Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008364.1 Hibiscus syriacus cultivar Beakdansim tig00111105_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5892847
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 27
Found at i:5168625 original size:79 final size:78
Alignment explanation
Indices: 5168421--5168647 Score: 339
Period size: 79 Copynumber: 2.9 Consensus size: 78
5168411 AATTAATTTT
* *
5168421 GCGAATTTGTAAATCGCGTTGCAATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
1 GCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
5168486 GAAA-ATCTCGTC
66 GAAATATCTCGTC
* * *
5168498 GCGAATTTGTAAATCGAGTTGTGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGTGAATTT
1 GCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
* * *
5168563 GAAAATATTTGGTT
66 G-AAATATCTCGTC
* *
5168577 GTGAATTTGTAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGCGTTGCGAATTT
1 GCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
5168642 GTAAAT
66 G-AAAT
5168648 CACGTTGCGA
Statistics
Matches: 134, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
77 61 0.46
78 3 0.02
79 70 0.52
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (78 bp):
GCGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT
GAAATATCTCGTC
Found at i:5168670 original size:57 final size:57
Alignment explanation
Indices: 5168574--5168748 Score: 251
Period size: 57 Copynumber: 3.1 Consensus size: 57
5168564 AAAATATTTG
*
5168574 GTTGTGAATTTGTAAATCGCGTTGCGATAGTACTATTTACCTATATCGGTAATTAGC
1 GTTGTGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
* * ** *
5168631 GTTGCGAATTTGTAAATCACGTTGCGATAAAACTGTTTACCTATATCAGTAATTAGC
1 GTTGTGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
* * * * *
5168688 GTTGTGAATTTGAAAATCGCGTCGCGATAGTATTGTTTACCTACATCGGTAATCAGC
1 GTTGTGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
5168745 GTTG
1 GTTG
5168749 AGATTTACAT
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 102 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.36
Consensus pattern (57 bp):
GTTGTGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
Found at i:5169745 original size:16 final size:16
Alignment explanation
Indices: 5169726--5169758 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5169716 GGGCGAGACC
5169726 CGATTCAGACGAGCCT
1 CGATTCAGACGAGCCT
5169742 CGATTCAGACGAGCCT
1 CGATTCAGACGAGCCT
5169758 C
1 C
5169759 CTGCTTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (16 bp):
CGATTCAGACGAGCCT
Found at i:5172107 original size:30 final size:30
Alignment explanation
Indices: 5172071--5172138 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
5172061 TTAGTCCTTA
*
5172071 AGCTTCAATTATAAATACCCTAACCCATTT
1 AGCTTCAACTATAAATACCCTAACCCATTT
5172101 AGCTTCAACTATAAATACCCTAACCCATTT
1 AGCTTCAACTATAAATACCCTAACCCATTT
5172131 AGCTTCAA
1 AGCTTCAA
5172139 AATCATCTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTAACCCATTT
Found at i:5172261 original size:34 final size:34
Alignment explanation
Indices: 5172202--5172268 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
5172192 TTCTTGAGAG
*
5172202 TTGTTTTCTCTTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCTTTTTGATC-AGAGAGAAGTTGTTA
5172236 TTGTTTTCTCTTTGTTAGATC-GAGAGAAGTTGT
1 TTGTTTTCTCTTT-TT-GATCAGAGAGAAGTTGT
5172269 AATTCCTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 20 0.69
35 6 0.21
36 3 0.10
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (34 bp):
TTGTTTTCTCTTTTTGATCAGAGAGAAGTTGTTA
Found at i:5173974 original size:22 final size:22
Alignment explanation
Indices: 5173933--5174013 Score: 126
Period size: 22 Copynumber: 3.6 Consensus size: 22
5173923 CTCGTATAAA
5173933 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
*
5173956 TGCACTGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
5173978 TGCACCTAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
5174000 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
5174014 ATATAATGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 42 0.79
23 11 0.21
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5174009 original size:13 final size:13
Alignment explanation
Indices: 5173947--5174009 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
5173937 CCGAAGTGCC
5173947 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
5173960 -C-T-GAAGTGC-
1 CCGTAGAATTGCA
5173969 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
5173982 CC-T--AAGTGC-
1 CCGTAGAATTGCA
5173991 CCGTAGAATTGCA
1 CCGTAGAATTGCA
5174004 CCGTAG
1 CCGTAG
5174010 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 2 0.05
10 13 0.34
11 2 0.05
12 13 0.34
13 8 0.21
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:5174673 original size:2 final size:2
Alignment explanation
Indices: 5174666--5174691 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5174656 TCTCTTAAAC
5174666 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5174692 TCACATGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5175731 original size:21 final size:21
Alignment explanation
Indices: 5175707--5175751 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
5175697 TCTTGTTCGT
* *
5175707 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5175728 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5175749 TTG
1 TTG
5175752 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5178965 original size:22 final size:22
Alignment explanation
Indices: 5178924--5179004 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
5178914 CTCGTATAAA
5178924 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
5178947 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
5178969 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
5178991 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
5179005 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:5179000 original size:13 final size:13
Alignment explanation
Indices: 5178938--5179000 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
5178928 CCGAAGTGCC
5178938 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
5178951 CC---GAAGTGC-
1 CCGTAGAATTGCA
5178960 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
5178973 CC---GAAGTGC-
1 CCGTAGAATTGCA
5178982 CCGTAGAATTGCA
1 CCGTAGAATTGCA
5178995 CCGTAG
1 CCGTAG
5179001 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:5180308 original size:18 final size:18
Alignment explanation
Indices: 5180287--5180334 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
5180277 CATTCAAAAG
*
5180287 CATGTCA-ACATATATATT
1 CATGTCATACATACA-ATT
5180305 CATG-CATACATACAATT
1 CATGTCATACATACAATT
*
5180322 CATGTCATTCATA
1 CATGTCATACATA
5180335 TACGTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (18 bp):
CATGTCATACATACAATT
Found at i:5180717 original size:21 final size:21
Alignment explanation
Indices: 5180693--5180737 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5180683 TCTTGTTCGT
*
5180693 TTGAAGGGGTACCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
5180714 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
5180735 TTG
1 TTG
5180738 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:5185720 original size:2 final size:2
Alignment explanation
Indices: 5185713--5185768 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
5185703 AATTGTGCCC
5185713 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5185755 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
5185769 CGTCATGTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5188603 original size:16 final size:17
Alignment explanation
Indices: 5188567--5188605 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
5188557 AATAAAATTT
5188567 TAAAATAAACAACTTTAA
1 TAAAATAAACAAC-TTAA
5188585 TAAAATAAACAAC-TAA
1 TAAAATAAACAACTTAA
5188601 TAAAA
1 TAAAA
5188606 ACAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (17 bp):
TAAAATAAACAACTTAA
Found at i:5188619 original size:90 final size:90
Alignment explanation
Indices: 5188450--5188625 Score: 271
Period size: 90 Copynumber: 2.0 Consensus size: 90
5188440 AGAAATTCAG
* * * *
5188450 ATTTTAGAACATACACAAATAAAATTTTAAAATAAACACCTTTAATAAAATAAATAATTAATAAA
1 ATTTCAGAACATACACAAATAAAATTTTAAAATAAACAACTTTAATAAAATAAACAACTAATAAA
* *
5188515 AATAAATTCGATTTCCAGAACAAAA
66 AACAAATTCAATTTCCAGAACAAAA
*
5188540 ATTTCAGAACTTACACAAATAAAATTTTAAAATAAACAACTTTAATAAAATAAACAACTAATAAA
1 ATTTCAGAACATACACAAATAAAATTTTAAAATAAACAACTTTAATAAAATAAACAACTAATAAA
* *
5188605 AACAAATTTAATTTCGAGAAC
66 AACAAATTCAATTTCCAGAAC
5188626 GCACGTGCTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.56, C:0.12, G:0.03, T:0.28
Consensus pattern (90 bp):
ATTTCAGAACATACACAAATAAAATTTTAAAATAAACAACTTTAATAAAATAAACAACTAATAAA
AACAAATTCAATTTCCAGAACAAAA
Found at i:5188839 original size:43 final size:43
Alignment explanation
Indices: 5188808--5188905 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 43
5188798 ATATTTTACA
5188808 TTTATAATTG-AGATTCTAATTTTTTTCAATCTCACTTTTTATC
1 TTTATAATTGAAG-TTCTAATTTTTTTCAATCTCACTTTTTATC
* * * *
5188851 TTTATGATTGAAGTCTCTAATTTTTTCCAAT-TCCATTTTTTACC
1 TTTATAATTGAAGT-TCTAATTTTTTTCAATCT-CACTTTTTATC
*
5188895 TTTATAGTTGA
1 TTTATAATTGA
5188906 GGCATTTTAG
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
43 11 0.24
44 35 0.76
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.54
Consensus pattern (43 bp):
TTTATAATTGAAGTTCTAATTTTTTTCAATCTCACTTTTTATC
Found at i:5190752 original size:3 final size:3
Alignment explanation
Indices: 5190739--5190791 Score: 74
Period size: 3 Copynumber: 18.0 Consensus size: 3
5190729 TTTTTTATCG
5190739 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
5190783 TTA ATA TTA
1 TTA TTA TTA
5190792 CATTTTACAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:5198398 original size:4 final size:4
Alignment explanation
Indices: 5198389--5198436 Score: 68
Period size: 4 Copynumber: 13.0 Consensus size: 4
5198379 AAAAGTATAC
5198389 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT AC-- ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
5198433 ACAT
1 ACAT
5198437 GATACATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.10
4 36 0.90
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:5198408 original size:18 final size:18
Alignment explanation
Indices: 5198385--5198436 Score: 104
Period size: 18 Copynumber: 2.9 Consensus size: 18
5198375 CGAGAAAAGT
5198385 ATACACATACATACATAC
1 ATACACATACATACATAC
5198403 ATACACATACATACATAC
1 ATACACATACATACATAC
5198421 ATACACATACATACAT
1 ATACACATACATACAT
5198437 GATACATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (18 bp):
ATACACATACATACATAC
Found at i:5198436 original size:14 final size:14
Alignment explanation
Indices: 5198393--5198435 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
5198383 GTATACACAT
5198393 ACATACATACATAC
1 ACATACATACATAC
5198407 ACATACATACATAC
1 ACATACATACATAC
* *
5198421 ATACACATACATAC
1 ACATACATACATAC
5198435 A
1 A
5198436 TGATACATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (14 bp):
ACATACATACATAC
Found at i:5199030 original size:105 final size:103
Alignment explanation
Indices: 5198889--5199128 Score: 299
Period size: 105 Copynumber: 2.3 Consensus size: 103
5198879 TGAGAATTTT
* * *
5198889 AAAACAAATTGCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
*
5198953 TTAAAACAAAATTAATCTCACCTT-AGATTGTTGTTTCTTTC-
66 TT-AAACAAAATTAATCTCACCTTGAGATCG-T-TTTC--TCA
* * *
5198994 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
5199059 TTAAACAAAGTTGATCTCACTTTGAGATCGTTTTCTCA
66 TTAAACAAAATTAATCTCACCTTGAGATCGTTTTCTCA
*
5199097 AAAACAAACTTT-GTCTCGCTTGAGACAATTTC
1 AAAACAAA-TTTCGTCTCGCTTGAGACATTTTC
5199129 TCTAAAAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
102 2 0.02
103 26 0.22
104 7 0.06
105 77 0.65
106 7 0.06
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (103 bp):
AAAACAAATTTCGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACCTTGAGATCGTTTTCTCA
Found at i:5199136 original size:36 final size:35
Alignment explanation
Indices: 5199090--5199193 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
5199080 TTGAGATCGT
5199090 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
** *
5199125 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAA-TTTGTCTCGCTTGAGACAA
* *
5199161 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTT-GTCTCGCTTGAGACA
5199194 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
33 3 0.05
34 19 0.33
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (35 bp):
TTTCTCTAAAAACAAATTTGTCTCGCTTGAGACAA
Found at i:5199462 original size:28 final size:29
Alignment explanation
Indices: 5199431--5199534 Score: 153
Period size: 29 Copynumber: 3.7 Consensus size: 29
5199421 ACAGTTTCTC
5199431 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
*
5199459 TTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAATAAAAATCTTTGAGTTTGTTCCTT
*
5199488 TTGAATAAATATCTTTGAG-TTG-TCTCTT
1 TTGAATAAAAATCTTTGAGTTTGTTC-CTT
5199516 TTGAA-AAAAATCTTTGAGT
1 TTGAATAAAAATCTTTGAGT
5199535 CTATTTATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
27 14 0.20
28 16 0.23
29 39 0.57
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.45
Consensus pattern (29 bp):
TTGAATAAAAATCTTTGAGTTTGTTCCTT
Found at i:5199767 original size:64 final size:65
Alignment explanation
Indices: 5199597--5199786 Score: 206
Period size: 64 Copynumber: 2.9 Consensus size: 65
5199587 TCTCTGAGTC
* * *
5199597 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTT-TTTTGAAACAAAAATCTTTGAGTTTGTTTCT
1 TGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTG-AA-AAAAATCTTTGAATATGTTTCT
*
5199661 TT
64 CT
* * *
5199663 TGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCT
1 TGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAAATCTTTGAATATGTTTCTCT
* * * * * **
5199728 T-AAA-ATGAATTTTGTATTTCTTGAGACAGTTTCTCTTGAAGTAAATCTTTGAATATGTT
1 TGAAACA-AAATTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAAATCTTTGAATATGTT
5199787 CATTTTGAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 46 0.43
65 22 0.21
66 32 0.30
67 5 0.05
ACGTcount: A:0.31, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
TGAAACAAAATTTTGTCTCTCTTGAGACAATTTCTTTTGAAAAAAATCTTTGAATATGTTTCTCT
Found at i:5200180 original size:31 final size:30
Alignment explanation
Indices: 5200145--5200205 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
5200135 GTTTCTCTAG
*
5200145 AAATACAAA-ATCTTTGAGTTTGTTTCACTTA
1 AAATA-AAACATCTTTGAG-TCGTTTCACTTA
*
5200176 AAATAAAACCATTTTTGAGTCGTTTCACTT
1 AAATAAAA-CATCTTTGAGTCGTTTCACTT
5200206 GAAACATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 3 0.12
31 15 0.58
32 8 0.31
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (30 bp):
AAATAAAACATCTTTGAGTCGTTTCACTTA
Found at i:5200221 original size:15 final size:15
Alignment explanation
Indices: 5200198--5200241 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
5200188 TTTTGAGTCG
*
5200198 TTTCACTTGAAACAT
1 TTTCTCTTGAAACAT
5200213 TTTCTCTTGAAACAT
1 TTTCTCTTGAAACAT
*
5200228 TTTCTCTTAAAACA
1 TTTCTCTTGAAACA
5200242 AGATCATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (15 bp):
TTTCTCTTGAAACAT
Found at i:5200533 original size:36 final size:35
Alignment explanation
Indices: 5200493--5200572 Score: 90
Period size: 36 Copynumber: 2.3 Consensus size: 35
5200483 TTTGAAAAAA
* * * *
5200493 ATCTTTGAGTTTGTTT-CTTTGTAAACAAAAATTACC
1 ATCTTTGAGTCTGTTTCCCTTG-AAAC-AAAATAAAC
*
5200529 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAGTCTGTTTCCCTTGAAACAAAATAAAC
5200564 ATCTTTGAG
1 ATCTTTGAG
5200573 AACGTTTCCC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
35 15 0.41
36 18 0.49
37 4 0.11
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (35 bp):
ATCTTTGAGTCTGTTTCCCTTGAAACAAAATAAAC
Found at i:5200567 original size:35 final size:35
Alignment explanation
Indices: 5200493--5200593 Score: 89
Period size: 36 Copynumber: 2.8 Consensus size: 35
5200483 TTTGAAAAAA
* * * * *
5200493 ATCTTTGAGTTTGTTT-CTTTGTAAACAAAAATTACC
1 ATCTTTGAATCTGTTTCCCTTG-AAAC-AAAATAAAC
5200529 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
* *
5200564 ATCTTTGAGAAC-GTTTCCCTTAAAAACAAA
1 ATCTTTGA-ATCTGTTTCCCTT-GAAACAAA
5200594 TTTTGTCTCA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 24 0.44
36 27 0.49
37 4 0.07
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (35 bp):
ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
Found at i:5200861 original size:43 final size:44
Alignment explanation
Indices: 5200772--5201007 Score: 170
Period size: 43 Copynumber: 5.5 Consensus size: 44
5200762 TGGCCAGTAG
* * ** *
5200772 TCCTCATCACATAGGAACCGTGTCAT-CCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* *
5200812 TCCTCATCACGTAGGAGTCGTGTCA-ACCATGGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
* * * ** *
5200854 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT-ACC-ATAGATAACCAGACC
* * * * ** *
5200901 TCTTCATCACGTATGAGCCGTGCCATTCCCCAG---ACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
5200942 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
*
5200984 GTCCTCATCACGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAGCCGTGT
5201008 TATCACTTTT
Statistics
Matches: 150, Mismatches: 33, Indels: 23
0.73 0.16 0.11
Matches are distributed among these distances:
40 29 0.19
41 28 0.19
42 2 0.01
43 54 0.36
44 2 0.01
45 5 0.03
46 29 0.19
47 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.19, T:0.22
Consensus pattern (44 bp):
TCCTCATCACGTAGGAGCCGTGTCATACCATAGATAACCAGACC
Found at i:5200913 original size:46 final size:45
Alignment explanation
Indices: 5200772--5201039 Score: 154
Period size: 43 Copynumber: 6.2 Consensus size: 45
5200762 TGGCCAGTAG
* * *
5200772 TCCTCATCACATAGGAACCGTGTCATC-CC---CA-GACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAAC
** * * * *
5200812 TCCTCATCACGTAGGAGTCGTGTCA--ACCATGGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAAC
* *
5200854 GTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATCACC-TTAGATGACCAGAAC
* * * * * *
5200901 TCTTCATCACGTATGAGCCGTGCCATTC-CC---CA-GACCAGATC
1 TCCTCATCACGTAGGAACCGTGTCA-TCACCTTAGATGACCAGAAC
* * * *
5200942 TCCTCATCACGTAGGAGCCGTGTCA--ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAAC
* * *
5200984 GTCCTCATCACGTAGGAACCGTGTTATCACTTTTAGACGACCAGAAC
1 -TCCTCATCACGTAGGAACCGTGTCATCAC-CTTAGATGACCAGAAC
*
5201031 TCTTCATCA
1 TCCTCATCA
5201040 TGTATGAGCA
Statistics
Matches: 171, Mismatches: 36, Indels: 36
0.70 0.15 0.15
Matches are distributed among these distances:
39 4 0.02
40 22 0.13
41 29 0.17
42 5 0.03
43 55 0.32
45 5 0.03
46 47 0.27
47 4 0.02
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (45 bp):
TCCTCATCACGTAGGAACCGTGTCATCACCTTAGATGACCAGAAC
Found at i:5200991 original size:130 final size:129
Alignment explanation
Indices: 5200759--5201048 Score: 454
Period size: 130 Copynumber: 2.2 Consensus size: 129
5200749 ATTATTCCTA
* * * * * * *
5200759 AGATGGCCAGTAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGT
1 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCAGACCAGATCTCCTCATCACGT
* *
5200824 AGGAGTCGTGTCAACCATGGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
66 AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
5200888 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATTCCCCAGACCAGATCTCCTCATCACG
1 AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCA-TCCCCAGACCAGATCTCCTCATCACG
*
5200953 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACTTTT
65 TAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
* * *
5201018 AGACGACCAGAACTCTTCATCATGTATGAGC
1 AGATGGCCAGAACTCTTCATCACGTATGAGC
5201049 AGTGTCGTCC
Statistics
Matches: 147, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
129 31 0.21
130 116 0.79
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (129 bp):
AGATGGCCAGAACTCTTCATCACGTATGAGCCGTGCCATCCCCAGACCAGATCTCCTCATCACGT
AGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTT
Found at i:5201223 original size:3 final size:3
Alignment explanation
Indices: 5201215--5201258 Score: 61
Period size: 3 Copynumber: 14.0 Consensus size: 3
5201205 TTATCGTTAT
*
5201215 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TATA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA TTA TTA
5201259 CATTTTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 31 0.84
4 6 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5201270 original size:23 final size:23
Alignment explanation
Indices: 5201222--5201271 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5201212 TATTTATTAT
* * *
5201222 TATTATTATTATTATTTATTATA
1 TATTATTAATATTAATTATTACA
5201245 TATTATTAATATTACATT-TTACA
1 TATTATTAATATTA-ATTATTACA
5201268 TATT
1 TATT
5201272 TGCAGGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 21 0.91
24 2 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTAATATTAATTATTACA
Found at i:5208044 original size:18 final size:19
Alignment explanation
Indices: 5208021--5208056 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5208011 CTTGATTAAG
5208021 AAGAAAC-CTTGAACGAAT
1 AAGAAACGCTTGAACGAAT
*
5208039 AAGAAACGGTTGAACGAA
1 AAGAAACGCTTGAACGAA
5208057 ACGTTAGGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.50, C:0.14, G:0.22, T:0.14
Consensus pattern (19 bp):
AAGAAACGCTTGAACGAAT
Found at i:5209860 original size:24 final size:24
Alignment explanation
Indices: 5209816--5209913 Score: 85
Period size: 24 Copynumber: 4.2 Consensus size: 24
5209806 TATTCATTTA
* *
5209816 TTTAT-TGTTCATGAACGTGTTCG
1 TTTATATGTTCATCAACATGTTCG
*
5209839 TTTATATATTCATCAACATGTTCG
1 TTTATATGTTCATCAACATGTTCG
* * * * *
5209863 CTTA-GTGTTC-GCGAACAAGTTTG
1 TTTATATGTTCATC-AACATGTTCG
*
5209886 TTTATATGTTCATGAACATGTTCG
1 TTTATATGTTCATCAACATGTTCG
5209910 TTTA
1 TTTA
5209914 GCGTTCATTT
Statistics
Matches: 56, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
22 1 0.02
23 20 0.36
24 35 0.62
ACGTcount: A:0.23, C:0.14, G:0.17, T:0.45
Consensus pattern (24 bp):
TTTATATGTTCATCAACATGTTCG
Found at i:5212673 original size:22 final size:21
Alignment explanation
Indices: 5212643--5212684 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
5212633 ATTATTGTAA
5212643 TATTAATTATTTAACTATTTT
1 TATTAATTATTTAACTATTTT
*
5212664 TATTACATTATTTAGCTATTT
1 TATTA-ATTATTTAACTATTT
5212685 CTAACCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.60
Consensus pattern (21 bp):
TATTAATTATTTAACTATTTT
Found at i:5218144 original size:50 final size:50
Alignment explanation
Indices: 5218069--5218224 Score: 174
Period size: 50 Copynumber: 3.1 Consensus size: 50
5218059 GTAGCAGTAA
* *
5218069 AGCGCGCCCCCTGAACCGCGCTATACGCTGATTTGGCGT-CACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGC-TACACGTGGGTAT
** *
5218119 AGCGCGCCCCCTGCCCCGCGATATACGGTGATCTGGCTACACGTGGGTAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCTACACGTGGGTAT
* * * **
5218169 AGCGCGCCCCCTGATCCGCGCTATAC-CT-ATGTATCTGACACGTGGGATAT
1 AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCT-ACACGTGGG-TAT
5218219 AGCGCG
1 AGCGCG
5218225 GTGCAGGGGG
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
48 5 0.05
49 11 0.12
50 75 0.82
ACGTcount: A:0.17, C:0.33, G:0.29, T:0.21
Consensus pattern (50 bp):
AGCGCGCCCCCTGAACCGCGATATACGCTGATCTGGCTACACGTGGGTAT
Found at i:5219740 original size:12 final size:12
Alignment explanation
Indices: 5219711--5219748 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
5219701 ATTTATAAGA
*
5219711 GAGGAGAGATGC
1 GAGGAGAGATGT
5219723 GA--AGAGATGT
1 GAGGAGAGATGT
5219733 GAGGAGAGATGT
1 GAGGAGAGATGT
5219745 GAGG
1 GAGG
5219749 TATTTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.34, C:0.03, G:0.50, T:0.13
Consensus pattern (12 bp):
GAGGAGAGATGT
Found at i:5230015 original size:9 final size:9
Alignment explanation
Indices: 5230001--5230038 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
5229991 GTAAAAAAAT
5230001 AATAATAAA
1 AATAATAAA
5230010 AATAATAAA
1 AATAATAAA
5230019 AATAA-ACAA
1 AATAATA-AA
5230028 AATGAATAAA
1 AAT-AATAAA
5230038 A
1 A
5230039 TGTTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 1 0.04
9 19 0.73
10 5 0.19
11 1 0.04
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (9 bp):
AATAATAAA
Found at i:5230016 original size:15 final size:14
Alignment explanation
Indices: 5229992--5230030 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
5229982 ACAGAACATG
*
5229992 TAAAAAAATAATAA
1 TAAAAAAATAAAAA
5230006 TAAAAATAATAAAAA
1 TAAAAA-AATAAAAA
5230021 TAAACAAAAT
1 TAAA-AAAAT
5230031 GAATAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 6 0.27
15 14 0.64
16 2 0.09
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAAAAAATAAAAA
Found at i:5230102 original size:10 final size:9
Alignment explanation
Indices: 5230083--5230125 Score: 50
Period size: 10 Copynumber: 4.4 Consensus size: 9
5230073 TTAATGGAGT
5230083 AAAAAAATA
1 AAAAAAATA
5230092 AAAAAAGATA
1 AAAAAA-ATA
*
5230102 AAAGAAATTA
1 AAA-AAAATA
5230112 AAAAAGAATA
1 AAAAA-AATA
5230122 AAAA
1 AAAA
5230126 TAATGTGTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
9 8 0.28
10 18 0.62
11 3 0.10
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:5230114 original size:19 final size:19
Alignment explanation
Indices: 5230082--5230125 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5230072 ATTAATGGAG
5230082 TAAAAAAATAAAAAAAG-A
1 TAAAAAAATAAAAAAAGAA
*
5230100 TAAAAGAAATTAAAAAAGAA
1 TAAAA-AAATAAAAAAAGAA
5230120 TAAAAA
1 TAAAAA
5230126 TAATGTGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 5 0.22
19 12 0.52
20 6 0.26
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.14
Consensus pattern (19 bp):
TAAAAAAATAAAAAAAGAA
Found at i:5230264 original size:16 final size:17
Alignment explanation
Indices: 5230232--5230319 Score: 56
Period size: 18 Copynumber: 5.1 Consensus size: 17
5230222 TATTAAGGAA
5230232 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
5230249 AAAATAA-AGTAAAAATAT
1 AAAATAATAG-AAAAA-AT
* * *
5230267 AATATATATATATATAAAT
1 AAAATA-ATAGA-AAAAAT
*
5230286 -AAATAA-ATAAAAAAT
1 AAAATAATAGAAAAAAT
* *
5230301 AGAATATTAAGAAAAAAT
1 AAAATAAT-AGAAAAAAT
5230319 A
1 A
5230320 TATACATAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
15 5 0.09
16 9 0.16
17 13 0.24
18 20 0.36
19 4 0.07
20 4 0.07
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:5230365 original size:2 final size:2
Alignment explanation
Indices: 5230353--5230411 Score: 68
Period size: 2 Copynumber: 30.0 Consensus size: 2
5230343 TTAATACATC
* *
5230353 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5230394 TGA TA TA -A GA TA TA TA TA
1 T-A TA TA TA TA TA TA TA TA
5230412 ATAAAAATAA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:5230429 original size:23 final size:22
Alignment explanation
Indices: 5230403--5230473 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
5230393 ATGATATAAG
5230403 ATATATATAATAAAAATAATATA
1 ATATATATAATAAAAA-AATATA
* *
5230426 ATATAAATAAAAAAAGAAGAATATA
1 ATATATAT-AATAAA-AA-AATATA
* *
5230451 GTAAATA-AATAAAAAAATATA
1 ATATATATAATAAAAAAATATA
5230472 AT
1 AT
5230474 TAAAAATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 7 0.18
22 2 0.05
23 12 0.32
24 5 0.13
25 12 0.32
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (22 bp):
ATATATATAATAAAAAAATATA
Found at i:5230433 original size:14 final size:14
Alignment explanation
Indices: 5230396--5230435 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
5230386 ATATATAATG
5230396 ATATAAGATATATATA
1 ATATAA-ATA-ATATA
*
5230412 ATAAAAATAATATA
1 ATATAAATAATATA
5230426 ATATAAATAA
1 ATATAAATAA
5230436 AAAAAGAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:5230450 original size:41 final size:42
Alignment explanation
Indices: 5230400--5230479 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 42
5230390 ATAATGATAT
* *
5230400 AAGATATATA-TAATAAAAATAATATAATATAAATAAAAAAAG
1 AAGATATATAGTAA-AAAAATAAAAAAATATAAATAAAAAAAG
* *
5230442 AAGA-ATATAGTAAATAAATAAAAAAATATAATTAAAAA
1 AAGATATATAGTAAAAAAATAAAAAAATATAAATAAAAA
5230480 TATATATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 26 0.79
42 7 0.21
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (42 bp):
AAGATATATAGTAAAAAAATAAAAAAATATAAATAAAAAAAG
Found at i:5232903 original size:67 final size:65
Alignment explanation
Indices: 5232787--5232969 Score: 224
Period size: 65 Copynumber: 2.8 Consensus size: 65
5232777 AAGATATATG
* * * **
5232787 TTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-
5232851 TTT
64 -TT
*
5232854 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * * *
5232919 TTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
5232970 CTGTCTCAAG
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
65 46 0.45
67 35 0.34
68 21 0.21
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:5232970 original size:36 final size:36
Alignment explanation
Indices: 5232918--5233036 Score: 157
Period size: 36 Copynumber: 3.3 Consensus size: 36
5232908 ATTCAAAGAT
* *
5232918 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACGAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
*
5232954 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
* * * * *
5232990 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
5233027 TTTGTTTCAA
1 TTTGTTTCAA
5233037 ATAAAACATA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
36 41 0.58
37 30 0.42
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAA
Found at i:5233014 original size:37 final size:36
Alignment explanation
Indices: 5232930--5233021 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
5232920 TGTTTCAAGG
* * * * *
5232930 GAAACTATCTCAAGAGAGACGAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
5232966 GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAA
*
5233003 GAAACTGTCTCAAGGGAGA
1 GAAACTGTCTCAAGAGAGA
5233022 TGAAATTTGT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
36 22 0.45
37 27 0.55
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (36 bp):
GAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAA
Found at i:5233966 original size:32 final size:33
Alignment explanation
Indices: 5233927--5234022 Score: 131
Period size: 32 Copynumber: 2.9 Consensus size: 33
5233917 ATTCCCAAAG
* *
5233927 ATGCCCCAATATTCGATGTTGAATCTCAAAA-A
1 ATGCCCCAACATTTGATGTTGAATCTCAAAATA
* * *
5233959 ATTCCCCAACATTTGATGTTAAATCTAAAAATA
1 ATGCCCCAACATTTGATGTTGAATCTCAAAATA
5233992 ATGCCCCAACATTTGATGTTGAATCTTCAAA
1 ATGCCCCAACATTTGATGTTGAATC-TCAAA
5234023 GATGCCCTCA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 26 0.48
33 24 0.44
34 4 0.07
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (33 bp):
ATGCCCCAACATTTGATGTTGAATCTCAAAATA
Found at i:5235050 original size:69 final size:69
Alignment explanation
Indices: 5234939--5235076 Score: 249
Period size: 69 Copynumber: 2.0 Consensus size: 69
5234929 TATCTCTCTC
*
5234939 TTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTCGATCAATC
1 TTGATGCTCTACGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTCGATCAATC
5235004 TCAT
66 TCAT
* *
5235008 TTGATGCTCTACGATCTTTGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTACGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTCGATCAATC
5235073 TCAT
66 TCAT
5235077 AGTTTGAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (69 bp):
TTGATGCTCTACGATCTTCGAGTGAAGTGATTCAGTGATTCGGAAATGATTGTGCTCGATCAATC
TCAT
Found at i:5235168 original size:13 final size:14
Alignment explanation
Indices: 5235152--5235216 Score: 75
Period size: 13 Copynumber: 4.9 Consensus size: 14
5235142 AATTTTCCTT
5235152 TTTTTTTC-CTTTG
1 TTTTTTTCTCTTTG
5235165 TTTTTTTCTCTTT-
1 TTTTTTTCTCTTTG
*
5235178 TTATTTTCTCTTTG
1 TTTTTTTCTCTTTG
*
5235192 -CTTTTTCTCTTTG
1 TTTTTTTCTCTTTG
*
5235205 -CTTTTTCTCTTT
1 TTTTTTTCTCTTT
5235217 TTGTTCTGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
13 43 0.91
14 4 0.09
ACGTcount: A:0.02, C:0.18, G:0.05, T:0.75
Consensus pattern (14 bp):
TTTTTTTCTCTTTG
Found at i:5235196 original size:26 final size:26
Alignment explanation
Indices: 5235144--5235216 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 26
5235134 TTTTTTTCAA
*
5235144 TTTTC-CTTTTTTTTTC-CTTTGTTT
1 TTTTCTCTTTTTTTTTCTCTTTGTCT
5235168 TTTTCTCTTTTTATTTTCTCTTTG-CT
1 TTTTCTCTTTTT-TTTTCTCTTTGTCT
*
5235194 TTTTCTCTTTGCTTTTTCTCTTT
1 TTTTCTCTTT-TTTTTTCTCTTT
5235217 TTGTTCTGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.12
25 6 0.14
26 26 0.60
27 6 0.14
ACGTcount: A:0.01, C:0.19, G:0.04, T:0.75
Consensus pattern (26 bp):
TTTTCTCTTTTTTTTTCTCTTTGTCT
Found at i:5238317 original size:25 final size:24
Alignment explanation
Indices: 5238287--5238353 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
5238277 AATAATAAAT
5238287 AAAACAAGAAAAAATGAAAAATAAC
1 AAAACAAGAAAAAAT-AAAAATAAC
* * *
5238312 AAAACACGTAAAAAATAATAATAAT
1 AAAACAAG-AAAAAATAAAAATAAC
* *
5238337 AAAATAA-TAAAAATAAA
1 AAAACAAGAAAAAATAAA
5238354 CAAAATGAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
23 8 0.24
25 19 0.56
26 7 0.21
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (24 bp):
AAAACAAGAAAAAATAAAAATAAC
Found at i:5238342 original size:14 final size:14
Alignment explanation
Indices: 5238323--5238353 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5238313 AAACACGTAA
*
5238323 AAAATAATAATAAT
1 AAAATAATAAAAAT
5238337 AAAATAATAAAAAT
1 AAAATAATAAAAAT
5238351 AAA
1 AAA
5238354 CAAAATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAATAATAAAAAT
Found at i:5238590 original size:16 final size:17
Alignment explanation
Indices: 5238558--5238613 Score: 60
Period size: 16 Copynumber: 3.2 Consensus size: 17
5238548 ATTATGGAAA
5238558 AAAATAATAGAAAAAAT
1 AAAATAATAGAAAAAAT
*
5238575 AAAATAA-AGTAAAAAT
1 AAAATAATAGAAAAAAT
* *
5238591 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAA-AAAT
5238610 AAAA
1 AAAA
5238614 ACAAAAATAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 13 0.42
17 8 0.26
18 3 0.10
19 7 0.23
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (17 bp):
AAAATAATAGAAAAAAT
Found at i:5238742 original size:25 final size:25
Alignment explanation
Indices: 5238714--5238762 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5238704 ACATCTATAC
*
5238714 ATATATAT-ATATATAATGATATAAG
1 ATATATATAATATA-AATAATATAAG
5238739 ATATATATAATATAAATAATATAA
1 ATATATATAATATAAATAATATAA
5238763 TATAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
ATATATATAATATAAATAATATAAG
Found at i:5238762 original size:14 final size:14
Alignment explanation
Indices: 5238732--5238771 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 14
5238722 ATATATAATG
5238732 ATATAAGATATATATA
1 ATATAA-ATA-ATATA
5238748 ATATAAATAATATA
1 ATATAAATAATATA
5238762 ATATAAATAA
1 ATATAAATAA
5238772 AAAAAGAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 15 0.62
15 3 0.12
16 6 0.25
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (14 bp):
ATATAAATAATATA
Found at i:5238823 original size:16 final size:14
Alignment explanation
Indices: 5238791--5238821 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5238781 AATATAGTAA
5238791 ATAATTAAAAATAT
1 ATAATTAAAAATAT
5238805 ATAATTAAAAATAT
1 ATAATTAAAAATAT
5238819 ATA
1 ATA
5238822 TATATGGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
ATAATTAAAAATAT
Found at i:5239954 original size:21 final size:22
Alignment explanation
Indices: 5239896--5239955 Score: 61
Period size: 21 Copynumber: 2.7 Consensus size: 22
5239886 ATGTTTCAAT
5239896 ATGTATAATATTATTAAATTTAAC
1 ATGT-TAAT-TTATTAAATTTAAC
* **
5239920 ATTTTAAAAT-TTAAATTTAAC
1 ATGTTAATTTATTAAATTTAAC
5239941 -TGTTAATTTATTAAA
1 ATGTTAATTTATTAAA
5239956 ATATGATGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 6 0.21
21 16 0.55
22 1 0.03
23 3 0.10
24 3 0.10
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (22 bp):
ATGTTAATTTATTAAATTTAAC
Found at i:5243801 original size:3 final size:3
Alignment explanation
Indices: 5243795--5243891 Score: 74
Period size: 3 Copynumber: 33.3 Consensus size: 3
5243785 GAGGATAAGG
* * * * * *
5243795 AGA AGA AGA AGA ACA AGA AGA ACA AGA ACA AGA ACA AGA ACA AGA ACA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
* * * * *
5243843 AGA ACA AGA A-A ATA AGA ATA AGA A-A ATA AGA AGA AGA A-A ATA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5243888 AGA A
1 AGA A
5243892 TAATAATAAT
Statistics
Matches: 72, Mismatches: 19, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
2 6 0.08
3 66 0.92
ACGTcount: A:0.69, C:0.07, G:0.20, T:0.04
Consensus pattern (3 bp):
AGA
Found at i:5243865 original size:14 final size:14
Alignment explanation
Indices: 5243803--5243888 Score: 90
Period size: 14 Copynumber: 6.4 Consensus size: 14
5243793 GGAGAAGAAG
*
5243803 AAGAACAAGAAGAAC
1 AAGAACAAGAA-AAT
*
5243818 AAGAACAAG--AAC
1 AAGAACAAGAAAAT
*
5243830 AAGAACAAG--AAC
1 AAGAACAAGAAAAT
5243842 AAGAACAAGAAAAT
1 AAGAACAAGAAAAT
*
5243856 AAGAATAAGAAAAT
1 AAGAACAAGAAAAT
*
5243870 AAGAAGAAGAAAAT
1 AAGAACAAGAAAAT
5243884 AAGAA
1 AAGAA
5243889 GAATAATAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
12 24 0.36
14 33 0.50
15 9 0.14
ACGTcount: A:0.70, C:0.08, G:0.17, T:0.05
Consensus pattern (14 bp):
AAGAACAAGAAAAT
Found at i:5243887 original size:11 final size:12
Alignment explanation
Indices: 5243859--5243897 Score: 55
Period size: 11 Copynumber: 3.4 Consensus size: 12
5243849 AGAAAATAAG
5243859 AATAAGAA-AAT
1 AATAAGAAGAAT
*
5243870 AAGAAGAAGAA-
1 AATAAGAAGAAT
5243881 AATAAGAAGAAT
1 AATAAGAAGAAT
5243893 AATAA
1 AATAA
5243898 TAATGAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.13
Consensus pattern (12 bp):
AATAAGAAGAAT
Found at i:5246853 original size:15 final size:15
Alignment explanation
Indices: 5246835--5246869 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5246825 CGAGGGTATT
5246835 GTAGTCATTCGGGAC
1 GTAGTCATTCGGGAC
*
5246850 GTAGTCCTTCGGGAC
1 GTAGTCATTCGGGAC
5246865 GTAGT
1 GTAGT
5246870 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (15 bp):
GTAGTCATTCGGGAC
Found at i:5256790 original size:8 final size:9
Alignment explanation
Indices: 5256762--5256787 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
5256752 GGCAGAACAC
5256762 CCCCAAAAA
1 CCCCAAAAA
5256771 CCCCAAAAA
1 CCCCAAAAA
5256780 CCCCAAAA
1 CCCCAAAA
5256788 CCCTTCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.54, C:0.46, G:0.00, T:0.00
Consensus pattern (9 bp):
CCCCAAAAA
Found at i:5259168 original size:21 final size:22
Alignment explanation
Indices: 5259144--5259199 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
5259134 CTCAGAGGGA
5259144 ACCGATTCCCCCCCAA-GGGGT
1 ACCGATTCCCCCCCAAGGGGGT
5259165 ACCGATTCCCCCCCAAGGGGGT
1 ACCGATTCCCCCCCAAGGGGGT
*
5259187 ACTGATTCCCCCC
1 ACCGATTCCCCCC
5259200 TAAATGGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 16 0.48
22 17 0.52
ACGTcount: A:0.18, C:0.45, G:0.21, T:0.16
Consensus pattern (22 bp):
ACCGATTCCCCCCCAAGGGGGT
Found at i:5261262 original size:278 final size:273
Alignment explanation
Indices: 5260483--5261436 Score: 953
Period size: 271 Copynumber: 3.5 Consensus size: 273
5260473 GTCATCTCAA
* * * * * *
5260483 TATTCAATGATTTAGCTACTTTTC-AGTGCTCAATTAATGCACTGTTTCAGTTACGATTT-AG-A
1 TATTCAATGATTCAACTACTTTTCGA-TACTCAATTAATGCACCGTTTCAGCTAC-TTTTCAGAA
* * * * * *
5260545 GCTCATTCAATGTAGC-A-AATGCACCATTTTAGCTTTTTCAGAGCTCATTTAATGCAGAATTCA
64 G-TCATTTATTGCAACAATAATGCA-CATTTCAGCTTTTTCAG-GCTCATTCAATGCAGAATTCA
* * * * ** *
5260608 AGCAA-TTATTCAAAAAACGAGTGAAAATAGTGATGCATTATCATCTTTTGCAGTTTTTCAGTGC
126 AGCAACTT-TTTAGAAAACGAGTGAAAATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGTGA
* *** * * * * *
5260672 TATATCAACTTAAATGTTAAAGCTTCTCAATGTTGAATTATCGCTTCAAAACAT--AAAAATGTG
190 TATATCAACTCAAATCAGAAAGCTTTTCAGTGTTGAATTATCACTTCAAAATATAAAAAAACGTG
5260735 TATTTTAACCAGGCCAAAT
255 TATTTTAACCAGGCCAAAT
* * * * * * * * * *
5260754 TATTCAATGATTTAGCTACTGTTC-ACTATTCAATTAATGCACTGTTTTAGTTACTTTCCAAAAA
1 TATTCAATGATTCAACTACTTTTCGA-TACTCAATTAATGCACCGTTTCAGCTACTTTTCAGAAG
* *
5260818 TCATTTATTGCAACAATAATGTACTATTTCAGCTTTTTCA-TCTCATTCAATGCAGAATTCAAGC
65 TCATTTATTGCAACAATAATGCAC-ATTTCAGCTTTTTCAGGCTCATTCAATGCAGAATTCAAGC
** * * *
5260882 AACTTTTTAGAAAATAAGTGAAAATAGTGGTGCACTATTATCTTCTGTAACTTTTCAGTGATATA
129 AACTTTTTAGAAAACGAGTGAAAATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGTGATATA
* **
5260947 TCAACTCAAATCAGAAAGCTTTTCAGTGTTGAATTATCTCTTCAATTAATATAAAAAAACACGTA
194 TCAACTCAAATCAGAAAGCTTTTCAGTGTTGAATTATCACTTCAA--AATATAAAAAAACGTGTA
5261012 TTTTAACCAGGCCAAAT
257 TTTTAACCAGGCCAAAT
* * * * *
5261029 TATTCAATGATTCAACTACTTTTCGGTACTAAATTAATGCACCCTTTCAACTACTTTTCAGATGT
1 TATTCAATGATTCAACTACTTTTCGATACTCAATTAATGCACCGTTTCAGCTACTTTTCAGAAGT
* * *
5261094 CGTTTATTGCAACAATAATGCATCATTTCAGTTTTTTCAAGGCTCATTCAATGCAGAACTTAAAG
66 CATTTATTGCAACAATAATGCA-CATTTCAGCTTTTTC-AGGCTCATTCAATGCAGAA-TTCAAG
* * * *
5261159 CAACTTTTTAGAAAACGGGTGAAAATAGTGGTGCATTATCATATTCTACAACTTTTCAATGATAT
128 CAACTTTTTAGAAAACGAGTGAAAATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGTGATAT
* * * *
5261224 ATCAACTCAAATCAGAAAGCTTTTTAGTGCTAAATTATCACTTC-AAATCATAAAAAAGCGTGTA
193 ATCAACTCAAATCAGAAAGCTTTTCAGTGTTGAATTATCACTTCAAAAT-ATAAAAAAACGTGTA
* *
5261288 TTTCAACTAGGCCAAAAT
257 TTTTAACCAGGCC-AAAT
* * * * * * * * *
5261306 T-TTCACTGTTTCAACTATTTTTCGATGCTCAATCAATGCAGCGTTTCAGCTAGTTTTTAGAGGT
1 TATTCAATGATTCAACTACTTTTCGATACTCAATTAATGCACCGTTTCAGCTACTTTTCAGAAGT
* * * *
5261370 CACTTATTGCAACAATAATGCACCTGTT-GGCTTTTTCAGGGCTCATTCAATGCAAAATTCAAGC
66 CATTTATTGCAACAATAATGCACAT-TTCAGCTTTTTCA-GGCTCATTCAATGCAGAATTCAAGC
5261434 AAC
129 AAC
5261437 ATTTCACAAA
Statistics
Matches: 566, Mismatches: 98, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
270 2 0.00
271 170 0.30
272 5 0.01
273 23 0.04
274 10 0.02
275 136 0.24
276 97 0.17
277 22 0.04
278 101 0.18
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (273 bp):
TATTCAATGATTCAACTACTTTTCGATACTCAATTAATGCACCGTTTCAGCTACTTTTCAGAAGT
CATTTATTGCAACAATAATGCACATTTCAGCTTTTTCAGGCTCATTCAATGCAGAATTCAAGCAA
CTTTTTAGAAAACGAGTGAAAATAGTGGTGCATTATCATCTTCTGCAACTTTTCAGTGATATATC
AACTCAAATCAGAAAGCTTTTCAGTGTTGAATTATCACTTCAAAATATAAAAAAACGTGTATTTT
AACCAGGCCAAAT
Found at i:5270427 original size:20 final size:19
Alignment explanation
Indices: 5270404--5270510 Score: 72
Period size: 20 Copynumber: 5.3 Consensus size: 19
5270394 AACGCGTATC
*
5270404 CGTAAATTGCAATGACAATA
1 CGTAAATCGCAATG-CAATA
* *
5270424 CGTAAAATCGCAACGC-GTA
1 CGT-AAATCGCAATGCAATA
* *
5270443 TCTGTAAATCGCAACGAGAATA
1 -C-GTAAATCGCAATG-CAATA
* *
5270465 CGTAAATCGCAATGCGTATC
1 CGTAAATCGCAATGC-AATA
*
5270485 CGTAAATAGCAATGCGAATA
1 CGTAAATCGCAATGC-AATA
5270505 CGTAAA
1 CGTAAA
5270511 ATTGCAACAC
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
19 2 0.03
20 53 0.77
21 12 0.17
22 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (19 bp):
CGTAAATCGCAATGCAATA
Found at i:5270428 original size:41 final size:41
Alignment explanation
Indices: 5270383--5270532 Score: 196
Period size: 41 Copynumber: 3.7 Consensus size: 41
5270373 AACGAGTATC
* *
5270383 CGTAAAATCACAACGCGTATCCGTAAATTGCAATGACAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATAGCAATGACAATA
* * * *
5270424 CGTAAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATAGCAATGACAATA
*
5270465 CGT-AAATCGCAATGCGTATCCGTAAATAGCAATG-CGAATA
1 CGTAAAATCGCAACGCGTATCCGTAAATAGCAATGAC-AATA
* *
5270505 CGTAAAATTGCAACACGTATCCGTAAAT
1 CGTAAAATCGCAACGCGTATCCGTAAAT
5270533 CGAAACGCGA
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
40 34 0.36
41 60 0.64
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.22
Consensus pattern (41 bp):
CGTAAAATCGCAACGCGTATCCGTAAATAGCAATGACAATA
Found at i:5270505 original size:81 final size:82
Alignment explanation
Indices: 5270368--5270539 Score: 240
Period size: 81 Copynumber: 2.1 Consensus size: 82
5270358 GATTCTGACT
* * *
5270368 ATCGCAACGAGTATCCGTAAAATCACAACGCGTATCCGTAAATTGCAATGACAATACGTAAAATC
1 ATCGCAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATAGCAATGACAATACGTAAAATC
* *
5270433 GCAACGCGTATCTGTAA
66 GCAACACGTATCCGTAA
* *
5270450 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATAGCAATG-CGAATACGTAAAAT
1 ATCGCAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATAGCAATGAC-AATACGTAAAAT
*
5270513 TGCAACACGTATCCGTAA
65 CGCAACACGTATCCGTAA
*
5270531 ATCGAAACG
1 ATCGCAACG
5270540 CGATTTTTAA
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
80 1 0.01
81 63 0.79
82 16 0.20
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (82 bp):
ATCGCAACGAGAATACGTAAAATCACAACGCGTATCCGTAAATAGCAATGACAATACGTAAAATC
GCAACACGTATCCGTAA
Found at i:5271197 original size:33 final size:33
Alignment explanation
Indices: 5271147--5271218 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
5271137 GAAATTGACT
* **
5271147 ATCGCAATGAGAGAATCGCAACGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAACCAAA
*
5271180 ATCGCAACGAGATAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAGAATCGCAACGCGAAACCAAA
5271213 ATCGCA
1 ATCGCA
5271219 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACGCGAAACCAAA
Found at i:5271293 original size:20 final size:20
Alignment explanation
Indices: 5271243--5271305 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
5271233 TCGCGTTGCG
**
5271243 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATTTTC
*
5271263 AATTC-CGCGTTGCGATTTTC
1 -ATTCTCTCGTTGCGATTTTC
5271283 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
5271303 ATT
1 ATT
5271306 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 4 0.11
20 29 0.78
21 4 0.11
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:5273981 original size:14 final size:14
Alignment explanation
Indices: 5273962--5273997 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
5273952 ATTGTTTAAT
5273962 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
5273976 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
5273990 TGATTTGT
1 TGATTTGT
5273998 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:5274203 original size:19 final size:19
Alignment explanation
Indices: 5274137--5274310 Score: 189
Period size: 19 Copynumber: 9.8 Consensus size: 19
5274127 GCGAAATGAA
*
5274137 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5274156 ATTTCCGCATTGCGA--TTC
1 ATTT-CGCATTGCGATTTTC
*
5274174 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5274190 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5274209 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
5274226 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5274242 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
5274260 A---CTCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5274276 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
5274295 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
5274311 CTCTCGTTGA
Statistics
Matches: 131, Mismatches: 7, Indels: 34
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.16
16 17 0.13
17 7 0.05
18 12 0.09
19 59 0.45
20 15 0.11
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:5274248 original size:53 final size:52
Alignment explanation
Indices: 5274137--5274310 Score: 219
Period size: 53 Copynumber: 3.3 Consensus size: 52
5274127 GCGAAATGAA
* *
5274137 ATTTCGCGTTGCGATTTTCATTTCCGCATTGCGATTCACTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATTTTC
5274190 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* * * * *
5274242 ATTTTCGCATTGCGATTCACTCATTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 A-TTTCGCATTGCGATT--TTCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
5274295 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
5274311 CTCTCGTTGA
Statistics
Matches: 110, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
52 44 0.40
53 52 0.47
54 4 0.04
55 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (52 bp):
ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:5274253 original size:34 final size:33
Alignment explanation
Indices: 5274196--5274291 Score: 165
Period size: 34 Copynumber: 2.9 Consensus size: 33
5274186 TTTCATTTCG
*
5274196 CATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CATTGCGATTTTCATTTCGCATTGCGATTCACT
*
5274229 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CATTGCGATTTTCA-TTTCGCATTGCGATTCACT
5274263 CATTGCGATTTTCATTTCGCATTGCGATT
1 CATTGCGATTTTCATTTCGCATTGCGATT
5274292 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 28 0.47
34 31 0.53
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
CATTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:5274271 original size:86 final size:86
Alignment explanation
Indices: 5274143--5274341 Score: 344
Period size: 86 Copynumber: 2.3 Consensus size: 86
5274133 TGAAATTTCG
*
5274143 CGTTGCGATTTTCATTTCCGCATTGCGATTCACTCGTTGCGATTTTCATTTCGCATTGCGATTTT
1 CGTTGCGATTTTCATTTCCGCATTGCGATTCACTCATTGCGATTTTCATTTCGCATTGCGATTTT
5274208 CATTTCGCATTGCGATTCTCT
66 CATTTCGCATTGCGATTCTCT
*
5274229 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCATTGCGATTTTCATTTCGCATTGCGATTTT
1 CGTTGCGATTTTCATTTCCGCATTGCGATTCACTCATTGCGATTTTCATTTCGCATTGCGATTTT
5274294 CATTTCGCATTGCGATTCTCT
66 CATTTCGCATTGCGATTCTCT
* ** *
5274315 CGTTGAGATAGTCATTTCCGCGTTGCG
1 CGTTGCGATTTTCATTTCCGCATTGCG
5274342 GTAGTCAATT
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 106 1.00
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (86 bp):
CGTTGCGATTTTCATTTCCGCATTGCGATTCACTCATTGCGATTTTCATTTCGCATTGCGATTTT
CATTTCGCATTGCGATTCTCT
Found at i:5274330 original size:52 final size:52
Alignment explanation
Indices: 5274177--5274341 Score: 192
Period size: 52 Copynumber: 3.1 Consensus size: 52
5274167 GCGATTCACT
* *
5274177 CGTTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCATTG-CGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCG-ATTGTC-ATT-TCG
* *
5274229 CGTTGCGATTTTCATTTTCGCATTGCGATTCACTCATTGCGATTTTCATTTCG
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCTCATTGCGATTGTCATTTCG
* * * *
5274282 CATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGAGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTGTCATTT-CG
5274335 CGTTGCG
1 CGTTGCG
5274342 GTAGTCAATT
Statistics
Matches: 97, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
52 45 0.46
53 38 0.39
54 6 0.06
55 8 0.08
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (52 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCATTGCGATTGTCATTTCG
Found at i:5274367 original size:19 final size:20
Alignment explanation
Indices: 5274321--5274368 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
5274311 CTCTCGTTGA
* *
5274321 GATAGTCATTTCCGCGTTGC
1 GATAGTCAATTCCGCATTGC
*
5274341 GGTAGTCAATTCCGCATT-C
1 GATAGTCAATTCCGCATTGC
5274360 GATAGTCAA
1 GATAGTCAA
5274369 ATGAATGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (20 bp):
GATAGTCAATTCCGCATTGC
Found at i:5276813 original size:24 final size:24
Alignment explanation
Indices: 5276779--5276832 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
5276769 CTGAAAAATC
5276779 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
5276803 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
5276827 ATCAAA
1 ATCAAA
5276833 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:5276846 original size:24 final size:24
Alignment explanation
Indices: 5276779--5276846 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
5276769 CTGAAAAATC
* * *
5276779 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
5276803 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
5276827 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
5276847 TATTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:5277707 original size:20 final size:20
Alignment explanation
Indices: 5277684--5277962 Score: 151
Period size: 20 Copynumber: 13.9 Consensus size: 20
5277674 TTGCGATAGT
*
5277684 CAGAATCTCGTTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
* *
5277704 CAGATTCGCATTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
* *
5277724 C-GTATTCGCATTGCGATTTA
1 CAG-ATTCTCGTTGCGATTTA
* *
5277744 C-GTATTCACATTGCGATTTA
1 CAG-ATTCTCGTTGCGATTTA
5277764 C-GTATTCTCGTTGCGATTTA
1 CAG-ATTCTCGTTGCGATTTA
* * *
5277784 CAGATACGCGTTACGATTTA
1 CAGATTCTCGTTGCGATTTA
*
5277804 CATATTC-CGTTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
** * *
5277823 TGGATACGT-GTTGCAATTTTA
1 CAGATTC-TCGTTGCGA-TTTA
* *
5277844 C-GTATTGTCGTTTCGATTTA
1 CAG-ATTCTCGTTGCGATTTA
* * *
5277864 CGGATACGCGTTGCGATTTTA
1 CAGATTCTCGTTGCGA-TTTA
* * *
5277885 CGGATACTCGTTGCGATAGT-
1 CAGATTCTCGTTGCGAT-TTA
* *
5277905 CAGAATCGCGTTGCGATTTA
1 CAGATTCTCGTTGCGATTTA
* * *
5277925 TATG-TTCGCGTTGCGATTTT
1 CA-GATTCTCGTTGCGATTTA
* *
5277945 CATATTCGCGTTGCGATT
1 CAGATTCTCGTTGCGATT
5277963 ATGGAAAATC
Statistics
Matches: 208, Mismatches: 38, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
19 16 0.08
20 158 0.76
21 34 0.16
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (20 bp):
CAGATTCTCGTTGCGATTTA
Found at i:5277738 original size:40 final size:40
Alignment explanation
Indices: 5277692--5277962 Score: 235
Period size: 40 Copynumber: 6.8 Consensus size: 40
5277682 GTCAGAATCT
*
5277692 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACAGATTCGCGTTGCGATTTACGTATTCG
* * * *
5277732 CATTGCGATTTAC-GTATTCACATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAG-ATTCGCGTTGCGATTTACGTATTCG
* * *
5277772 CGTTGCGATTTACAGATACGCGTTACGATTTACATATTC-
1 CGTTGCGATTTACAGATTCGCGTTGCGATTTACGTATTCG
** * * *
5277811 CGTTGCGATTTATGGATACGTGTTGCAATTTTACGTATT-G
1 CGTTGCGATTTACAGATTCGCGTTGCGA-TTTACGTATTCG
* * * * * *
5277851 TCGTTTCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 -CGTTGCGATTTACAGATTCGCGTTGCGA-TTTACGTATTCG
* * ** *
5277893 CGTTGCGATAGT-CAGAATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATTCGCGTTGCGATTTACGTATTCG
* *
5277933 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATTCGCGTTGCGATT
5277963 ATGGAAAATC
Statistics
Matches: 187, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
39 25 0.13
40 106 0.57
41 55 0.29
42 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACAGATTCGCGTTGCGATTTACGTATTCG
Found at i:5280786 original size:19 final size:20
Alignment explanation
Indices: 5280743--5280790 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
5280733 TCTAAATCCT
*
5280743 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
5280763 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
5280782 TTTTCAAAA
1 TTTTCAAAA
5280791 GAAGATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:5282088 original size:17 final size:18
Alignment explanation
Indices: 5282037--5282080 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
5282027 GTTATACAGA
*
5282037 GGGGAATCGATACCCCTG
1 GGGGAATCGGTACCCCTG
5282055 GGGGAATCGGTACCCCTG
1 GGGGAATCGGTACCCCTG
5282073 GGGGAATC
1 GGGGAATC
5282081 TGTTCCCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.25, G:0.39, T:0.16
Consensus pattern (18 bp):
GGGGAATCGGTACCCCTG
Found at i:5284219 original size:22 final size:21
Alignment explanation
Indices: 5284185--5284324 Score: 91
Period size: 21 Copynumber: 6.8 Consensus size: 21
5284175 TATTAATTTT
*
5284185 TTAATATT-ATATTATAGATA
1 TTAATTTTAATATTATAGATA
5284205 TTAATTTTTAATATTATAGATA
1 TTAA-TTTTAATATTATAGATA
* *
5284227 TTAATTTTAATATTA-AAATT
1 TTAATTTTAATATTATAGATA
*
5284247 TTAA--ATAA-ATTA-A-ATA
1 TTAATTTTAATATTATAGATA
5284263 TTAATTTTTAATATTATTATAGATA
1 TTAA-TTTT-A-A-TATTATAGATA
* * *
5284288 TTTAATTTT-ATATCATATAAA
1 -TTAATTTTAATATTATAGATA
5284309 TT-ATTTTATATATTAT
1 TTAATTTTA-ATATTAT
5284325 TAAAATTTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
16 6 0.06
17 5 0.05
18 3 0.03
19 6 0.06
20 14 0.15
21 29 0.30
22 17 0.18
23 4 0.04
24 1 0.01
25 7 0.07
26 4 0.04
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (21 bp):
TTAATTTTAATATTATAGATA
Found at i:5284242 original size:27 final size:27
Alignment explanation
Indices: 5284174--5284242 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 27
5284164 AATAAATAAA
5284174 ATATTAATTTTTTAATATT-ATATTATAG
1 ATATTAA--TTTTAATATTAATATTATAG
5284202 ATATTAA--TT--T-TTAATATTATAG
1 ATATTAATTTTAATATTAATATTATAG
5284224 ATATTAATTTTAATATTAA
1 ATATTAATTTTAATATTAA
5284243 AATTTTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
24 4 0.11
26 1 0.03
27 4 0.11
28 7 0.20
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (27 bp):
ATATTAATTTTAATATTAATATTATAG
Found at i:5284247 original size:36 final size:36
Alignment explanation
Indices: 5284207--5284278 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
5284197 TATAGATATT
*
5284207 AATTTTTAAT-ATTATAGATATTAA-TTTTAATATTAA
1 AATTTTAAATAATTA-A-ATATTAATTTTTAATATTAA
5284243 AATTTTAAATAAATTAAATATTAATTTTTAATATTA
1 AATTTTAAAT-AATTAAATATTAATTTTTAATATTA
5284279 TTATAGATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 16 0.50
37 12 0.38
38 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (36 bp):
AATTTTAAATAATTAAATATTAATTTTTAATATTAA
Found at i:5284334 original size:85 final size:86
Alignment explanation
Indices: 5284141--5284334 Score: 254
Period size: 86 Copynumber: 2.3 Consensus size: 86
5284131 ATATTTGAAT
**
5284141 TTAATTTTAATATTAATTTTTTAAATAAATAAAATATTAATTTTTTAATATTATATTATAGATAT
1 TTAATTTTAATATTAAAATTTTAAATAAATAAAATATTAATTTTTTAATATTATATTATAGATAT
* *
5284206 TAATTTTTAATATTATAGATA
66 TAATTTTTAATATCATAGAAA
*
5284227 TTAATTTTAATATTAAAATTTTAAATAAATTAAATATTAA-TTTTTAATA-T-TATTATAGATAT
1 TTAATTTTAATATTAAAATTTTAAATAAATAAAATATTAATTTTTTAATATTATATTATAGATA-
*
5284289 TTAA-TTTT-ATATCATATAAA
65 TTAATTTTTAATATCATAGAAA
*
5284309 TTATTTTATATATTATTAAAATTTTA
1 TTAATTT-TA-A-TATTAAAATTTTA
5284335 TATTTATTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
82 15 0.15
83 17 0.18
84 6 0.06
85 22 0.23
86 37 0.38
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (86 bp):
TTAATTTTAATATTAAAATTTTAAATAAATAAAATATTAATTTTTTAATATTATATTATAGATAT
TAATTTTTAATATCATAGAAA
Found at i:5284848 original size:31 final size:31
Alignment explanation
Indices: 5284813--5284872 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
5284803 TAGTTGTATG
*
5284813 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATTTCAGTATTGCAAAACTAA
5284844 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTGCAAAACT
5284873 CATTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTGCAAAACTAA
Found at i:5285537 original size:84 final size:85
Alignment explanation
Indices: 5285436--5285598 Score: 292
Period size: 84 Copynumber: 1.9 Consensus size: 85
5285426 AATTAGAACG
*
5285436 GACACGTGTCAATACATGATTGAAAGGTTTTATTTATGAATTTTAAATTATTTAATTAAAT-ATT
1 GACACGTGTCAATACATGATTGAAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATAATT
*
5285500 TTTTTATCCATTCAAGACTT
66 TTTCTATCCATTCAAGACTT
*
5285520 GACACGTGTCAATACATGATTGAAATATTTTATTTATGAATTTTAAATTATTTAATTAAATAATT
1 GACACGTGTCAATACATGATTGAAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATAATT
5285585 TTTCTATCCATTCA
66 TTTCTATCCATTCA
5285599 GATGGTGACG
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 59 0.79
85 16 0.21
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (85 bp):
GACACGTGTCAATACATGATTGAAAGATTTTATTTATGAATTTTAAATTATTTAATTAAATAATT
TTTCTATCCATTCAAGACTT
Found at i:5291942 original size:40 final size:40
Alignment explanation
Indices: 5291896--5291977 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
5291886 AAATTAAAGT
5291896 TTTATCTATATAATTATACAAAATCAAAATTCATATCACA
1 TTTATCTATATAATTATACAAAATCAAAATTCATATCACA
*
5291936 TTTATCTATATAATTATACAAAATCCAAATTCATATCACA
1 TTTATCTATATAATTATACAAAATCAAAATTCATATCACA
5291976 TT
1 TT
5291978 ACATATTTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (40 bp):
TTTATCTATATAATTATACAAAATCAAAATTCATATCACA
Found at i:5298133 original size:65 final size:63
Alignment explanation
Indices: 5298059--5298224 Score: 174
Period size: 65 Copynumber: 2.6 Consensus size: 63
5298049 AAATAGCCAG
* *
5298059 AGTGTATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTC-A-TAAAATCC
1 AGTGCATCGATGCATGG-TGGTGCATCGATGCATCAAATGCATTCGATG--TTCAATTAAAATCA
5298122 T
63 T
* * * * * *
5298123 CAGTGCATCGATGTATGGTATGTGCATCGATGCATGAAATGCATTCTATGTTCAATTTAATTCAT
1 -AGTGCATCGATGCATGGT-GGTGCATCGATGCATCAAATGCATTCGATGTTCAATTAAAATCAT
*
5298188 AGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 AGTGCATCGATGCATGG--TGGTGCATCGATGCATCA
5298225 CTTTGATAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
63 3 0.04
64 18 0.21
65 62 0.74
66 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.33
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTGGTGCATCGATGCATCAAATGCATTCGATGTTCAATTAAAATCAT
Found at i:5298902 original size:14 final size:15
Alignment explanation
Indices: 5298883--5298911 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5298873 TCAAGCATTT
5298883 AACAATCCA-AAACA
1 AACAATCCAGAAACA
5298897 AACAATCCAGAAACA
1 AACAATCCAGAAACA
5298912 TCAAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.28, G:0.03, T:0.07
Consensus pattern (15 bp):
AACAATCCAGAAACA
Found at i:5299740 original size:15 final size:15
Alignment explanation
Indices: 5299722--5299754 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5299712 TTTCATTATA
5299722 TAACCCATCATCATC
1 TAACCCATCATCATC
5299737 TAACCCATCATCATC
1 TAACCCATCATCATC
5299752 TAA
1 TAA
5299755 ACCAAAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (15 bp):
TAACCCATCATCATC
Found at i:5300585 original size:20 final size:21
Alignment explanation
Indices: 5300542--5300625 Score: 116
Period size: 21 Copynumber: 4.0 Consensus size: 21
5300532 CGTTAGGCAT
5300542 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
5300563 GGGGGAATCGGTACCCACTGG
1 GGGGGAATCGGTACCCCCTGG
** *
5300584 GGGGGAATTTGTTCCCCCT-G
1 GGGGGAATCGGTACCCCCTGG
*
5300604 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
5300625 G
1 G
5300626 CAATCTGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 18 0.33
21 37 0.67
ACGTcount: A:0.14, C:0.26, G:0.40, T:0.19
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:5304062 original size:21 final size:21
Alignment explanation
Indices: 5304037--5304079 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5304027 CCGTTAGACA
*
5304037 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCATGG
*
5304058 GGGGGAATCTGTACCCCATGG
1 GGGGGAATCGGTACCCCATGG
5304079 G
1 G
5304080 CAATCTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.26, G:0.42, T:0.16
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCATGG
Found at i:5305357 original size:21 final size:21
Alignment explanation
Indices: 5305328--5305399 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
5305318 CAAGGCGTGC
*
5305328 ATCGGTGCACCTTCATGGTGT
1 ATCGATGCACCTTCATGGTGT
* * *
5305349 ATCGATGCACATTCAAGGATGC
1 ATCGATGCACCTTCATGG-TGT
*
5305371 ATCGATGCA-CTGTTAT-GTGT
1 ATCGATGCACCT-TCATGGTGT
5305391 ATCGATGCA
1 ATCGATGCA
5305400 TGAAGCACAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 11 0.27
21 17 0.41
22 13 0.32
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (21 bp):
ATCGATGCACCTTCATGGTGT
Found at i:5305372 original size:43 final size:43
Alignment explanation
Indices: 5305281--5305399 Score: 118
Period size: 43 Copynumber: 2.8 Consensus size: 43
5305271 AACCCGATCG
* * * **
5305281 ATGCATCGATGCA-TGGCCTTGTGCATCGATATACATTCAAGGC
1 ATGCATCGATGCACT-GTCATGTGTATCGATGCACATTCAAGGC
* *
5305324 GTGCATCGGTGCACCT-TCATGGTGTATCGATGCACATTCAAGG-
1 ATGCATCGATGCA-CTGTCAT-GTGTATCGATGCACATTCAAGGC
*
5305367 ATGCATCGATGCACTGTTATGTGTATCGATGCA
1 ATGCATCGATGCACTGTCATGTGTATCGATGCA
5305400 TGAAGCACAA
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
42 15 0.24
43 27 0.44
44 19 0.31
45 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (43 bp):
ATGCATCGATGCACTGTCATGTGTATCGATGCACATTCAAGGC
Found at i:5305398 original size:42 final size:44
Alignment explanation
Indices: 5305313--5305399 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 44
5305303 GCATCGATAT
* *
5305313 ACATTCAAGGCGTGCATCGGTGCACCTTCATGGTGTATCGATGC
1 ACATTCAAGGCATGCATCGATGCACCTTCATGGTGTATCGATGC
*
5305357 ACATTCAAGG-ATGCATCGATGCA-CTGTTAT-GTGTATCGATGC
1 ACATTCAAGGCATGCATCGATGCACCT-TCATGGTGTATCGATGC
5305399 A
1 A
5305400 TGAAGCACAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
42 15 0.38
43 14 0.36
44 10 0.26
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (44 bp):
ACATTCAAGGCATGCATCGATGCACCTTCATGGTGTATCGATGC
Found at i:5311324 original size:65 final size:65
Alignment explanation
Indices: 5311191--5311351 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
5311181 TGCACTAAGA
* * *
5311191 GTGCATCGATGCATCAAGTGCATTTGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
* *
5311255 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCACAGTGCATCGATGCATGGCT
*
5311318 AT
65 -G
*
5311320 GTGCATCGATGCATGAAATGCATTCGATGTTT
1 GTGCATCGATGCATCAAATGCATTCGATGTTT
5311352 AATTTAATTC
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 28 0.32
65 56 0.64
66 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:5311390 original size:65 final size:65
Alignment explanation
Indices: 5311191--5311400 Score: 180
Period size: 65 Copynumber: 3.2 Consensus size: 65
5311181 TGCACTAAGA
* * * ** * * *
5311191 GTGCATCGATGCATCAAGTGCATTTGATGTTTCAA-AATAGCCA-GAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAA-AATCATCAGTGCATCAATGCAT-GAT
*
5311254 -G
64 AT
* * * *
5311255 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGATGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAAAATCATCAGTGCATCAATGCATGATAT
* * *
5311320 GTGCATCGATGCATGAAATGCATTCGATG-TTTAATTTAATTCAT-AGTGCATCAATGCATAGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTAA-TAAAATCATCAGTGCATCAATGCAT-GAT
5311383 -T
64 AT
*
5311384 GATGCATCGGTGCATCA
1 G-TGCATCGATGCATCA
5311401 CTTTGATAAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
64 55 0.45
65 66 0.55
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTAATAAAATCATCAGTGCATCAATGCATGATAT
Found at i:5312258 original size:15 final size:16
Alignment explanation
Indices: 5312232--5312272 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
5312222 AATATTCATT
5312232 TTAAATATATTATAAA
1 TTAAATATATTATAAA
*
5312248 TTAAATA-ATTATGAA
1 TTAAATATATTATAAA
5312263 TTACAATATA
1 TTA-AATATA
5312273 ATTTTATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 10 0.45
16 11 0.50
17 1 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
TTAAATATATTATAAA
Found at i:5313739 original size:4 final size:4
Alignment explanation
Indices: 5313730--5313758 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
5313720 CAACCACACG
5313730 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
5313759 CAACTGAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:5315762 original size:13 final size:12
Alignment explanation
Indices: 5315728--5315752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5315718 TCTAATAAAA
5315728 AAATAATATTTT
1 AAATAATATTTT
5315740 AAATAATATTTT
1 AAATAATATTTT
5315752 A
1 A
5315753 CCAAAATATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:5319865 original size:44 final size:44
Alignment explanation
Indices: 5319817--5319913 Score: 131
Period size: 44 Copynumber: 2.2 Consensus size: 44
5319807 GAACTAGAAG
* * *
5319817 GCCAAAGGTTAATGATTCTTCTACTGTTTTTTTTAGTGTTGGAA
1 GCCAAAGATTAATGATTATTCTACTGTTTTTGTTAGTGTTGGAA
* * * *
5319861 GCCAAAGATTAATGTTTATTTTTCTGTTTTTGTTAGTTTTGGAA
1 GCCAAAGATTAATGATTATTCTACTGTTTTTGTTAGTGTTGGAA
5319905 GCCAAAGAT
1 GCCAAAGAT
5319914 GGAACCATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (44 bp):
GCCAAAGATTAATGATTATTCTACTGTTTTTGTTAGTGTTGGAA
Found at i:5321463 original size:44 final size:44
Alignment explanation
Indices: 5321393--5321494 Score: 152
Period size: 44 Copynumber: 2.3 Consensus size: 44
5321383 CTCAGAACTA
* *
5321393 GGAAGCCAAA-AGTTAATGATTCTTTTGCCGTTTTTGTTAGTGTT
1 GGAAGCCAAAGA-TTAATGATTATTTTGACGTTTTTGTTAGTGTT
* *
5321437 GGAAGCCAAAGATTAATGTTTATTTTGATGTTTTTGTTAGTGTT
1 GGAAGCCAAAGATTAATGATTATTTTGACGTTTTTGTTAGTGTT
5321481 GGAAGCCAAAGATT
1 GGAAGCCAAAGATT
5321495 CTGCTTTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 52 0.98
45 1 0.02
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (44 bp):
GGAAGCCAAAGATTAATGATTATTTTGACGTTTTTGTTAGTGTT
Found at i:5321704 original size:42 final size:42
Alignment explanation
Indices: 5321650--5321753 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
5321640 AATTTTCGTG
* * *
5321650 TGTTTCGCGTAATTCGTTTTTCGAAAAATATTTTCTCGTGTT
1 TGTTTCACGTAATTCGTTTTTCGAAAAATATTTTCCCATGTT
*
5321692 TGTTTCACGTAATTCGTTTTTTGAAAAATATTTTCCCATGTT
1 TGTTTCACGTAATTCGTTTTTCGAAAAATATTTTCCCATGTT
* *
5321734 TGTTTAACGTAATTGGTTTT
1 TGTTTCACGTAATTCGTTTT
5321754 CCGGAATGTA
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.21, C:0.12, G:0.15, T:0.51
Consensus pattern (42 bp):
TGTTTCACGTAATTCGTTTTTCGAAAAATATTTTCCCATGTT
Found at i:5321978 original size:22 final size:23
Alignment explanation
Indices: 5321953--5322095 Score: 81
Period size: 28 Copynumber: 5.5 Consensus size: 23
5321943 ATTTATTTAT
5321953 TAATATTTATAATAATATAAT-A
1 TAATATTTATAATAATATAATAA
5321975 TAATATTTATAATATTATATAAATAA
1 TAATATTTATAATA--ATAT-AATAA
*
5322001 TCAATTATATTATAATAATATAAGATAT
1 T-AA-TAT-TTATAATAATAT-A-ATAA
*
5322029 TATATTTTTATTTTAATAATATATATAA
1 TA-ATATTTA---TAATAATATA-ATAA
*
5322057 TAAAATTTATATATTTAATAATGAATAA
1 TAATATTTATA-A--TAAT-AT-AATAA
*
5322085 TATTATTTATA
1 TAATATTTATA
5322096 TATTTAAATT
Statistics
Matches: 96, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
22 14 0.15
24 6 0.06
25 4 0.04
26 5 0.05
27 20 0.21
28 29 0.30
29 18 0.19
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (23 bp):
TAATATTTATAATAATATAATAA
Found at i:5322137 original size:23 final size:23
Alignment explanation
Indices: 5322095--5322156 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
5322085 TATTATTTAT
*
5322095 ATATTTAAATTATATTTTAATAAAG
1 ATATTTAAA--ATATATTAATAAAG
* *
5322120 ATATTTAAAATATATTAATTAAT
1 ATATTTAAAATATATTAATAAAG
5322143 AT-TTATAAAATATA
1 ATATT-TAAAATATA
5322157 ATATAACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 2 0.06
23 22 0.67
25 9 0.27
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTTAAAATATATTAATAAAG
Found at i:5324528 original size:31 final size:32
Alignment explanation
Indices: 5324466--5324543 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 32
5324456 TTGGGGTCGT
* *
5324466 AGGGCCTACCTAAGAATACATCTTAGGGCCGC
1 AGGGCCTACCCAAGAATACATCTCAGGGCCGC
* *
5324498 AGGGCCTACCCGAGAAT-GATCTCAGGGCCGC
1 AGGGCCTACCCAAGAATACATCTCAGGGCCGC
* *
5324529 AGAGCCTACCTAAGA
1 AGGGCCTACCCAAGA
5324544 GTCACATTAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.62
32 15 0.38
ACGTcount: A:0.28, C:0.29, G:0.27, T:0.15
Consensus pattern (32 bp):
AGGGCCTACCCAAGAATACATCTCAGGGCCGC
Found at i:5333319 original size:18 final size:18
Alignment explanation
Indices: 5333296--5333348 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
5333286 AGGGATTATC
5333296 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
5333314 AGTGGTTCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
5333332 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
5333349 AATATTCAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.34, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:5339442 original size:22 final size:22
Alignment explanation
Indices: 5339412--5339456 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5339402 TTTATTTCAT
* *
5339412 AATTATTTATTTTTAATCATTA
1 AATTATTTATTTTCAACCATTA
*
5339434 AATTGTTTATTTTCAACCATTA
1 AATTATTTATTTTCAACCATTA
5339456 A
1 A
5339457 GTTACAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTATTTATTTTCAACCATTA
Found at i:5339530 original size:32 final size:32
Alignment explanation
Indices: 5339465--5339552 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
5339455 AAGTTACAAC
* * *
5339465 AAATTTTAATTTAAC--CT-ATTGTTTTAAAT
1 AAATATTAATTTAACTTCTAATTTTTTTAAAA
5339494 AAATATTAATTTAACTTCTAATTTTTTTAAAA
1 AAATATTAATTTAACTTCTAATTTTTTTAAAA
* *
5339526 AAATATTAATTTATATTTTTAATTTTT
1 AAATATTAATTTA-ACTTCTAATTTTT
5339553 AAATAAAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
29 14 0.28
31 2 0.04
32 23 0.46
33 11 0.22
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.55
Consensus pattern (32 bp):
AAATATTAATTTAACTTCTAATTTTTTTAAAA
Found at i:5339561 original size:32 final size:32
Alignment explanation
Indices: 5339465--5339571 Score: 100
Period size: 32 Copynumber: 3.4 Consensus size: 32
5339455 AAGTTACAAC
*
5339465 AAATTTTAATTTAAC--CT-ATTGTTTTAAAT-
1 AAATATTAATTTAACTTCTAATT-TTTTAAATA
5339494 AAATATTAATTTAACTTCTAATTTTTTTAAA-A
1 AAATATTAATTTAACTTCTAA-TTTTTTAAATA
* *
5339526 AAATATTAATTTATATTTTTAA-TTTTTAAATA
1 AAATATTAATTTA-ACTTCTAATTTTTTAAATA
**
5339558 AAATACCAATTTAA
1 AAATATTAATTTAA
5339572 TCTTTAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
29 14 0.21
31 11 0.17
32 33 0.50
33 8 0.12
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.50
Consensus pattern (32 bp):
AAATATTAATTTAACTTCTAATTTTTTAAATA
Found at i:5339578 original size:31 final size:32
Alignment explanation
Indices: 5339486--5339578 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 32
5339476 TAACCTATTG
5339486 TTTTAAAT-AAATATTAATTTAA-CTTCTAATTT
1 TTTTAAATAAAATATTAATTTAATCTT-TAA-TT
*
5339518 TTTTAAA-AAAATATTAATTTATATTTTTAA-T
1 TTTTAAATAAAATATTAATTTA-ATCTTTAATT
**
5339549 TTTTAAATAAAATACCAATTTAATCTTTAA
1 TTTTAAATAAAATATTAATTTAATCTTTAA
5339579 ATTCGACCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
31 15 0.28
32 32 0.60
33 4 0.08
34 2 0.04
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTTAAATAAAATATTAATTTAATCTTTAATT
Found at i:5348548 original size:165 final size:165
Alignment explanation
Indices: 5348276--5348606 Score: 653
Period size: 165 Copynumber: 2.0 Consensus size: 165
5348266 AGTTGAGGCC
5348276 TGCAAAATGAACTAACTGATTATCAATTTGATTGCTAATGTTAATTCATAAAAGTTCCAATCTTC
1 TGCAAAATGAACTAACTGATTATCAATTTGATTGCTAATGTTAATTCATAAAAGTTCCAATCTTC
5348341 TCTGTTGTGAAAAAGAATAATTTATTTGGAAATTTGGGTTGTGGTTATGCCGAAAAAGGGGGTTT
66 TCTGTTGTGAAAAAGAATAATTTATTTGGAAATTTGGGTTGTGGTTATGCCGAAAAAGGGGGTTT
5348406 CCTGGACATGTTTCGGCATCAAACTTTACTTGTTT
131 CCTGGACATGTTTCGGCATCAAACTTTACTTGTTT
*
5348441 TGCAAAATGAACTAACTGGTTATCAATTTGATTGCTAATGTTAATTCATAAAAGTTCCAATCTTC
1 TGCAAAATGAACTAACTGATTATCAATTTGATTGCTAATGTTAATTCATAAAAGTTCCAATCTTC
5348506 TCTGTTGTGAAAAAGAATAATTTATTTGGAAATTTGGGTTGTGGTTATGCCGAAAAAGGGGGTTT
66 TCTGTTGTGAAAAAGAATAATTTATTTGGAAATTTGGGTTGTGGTTATGCCGAAAAAGGGGGTTT
5348571 CCTGGACATGTTTCGGCATCAAACTTTACTTGTTT
131 CCTGGACATGTTTCGGCATCAAACTTTACTTGTTT
5348606 T
1 T
5348607 AGAAATTTAG
Statistics
Matches: 165, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 165 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (165 bp):
TGCAAAATGAACTAACTGATTATCAATTTGATTGCTAATGTTAATTCATAAAAGTTCCAATCTTC
TCTGTTGTGAAAAAGAATAATTTATTTGGAAATTTGGGTTGTGGTTATGCCGAAAAAGGGGGTTT
CCTGGACATGTTTCGGCATCAAACTTTACTTGTTT
Found at i:5350292 original size:9 final size:10
Alignment explanation
Indices: 5350252--5350292 Score: 50
Period size: 9 Copynumber: 4.1 Consensus size: 10
5350242 TTATATTTTG
5350252 TTCTATATAT
1 TTCTATATAT
5350262 TTCAATATATAT
1 TTC--TATATAT
5350274 TTCT-TATAT
1 TTCTATATAT
5350283 TTCTAT-TAT
1 TTCTATATAT
5350292 T
1 T
5350293 ATTTTTATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
9 13 0.46
10 5 0.18
12 10 0.36
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (10 bp):
TTCTATATAT
Done.