 GAG
130 GAG
*
2542860 AGATAAGGCTTGCCATTTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTC
1 AGATAAGGCTTGCCA-TTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTC
* * *
2542925 AGTCTGTTACCCTACTGCTTAGGGGGTTAAAACTTGTATCTTCAACCTGCTCTCTTGCTACCTCA
65 AGCCTGTTACCCTACTGCTTAGGGGGTTAAAACTCGTATCTCCAACCTGCTCTCTTGCTACCTCA
*
2542990 GGG
130 GAG
* * ***
2542993 AGATAAGGTCGGTGGC--TAAAATCTGCTCCATAGCCGATACATGGAGATAAGA
1 AGATAAGG-C-TTGCCATTTCGATCTGCTCCATAGCCGATACATGGAGATAAGA
2543045 CTCGCAATCT
Statistics
Matches: 167, Mismatches: 15, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
132 33 0.20
133 129 0.77
134 2 0.01
135 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (132 bp):
AGATAAGGCTTGCCATTTCGATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTCA
GCCTGTTACCCTACTGCTTAGGGGGTTAAAACTCGTATCTCCAACCTGCTCTCTTGCTACCTCAG
AG
Found at i:2543166 original size:88 final size:88
Alignment explanation
Indices: 2543057--2543220 Score: 274
Period size: 88 Copynumber: 1.9 Consensus size: 88
2543047 CGCAATCTTT
* *
2543057 AATCTGCTCCATAGCCAATACATGGAGATAAGATCTGTAATTTTCAACCTGTTACCCTACTGCTT
1 AATCTGCTCCATAGCCAATACATGGAGATAAGATCTATAATTTTCAACCTATTACCCTACTGCTT
2543122 AGAGGGTTAAGACTTGTGGCTAA
66 AGAGGGTTAAGACTTGTGGCTAA
* * *
2543145 AATCTGCTCCATAGCCGATACATGGAGATAAGATCTATAATTTTTAGCCTATTACCCTACTGCTT
1 AATCTGCTCCATAGCCAATACATGGAGATAAGATCTATAATTTTCAACCTATTACCCTACTGCTT
*
2543210 AGGGGGTTAAG
66 AGAGGGTTAAG
2543221 GCTCGCAACT
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 70 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (88 bp):
AATCTGCTCCATAGCCAATACATGGAGATAAGATCTATAATTTTCAACCTATTACCCTACTGCTT
AGAGGGTTAAGACTTGTGGCTAA
Found at i:2543394 original size:64 final size:64
Alignment explanation
Indices: 2543292--2543418 Score: 175
Period size: 64 Copynumber: 2.0 Consensus size: 64
2543282 TCATGTGTCT
* * * *
2543292 ATGCTTATGCTAAATAGTTAGGATACTATGATCGAAATGAATCAACCGCTCCTAGCTAGATGTG
1 ATGCTTATGCTAAATAATTAGGATACTATGATCAAAATGAATCAAACGCTCCTAACTAGATGTG
* * *
2543356 ATGCTTATG-TCAAATAATTAGGATGCTATGATCAAAATGAATCAAATGCTCTTAACTAGATGT
1 ATGCTTATGCT-AAATAATTAGGATACTATGATCAAAATGAATCAAACGCTCCTAACTAGATGT
2543419 ATTATGAATG
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
63 1 0.02
64 54 0.98
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (64 bp):
ATGCTTATGCTAAATAATTAGGATACTATGATCAAAATGAATCAAACGCTCCTAACTAGATGTG
Found at i:2554161 original size:21 final size:22
Alignment explanation
Indices: 2554135--2554178 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
2554125 ATAATGGTAA
2554135 ACTAATAATAGTA-A-AAATAGT
1 ACTAATAAT-GTATATAAATAGT
2554156 ACTAATAATGTATATAAATAGT
1 ACTAATAATGTATATAAATAGT
2554178 A
1 A
2554179 GTATAAGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.14
21 10 0.48
22 8 0.38
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.32
Consensus pattern (22 bp):
ACTAATAATGTATATAAATAGT
Found at i:2556667 original size:9 final size:9
Alignment explanation
Indices: 2556653--2556685 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
2556643 ACTCGGTTAG
2556653 GGAAATTAT
1 GGAAATTAT
2556662 GGAAATTAT
1 GGAAATTAT
2556671 GGAAATTAT
1 GGAAATTAT
2556680 GGAAAT
1 GGAAAT
2556686 AATCTTTCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.24, T:0.30
Consensus pattern (9 bp):
GGAAATTAT
Found at i:2558699 original size:113 final size:113
Alignment explanation
Indices: 2558389--2558830 Score: 676
Period size: 114 Copynumber: 3.9 Consensus size: 113
2558379 TTTTATAGTT
* *
2558389 GATTAGGTTATATAAATTGTTAATGTTTAGTAGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
2558454 TAATATA-TTTAAAAAATAATAATTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAT-AT--TTTTATAGCTATTTTATTAGTAATTTAA
* * *
2558504 GATTAGGTT-TATAAATTCTTAGTGTTTAGTGGTTTAGTGTATTAATGTATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
*
2558568 TAATATATTTTTAAAAAATATTTTTATAGCTATTTTATTTGTAATTTAA
66 TAATATA-TTTTAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
* *
2558617 GGTTAGATTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
2558682 TAATATATTTTAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
*
2558730 GATTAGGTTATAT--ATTGTTAGTGTTTAGTGGTTTAGTGTGTGTTAGTGTATTGTGATTTTTTT
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTA--GTGTATTAGTGTATTGTGA-TTTTTT
* * * *
2558793 TAGTAATGTATTTAAAAAAATAATTTTATAGTTATTTT
63 TAGTAATATATTTTAAAAAATATTTTTATAGCTATTTT
2558831 GTGTTAGTAT
Statistics
Matches: 302, Mismatches: 19, Indels: 13
0.90 0.06 0.04
Matches are distributed among these distances:
111 22 0.07
113 103 0.34
114 156 0.52
115 11 0.04
116 10 0.03
ACGTcount: A:0.31, C:0.01, G:0.16, T:0.52
Consensus pattern (113 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTGATTTTTTTAG
TAATATATTTTAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
Found at i:2558909 original size:21 final size:20
Alignment explanation
Indices: 2558885--2558946 Score: 52
Period size: 22 Copynumber: 2.9 Consensus size: 20
2558875 TTTTGTGATT
2558885 TTTAATGTAATTTTTATATAA
1 TTTAATGTAATTTTTATAT-A
* *
2558906 TTTAATTTTATATTATTATATA
1 TTTAA-TGTA-ATTTTTATATA
*
2558928 TTTATTTGATAATTTTTAT
1 TTTA-ATG-TAATTTTTAT
2558947 TGATTTATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
21 5 0.16
22 16 0.50
23 11 0.34
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTAATGTAATTTTTATATA
Found at i:2558946 original size:22 final size:23
Alignment explanation
Indices: 2558892--2558955 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
2558882 ATTTTTAATG
*
2558892 TAATTTTTATATAATTTAATTTTA
1 TAATTTTTATATAATTT-ATTTGA
*
2558916 T-ATTATTATAT-ATTTATTTGA
1 TAATTTTTATATAATTTATTTGA
*
2558937 TAATTTTTAT-TGATTTATT
1 TAATTTTTATATAATTTATT
2558956 AAAATGTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 7 0.20
22 18 0.51
23 9 0.26
24 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (23 bp):
TAATTTTTATATAATTTATTTGA
Found at i:2565410 original size:22 final size:22
Alignment explanation
Indices: 2565382--2565448 Score: 125
Period size: 22 Copynumber: 3.0 Consensus size: 22
2565372 TACTTTGATC
*
2565382 AAATAATTTTATTGTAAAATTT
1 AAATAATTTTATTATAAAATTT
2565404 AAATAATTTTATTATAAAATTT
1 AAATAATTTTATTATAAAATTT
2565426 AAATAATTTTATTATAAAATTT
1 AAATAATTTTATTATAAAATTT
2565448 A
1 A
2565449 CCTTTTTCGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 44 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (22 bp):
AAATAATTTTATTATAAAATTT
Found at i:2566413 original size:11 final size:11
Alignment explanation
Indices: 2566397--2566427 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2566387 ATACCCATAC
2566397 CCCATACCTTG
1 CCCATACCTTG
*
2566408 CCCATACCTTT
1 CCCATACCTTG
2566419 CCCATACCT
1 CCCATACCT
2566428 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:2570192 original size:11 final size:11
Alignment explanation
Indices: 2570176--2570206 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2570166 ATACCCATAC
2570176 CCCATACCTTG
1 CCCATACCTTG
*
2570187 CCCATACCTTT
1 CCCATACCTTG
2570198 CCCATACCT
1 CCCATACCT
2570207 ACCCATACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.48, G:0.03, T:0.29
Consensus pattern (11 bp):
CCCATACCTTG
Found at i:2573812 original size:17 final size:16
Alignment explanation
Indices: 2573775--2573813 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2573765 AATAAACAAT
2573775 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
2573790 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
2573808 TAAATT
1 TAAATT
2573814 CGGATTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:2575694 original size:22 final size:22
Alignment explanation
Indices: 2575666--2575728 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
2575656 CCTTTTTCTT
2575666 TTTTTCTTTATTATTTGTTTTA
1 TTTTTCTTTATTATTTGTTTTA
* *
2575688 TTTTTCTTTTTTCTATT-TTTTA
1 TTTTTCTTTATTAT-TTGTTTTA
2575710 TTTGTTC---ATTATTTGTTTT
1 TTT-TTCTTTATTATTTGTTTT
2575729 TATAATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 2 0.06
20 7 0.21
22 20 0.59
23 5 0.15
ACGTcount: A:0.11, C:0.06, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTTTCTTTATTATTTGTTTTA
Found at i:2575713 original size:31 final size:30
Alignment explanation
Indices: 2575658--2575715 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
2575648 CTATTTGTCC
*
2575658 TTTTTCTTTTTTTCTTTATTATTTGTTTTA
1 TTTTTCTTTTTTTATTTATTATTTGTTTTA
*
2575688 TTTTTCTTTTTTCTATTTTTTATTTGTT
1 TTTTTCTTTTTT-TATTTATTATTTGTT
2575716 CATTATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.09, C:0.07, G:0.03, T:0.81
Consensus pattern (30 bp):
TTTTTCTTTTTTTATTTATTATTTGTTTTA
Found at i:2579290 original size:41 final size:41
Alignment explanation
Indices: 2579239--2579447 Score: 174
Period size: 41 Copynumber: 5.1 Consensus size: 41
2579229 CAAAAATTGT
*
2579239 AAAACACAGAGCAATAGCGGCTTTTTACCAAAAACGCCGCTA
1 AAAAC-CAGAGCAATAGCGGCGTTTTACCAAAAACGCCGCTA
*
2579281 AAAACCAGAGCAATAGCGGCGTTTTACCAAAAACACCGCTA
1 AAAACCAGAGCAATAGCGGCGTTTTACCAAAAACGCCGCTA
* * * * ** *
2579322 AAAACCAAAGCATTAGCTGCGCTTT-CGGTAAAACGCCACTA
1 AAAACCAGAGCAATAGCGGCGTTTTAC-CAAAAACGCCGCTA
* * * * ** *
2579363 AAAACCAGAGCATTAGTGTCGCTTT-CGGTAAAACGCTGCTA
1 AAAACCAGAGCAATAGCGGCGTTTTAC-CAAAAACGCCGCTA
* * *
2579404 AAAACCAGAGC-ATCAGCGACGTTTT-CGATAAAACGCCGTTA
1 AAAACCAGAGCAAT-AGCGGCGTTTTACCA-AAAACGCCGCTA
2579445 AAA
1 AAA
2579448 GTCATATAAC
Statistics
Matches: 141, Mismatches: 23, Indels: 7
0.82 0.13 0.04
Matches are distributed among these distances:
40 3 0.02
41 133 0.94
42 5 0.04
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AAAACCAGAGCAATAGCGGCGTTTTACCAAAAACGCCGCTA
Found at i:2579447 original size:82 final size:82
Alignment explanation
Indices: 2579269--2579447 Score: 200
Period size: 82 Copynumber: 2.2 Consensus size: 82
2579259 CTTTTTACCA
*
2579269 AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGTTTTACCAAAAACACCGCTAAAAACCAAAGCA
1 AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTACCAAAAACACCGCTAAAAACCAAAGCA
* *
2579334 TTAGCTGCGCTTTCGGT
66 TCAGCTGCGCTTTCGAT
* * * * ** * * *
2579351 AAAACGCCACTAAAAACCAGAGCATTAGTGTCGCTTT-CGGTAAAACGCTGCTAAAAACCAGAGC
1 AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTAC-CAAAAACACCGCTAAAAACCAAAGC
*
2579415 ATCAGC-GACGTTTTCGAT
65 ATCAGCTG-CGCTTTCGAT
*
2579433 AAAACGCCGTTAAAA
1 AAAACGCCGCTAAAA
2579448 GTCATATAAC
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 2 0.03
82 78 0.98
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (82 bp):
AAAACGCCGCTAAAAACCAGAGCAATAGCGGCGCTTTACCAAAAACACCGCTAAAAACCAAAGCA
TCAGCTGCGCTTTCGAT
Found at i:2579773 original size:28 final size:28
Alignment explanation
Indices: 2579742--2579811 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
2579732 TATGGATTAT
* *
2579742 GGGTTTAGGGATTATGGTTTAAAGGTT-G
1 GGGTTTA-GGATTAGGGGTTAAAGGTTAG
* **
2579770 GGGTTTAAGGTTTAGGGGTTATGGGTTAG
1 GGGTTT-AGGATTAGGGGTTAAAGGTTAG
2579799 GGGTTTAGGATTA
1 GGGTTTAGGATTA
2579812 AGAGTTTATA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 26 0.76
29 8 0.24
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (28 bp):
GGGTTTAGGATTAGGGGTTAAAGGTTAG
Found at i:2579827 original size:50 final size:50
Alignment explanation
Indices: 2579773--2579869 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
2579763 AAGGTTGGGG
* * *
2579773 TTTAAGGTTTAGGGGTTATGGGTTAGGGGTTTAGGATTAAGAGTTTATAT
1 TTTAAGATTTAGGGGTTATGGGTTAAGGGTTAAGGATTAAGAGTTTATAT
* * *
2579823 TTTAAGATTTAGGGTTTATGGGTTAAGGGTTAAGGGTTAGGAGTTTA
1 TTTAAGATTTAGGGGTTATGGGTTAAGGGTTAAGGATTAAGAGTTTA
2579870 GGGTTTAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (50 bp):
TTTAAGATTTAGGGGTTATGGGTTAAGGGTTAAGGATTAAGAGTTTATAT
Found at i:2579831 original size:21 final size:21
Alignment explanation
Indices: 2579802--2579841 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2579792 GGGTTAGGGG
*
2579802 TTTAGGATTAAGAGTTTATAT
1 TTTAAGATTAAGAGTTTATAT
* *
2579823 TTTAAGATTTAGGGTTTAT
1 TTTAAGATTAAGAGTTTAT
2579842 GGGTTAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (21 bp):
TTTAAGATTAAGAGTTTATAT
Found at i:2579845 original size:8 final size:7
Alignment explanation
Indices: 2579830--2579877 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
2579820 TATTTTAAGA
2579830 TTTAGGG
1 TTTAGGG
2579837 TTTATGGG
1 TTTA-GGG
*
2579845 TTAAGGG
1 TTTAGGG
*
2579852 TTAAGGG
1 TTTAGGG
2579859 -TTAGGAG
1 TTTAGG-G
2579866 TTTAGGG
1 TTTAGGG
2579873 TTTAG
1 TTTAG
2579878 TTAATTAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 4 0.11
7 21 0.58
8 11 0.31
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:2580254 original size:19 final size:19
Alignment explanation
Indices: 2580219--2580281 Score: 99
Period size: 19 Copynumber: 3.3 Consensus size: 19
2580209 GTAGATTTAA
2580219 AAAAACATTGATAAATAAAT
1 AAAAACATTGAT-AATAAAT
2580239 AAAAACATTGATAATAAAT
1 AAAAACATTGATAATAAAT
* *
2580258 AAAAACATTAATAACAAAT
1 AAAAACATTGATAATAAAT
2580277 AAAAA
1 AAAAA
2580282 TGAAATACAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.22
Consensus pattern (19 bp):
AAAAACATTGATAATAAAT
Found at i:2580326 original size:15 final size:15
Alignment explanation
Indices: 2580306--2580357 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
2580296 AAAAATGAAA
2580306 TATGGGTTTATGGAT
1 TATGGGTTTATGGAT
*
2580321 TATGGGTTTAGGGAT
1 TATGGGTTTATGGAT
* *
2580336 TAT-GATTTATGGTT
1 TATGGGTTTATGGAT
*
2580350 TAAGGGTT
1 TATGGGTT
2580358 GGGGTTTAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
14 10 0.33
15 20 0.67
ACGTcount: A:0.21, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
TATGGGTTTATGGAT
Found at i:2581178 original size:17 final size:17
Alignment explanation
Indices: 2581136--2581179 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
2581126 TTCTCTTCCT
*
2581136 CCATTCCCTTTTCTTTC
1 CCATTTCCTTTTCTTTC
2581153 CCAATTTCCTTTTCTTTC
1 CC-ATTTCCTTTTCTTTC
*
2581171 TCATTTCCT
1 CCATTTCCT
2581180 CAGTCTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (17 bp):
CCATTTCCTTTTCTTTC
Found at i:2581455 original size:62 final size:63
Alignment explanation
Indices: 2581385--2581516 Score: 187
Period size: 65 Copynumber: 2.1 Consensus size: 63
2581375 CTTTCTTTAT
2581385 TTTTCAATCGTCTTA-AAATTTTAGA-ATTTTTAATTTGGGTTTCTTATTTTCTATTATATTAG
1 TTTTCAATCGTCTTAGAAATTTTAGATATTTTTAATTTGGGTTTCTTA-TTTCTATTATATTAG
* * **
2581447 TTTTCAATCGTCTTAGAAATTTTTGATTTTTTTTTTGTTTGGGTTTCTTATTTCTATTATATTAG
1 TTTTCAATCGTCTTAGAAATTTTAGA--TATTTTTAATTTGGGTTTCTTATTTCTATTATATTAG
2581512 TTTTC
1 TTTTC
2581517 TAGTTTCCTG
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
62 15 0.24
63 9 0.15
65 20 0.32
66 18 0.29
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.60
Consensus pattern (63 bp):
TTTTCAATCGTCTTAGAAATTTTAGATATTTTTAATTTGGGTTTCTTATTTCTATTATATTAG
Found at i:2584671 original size:23 final size:23
Alignment explanation
Indices: 2584641--2584742 Score: 150
Period size: 23 Copynumber: 4.4 Consensus size: 23
2584631 TGGTTGCTGC
*
2584641 TGTTTAAATGCTGTAAATTGAAG
1 TGTTTAAATGCTGTAAATTAAAG
* *
2584664 TGTTTAAATGCTATAAATTGAAG
1 TGTTTAAATGCTGTAAATTAAAG
* *
2584687 TGTTTAAATGTTGTAAACTAAAG
1 TGTTTAAATGCTGTAAATTAAAG
*
2584710 TATTTAAATGCTGTAAATTAAAG
1 TGTTTAAATGCTGTAAATTAAAG
2584733 TGTTTAAATG
1 TGTTTAAATG
2584743 TTCTTTGTGT
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (23 bp):
TGTTTAAATGCTGTAAATTAAAG
Found at i:2585276 original size:42 final size:43
Alignment explanation
Indices: 2585221--2585323 Score: 118
Period size: 42 Copynumber: 2.4 Consensus size: 43
2585211 ATATATATGG
* ** * * *
2585221 TCTTTAGCGGCGTTTTTGGGGAAAGCGTTGTTAAAGGTTA-TA
1 TCTTTAGCGGCGTTTTTGGAGAAAGCGCCGCTAAAGGTCACAA
* * *
2585263 TTTTTAGCGGCGTTCTTAGAGAAAGCGCCGCTAAAGGTCACAA
1 TCTTTAGCGGCGTTTTTGGAGAAAGCGCCGCTAAAGGTCACAA
2585306 TCTTTAGCGGCGTTTTTG
1 TCTTTAGCGGCGTTTTTG
2585324 AAAAAAAAAT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
42 32 0.67
43 16 0.33
ACGTcount: A:0.21, C:0.16, G:0.28, T:0.35
Consensus pattern (43 bp):
TCTTTAGCGGCGTTTTTGGAGAAAGCGCCGCTAAAGGTCACAA
Found at i:2588939 original size:41 final size:43
Alignment explanation
Indices: 2588876--2588959 Score: 102
Period size: 41 Copynumber: 2.0 Consensus size: 43
2588866 CTTTAAACTC
*
2588876 AAACCCTAAATCTCAAATCCTTAAACCCTCG-ACCTAAACCTTG
1 AAACCCTAAACCTCAAATCCTTAAA-CCTCGAACCTAAACCTTG
* **
2588919 AAACCC-AAACCTTAAA-CCTTAAATTTCGAACCTAAACCTTG
1 AAACCCTAAACCTCAAATCCTTAAACCTCGAACCTAAACCTTG
2588960 GGGTTCAAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 3 0.08
41 19 0.53
42 8 0.22
43 6 0.17
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.24
Consensus pattern (43 bp):
AAACCCTAAACCTCAAATCCTTAAACCTCGAACCTAAACCTTG
Found at i:2601075 original size:20 final size:21
Alignment explanation
Indices: 2601052--2601170 Score: 71
Period size: 23 Copynumber: 5.2 Consensus size: 21
2601042 AATACTACAT
*
2601052 AAATATGTACATAT-ATATTA
1 AAATATATACATATAATATTA
*
2601072 AAATAAATACATAATAATATTA
1 AAATATATACAT-ATAATATTA
*
2601094 AAAGTATATACATAAAATAGTGTTAA
1 AAA-TATATACATATAATA---TT-A
*
2601120 AAATACATACATA-ATATAGTTA
1 AAATATATACATATA-ATA-TTA
* *
2601142 TTAATATATATATATACATATTA
1 -AAATATATACATATA-ATATTA
2601165 GAAATA
1 -AAATA
2601171 ATAATAATGT
Statistics
Matches: 78, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
20 10 0.13
21 2 0.03
22 15 0.19
23 28 0.36
24 5 0.06
25 14 0.18
26 4 0.05
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
AAATATATACATATAATATTA
Found at i:2601108 original size:23 final size:22
Alignment explanation
Indices: 2601059--2601135 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
2601049 CATAAATATG
2601059 TACAT-AT-ATATTAAAATAAA
1 TACATAATAATATTAAAATAAA
*
2601079 TACATAATAATATTAAAAGTATA
1 TACATAATAATATTAAAA-TAAA
*
2601102 TACATAA-AATAGTGTTAAAAATACA
1 TACATAATAATA---TT-AAAATAAA
2601127 TACATAATA
1 TACATAATA
2601136 TAGTTATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.11
21 2 0.04
22 13 0.28
23 10 0.21
25 12 0.26
26 5 0.11
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (22 bp):
TACATAATAATATTAAAATAAA
Found at i:2601141 original size:23 final size:22
Alignment explanation
Indices: 2601059--2601137 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 22
2601049 CATAAATATG
2601059 TACAT-ATATATT-AAAATAAA
1 TACATAATATATTAAAAATAAA
* *
2601079 TACATAATAATATTAAAAGTATA
1 TACATAAT-ATATTAAAAATAAA
* *
2601102 TACATAAAATAGTGTTAAAAATACA
1 TACAT--AATA-TATTAAAAATAAA
2601127 TACATAATATA
1 TACATAATATA
2601138 GTTATTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 5 0.11
21 2 0.04
22 6 0.13
23 15 0.32
24 1 0.02
25 18 0.38
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (22 bp):
TACATAATATATTAAAAATAAA
Found at i:2601253 original size:21 final size:22
Alignment explanation
Indices: 2601213--2601259 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2601203 CTGCATAAAC
* *
2601213 ATATACATATATATGTTAAAGAT
1 ATATACATATATA-GATAAACAT
2601236 ATATACATATATA-ATAAACAT
1 ATATACATATATAGATAAACAT
2601257 ATA
1 ATA
2601260 CTACTACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
23 13 0.59
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.36
Consensus pattern (22 bp):
ATATACATATATAGATAAACAT
Found at i:2601264 original size:3 final size:3
Alignment explanation
Indices: 2601258--2601286 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2601248 AATAAACATA
2601258 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
2601287 ATAATAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:2601652 original size:11 final size:10
Alignment explanation
Indices: 2601634--2601704 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 10
2601624 ATAACATTAA
2601634 AAATATATAT
1 AAATATATAT
2601644 -AATATATAT
1 AAATATATAT
2601653 AAA-ATATAT
1 AAATATATAT
*
2601662 ACAATATATAC
1 A-AATATATAT
* * *
2601673 ATATATTTAG
1 AAATATATAT
2601683 AAATGATA-AT
1 AAAT-ATATAT
2601693 -AATATATAT
1 AAATATATAT
2601702 AAA
1 AAA
2601705 AAACTATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
8 3 0.06
9 21 0.44
10 16 0.33
11 8 0.17
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (10 bp):
AAATATATAT
Found at i:2601812 original size:23 final size:25
Alignment explanation
Indices: 2601778--2601841 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 25
2601768 TACAATATAG
* *
2601778 TATTAGAA-ATATACATAC-AATAG
1 TATTAAAAGATATACATACTAATAA
*
2601801 TA-TAAAAGATATATA-ACTAATAA
1 TATTAAAAGATATACATACTAATAA
*
2601824 TATTAAAATATATACATA
1 TATTAAAAGATATACATA
2601842 ATATATGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 6 0.19
23 14 0.44
24 11 0.34
25 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (25 bp):
TATTAAAAGATATACATACTAATAA
Found at i:2601924 original size:21 final size:21
Alignment explanation
Indices: 2601889--2601978 Score: 73
Period size: 21 Copynumber: 4.2 Consensus size: 21
2601879 ATACTTCATG
*
2601889 AATATATACATATATATATTAA
1 AATATATACA-ATATATAATAA
2601911 AGATATATAC-ATATATAATAA
1 A-ATATATACAATATATAATAA
*
2601932 AACATATACTAATA-ATAATAA
1 AATATATAC-AATATATAATAA
2601953 TAATA-AT--AATAATATAATAA
1 -AATATATACAAT-ATATAATAA
2601973 TAATAT
1 -AATAT
2601979 TATTAAAAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
18 3 0.05
19 1 0.02
20 19 0.33
21 20 0.34
22 7 0.12
23 8 0.14
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
AATATATACAATATATAATAA
Found at i:2601946 original size:15 final size:14
Alignment explanation
Indices: 2601919--2601972 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
2601909 AAAGATATAT
2601919 ACATATATAATAAA
1 ACATATATAATAAA
*
2601933 ACATATACTAATAAT
1 ACATATA-TAATAAA
*
2601948 A-ATA-ATAATAAT
1 ACATATATAATAAA
2601960 A-ATAATATAATAA
1 ACAT-ATATAATAA
2601973 TAATATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
12 10 0.28
13 2 0.06
14 17 0.47
15 7 0.19
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
ACATATATAATAAA
Found at i:2601947 original size:3 final size:3
Alignment explanation
Indices: 2601941--2601977 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
2601931 AAACATATAC
2601941 TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2601978 TTATTAAAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2602640 original size:18 final size:18
Alignment explanation
Indices: 2602604--2602642 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2602594 CGAAAACAGA
2602604 AAAGGAAAAAAAATAAAT
1 AAAGGAAAAAAAATAAAT
*
2602622 AAAGAGAAAGAAAAT-AAT
1 AAAG-GAAAAAAAATAAAT
2602640 AAA
1 AAA
2602643 AATGTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (18 bp):
AAAGGAAAAAAAATAAAT
Found at i:2603823 original size:75 final size:73
Alignment explanation
Indices: 2603721--2603990 Score: 291
Period size: 75 Copynumber: 3.6 Consensus size: 73
2603711 TGGCCTGAGA
* *
2603721 CTCAACTCACCTATCGCAATATGAGTTGA-TTTTTGACGAACAGAAATTGAAAATACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AAACAGAAATTGAAAATACCTCAGCGT
2603785 GTGAGCCAAGG
65 GT--GCCAAGG
* *
2603796 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTATGAACAGAAATT-AAAATTACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGA-AAACAGAAATTGAAAA-TACCTCAGC
2603860 GTGT-CCTGAA-G
63 GTGTGCC--AAGG
* * * *
2603871 CTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAAAGATAGAAATTGAAAATACCTCAACGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA-ACAGAAATTGAAAATACCTCAGCGT
**
2603936 GT-CTTGAGG
65 GTGC-CAAGG
* * *
2603945 CTTAACTTATCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAAT
2603991 AAGAACATCA
Statistics
Matches: 172, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
72 7 0.04
73 11 0.06
74 57 0.33
75 61 0.35
76 6 0.03
77 30 0.17
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (73 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTG
TGCCAAGG
Found at i:2611317 original size:22 final size:22
Alignment explanation
Indices: 2611289--2611333 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2611279 AATGGATGAA
2611289 TGAATAAATGACAAATGAATGT
1 TGAATAAATGACAAATGAATGT
*
2611311 TGAATAAATGACGAATGAATGT
1 TGAATAAATGACAAATGAATGT
2611333 T
1 T
2611334 AGTCATGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.20, T:0.29
Consensus pattern (22 bp):
TGAATAAATGACAAATGAATGT
Found at i:2614961 original size:23 final size:23
Alignment explanation
Indices: 2614930--2615023 Score: 179
Period size: 23 Copynumber: 4.1 Consensus size: 23
2614920 AGAGTTAGAA
2614930 ATACATCGAAGCAAATAATAAAT
1 ATACATCGAAGCAAATAATAAAT
*
2614953 ATAAATCGAAGCAAATAATAAAT
1 ATACATCGAAGCAAATAATAAAT
2614976 ATACATCGAAGCAAATAATAAAT
1 ATACATCGAAGCAAATAATAAAT
2614999 ATACATCGAAGCAAATAATAAAT
1 ATACATCGAAGCAAATAATAAAT
2615022 AT
1 AT
2615024 GACAATAATA
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.57, C:0.12, G:0.09, T:0.22
Consensus pattern (23 bp):
ATACATCGAAGCAAATAATAAAT
Found at i:2615245 original size:14 final size:14
Alignment explanation
Indices: 2615226--2615274 Score: 71
Period size: 14 Copynumber: 3.3 Consensus size: 14
2615216 TGTAAACATA
2615226 ATAATACTAAATAT
1 ATAATACTAAATAT
2615240 ATAATACTAAATAT
1 ATAATACTAAATAT
2615254 ATATATACATAATATAT
1 ATA-ATAC-TAA-ATAT
2615271 ATAA
1 ATAA
2615275 AATGAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 17 0.53
15 4 0.12
16 4 0.12
17 7 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAATACTAAATAT
Found at i:2615351 original size:20 final size:21
Alignment explanation
Indices: 2615328--2615388 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 21
2615318 AATACTACAT
*
2615328 AAATATGTACATAT-ATATTA
1 AAATATATACATATAATATTA
*
2615348 AAATAAATACATAATAATATTA
1 AAATATATACAT-ATAATATTA
*
2615370 AAAGTATATACATAAAATA
1 AAA-TATATACATATAATA
2615389 GTGTTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 10 0.29
21 2 0.06
22 14 0.41
23 8 0.24
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (21 bp):
AAATATATACATATAATATTA
Found at i:2615384 original size:23 final size:22
Alignment explanation
Indices: 2615335--2615411 Score: 70
Period size: 22 Copynumber: 3.4 Consensus size: 22
2615325 CATAAATATG
2615335 TACAT-AT-ATATTAAAATAAA
1 TACATAATAATATTAAAATAAA
*
2615355 TACATAATAATATTAAAAGTATA
1 TACATAATAATATTAAAA-TAAA
*
2615378 TACATAA-AATAGTGTTAAAAATACA
1 TACATAATAATA---TT-AAAATAAA
2615403 TACATAATA
1 TACATAATA
2615412 TAGTTATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.11
21 2 0.04
22 13 0.28
23 10 0.21
25 12 0.26
26 5 0.11
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (22 bp):
TACATAATAATATTAAAATAAA
Found at i:2615417 original size:23 final size:22
Alignment explanation
Indices: 2615335--2615413 Score: 72
Period size: 25 Copynumber: 3.5 Consensus size: 22
2615325 CATAAATATG
2615335 TACAT-ATATATT-AAAATAAA
1 TACATAATATATTAAAAATAAA
* *
2615355 TACATAATAATATTAAAAGTATA
1 TACATAAT-ATATTAAAAATAAA
* *
2615378 TACATAAAATAGTGTTAAAAATACA
1 TACAT--AATA-TATTAAAAATAAA
2615403 TACATAATATA
1 TACATAATATA
2615414 GTTATTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 5 0.11
21 2 0.04
22 6 0.13
23 15 0.32
24 1 0.02
25 18 0.38
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (22 bp):
TACATAATATATTAAAAATAAA
Found at i:2615542 original size:3 final size:3
Alignment explanation
Indices: 2615536--2615563 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2615526 TAAACATATT
2615536 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2615564 AAAGATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2615905 original size:11 final size:10
Alignment explanation
Indices: 2615889--2615959 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 10
2615879 ATAACATTAA
2615889 AAATATATAT
1 AAATATATAT
2615899 -AATATATAT
1 AAATATATAT
2615908 AAA-ATATAT
1 AAATATATAT
*
2615917 ACAATATATAC
1 A-AATATATAT
* * *
2615928 ATATATTTAG
1 AAATATATAT
2615938 AAATGATA-AT
1 AAAT-ATATAT
2615948 -AATATATAT
1 AAATATATAT
2615957 AAA
1 AAA
2615960 AAACAATTCA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
8 3 0.06
9 21 0.44
10 16 0.33
11 8 0.17
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (10 bp):
AAATATATAT
Found at i:2616067 original size:23 final size:25
Alignment explanation
Indices: 2616033--2616096 Score: 64
Period size: 23 Copynumber: 2.7 Consensus size: 25
2616023 TACAATATAG
* *
2616033 TATTAGAA-ATATACATAC-AATAG
1 TATTAAAAGATATACATACTAATAA
*
2616056 TA-TAAAAGATATATA-ACTAATAA
1 TATTAAAAGATATACATACTAATAA
*
2616079 TATTAAAATATATACATA
1 TATTAAAAGATATACATA
2616097 ATATATGCAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 6 0.19
23 14 0.44
24 11 0.34
25 1 0.03
ACGTcount: A:0.56, C:0.06, G:0.05, T:0.33
Consensus pattern (25 bp):
TATTAAAAGATATACATACTAATAA
Found at i:2616885 original size:18 final size:18
Alignment explanation
Indices: 2616853--2616887 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2616843 AAAATAGAAA
2616853 AGAAAAAAATAAATAAAG
1 AGAAAAAAATAAATAAAG
2616871 AGAAAGAAAAT-AATAAA
1 AGAAA-AAAATAAATAAA
2616888 AATGTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AGAAAAAAATAAATAAAG
Found at i:2618078 original size:75 final size:73
Alignment explanation
Indices: 2617976--2618245 Score: 291
Period size: 75 Copynumber: 3.6 Consensus size: 73
2617966 TGGCCTGAGA
* *
2617976 CTCAACTCACCTATCGCAATATGAGTTGA-TTTTTGACGAACAGAAATTGAAAATACCTCAGCGT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AAACAGAAATTGAAAATACCTCAGCGT
2618040 GTGAGCCAAGG
65 GT--GCCAAGG
* *
2618051 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTATGAACAGAAATT-AAAATTACCTCAGC
1 CTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTGA-AAACAGAAATTGAAAA-TACCTCAGC
2618115 GTGT-CCTGAA-G
63 GTGTGCC--AAGG
* * * *
2618126 CTCAACTCATCTCTCGCAATATGAGTTGATTTTTTGAAAGATAGAAATTGAAAATACCTCAACGC
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAA-ACAGAAATTGAAAATACCTCAGCGT
**
2618191 GT-CTTGAGG
65 GTGC-CAAGG
* * *
2618200 CTTAACTTATCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAAT
1 CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAAT
2618246 AAGAACATCA
Statistics
Matches: 172, Mismatches: 14, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
72 7 0.04
73 11 0.06
74 57 0.33
75 61 0.35
76 6 0.03
77 30 0.17
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (73 bp):
CTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGCGTG
TGCCAAGG
Found at i:2625441 original size:30 final size:30
Alignment explanation
Indices: 2625407--2625469 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
2625397 ACTTAACAAG
2625407 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
2625437 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
2625467 CAA
1 CAA
2625470 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:2630997 original size:26 final size:24
Alignment explanation
Indices: 2630953--2631002 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
2630943 ATTTGTTTTA
*
2630953 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
2630977 ATATTTGATTTATTATATTTTTAAAT
1 ATATTTG-TTT-TTATATTTTTAAAT
2631003 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:2631546 original size:22 final size:22
Alignment explanation
Indices: 2631521--2631572 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
2631511 AAAAAGATTC
2631521 GAAA-TAAAAAAAATAAGAACAA
1 GAAATTAAAAAAAATAAGAA-AA
*
2631543 GAAATTGAAAAAAATAAGAAAA
1 GAAATTAAAAAAAATAAGAAAA
2631565 GAAGATTA
1 GAA-ATTA
2631573 CAGTCAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 9 0.35
23 17 0.65
ACGTcount: A:0.71, C:0.02, G:0.13, T:0.13
Consensus pattern (22 bp):
GAAATTAAAAAAAATAAGAAAA
Found at i:2632327 original size:50 final size:49
Alignment explanation
Indices: 2632264--2632411 Score: 201
Period size: 47 Copynumber: 3.0 Consensus size: 49
2632254 TTGTCCATCC
2632264 GAAACACCATTTGTGGACAAGCCACCACTGATTTGCAGATAAACTGCCACT
1 GAAACA-C-TTTGTGGACAAGCCACCACTGATTTGCAGATAAACTGCCACT
* * * *
2632315 GATAACACTTTGTGGACTAGCCACCAC--ATATGCAGATATACTGCCATT
1 GA-AACACTTTGTGGACAAGCCACCACTGATTTGCAGATAAACTGCCACT
* *
2632363 GAAATACTTTGTGGACAAGCCACCACTGATTTGTAGATAAACTGCCACT
1 GAAACACTTTGTGGACAAGCCACCACTGATTTGCAGATAAACTGCCACT
2632412 ACTTCCACCT
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
47 22 0.26
48 20 0.24
49 17 0.20
50 18 0.21
51 3 0.04
52 4 0.05
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (49 bp):
GAAACACTTTGTGGACAAGCCACCACTGATTTGCAGATAAACTGCCACT
Found at i:2633836 original size:21 final size:21
Alignment explanation
Indices: 2633810--2633864 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
2633800 TGTTTCTCAG
2633810 CCACACAGATGTGTGGTTTAA
1 CCACACAGATGTGTGGTTTAA
* * *
2633831 CGACACATATGTGTGGTTTAG
1 CCACACAGATGTGTGGTTTAA
2633852 CCACACAG-TGTGT
1 CCACACAGATGTGT
2633865 CCATTCTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (21 bp):
CCACACAGATGTGTGGTTTAA
Found at i:2635310 original size:15 final size:15
Alignment explanation
Indices: 2635290--2635319 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2635280 CATTTTATTT
*
2635290 ATATTAGGATAATTA
1 ATATTAAGATAATTA
2635305 ATATTAAGATAATTA
1 ATATTAAGATAATTA
2635320 TGAGGATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:2640442 original size:17 final size:16
Alignment explanation
Indices: 2640415--2640490 Score: 55
Period size: 17 Copynumber: 4.3 Consensus size: 16
2640405 TATATTTTAA
2640415 AAAAGTATTTAATATAT
1 AAAA-TATTTAATATAT
*
2640432 ATAAATATTTACAAATAT
1 A-AAATATTTA-ATATAT
2640450 AAAATATTCATTAATTATAT
1 AAAATA-T--TTAA-TATAT
*
2640470 AAAAATATTTATTA-AT
1 -AAAATATTTAATATAT
2640486 AAAAT
1 AAAAT
2640491 TCTATCATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
15 5 0.10
16 2 0.04
17 14 0.29
18 13 0.27
19 1 0.02
20 8 0.16
21 6 0.12
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (16 bp):
AAAATATTTAATATAT
Found at i:2640469 original size:20 final size:21
Alignment explanation
Indices: 2640446--2640485 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2640436 ATATTTACAA
2640446 ATAT-AAAATATTCATTAATT
1 ATATAAAAATATTCATTAATT
*
2640466 ATATAAAAATATTTATTAAT
1 ATATAAAAATATTCATTAAT
2640486 AAAATTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAAAAATATTCATTAATT
Found at i:2646882 original size:23 final size:23
Alignment explanation
Indices: 2646801--2646902 Score: 75
Period size: 23 Copynumber: 4.3 Consensus size: 23
2646791 TACCGATATA
2646801 TCAGCTC-ATAAGAGCTTACTGTT
1 TCAGCTCAAT-AGAGCTTACTGTT
** *
2646824 CTCAGCT-TGTATGGGCTTACTG-T
1 -TCAGCTCAATA-GAGCTTACTGTT
**
2646847 TCAGCTCGTTAGAGCTTACTGTT
1 TCAGCTCAATAGAGCTTACTGTT
* *
2646870 TTAGCTCAATAGAGATTACTGTT
1 TCAGCTCAATAGAGCTTACTGTT
2646893 CATCAGCTCA
1 --TCAGCTCA
2646903 GGAGGAGCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
22 15 0.24
23 24 0.39
24 16 0.26
25 7 0.11
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.36
Consensus pattern (23 bp):
TCAGCTCAATAGAGCTTACTGTT
Found at i:2652355 original size:26 final size:28
Alignment explanation
Indices: 2652305--2652359 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
2652295 ATAGAAGATG
*
2652305 AAATATATACACAATATAATAATATAAT
1 AAATATATACACAATATAAAAATATAAT
*
2652333 AAATA-ATACA-AATTTAAAAATATAAT
1 AAATATATACACAATATAAAAATATAAT
2652359 A
1 A
2652360 CTTAATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 5 0.20
28 5 0.20
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATATATACACAATATAAAAATATAAT
Found at i:2663993 original size:31 final size:31
Alignment explanation
Indices: 2663958--2664016 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2663948 ATAACTTTGC
*
2663958 TCTCGATTTTATTTATCATATGACATCCTGT
1 TCTCGATTTTAATTATCATATGACATCCTGT
*
2663989 TCTCGGTTTTAATTATCATATGACATCC
1 TCTCGATTTTAATTATCATATGACATCC
2664017 AGATACACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (31 bp):
TCTCGATTTTAATTATCATATGACATCCTGT
Found at i:2664825 original size:28 final size:26
Alignment explanation
Indices: 2664769--2664825 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
2664759 TTAGGGACAA
*
2664769 TATGTGTATGCATGAATGATTTAAGT
1 TATGTGTATGCATGAATGAATTAAGT
*
2664795 TATGTTTATGCTATTGAATGAAATTAA-T
1 TATGTGTATGC-A-TGAATG-AATTAAGT
2664823 TAT
1 TAT
2664826 AGATGTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 10 0.38
27 1 0.04
28 10 0.38
29 5 0.19
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (26 bp):
TATGTGTATGCATGAATGAATTAAGT
Found at i:2666271 original size:17 final size:15
Alignment explanation
Indices: 2666221--2666294 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 15
2666211 GTTTATTTTA
*
2666221 ATTTTACTTTTATATT
1 ATTTTA-TTATATATT
* *
2666237 A-TATATTATAAAATT
1 ATTTTATTAT-ATATT
2666252 ATTTTATTATGAGTATT
1 ATTTTATTAT-A-TATT
2666269 ATTTTTAATTATATATT
1 A-TTTT-ATTATATATT
2666286 ATTATTATT
1 ATT-TTATT
2666295 TATTATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
14 3 0.07
15 8 0.17
16 14 0.30
17 11 0.24
18 5 0.11
19 5 0.11
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTTATTATATATT
Found at i:2666290 original size:20 final size:18
Alignment explanation
Indices: 2666240--2666312 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 18
2666230 TTATATTATA
*
2666240 TATTATA-AAATTA-TTT
1 TATTATATATATTATTTT
*
2666256 TATTATGA-GTATTATTTT
1 TATTAT-ATATATTATTTT
2666274 TAATTATATATTATTATTATT
1 T-ATTATATA-TATTATT-TT
2666295 TATTATATATATTATTTT
1 TATTATATATATTATTTT
2666313 CCTTAAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 6 0.12
17 5 0.10
18 7 0.15
19 12 0.25
20 15 0.31
21 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTATATATATTATTTT
Found at i:2666292 original size:55 final size:54
Alignment explanation
Indices: 2666173--2666312 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 54
2666163 TTTAGTCCTA
* * ** *
2666173 TATT-TATTATATTATTCTATATATATATTTTATTATTTGTTTATTTTAATTTTAC
1 TATTATATTATA-TATTATATAAAT-TATTTTATTATGAGTTTATTTTAATTATAC
*
2666228 TTTTATATTATATATTATA-AAATTATTTTATTATGAGTATTATTTTTAATTATA-
1 TATTATATTATATATTATATAAATTATTTTATTATGAGT-TTA-TTTTAATTATAC
* *
2666282 TATTATTATTATTTATTATATATATTATTTT
1 TATTA-TATTATATATTATATAAATTATTTT
2666313 CCTTAAATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
53 13 0.18
54 10 0.14
55 32 0.45
56 16 0.23
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (54 bp):
TATTATATTATATATTATATAAATTATTTTATTATGAGTTTATTTTAATTATAC
Found at i:2666330 original size:55 final size:54
Alignment explanation
Indices: 2666198--2666330 Score: 128
Period size: 55 Copynumber: 2.4 Consensus size: 54
2666188 TCTATATATA
** * *
2666198 TATTTTATTATTTGT-TTATTTTAATTTTACTTTTATATTATATATTATAAAAT
1 TATTTTATTATAAGTATTATTTTAATTATACTATTATATTATATATTATAAAAT
* * *
2666251 TATTTTATTATGAGTATTATTTTTAATTATA-TATTATTATTATTTATTATATATAT
1 TATTTTATTATAAGTATTA-TTTTAATTATACTATTA-TATTATATATTATA-AAAT
* *
2666307 TATTTTCCTTA-AATTATTATTTTA
1 TATTTT-ATTATAAGTATTATTTTA
2666331 CATCCTTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
53 13 0.20
54 7 0.11
55 28 0.42
56 15 0.23
57 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (54 bp):
TATTTTATTATAAGTATTATTTTAATTATACTATTATATTATATATTATAAAAT
Found at i:2666944 original size:715 final size:716
Alignment explanation
Indices: 2665671--2667102 Score: 2751
Period size: 715 Copynumber: 2.0 Consensus size: 716
2665661 CAGGACGGCG
*
2665671 CGTGAGCGCGTGAGGAGACCCCTGGATGGAGGCTCAGCAGCTCCGGGATCGGCCCCCGAATCCTC
1 CGTGAGCGCGTGAGGAGACCCCTGGACGGAGGCTCAGCAGCTCCGGGATCGGCCCCCGAATCCTC
*
2665736 TTCCAGAGGATTTTTTCTTTTTTTTTTTTTAAAAAACGGATGTTAAAATGATTTTTAGGGGCGAA
66 TTCCAGAGGA-TTTTTCTTTTCTTTTTTTTAAAAAACGGATGTTAAAATGATTTTTAGGGGCGAA
2665801 ATTTGACTTATATAGTCTATTTAAAACGGTGTCGTTTTACAACTATAGGATCCGCGCGTTGACCC
130 ATTTGACTTATATAGTCTATTTAAAACGGTGTCGTTTTACAACTATAGGATCCGCGCGTTGACCC
*
2665866 GATTACCCGGGGAGGATCCGCGCATTTTTTAAAATTGGGTTAATTGCCCAATTGGTCCTCTCGCA
195 GATTACCCGGGGAGGATCCGCGCATTTTTGAAAATTGGGTTAATTGCCCAATTGGTCCTCTCGCA
2665931 ATTTTTATACTTTTAATTTCATTTTATTTATTTGTTTATTTGGTATTAATATTTTAATTCTGTTT
260 ATTTTTATACTTTTAATTTCATTTTATTTATTTGTTTATTTGGTATTAATATTTTAATTCTGTTT
2665996 CAATTCGACCCTCCCAATGATTTACAATCGTATTAGGGGAAACGGTGACGTTTTGGGAATAGGGC
325 CAATTCGACCCTCCCAATGATTTACAATCGTATTAGGGGAAACGGTGACGTTTTGGGAATAGGGC
2666061 TATTTGCCCAGTGACCCCCTTTGATTTCGCGAATGTTTCAAATCGGGTCTTAATTCAGTTTTAGC
390 TATTTGCCCAGTGACCCCCTTTGATTTCGCGAATGTTTCAAATCGGGTCTTAATTCAGTTTTAGC
*
2666126 TTTGTAAATTTGCCCCATAATTTTGTTAAACTTTAAATTTAGTCCTATATTTATTATATTATTCT
455 TTTGTAAATTTGCCCCATAATTTTGTTAAACTTTAAATTTAGTCCTATATCTATTATATTATTCT
2666191 ATATATATATTTTATTATTTGTTTATTTTAATTTTACTTTTATATTATATATTATAAAATTATTT
520 ATATATATATTTTATTATTTGTTTATTTTAATTTTACTTTTATATTATATATTATAAAATTATTT
2666256 TATTATGAGTATTATTTTTAATTATATATTATTATTATTTATTATATATATTATTTTCCTTAAAT
585 TATTATGAGTATTATTTTTAATTATATATTATTATTATTTATTATATATATTATTTTCCTTAAAT
2666321 TATTATTTTACATCCTTTTTATATATTATTATATTTTCACATATATTATATTTATTAATTACTTA
650 TATTATTTTACATCCTTTTTATATATTATTATATTTTCACATATATTATATTTATTAATTACTTA
2666386 TA
715 TA
* *
2666388 CGTGAGCGCGTGAGGAGACCCCTGGACGGAGGCTTAGCAGCTCCGGGATCGGCCTCCGAATCCTC
1 CGTGAGCGCGTGAGGAGACCCCTGGACGGAGGCTCAGCAGCTCCGGGATCGGCCCCCGAATCCTC
2666453 TTCCAGAGGA-TTTT-TTTTCTTTTTTTTAAAAAACGGATGTTAAAATGATTTTTAGGGGCGAAA
66 TTCCAGAGGATTTTTCTTTTCTTTTTTTTAAAAAACGGATGTTAAAATGATTTTTAGGGGCGAAA
2666516 TTTGACTTATATAGTCTATTTAAAACGGTGTCGTTTTACAACTATAGGATCCGCGCGTTGACCCG
131 TTTGACTTATATAGTCTATTTAAAACGGTGTCGTTTTACAACTATAGGATCCGCGCGTTGACCCG
*
2666581 ATTACCCGGGGAGGATCCGCGCATTTTTGAGAATTGGGTTAATTGCCCAATTGGTCCTCTCGCAA
196 ATTACCCGGGGAGGATCCGCGCATTTTTGAAAATTGGGTTAATTGCCCAATTGGTCCTCTCGCAA
*
2666646 TTTTTATACTTTTAATTTCATTTTATTTATTTTTTGTATTTGGTATTAATATTTTAATTCTGTTT
261 TTTTTATACTTTTAATTTCATTTTATTTATTTGTT-TATTTGGTATTAATATTTTAATTCTGTTT
*
2666711 CAATTCGACCCTCCCAATGATTTACAATCGTATTAGGGGAAATGGTGACGTTTTGGGAATAGGGC
325 CAATTCGACCCTCCCAATGATTTACAATCGTATTAGGGGAAACGGTGACGTTTTGGGAATAGGGC
2666776 TATTTGCCCAGTGACCCCCTTTGATTTCGCGAATGTTTCAAATCGGGTCTTAATTCAGTTTTAGC
390 TATTTGCCCAGTGACCCCCTTTGATTTCGCGAATGTTTCAAATCGGGTCTTAATTCAGTTTTAGC
2666841 TTTGTAAATTTGCCCCATAATTTTGTTAAACTTTAAATTTAGTCCTATATCTATTATATTATTCT
455 TTTGTAAATTTGCCCCATAATTTTGTTAAACTTTAAATTTAGTCCTATATCTATTATATTATTCT
2666906 ATATATATATTTTATTATTTGTTTATTTTAATTTTACTTTTATATTATATATTATAAAATTATTT
520 ATATATATATTTTATTATTTGTTTATTTTAATTTTACTTTTATATTATATATTATAAAATTATTT
2666971 TATTATGAGTATTATTTTTAATTATATATTATTATTATTTATTATATATATTATTTTCCTTAAAT
585 TATTATGAGTATTATTTTTAATTATATATTATTATTATTTATTATATATATTATTTTCCTTAAAT
2667036 TATTATTTTACATCCTTTTTATATATTATTATATTTTCACATATATTATATTTATTAATTACTTA
650 TATTATTTTACATCCTTTTTATATATTATTATATTTTCACATATATTATATTTATTAATTACTTA
2667101 TA
715 TA
2667103 TATATATATT
Statistics
Matches: 705, Mismatches: 9, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
714 210 0.30
715 423 0.60
717 72 0.10
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (716 bp):
CGTGAGCGCGTGAGGAGACCCCTGGACGGAGGCTCAGCAGCTCCGGGATCGGCCCCCGAATCCTC
TTCCAGAGGATTTTTCTTTTCTTTTTTTTAAAAAACGGATGTTAAAATGATTTTTAGGGGCGAAA
TTTGACTTATATAGTCTATTTAAAACGGTGTCGTTTTACAACTATAGGATCCGCGCGTTGACCCG
ATTACCCGGGGAGGATCCGCGCATTTTTGAAAATTGGGTTAATTGCCCAATTGGTCCTCTCGCAA
TTTTTATACTTTTAATTTCATTTTATTTATTTGTTTATTTGGTATTAATATTTTAATTCTGTTTC
AATTCGACCCTCCCAATGATTTACAATCGTATTAGGGGAAACGGTGACGTTTTGGGAATAGGGCT
ATTTGCCCAGTGACCCCCTTTGATTTCGCGAATGTTTCAAATCGGGTCTTAATTCAGTTTTAGCT
TTGTAAATTTGCCCCATAATTTTGTTAAACTTTAAATTTAGTCCTATATCTATTATATTATTCTA
TATATATATTTTATTATTTGTTTATTTTAATTTTACTTTTATATTATATATTATAAAATTATTTT
ATTATGAGTATTATTTTTAATTATATATTATTATTATTTATTATATATATTATTTTCCTTAAATT
ATTATTTTACATCCTTTTTATATATTATTATATTTTCACATATATTATATTTATTAATTACTTAT
A
Found at i:2666986 original size:17 final size:15
Alignment explanation
Indices: 2666936--2667009 Score: 51
Period size: 16 Copynumber: 4.5 Consensus size: 15
2666926 GTTTATTTTA
*
2666936 ATTTTACTTTTATATT
1 ATTTTA-TTATATATT
* *
2666952 A-TATATTATAAAATT
1 ATTTTATTAT-ATATT
2666967 ATTTTATTATGAGTATT
1 ATTTTATTAT-A-TATT
2666984 ATTTTTAATTATATATT
1 A-TTTT-ATTATATATT
2667001 ATTATTATT
1 ATT-TTATT
2667010 TATTATATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
14 3 0.07
15 8 0.17
16 14 0.30
17 11 0.24
18 5 0.11
19 5 0.11
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (15 bp):
ATTTTATTATATATT
Found at i:2667005 original size:20 final size:18
Alignment explanation
Indices: 2666955--2667027 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 18
2666945 TTATATTATA
*
2666955 TATTATA-AAATTA-TTT
1 TATTATATATATTATTTT
*
2666971 TATTATGA-GTATTATTTT
1 TATTAT-ATATATTATTTT
2666989 TAATTATATATTATTATTATT
1 T-ATTATATA-TATTATT-TT
2667010 TATTATATATATTATTTT
1 TATTATATATATTATTTT
2667028 CCTTAAATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
16 6 0.12
17 5 0.10
18 7 0.15
19 12 0.25
20 15 0.31
21 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTATATATATTATTTT
Found at i:2667007 original size:55 final size:54
Alignment explanation
Indices: 2666892--2667027 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 54
2666882 GTCCTATATC
* * ** * *
2666892 TATTATATTATTCTATATATATATTTTATTATTTGTTTATTTTAATTTTACTTTTA
1 TATTATA-TATTATATAAAT-TATTTTATTATGAGTTTATTTTAATTATACTATTA
2666948 TATTATATATTATA-AAATTATTTTATTATGAGTATTATTTTTAATTATA-TATTA
1 TATTATATATTATATAAATTATTTTATTATGAGT-TTA-TTTTAATTATACTATTA
* *
2667002 TTATTATTTATTATATATATTATTTT
1 -TATTATATATTATATAAATTATTTT
2667028 CCTTAAATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
53 13 0.19
54 10 0.15
55 29 0.43
56 16 0.24
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.63
Consensus pattern (54 bp):
TATTATATATTATATAAATTATTTTATTATGAGTTTATTTTAATTATACTATTA
Found at i:2667045 original size:55 final size:54
Alignment explanation
Indices: 2666913--2667045 Score: 128
Period size: 55 Copynumber: 2.4 Consensus size: 54
2666903 TCTATATATA
** * *
2666913 TATTTTATTATTTGT-TTATTTTAATTTTACTTTTATATTATATATTATAAAAT
1 TATTTTATTATAAGTATTATTTTAATTATACTATTATATTATATATTATAAAAT
* * *
2666966 TATTTTATTATGAGTATTATTTTTAATTATA-TATTATTATTATTTATTATATATAT
1 TATTTTATTATAAGTATTA-TTTTAATTATACTATTA-TATTATATATTATA-AAAT
* *
2667022 TATTTTCCTTA-AATTATTATTTTA
1 TATTTT-ATTATAAGTATTATTTTA
2667046 CATCCTTTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
53 13 0.20
54 7 0.11
55 28 0.42
56 15 0.23
57 3 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.63
Consensus pattern (54 bp):
TATTTTATTATAAGTATTATTTTAATTATACTATTATATTATATATTATAAAAT
Found at i:2667212 original size:25 final size:25
Alignment explanation
Indices: 2667169--2667231 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 25
2667159 TTATATTACA
* *
2667169 TTTTA-TTATATAATCTTTATTATG
1 TTTTATTTATATATTATTTATTATG
* * *
2667193 TTTTATTTTTATATTATTTATTGTT
1 TTTTATTTATATATTATTTATTATG
2667218 TTTTATTTATATAT
1 TTTTATTTATATAT
2667232 GTTATGTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.25, C:0.02, G:0.03, T:0.70
Consensus pattern (25 bp):
TTTTATTTATATATTATTTATTATG
Found at i:2676369 original size:27 final size:26
Alignment explanation
Indices: 2676339--2676401 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 26
2676329 GAAAGATTTT
2676339 TATTAAGATTCCCTACAAATTTTCTAG
1 TATTAA-ATTCCCTACAAATTTTCTAG
2676366 TATTTAAATTCCCTACAAATTTTCTAG
1 TA-TTAAATTCCCTACAAATTTTCTAG
2676393 TATTTAAAT
1 TA-TTAAAT
2676402 ATGTTAGGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 31 0.89
28 4 0.11
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (26 bp):
TATTAAATTCCCTACAAATTTTCTAG
Found at i:2681422 original size:22 final size:22
Alignment explanation
Indices: 2681397--2681466 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
2681387 TAAAAATATT
2681397 TAAAATTATTAAATTTTTAATA
1 TAAAATTATTAAATTTTTAATA
**
2681419 TAAAA-TATTAAATCATTTT-GCA
1 TAAAATTATTAAAT--TTTTAATA
*
2681441 -AAAATCATTAAATTTTTAATA
1 TAAAATTATTAAATTTTTAATA
2681462 TAAAA
1 TAAAA
2681467 GTTAATACCC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
20 4 0.11
21 13 0.34
22 17 0.45
23 4 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
TAAAATTATTAAATTTTTAATA
Found at i:2685033 original size:19 final size:19
Alignment explanation
Indices: 2684989--2685038 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
2684979 TTTTTACTGC
2684989 ATTTTATTTT-TATTTTTA
1 ATTTTATTTTCTATTTTTA
2685007 ATTCTTATTTTCTAATTTTT-
1 ATT-TTATTTTCT-ATTTTTA
*
2685027 CTTTTATTTTCT
1 ATTTTATTTTCT
2685039 TCTAGCAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 3 0.11
19 16 0.57
20 3 0.11
21 6 0.21
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (19 bp):
ATTTTATTTTCTATTTTTA
Found at i:2691177 original size:124 final size:124
Alignment explanation
Indices: 2690946--2691179 Score: 269
Period size: 124 Copynumber: 1.9 Consensus size: 124
2690936 TCACAGGGCG
* * * *
2690946 TGGGAGAAGCGAAGGAGATTGCACACGACTGTGCCACAAGGCCGTGTGGACCACCCGACCTGAAC
1 TGGGAGAAGCGAAGGAGATTGCACACAACCGCGCCACAAGGCCGTGTGGACCACACGACCTGAAC
* *
2691011 ACATGGGCGTGTCCTAGGCTGTGTGAAGACTGGGCTTGAATTTTTAATGCACACGGACA
66 ACACGGGCGTGTCCTAGGCTGTGTGAAGACTGAGCTTGAATTTTTAATGCACACGGACA
* * ** * * **
2691070 TGGGAGAAGTGAAGGAGATTTCACACAACCGCGTGACACGGTCGTGTGGACCACACGGTCT-AGA
1 TGGGAGAAGCGAAGGAGATTGCACACAACCGCGCCACAAGGCCGTGTGGACCACACGACCTGA-A
*
2691134 CACACGGGCGTGTCTTAGGCAT-TGTGAA-ACCTAGAGCTT-AATTTTT
65 CACACGGGCGTGTCCTAGGC-TGTGTGAAGA-CT-GAGCTTGAATTTTT
2691180 CAAATTTAAA
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
123 2 0.02
124 83 0.91
125 6 0.07
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.21
Consensus pattern (124 bp):
TGGGAGAAGCGAAGGAGATTGCACACAACCGCGCCACAAGGCCGTGTGGACCACACGACCTGAAC
ACACGGGCGTGTCCTAGGCTGTGTGAAGACTGAGCTTGAATTTTTAATGCACACGGACA
Found at i:2693769 original size:18 final size:18
Alignment explanation
Indices: 2693739--2693789 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
2693729 CTATGTATCA
2693739 TTTATTTTATTTTTA-GT
1 TTTATTTTATTTTTATGT
2693756 TTTATTTCTATTTTTATG-
1 TTTATTT-TATTTTTATGT
2693774 TTTATTATTATGTTTT
1 TTTATT-TTAT-TTTT
2693790 TAGACTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 7 0.23
18 17 0.57
19 6 0.20
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.75
Consensus pattern (18 bp):
TTTATTTTATTTTTATGT
Found at i:2701753 original size:14 final size:14
Alignment explanation
Indices: 2701734--2701761 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2701724 TTCTCTTGCA
2701734 CACTTGTATTTTAT
1 CACTTGTATTTTAT
2701748 CACTTGTATTTTAT
1 CACTTGTATTTTAT
2701762 TTCATCATGA
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:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CACTTGTATTTTAT
Found at i:2701994 original size:44 final size:44
Alignment explanation
Indices: 2701906--2701996 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
2701896 GTAATTGTAA
* * *
2701906 ATTAAATTATAAATATTTTTAAATGTAAAATTATCTCAACTTCT
1 ATTAAATTATAAATATTCTTAAACGTAAAATTATCTCAAATTCT
* *
2701950 ATTAAATTATAATTATTCTTAAACGTATAATTATCAT-AAATTCT
1 ATTAAATTATAAATATTCTTAAACGTAAAATTATC-TCAAATTCT
2701994 ATT
1 ATT
2701997 TTTTATTAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.46
Consensus pattern (44 bp):
ATTAAATTATAAATATTCTTAAACGTAAAATTATCTCAAATTCT
Found at i:2704794 original size:24 final size:24
Alignment explanation
Indices: 2704728--2704794 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
2704718 GAGCGTCCCA
*
2704728 TTATTAGCTC-TCATGAGCTTCCTG
1 TTATTAGCTCTTC-GGAGCTTCCTG
* *
2704752 TTATATGGTTCTT-GCGAGCTTCCTG
1 TTAT-TAGCTCTTCG-GAGCTTCCTG
2704777 TTATTAGCTCTTCGGAGC
1 TTATTAGCTCTTCGGAGC
2704795 ATCCCGATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
24 14 0.41
25 19 0.56
26 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (24 bp):
TTATTAGCTCTTCGGAGCTTCCTG
Found at i:2704973 original size:24 final size:23
Alignment explanation
Indices: 2704920--2704973 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2704910 ATGCTCTCCA
2704920 GAGCTTCTCGATATTGCTCGCTT
1 GAGCTTCTCGATATTGCTCGCTT
*
2704943 GAACTTCTCGATATTGGCTCG-TAT
1 GAGCTTCTCGATATT-GCTCGCT-T
2704967 GAGCTTC
1 GAGCTTC
2704974 CGGTTAATGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (23 bp):
GAGCTTCTCGATATTGCTCGCTT
Found at i:2704984 original size:24 final size:25
Alignment explanation
Indices: 2704957--2705011 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
2704947 TTCTCGATAT
2704957 TGGCTCGTAT-GAGC-TTCCGGTTA-A
1 TGGCTC-TATAGAGCTTTCC-GTTACA
*
2704981 TGGCTCTCTAGAGCTTTCCGTTACA
1 TGGCTCTATAGAGCTTTCCGTTACA
2705006 TGGCTC
1 TGGCTC
2705012 ACATAAGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 2 0.07
24 14 0.52
25 11 0.41
ACGTcount: A:0.15, C:0.25, G:0.25, T:0.35
Consensus pattern (25 bp):
TGGCTCTATAGAGCTTTCCGTTACA
Found at i:2705023 original size:24 final size:24
Alignment explanation
Indices: 2704967--2705023 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
2704957 TGGCTCGTAT
*
2704967 GAGCTTCCGGTTAATGGCTCTCTA
1 GAGCTTCCGGTTAATGGCTCACTA
2704991 GAGCTTTCC-GTTACATGGCTCACATA
1 GAGC-TTCCGGTTA-ATGGCTCAC-TA
2705017 -AGCTTCC
1 GAGCTTCC
2705024 CGTTTTTTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 12 0.41
25 15 0.52
26 2 0.07
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (24 bp):
GAGCTTCCGGTTAATGGCTCACTA
Found at i:2705601 original size:68 final size:68
Alignment explanation
Indices: 2705492--2705624 Score: 178
Period size: 68 Copynumber: 2.0 Consensus size: 68
2705482 ATCTACTCTA
* * *
2705492 CTGAAACTTCAAGGAGATCTGATGTGGCTTCAAGCCGCTCCAACACTATTTCAGGAAGAAGAGAT
1 CTGAAACTTCAAGGAGATCCGATGTAGCTTCAAGCCGCTCCAACACCATTTCAGGAAGAAGAGAT
2705557 TCG
66 TCG
* * * * *
2705560 CTGAAACTTCAAGGAGATCCGCTGTAGCTTCGAA-CCGCTCCATCCCCATTTTAGGGAGAAGAGA
1 CTGAAACTTCAAGGAGATCCGATGTAGCTTC-AAGCCGCTCCAACACCATTTCAGGAAGAAGAGA
2705624 T
65 T
2705625 CTGTAGGCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 54 0.96
69 2 0.04
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.23
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCCGATGTAGCTTCAAGCCGCTCCAACACCATTTCAGGAAGAAGAGAT
TCG
Found at i:2705775 original size:88 final size:88
Alignment explanation
Indices: 2705682--2706324 Score: 581
Period size: 86 Copynumber: 7.5 Consensus size: 88
2705672 TAGTTTCGAC
* * * * *
2705682 CTGCTCCACTACTGCTTAGGGAGACACGATCTGTAATTTTCAACCTGTTGCCCTATTGCTTAGGG
1 CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGG
* *
2705747 GGTTAAGGCTCACTGCCTTCGAT
66 GGTTAAGGCTCACTGTCTTTGAT
* * *
2705770 CTGCTCCACTACTACTTTGGGAGATAAGATCTGTAA---T-----TGTTACCTTACTGCTTAGGG
1 CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGG
*
2705827 GGTTAAGGCTCACCGTCTTTGAT
66 GGTTAAGGCTCACTGTCTTTGAT
* * * * * * *
2705850 CTGCTCCACTACTTCTTAGGGAGATAAGATTTGTAA--TTCGGCCTATTATCCTACTGCTCAGGG
1 CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGG
* *
2705913 GGTTAAGGCTCACCGTCTTCGAT
66 GGTTAAGGCTCACTGTCTTTGAT
* * *
2705936 CTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAA-TTT-GGCCTGTTACCCTACTGCTTAGAG
1 CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGG
* **
2705999 GGTCAAGGCTCACCATCTTTGAT
66 GGTTAAGGCTCACTGTCTTTGAT
* * * * *
2706022 CTGTTCCACT-GTAACTTCA-GGAGACAAGAT-TCGCAATCTTCAGCCTGTTACCCTACTACTTA
1 CTGCTCCACTACT-ACTT-AGGGAGACAAGATCT-GTAATTTTCAGCCTGTTACCCTACTGCTTA
**
2706084 GGGGGTTAAGGCTTGCT-TCTTTGAT
63 GGGGGTTAAGGCTCACTGTCTTTGAT
* * * ** *
2706109 TTGCTCCACTACTATTTAGGGAGACAAGATTTACAATCTTT-AGCCTGTTACCCTACTACTTAGG
1 CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAAT-TTTCAGCCTGTTACCCTACTGCTTAGG
** *
2706173 GGGTTAAGGCTTGCTTTCTTTGAT
65 GGGTTAAGGCTCACTGTCTTTGAT
** * * ** * *
2706197 CTTTTCCACTGCAACTTCAGGGAGACAAGATCTGCGATCTTCAGCCTGTTACCCTACTACTTAGG
1 CTGCTCCACTACTACTT-AGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGG
* *
2706262 GGGCTAAGGCTTC-CT-TCTTTTAT
65 GGGTTAAGGC-TCACTGTCTTTGAT
** * *
2706285 CTGCTCCACTACTGTTTA-GG-GATAAGATCTATAATTTTCA
1 CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTTTCA
2706325 CCGATGTCGC
Statistics
Matches: 465, Mismatches: 70, Indels: 43
0.80 0.12 0.07
Matches are distributed among these distances:
80 70 0.15
81 1 0.00
85 18 0.04
86 140 0.30
87 78 0.17
88 106 0.23
89 51 0.11
90 1 0.00
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.34
Consensus pattern (88 bp):
CTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTTTCAGCCTGTTACCCTACTGCTTAGGG
GGTTAAGGCTCACTGTCTTTGAT
Found at i:2705967 original size:166 final size:169
Alignment explanation
Indices: 2705682--2706306 Score: 537
Period size: 176 Copynumber: 3.6 Consensus size: 169
2705672 TAGTTTCGAC
* * * * * *
2705682 CTGCTCCACTACTGCTTAGGGAGACACGATCTGTAATTTTCAACCTGTTGCCCTATTGCTTAGGG
1 CTGCTCCACTACTTCTTAGGGAGACAAGATTTGTAA-TTTCAGCCTGTTACCCTACTGCTTAGGG
* * * *
2705747 GGTTAAGGCTCACTGCCTTCGATCTGCTCCACTACTACTTTGGGAGATAAGATCTGTAA-T-TGT
65 GGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTCTGT
* * * *
2705810 TACCTTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGAT
130 TACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
* * * * *
2705850 CTGCTCCACTACTTCTTAGGGAGATAAGATTTGTAA-TTCGGCCTATTATCCTACTGCTCAGGGG
1 CTGCTCCACTACTTCTTAGGGAGACAAGATTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGG
*
2705914 GTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTGGCC
66 GTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAA-TT---C
2705979 TGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
127 TGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
* * * *
2706022 CTGTTCCACTGTAACTTC--A-GGAGACAAGATTCGCAATCTTCAGCCTGTTACCCTACTACTTA
1 CTGCTCCAC--T-ACTTCTTAGGGAGACAAGATTTGTAAT-TTCAGCCTGTTACCCTACTGCTTA
** * * * * * **
2706084 GGGGGTTAAGGCT-TGCTTCTTTGATTTGCTCCACTACTATTTAGGGAGACAAGATTTACAATCT
62 GGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAA---
* * * ** **
2706148 TTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTTCTTTGAT
124 TT---CTGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
** * ** * ** *
2706197 CTTTTCCACTGCAACTTCAGGGAGACAAGATCTGCGATCTTCAGCCTGTTACCCTACTACTTAGG
1 CTGCTCCACTACTTCTT-AGGGAGACAAGATTTGTAAT-TTCAGCCTGTTACCCTACTGCTTAGG
* * * ** **
2706262 GGGCTAAGGCT-TCCTTCTTTTATCTGCTCCACTACTGTTTAGGGA
64 GGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGA
2706307 TAAGATCTAT
Statistics
Matches: 381, Mismatches: 59, Indels: 26
0.82 0.13 0.06
Matches are distributed among these distances:
166 74 0.19
168 33 0.09
172 63 0.17
173 40 0.10
174 33 0.09
175 56 0.15
176 82 0.22
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (169 bp):
CTGCTCCACTACTTCTTAGGGAGACAAGATTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGG
GTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTCTGTT
ACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
Found at i:2706193 original size:44 final size:43
Alignment explanation
Indices: 2706058--2706281 Score: 116
Period size: 44 Copynumber: 5.1 Consensus size: 43
2706048 AGATTCGCAA
*
2706058 TCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
1 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
** * * * ** ** * *
2706101 TCTTT-GATTTGCT-CCACTACTATTTAGGGAGACAAGATTTACAA
1 TCTTTAG-CCTGTTACC-CTACTACTTAGGGGGTTAAGGCTTGC-T
2706145 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTT
1 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGC-T
* * * * * ** * *
2706189 TCTTT-GATCT-TTTCCACTGCAACTTCAGGGAGACAA-GATCTGCGA
1 TCTTTAG-CCTGTTACC-CTACTACTT-AGGGGGTTAAGGCT-TGC-T
* * *
2706234 TCTTCAGCCTGTTACCCTACTACTTAGGGGGCTAAGGCTTCCT
1 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
2706277 TCTTT
1 TCTTT
2706282 TATCTGCTCC
Statistics
Matches: 123, Mismatches: 46, Indels: 24
0.64 0.24 0.12
Matches are distributed among these distances:
42 3 0.02
43 35 0.28
44 52 0.42
45 28 0.23
46 5 0.04
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (43 bp):
TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
Found at i:2706481 original size:64 final size:64
Alignment explanation
Indices: 2706374--2706497 Score: 178
Period size: 64 Copynumber: 1.9 Consensus size: 64
2706364 ATGTCTATGT
*
2706374 TTATGCCAAATGACTAGGATGCTATGACCAAAATGAACTAAATGCTCCTAACTAGATGTGATGC
1 TTATGCCAAATAACTAGGATGCTATGACCAAAATGAACTAAATGCTCCTAACTAGATGTGATGC
* * * * *
2706438 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAA-TCAAATGCTTCTAACTAGATGTG
1 TTATGCCAAATAACTAGGATGCTATGACCAAAATGAACT-AAATGCTCCTAACTAGATGTG
2706498 TTACGAAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 1 0.02
64 52 0.98
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (64 bp):
TTATGCCAAATAACTAGGATGCTATGACCAAAATGAACTAAATGCTCCTAACTAGATGTGATGC
Found at i:2707781 original size:24 final size:24
Alignment explanation
Indices: 2707715--2707781 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
2707705 GAGCGTCCCA
*
2707715 TTATTAGCTC-TCATGAGCTTCCTG
1 TTATTAGCTCTTC-GGAGCTTCCTG
* *
2707739 TTATATGGTTCTT-GCGAGCTTCCTG
1 TTAT-TAGCTCTTCG-GAGCTTCCTG
2707764 TTATTAGCTCTTCGGAGC
1 TTATTAGCTCTTCGGAGC
2707782 ATCCCGATAG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
24 14 0.41
25 19 0.56
26 1 0.03
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (24 bp):
TTATTAGCTCTTCGGAGCTTCCTG
Found at i:2719589 original size:44 final size:43
Alignment explanation
Indices: 2719445--2719644 Score: 177
Period size: 44 Copynumber: 4.6 Consensus size: 43
2719435 ATCCTGCTTT
* * * *
2719445 ACTGCAACTTCAGAGAG-TAAGGATTGTGACTTCGATCTGCTCC
1 ACTGCAACTTCAGGGAGATAA-GATTGTGACTTCAACCCGCTCC
* ** * *
2719488 ACTGCAACTTCAGGGAGATAAGATCTGCTAACTTCAGTCTGGTCC
1 ACTGCAACTTCAGGGAGATAAGAT-TG-TGACTTCAACCCGCTCC
* * * *
2719533 ATTGCAGCTTCAGGGAGATAAGACTTGTTACTTCAACCCGCTCT
1 ACTGCAACTTCAGGGAGATAAGA-TTGTGACTTCAACCCGCTCC
* ** * * *
2719577 ACTGTAACTTCAGAAAGATAAGGATTGTGACTTCGATCTGCTCC
1 ACTGCAACTTCAGGGAGATAA-GATTGTGACTTCAACCCGCTCC
2719621 ACTGCAACTTCAGGGAGATAAGAT
1 ACTGCAACTTCAGGGAGATAAGAT
2719645 CTGCTAATTT
Statistics
Matches: 126, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
43 22 0.17
44 65 0.52
45 38 0.30
46 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (43 bp):
ACTGCAACTTCAGGGAGATAAGATTGTGACTTCAACCCGCTCC
Found at i:2719840 original size:68 final size:68
Alignment explanation
Indices: 2719756--2719889 Score: 198
Period size: 68 Copynumber: 2.0 Consensus size: 68
2719746 ATCTACTCTA
*
2719756 CTGAAACTTCAAGGAGATCTGATGTGGCTTC-AAGCCGCTCAAACACCATTTCAGGAAGAAGAGA
1 CTGAAACTTCAAGGAGATCCGATGTGGCTTCGAA-CCGCTCAAACACCATTTCAGGAAGAAGAGA
2719820 TTCG
65 TTCG
* * * * *
2719824 CTGAAACTTCAAGGAGATCCGCTGTGGCTTCGAACCGCTCCAACCCCATTTTAGGGAGAAGAGAT
1 CTGAAACTTCAAGGAGATCCGATGTGGCTTCGAACCGCTCAAACACCATTTCAGGAAGAAGAGAT
2719889 T
66 T
2719890 TGTAGCCTTG
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 57 0.97
69 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCCGATGTGGCTTCGAACCGCTCAAACACCATTTCAGGAAGAAGAGAT
TCG
Found at i:2720136 original size:80 final size:79
Alignment explanation
Indices: 2719997--2720295 Score: 328
Period size: 86 Copynumber: 3.6 Consensus size: 79
2719987 AACCTGTTGC
* * * *
2719997 CCTATTGCTTAGGGGGTTAAGGCTCACTGCCTTCGATCTGCTCCACTACTACTTTGGGAGATAAG
1 CCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAG
2720062 ATCTGTAATTGTTA
66 ATCTGTAATTGTTA
* *
2720076 CCTTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACTTCTTAGGGAGATAA
1 CC-TACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAA
*
2720141 GATTTGTAATTCAGCCTATTA
65 GATCTGTAATT--G----TTA
* * *
2720162 TCCTACTGCTCAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAA
1 -CCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAA
2720227 GATCTGTAATTTGGCCTGTTA
65 GATCTGTAA--T----TGTTA
* * * * *
2720248 CCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGATCTGTTCCACT
1 -CCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACT
2720296 GTAACTTCAG
Statistics
Matches: 187, Mismatches: 19, Indels: 21
0.82 0.08 0.09
Matches are distributed among these distances:
79 2 0.01
80 66 0.35
82 1 0.01
86 113 0.60
87 2 0.01
88 1 0.01
90 1 0.01
92 1 0.01
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (79 bp):
CCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAG
ATCTGTAATTGTTA
Found at i:2720231 original size:166 final size:169
Alignment explanation
Indices: 2719946--2720570 Score: 537
Period size: 176 Copynumber: 3.6 Consensus size: 169
2719936 TAGTTTCGAC
* * * * * *
2719946 CTGCTCCACTACTGCTTAGGGAGACACGATCTGTAATTTTCAACCTGTTGCCCTATTGCTTAGGG
1 CTGCTCCACTACTTCTTAGGGAGACAAGATTTGTAA-TTTCAGCCTGTTACCCTACTGCTTAGGG
* * * *
2720011 GGTTAAGGCTCACTGCCTTCGATCTGCTCCACTACTACTTTGGGAGATAAGATCTGTAA-T-TGT
65 GGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTCTGT
* * * *
2720074 TACCTTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGAT
130 TACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
* * * *
2720114 CTGCTCCACTACTTCTTAGGGAGATAAGATTTGTAA-TTCAGCCTATTATCCTACTGCTCAGGGG
1 CTGCTCCACTACTTCTTAGGGAGACAAGATTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGG
*
2720178 GTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTGGCC
66 GTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAA-TT---C
2720243 TGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
127 TGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
* * * *
2720286 CTGTTCCACTGTAACTTC--A-GGAGACAAGATTCGCAATCTTCAGCCTGTTACCCTACTACTTA
1 CTGCTCCAC--T-ACTTCTTAGGGAGACAAGATTTGTAAT-TTCAGCCTGTTACCCTACTGCTTA
** * * * * * * **
2720348 GGGGGTTAAGGCT-TGCTTCTTTGATTTGCTCCACTACTATTTAGGGAGACAATATTTACAATCT
62 GGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAA---
* * * ** **
2720412 TTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTTCTTTGAT
124 TT---CTGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
** * ** * ** *
2720461 CTTTTCCACTGCAACTTCAGGGAGACAAGATCTGCGATCTTCAGCCTGTTACCCTACTACTTAGG
1 CTGCTCCACTACTTCTT-AGGGAGACAAGATTTGTAAT-TTCAGCCTGTTACCCTACTGCTTAGG
* * * ** **
2720526 GGGCTAAGGCT-TCCTTCTTTTATCTGCTCCACTACTGTTTAGGGA
64 GGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGA
2720571 TAAGATCTAT
Statistics
Matches: 382, Mismatches: 58, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
166 75 0.20
168 33 0.09
172 63 0.16
173 39 0.10
174 34 0.09
175 56 0.15
176 82 0.21
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.33
Consensus pattern (169 bp):
CTGCTCCACTACTTCTTAGGGAGACAAGATTTGTAATTTCAGCCTGTTACCCTACTGCTTAGGGG
GTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGACAAGATCTGTAATTCTGTT
ACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGAT
Found at i:2720410 original size:87 final size:88
Alignment explanation
Indices: 2720071--2720570 Score: 505
Period size: 86 Copynumber: 5.7 Consensus size: 88
2720061 GATCTGTAAT
* * *
2720071 TGTTACCTTACTGCTTAGGGGGTTAAGGCTCACCGTCTTTGATCTGCTCCACTACT-TCTTAGGG
1 TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACTAT-TTAGGG
* *
2720135 AGATAAGATTTGTAA--TTCAGCC
65 AGACAAGATTTGCAATCTTCAGCC
* * * * * * **
2720157 TATTATCCTACTGCTCAGGGGGTTAAGGCTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGA
1 TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACTATTTAGGGA
* * *
2720222 GACAAGATCTGTAAT-TT-GGCC
66 GACAAGATTTGCAATCTTCAGCC
* * * * * * *
2720243 TGTTACCCTACTGCTTAGAGGGTCAAGGCTCACCATCTTTGATCTGTTCCACT-GTAACTTCA-G
1 TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACT-A-TTTAGG
*
2720306 GAGACAAGATTCGCAATCTTCAGCC
64 GAGACAAGATTTGCAATCTTCAGCC
** *
2720331 TGTTACCCTACTACTTAGGGGGTTAAGGCT-TGCTTCTTTGATTTGCTCCACTACTATTTAGGGA
1 TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACTATTTAGGGA
* * *
2720395 GACAATATTTACAATCTTTAGCC
66 GACAAGATTTGCAATCTTCAGCC
** * ** * * *
2720418 TGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTTTCTTTGATCTTTTCCACTGCAACTTCAGGG
1 TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACTA-TTTAGGG
* *
2720483 AGACAAGATCTGCGATCTTCAGCC
65 AGACAAGATTTGCAATCTTCAGCC
* * * *
2720507 TGTTACCCTACTACTTAGGGGGCTAAGGCT-TCCTTCTTTTATCTGCTCCACTACTGTTTAGGGA
1 TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACTATTTAGGGA
2720571 TAAGATCTAT
Statistics
Matches: 341, Mismatches: 63, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
85 1 0.00
86 136 0.40
87 83 0.24
88 67 0.20
89 54 0.16
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (88 bp):
TGTTACCCTACTACTTAGGGGGTTAAGGCTCACCTTCTTTGATCTGCTCCACTACTATTTAGGGA
GACAAGATTTGCAATCTTCAGCC
Found at i:2720457 original size:44 final size:43
Alignment explanation
Indices: 2720322--2720545 Score: 107
Period size: 44 Copynumber: 5.1 Consensus size: 43
2720312 AGATTCGCAA
*
2720322 TCTTCAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
1 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
** * * * ** *** * *
2720365 TCTTT-GATTTGCT-CCACTACTATTTAGGGAGACAATATTTACAA
1 TCTTTAG-CCTGTTACC-CTACTACTTAGGGGGTTAAGGCTTGC-T
2720409 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCTT
1 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGC-T
* * * * * ** * *
2720453 TCTTT-GATCT-TTTCCACTGCAACTTCAGGGAGACAA-GATCTGCGA
1 TCTTTAG-CCTGTTACC-CTACTACTT-AGGGGGTTAAGGCT-TGC-T
* * *
2720498 TCTTCAGCCTGTTACCCTACTACTTAGGGGGCTAAGGCTTCCT
1 TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
2720541 TCTTT
1 TCTTT
2720546 TATCTGCTCC
Statistics
Matches: 121, Mismatches: 48, Indels: 24
0.63 0.25 0.12
Matches are distributed among these distances:
42 3 0.02
43 34 0.28
44 51 0.42
45 28 0.23
46 5 0.04
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (43 bp):
TCTTTAGCCTGTTACCCTACTACTTAGGGGGTTAAGGCTTGCT
Found at i:2724035 original size:45 final size:44
Alignment explanation
Indices: 2723977--2724278 Score: 198
Period size: 45 Copynumber: 6.8 Consensus size: 44
2723967 TTTAGTCTGC
* * * *
2723977 TCCACTGCTACTTCAAAGAGATAAGGTTTGCTATCTTCGATCTAT
1 TCCACTACAACTTCAGAGAGATAAGATTTGCTATCTTC-ATCTAT
* * * * *
2724022 TCCACTATAACTTCAGGGAGATAAGATCTACTATCTTCAGTCTGT
1 TCCACTACAACTTCAGAGAGATAAGATTTGCTATCTTCA-TCTAT
* * * * * **
2724067 TCCACTGCAACTTTA-AGTAGATAAGACTTGGTA-CTTCAACCTGC
1 TCCACTACAACTTCAGAG-AGATAAGATTTGCTATCTTC-ATCTAT
* *** * *
2724111 TCTACCGTAACTTCAGAGAGATAAGGTTTGTTATCTTCGATCTAT
1 TCCACTACAACTTCAGAGAGATAAGATTTGCTATCTTC-ATCTAT
* * * ** *
2724156 TCCACTGCAACTTCAGGGAGATAAGATCTATTATCTTCAGTCTGT
1 TCCACTACAACTTCAGAGAGATAAGATTTGCTATCTTCA-TCTAT
* * * *
2724201 TCCACTACAACTTCA-AGGAGATAAGACTTGGTA-CTTCAACCTAC
1 TCCACTACAACTTCAGA-GAGATAAGATTTGCTATCTTC-ATCTAT
* *
2724245 TCTACTACAACTTCAGAGAGATAAGGTTTGCTAT
1 TCCACTACAACTTCAGAGAGATAAGATTTGCTAT
2724279 GATGACTTAA
Statistics
Matches: 196, Mismatches: 51, Indels: 20
0.73 0.19 0.07
Matches are distributed among these distances:
44 66 0.34
45 130 0.66
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.32
Consensus pattern (44 bp):
TCCACTACAACTTCAGAGAGATAAGATTTGCTATCTTCATCTAT
Found at i:2724136 original size:134 final size:134
Alignment explanation
Indices: 2723986--2724278 Score: 478
Period size: 134 Copynumber: 2.2 Consensus size: 134
2723976 CTCCACTGCT
* *
2723986 ACTTCAAAGAGATAAGGTTTGCTATCTTCGATCTATTCCACTATAACTTCAGGGAGATAAGATCT
1 ACTTCAGAGAGATAAGGTTTGCTATCTTCGATCTATTCCACTACAACTTCAGGGAGATAAGATCT
* * * *
2724051 ACTATCTTCAGTCTGTTCCACTGCAACTTTAAGTAGATAAGACTTGGTACTTCAACCTGCTCTAC
66 ACTATCTTCAGTCTGTTCCACTACAACTTCAAGGAGATAAGACTTGGTACTTCAACCTACTCTAC
**
2724116 CGTA
131 CACA
* *
2724120 ACTTCAGAGAGATAAGGTTTGTTATCTTCGATCTATTCCACTGCAACTTCAGGGAGATAAGATCT
1 ACTTCAGAGAGATAAGGTTTGCTATCTTCGATCTATTCCACTACAACTTCAGGGAGATAAGATCT
*
2724185 ATTATCTTCAGTCTGTTCCACTACAACTTCAAGGAGATAAGACTTGGTACTTCAACCTACTCTAC
66 ACTATCTTCAGTCTGTTCCACTACAACTTCAAGGAGATAAGACTTGGTACTTCAACCTACTCTAC
*
2724250 TACA
131 CACA
2724254 ACTTCAGAGAGATAAGGTTTGCTAT
1 ACTTCAGAGAGATAAGGTTTGCTAT
2724279 GATGACTTAA
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 146 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (134 bp):
ACTTCAGAGAGATAAGGTTTGCTATCTTCGATCTATTCCACTACAACTTCAGGGAGATAAGATCT
ACTATCTTCAGTCTGTTCCACTACAACTTCAAGGAGATAAGACTTGGTACTTCAACCTACTCTAC
CACA
Found at i:2729747 original size:46 final size:46
Alignment explanation
Indices: 2729697--2729914 Score: 400
Period size: 46 Copynumber: 4.7 Consensus size: 46
2729687 TGGTTGAGCA
2729697 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
2729743 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
2729789 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
*
2729835 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2729881 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
2729915 GGGGTGGGTT
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 168 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2735122 original size:19 final size:19
Alignment explanation
Indices: 2735098--2735138 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
2735088 TTATGACCTT
*
2735098 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATG-AATG
2735117 TAATGCAAATGCATGAATG
1 TAATGCAAATGCATGAATG
2735136 TAA
1 TAA
2735139 AGGAGGCATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (19 bp):
TAATGCAAATGCATGAATG
Found at i:2741401 original size:38 final size:38
Alignment explanation
Indices: 2741342--2741447 Score: 105
Period size: 37 Copynumber: 2.8 Consensus size: 38
2741332 CATTTTTAAG
*
2741342 AATAT-AAAGAATATATATAAGTATGTATATG-ATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAGAAT-TAGA
* *
2741379 AATATGCATAAATATATGTAAGTA--TATAAGAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAGAATTA-GA
*
2741417 AATATGAAAAATATATTTAAGTATGTATAAG
1 AATATGAAAAATATATATAAGTATGTATAAG
2741448 TACGTATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
36 7 0.12
37 22 0.39
38 20 0.35
39 8 0.14
ACGTcount: A:0.51, C:0.01, G:0.13, T:0.35
Consensus pattern (38 bp):
AATATGAAAAATATATATAAGTATGTATAAGAATTAGA
Found at i:2745868 original size:15 final size:15
Alignment explanation
Indices: 2745845--2745875 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2745835 AAGGTTATAA
*
2745845 AAATCATATAAATAT
1 AAATAATATAAATAT
2745860 AAATAATATAAATAT
1 AAATAATATAAATAT
2745875 A
1 A
2745876 CTATAACCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAATATAAATAT
Found at i:2746566 original size:24 final size:23
Alignment explanation
Indices: 2746530--2746574 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
2746520 TAAAAGACAA
*
2746530 AAATATATAAATTTCAGTTAATTG
1 AAATATATAAATTCCA-TTAATTG
* *
2746554 AAATATTTCAATTCCATTAAT
1 AAATATATAAATTCCATTAAT
2746575 GTATGTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (23 bp):
AAATATATAAATTCCATTAATTG
Found at i:2749944 original size:1 final size:1
Alignment explanation
Indices: 2749940--2749970 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
2749930 AATTAGAATT
*
2749940 AAAAAAAAAAGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2749971 GAGAGGGGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:2749952 original size:15 final size:15
Alignment explanation
Indices: 2749921--2749962 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2749911 TGTATTCAGT
*
2749921 ATTAAAAAAAATTAGA
1 ATTAAAAAAAA-AAGA
2749937 ATTAAAAAAAAAAGA
1 ATTAAAAAAAAAAGA
2749952 A--AAAAAAAAAA
1 ATTAAAAAAAAAA
2749963 AAAAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 10 0.40
15 4 0.16
16 11 0.44
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (15 bp):
ATTAAAAAAAAAAGA
Found at i:2750066 original size:20 final size:22
Alignment explanation
Indices: 2750041--2750086 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 22
2750031 TAAAAAAATA
2750041 TTTTTTTAT-TTAT-TT-TTAT
1 TTTTTTTATATTATATTGTTAT
2750060 TTTTTTTATATTATATTGTTAT
1 TTTTTTTATATTATATTGTTAT
2750082 TTTTT
1 TTTTT
2750087 ATATTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.38
20 4 0.17
21 2 0.08
22 9 0.38
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTTTATATTATATTGTTAT
Found at i:2750076 original size:22 final size:20
Alignment explanation
Indices: 2750041--2750086 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 20
2750031 TAAAAAAATA
*
2750041 TTTTTTTATTTATTTTTATT
1 TTTTTTTATTTATTGTTATT
2750061 TTTTTTATATTATATTGTTATT
1 TTTTTT-TATT-TATTGTTATT
2750083 TTTT
1 TTTT
2750087 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.26
21 4 0.17
22 13 0.57
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (20 bp):
TTTTTTTATTTATTGTTATT
Found at i:2750087 original size:20 final size:19
Alignment explanation
Indices: 2750039--2750092 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
2750029 GGTAAAAAAA
*
2750039 TATTTTTT-TATTTATTTT
1 TATTTTTTATATTTATTGT
2750057 TATTTTTTTTATATTATATTGT
1 TA--TTTTTTATATT-TATTGT
2750079 TATTTTTTATATTT
1 TATTTTTTATATTT
2750093 TTTTAGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.06
19 1 0.03
20 17 0.55
21 4 0.13
22 7 0.23
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TATTTTTTATATTTATTGT
Found at i:2750313 original size:12 final size:12
Alignment explanation
Indices: 2750296--2750320 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2750286 GAGAGAAGAA
2750296 GAAAAAAAAAAG
1 GAAAAAAAAAAG
2750308 GAAAAAAAAAAG
1 GAAAAAAAAAAG
2750320 G
1 G
2750321 GTCCCCCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAAG
Found at i:2757223 original size:6 final size:6
Alignment explanation
Indices: 2757187--2757234 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
2757177 AAATTAGTTG
* * *
2757187 TTTTAT TTTTAA TTTAAT TTAATACT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TT-TTA-T TTTTAT TTTTAT TTTTAT TTTT
2757235 GAAGTACGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 28 0.82
7 3 0.09
8 3 0.09
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (6 bp):
TTTTAT
Done.