Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007867.1 Hibiscus syriacus cultivar Beakdansim tig00110239_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: 3477501
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:2523874 original size:2 final size:2
Alignment explanation
Indices: 2523867--2523891 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2523857 TCCCAATGAC
2523867 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2523892 ACTTTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2527857 original size:20 final size:19
Alignment explanation
Indices: 2527826--2527863 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2527816 GACTAATATC
*
2527826 ATATATTCATATTTTTATG
1 ATATATTCATATATTTATG
2527845 ATATATATCATATATTTAT
1 ATATAT-TCATATATTTAT
2527864 AATAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
ATATATTCATATATTTATG
Found at i:2527872 original size:20 final size:20
Alignment explanation
Indices: 2527832--2527872 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2527822 TATCATATAT
* * *
2527832 TCATATTTTTATGATATATA
1 TCATATATTTATAATAAATA
2527852 TCATATATTTATAATAAATA
1 TCATATATTTATAATAAATA
2527872 T
1 T
2527873 AAAATTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (20 bp):
TCATATATTTATAATAAATA
Found at i:2530533 original size:18 final size:17
Alignment explanation
Indices: 2530512--2530553 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2530502 AAATATTTTG
2530512 AATAAAAAAATGAAAATA
1 AATAAAAAAA-GAAAATA
*
2530530 AATAGAATAAAGAAAATA
1 AATA-AAAAAAGAAAATA
2530548 AA-AAAA
1 AATAAAA
2530554 CGACCGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.10
17 1 0.05
18 13 0.62
19 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (17 bp):
AATAAAAAAAGAAAATA
Found at i:2531199 original size:23 final size:23
Alignment explanation
Indices: 2531173--2531241 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
2531163 CACCACAGCT
*
2531173 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
2531196 CGTAGAATTGCA-CAAGAGTGTCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
2531219 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2531242 TATAATAATG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
22 2 0.06
23 33 0.92
24 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2536453 original size:23 final size:22
Alignment explanation
Indices: 2536427--2536495 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
2536417 CACCACAGCT
*
2536427 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCA-CGAAGTGCCA
* *
2536450 CGTAGAATTGCACCAGAGTGCCG
1 CGTAGAATTGCACGA-AGTGCCA
*
2536473 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCA-CGAAGTGCCA
2536496 TATAATAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 2 0.05
23 35 0.92
24 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.22
Consensus pattern (22 bp):
CGTAGAATTGCACGAAGTGCCA
Found at i:2539163 original size:168 final size:168
Alignment explanation
Indices: 2538879--2539273 Score: 589
Period size: 168 Copynumber: 2.3 Consensus size: 168
2538869 AGTGTAATCG
* * *
2538879 AACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCC
1 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
* *
2538944 TTGAAGCTGAGTGTAATCGAAATCGAAGATCTTTGGTTGGCAGATAGCCCTTCTTGA-CTT-ATG
66 TCGAAGCTGAGTGTAATCGAAATCGAAGATCTTTGGTTGGCAGATAGCCCTTC-TAACCTTGA-G
* * * *
2539007 CTATGCTACAAATGATGTGTCTTTGAGCTGATCGTAGTCA
129 CTATGCTACAAATGATATGCCTTGGAGCTGAACGTAGTCA
2539047 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
1 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
* *
2539112 TCGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGG-TGGCAGATAGCCCTTCTAACCTTGAGC
66 TCGAAGCTGAGTGTAATCGAAATCGAAGATC-TTTGGTTGGCAGATAGCCCTTCTAACCTTGAGC
*
2539176 TATGCTGCAAATGATATGCCTTGGAGCTGAACGTAGTCA
130 TATGCTACAAATGATATGCCTTGGAGCTGAACGTAGTCA
* * * *
2539215 AACTCGAAGGTCTTTTGGTGGCAGATAGCCCATCTAGCCTTGAGCTATGCTGCAAATGA
1 AACTCGAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
2539274 ACACGATATC
Statistics
Matches: 207, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
167 2 0.01
168 157 0.76
169 48 0.23
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (168 bp):
AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCC
TCGAAGCTGAGTGTAATCGAAATCGAAGATCTTTGGTTGGCAGATAGCCCTTCTAACCTTGAGCT
ATGCTACAAATGATATGCCTTGGAGCTGAACGTAGTCA
Found at i:2539224 original size:84 final size:84
Alignment explanation
Indices: 2538866--2539273 Score: 482
Period size: 84 Copynumber: 4.8 Consensus size: 84
2538856 CACTTGGAGC
* * * * * * * *
2538866 CTGAGTGTAATCGAACTCAAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
1 CTGAGCGTAATCAAACTCGAAGGTCTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGC
2538931 AAATGATGTGCCCTTGAAG
66 AAATGATGTGCCCTTGAAG
* * * *
2538950 CTGAGTGTAATCGAAA-TCGAAGATCTTTGGTTGGCAGATAGCCCTTCTTGACTT-ATGCTATGC
1 CTGAGCGTAATC-AAACTCGAAGGTCTTTGG-TGGCAGATAGCCCTTCTAGCCTTGA-GCTATGC
* * *
2539013 TACAAATGATGTGTCTTTG-AG
63 TGCAAATGATGTGCCCTTGAAG
* * * * *
2539034 CTGATCGTAGTCAAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGC
1 CTGAGCGTAATCAAACTCGAAGGTCTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGC
*
2539099 AAATGATGTGCCCTCGAAG
66 AAATGATGTGCCCTTGAAG
* * *
2539118 CTGAGTGTAATCGAACTCGAAGGTCTTTTGGTGGCAGATAGCCCTTCTAACCTTGAGCTATGCTG
1 CTGAGCGTAATCAAACTCGAAGGTC-TTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTG
* *
2539183 CAAATGATATG-CCTTGGAG
65 CAAATGATGTGCCCTTGAAG
* * *
2539202 CTGAACGTAGTCAAACTCGAAGGTCTTTTGGTGGCAGATAGCCCATCTAGCCTTGAGCTATGCTG
1 CTGAGCGTAATCAAACTCGAAGGTC-TTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTG
2539267 CAAATGA
65 CAAATGA
2539274 ACACGATATC
Statistics
Matches: 274, Mismatches: 43, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
83 44 0.16
84 143 0.52
85 87 0.32
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
CTGAGCGTAATCAAACTCGAAGGTCTTTGGTGGCAGATAGCCCTTCTAGCCTTGAGCTATGCTGC
AAATGATGTGCCCTTGAAG
Found at i:2539584 original size:43 final size:43
Alignment explanation
Indices: 2539537--2539680 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
2539527 CGTCATGAAG
* * * * *
2539537 TTGAAATCGTGGATGCGTGGGCACGATATCCTCTGTCGTGGAA
1 TTGAAATCATGGATGTGTGGGTACGATATCCTCCGTCGTAGAA
* *
2539580 TTGAAATCTTGGA-GTTGTGGGTACGATATCCTCCGTCGTAGAG
1 TTGAAATCATGGATG-TGTGGGTACGATATCCTCCGTCGTAGAA
* * * *
2539623 TTGAAATCATGGATTTGTGGGTACGATATCCTCCTTTGTAGAG
1 TTGAAATCATGGATGTGTGGGTACGATATCCTCCGTCGTAGAA
* *
2539666 TTAAAATCGTGGATG
1 TTGAAATCATGGATG
2539681 GCCCCTTCGT
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
42 1 0.01
43 85 0.99
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (43 bp):
TTGAAATCATGGATGTGTGGGTACGATATCCTCCGTCGTAGAA
Found at i:2545754 original size:12 final size:12
Alignment explanation
Indices: 2545729--2545785 Score: 75
Period size: 12 Copynumber: 4.9 Consensus size: 12
2545719 GGCTAAGAAA
2545729 AAAATAATAA-T
1 AAAATAATAATT
2545740 AAAATAATAATT
1 AAAATAATAATT
*
2545752 AAAGTAATAATT
1 AAAATAATAATT
2545764 AAAAT-AT-ATT
1 AAAATAATAATT
2545774 AAAAGTAATAAT
1 AAAA-TAATAAT
2545786 AATATTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
10 7 0.17
11 13 0.32
12 18 0.45
13 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.32
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:2545759 original size:23 final size:22
Alignment explanation
Indices: 2545728--2545787 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 22
2545718 AGGCTAAGAA
*
2545728 AAAAATAATAATAAAATAATAATT
1 AAAAGTAATAATAAAAT-AT-ATT
2545752 -AAAGTAATAATTAAAATATATT
1 AAAAGTAATAA-TAAAATATATT
2545774 AAAAGTAATAATAA
1 AAAAGTAATAATAA
2545788 TATTACAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 6 0.18
23 21 0.64
24 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (22 bp):
AAAAGTAATAATAAAATATATT
Found at i:2545820 original size:4 final size:5
Alignment explanation
Indices: 2545729--2545833 Score: 50
Period size: 5 Copynumber: 18.8 Consensus size: 5
2545719 GGCTAAGAAA
* * *
2545729 AAAAT AATAAT AAAAT AATAATT AAAGT AATAATT AAAAT ATATT AAAAGT
1 AAAAT AA-AAT AAAAT AA-AA-T AAAAT AA-AA-T AAAAT AAAAT AAAA-T
* *
2545780 AATAAT AATATT ACAAAT AAGTAAT GAAAT AAAAT -AAAT AAAAT AAAATT
1 AA-AAT AA-AAT A-AAAT AA--AAT AAAAT AAAAT AAAAT AAAAT AAAA-T
2545830 AAAA
1 AAAA
2545834 CTACAATCTA
Statistics
Matches: 78, Mismatches: 10, Indels: 23
0.70 0.09 0.21
Matches are distributed among these distances:
4 4 0.05
5 32 0.41
6 29 0.37
7 13 0.17
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (5 bp):
AAAAT
Found at i:2546191 original size:14 final size:14
Alignment explanation
Indices: 2546158--2546193 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2546148 TTGGGAAAGT
*
2546158 ATTAAAATAAAACA
1 ATTAAATTAAAACA
2546172 ATTTAAATTAAAACA
1 A-TTAAATTAAAACA
2546187 ATTAAAT
1 ATTAAAT
2546194 CATATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAATTAAAACA
Found at i:2547446 original size:3 final size:3
Alignment explanation
Indices: 2547438--2547511 Score: 107
Period size: 3 Copynumber: 24.3 Consensus size: 3
2547428 ATTTTTTATT
2547438 TAA TAA TAA TAA T-A TAA TAA TAA TAA TATA TATA TAA TAA TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TA-A
2547485 TAA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2547512 GAAAAAAATT
Statistics
Matches: 67, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.06
3 53 0.79
4 10 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:2547460 original size:17 final size:16
Alignment explanation
Indices: 2547438--2547511 Score: 116
Period size: 17 Copynumber: 4.6 Consensus size: 16
2547428 ATTTTTTATT
2547438 TAATAATAATAATATAA
1 TAATAATAAT-ATATAA
2547455 TAATAATAATATATATA
1 TAATAATAATATATA-A
2547472 TAATAATAATATATAA
1 TAATAATAATATATAA
2547488 T-ATAATAATA-ATAA
1 TAATAATAATATATAA
2547502 TAATAATAAT
1 TAATAATAAT
2547512 GAAAAAAATT
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.09
15 17 0.31
16 7 0.13
17 26 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAATAATAATATATAA
Found at i:2547695 original size:45 final size:45
Alignment explanation
Indices: 2547631--2548748 Score: 1434
Period size: 45 Copynumber: 24.8 Consensus size: 45
2547621 GATGGAAATG
*
2547631 TTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
2547676 TTTGAAAATATCATGCACTGAAGGGCTTATAGACGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
* *
2547722 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCAGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
2547767 TTTGAAAACATCATGCACTGAAGGGCTTATAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
2547812 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
2547857 TTTGAGAACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
2547902 TTTAAAAACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
2547947 TTTGAAGACATCAAGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
2547992 TTTGAAGACATCAAGCACTGAAGGACTTACAAATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
2548037 TTTGAAGACATTAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * * *
2548082 TTTGAAGACATCAAGTACTGAAGGACTTACAAATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
2548127 TTTGTAGACATCATGCACTGAAGGGCTTACAGATAACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * *
2548172 TTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGA
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * * ** * * *
2548217 CTT----ACA-GATG-ACCCGAAGGTTTTGA-AGACATCAAGCACTGAAGGA
1 TTTGAAAACATCATGCA-CTGAAGGGCTT-ACAG--AT-GA-C-CCGAAGGT
* * * *
2548262 CTT----ACA-GATG-ACCCGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCA-CTGAAGGGCTTACAGATGACCCGAAGGT
* * *
2548302 TTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
2548347 TTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
2548392 TTTGATTTTGAAGACCTCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGA-----AA-ACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
*
2548443 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* *
2548488 TTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCCGAAAGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
2548533 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
* * *
2548578 TTTGAAAACATCAAGCAATGAAGGACTTACAGATGACCCGAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
** * * *
2548623 TTTGAAAACATCAACCACTGAAGGACTTACAAATGACCCAAAGGT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
2548668 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-T
2548714 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
1 TTTGAAAACATCATGCACTGAAGGGCTTACAGATG
2548749 TTGGAAATAG
Statistics
Matches: 974, Mismatches: 77, Indels: 43
0.89 0.07 0.04
Matches are distributed among these distances:
39 1 0.00
40 20 0.02
41 5 0.01
42 3 0.00
43 3 0.00
44 5 0.01
45 815 0.84
46 79 0.08
50 1 0.00
51 42 0.04
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (45 bp):
TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGT
Found at i:2548216 original size:20 final size:20
Alignment explanation
Indices: 2548191--2548300 Score: 123
Period size: 20 Copynumber: 5.2 Consensus size: 20
2548181 ATCAAGCACT
2548191 GAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCC
2548211 GAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCC
** * *
2548231 GAAGGTTTTGA-AGACATCAAGCACT
1 GAAGGACTT-ACAG--AT-GA-C-CC
2548256 GAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCC
2548276 GAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCC
2548296 GAAGG
1 GAAGG
2548301 TTTTGAAGAC
Statistics
Matches: 75, Mismatches: 8, Indels: 14
0.77 0.08 0.14
Matches are distributed among these distances:
20 55 0.73
21 2 0.03
22 3 0.04
23 3 0.04
24 2 0.03
25 10 0.13
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.16
Consensus pattern (20 bp):
GAAGGACTTACAGATGACCC
Found at i:2548223 original size:65 final size:65
Alignment explanation
Indices: 2548146--2548345 Score: 382
Period size: 65 Copynumber: 3.1 Consensus size: 65
2548136 ATCATGCACT
* *
2548146 GAAGGGCTTACAGATAACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
2548211 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
2548276 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
2548341 GAAGG
1 GAAGG
2548346 TTTTGAAGAC
Statistics
Matches: 133, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 133 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.18
Consensus pattern (65 bp):
GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
Found at i:2548249 original size:110 final size:110
Alignment explanation
Indices: 2548101--2548441 Score: 379
Period size: 110 Copynumber: 3.0 Consensus size: 110
2548091 ATCAAGTACT
* * *
2548101 GAAGGACTTACAAATGACCCGAAGGTTTTGTAGACATCATGCACTGAAGGGCTTACAGATAACCC
1 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCC
2548166 GAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
66 GAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
* *
2548211 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
1 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCC
** * * *** * *
2548276 GAAGGACTT-ACAGATGACCCGAAGGTTTTGAA-GACAT-CA-A-G-CACT
66 GAAGGTTTTGA-AGA-CA-TC-AA-GCACTGAAGGACTTACAGATGAC-CC
2548321 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCC
1 GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCC
* * *
2548386 GAAGGTTTTGATTTTGAAGACCTCATGCACTGAAGGGCTTACAGATGACCC
66 GAA-G----G-TTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
2548437 GAAGG
1 GAAGG
2548442 TTTTGAAAAC
Statistics
Matches: 185, Mismatches: 28, Indels: 30
0.76 0.12 0.12
Matches are distributed among these distances:
109 2 0.01
110 138 0.75
111 3 0.02
112 8 0.04
113 10 0.05
114 8 0.04
115 2 0.01
116 12 0.06
117 2 0.01
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (110 bp):
GAAGGACTTACAGATGACCCGAAGGTTTTGAAGACATCATGCACTGAAGGGCTTACAGATGACCC
GAAGGTTTTGAAGACATCAAGCACTGAAGGACTTACAGATGACCC
Found at i:2549434 original size:22 final size:22
Alignment explanation
Indices: 2549409--2549488 Score: 85
Period size: 22 Copynumber: 3.6 Consensus size: 22
2549399 AATAAAGCTT
*
2549409 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAAAGAGAATCTA
*
2549431 TCATCTTT--AAAGAGATAGGCTA
1 TCATCTTTGAAAAGAGA-A-TCTA
*
2549453 TCATCTTTGAAGAA-AGAGTCTA
1 TCATCTTTGAA-AAGAGAATCTA
2549475 TCATCTTTGAAAAG
1 TCATCTTTGAAAAG
2549489 TGTAGATGTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.15
21 3 0.06
22 32 0.67
24 4 0.08
25 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:2550854 original size:75 final size:75
Alignment explanation
Indices: 2550725--2550890 Score: 237
Period size: 75 Copynumber: 2.2 Consensus size: 75
2550715 TATGACGATG
* * * * *
2550725 TGGGCTTTCAGCATGTCCCAACATTGGCTAATACAAATGTTCAAAATGTTTCAACATTCTTGATT
1 TGGGCTTTCAGCATGCCCCAACATTAGCTAATACAAACGTTCAAAATGTGTCAACATTCCTG-TT
*
2550790 C-TGATTGAAA
65 CATGAATGAAA
*
2550800 -GAGGTTTTCAGCATGCCCCAACATTAGCTAATACAAACGTTCAAAATGTGTCAACATTCCTGTT
1 TG-GGCTTTCAGCATGCCCCAACATTAGCTAATACAAACGTTCAAAATGTGTCAACATTCCTGTT
2550864 CATGAATGAAA
65 CATGAATGAAA
2550875 TGGGCTTTCAGCATGC
1 TGGGCTTTCAGCATGC
2550891 TTCATCATTT
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
74 4 0.05
75 75 0.94
76 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (75 bp):
TGGGCTTTCAGCATGCCCCAACATTAGCTAATACAAACGTTCAAAATGTGTCAACATTCCTGTTC
ATGAATGAAA
Found at i:2554515 original size:21 final size:21
Alignment explanation
Indices: 2554489--2554528 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2554479 CAGAACCCCA
*
2554489 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
2554510 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
2554529 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:2554557 original size:20 final size:21
Alignment explanation
Indices: 2554511--2554571 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2554501 TTCCCCTGTG
2554511 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2554534 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2554554 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2554572 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2563643 original size:8 final size:8
Alignment explanation
Indices: 2563632--2563727 Score: 84
Period size: 8 Copynumber: 12.9 Consensus size: 8
2563622 CTTTATTCTT
2563632 CTTTTTTC
1 CTTTTTTC
2563640 CTTTTTT-
1 CTTTTTTC
*
2563647 TTCTTTTTC
1 CT-TTTTTC
2563656 C-TTTTTC
1 CTTTTTTC
2563663 CTTTTTTTC
1 C-TTTTTTC
2563672 C-TTTTTC
1 CTTTTTTC
2563679 CTTTTTTC
1 CTTTTTTC
2563687 C-TTTTTC
1 CTTTTTTC
*
2563694 GTTTTTT-
1 CTTTTTTC
*
2563701 C-GTTTT-
1 CTTTTTTC
2563707 -TTTTTT-
1 CTTTTTTC
2563713 CTTTTTTC
1 CTTTTTTC
2563721 CTTTTTT
1 CTTTTTT
2563728 TCAAGTATAA
Statistics
Matches: 73, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
6 8 0.11
7 27 0.37
8 31 0.42
9 7 0.10
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (8 bp):
CTTTTTTC
Found at i:2563644 original size:7 final size:7
Alignment explanation
Indices: 2563643--2563726 Score: 82
Period size: 7 Copynumber: 11.7 Consensus size: 7
2563633 TTTTTTCCTT
*
2563643 TTTTTTC
1 TTTTTCC
2563650 TTTTTCC
1 TTTTTCC
2563657 TTTTTCC
1 TTTTTCC
2563664 TTTTTTTCC
1 --TTTTTCC
2563673 TTTTTCC
1 TTTTTCC
2563680 TTTTTTCC
1 -TTTTTCC
*
2563688 TTTTTCGT
1 TTTTTC-C
*
2563696 TTTTTCG
1 TTTTTCC
2563703 TTTTT--
1 TTTTTCC
*
2563708 TTTTTCT
1 TTTTTCC
2563715 TTTTTCC
1 TTTTTCC
2563722 TTTTT
1 TTTTT
2563727 TTCAAGTATA
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
5 5 0.07
7 42 0.63
8 13 0.19
9 7 0.10
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTTTCC
Found at i:2563655 original size:16 final size:15
Alignment explanation
Indices: 2563633--2563729 Score: 101
Period size: 15 Copynumber: 6.5 Consensus size: 15
2563623 TTTATTCTTC
*
2563633 TTTTTTCCTTTTTTT
1 TTTTTTCCTTTTTCT
2563648 TCTTTTTCCTTTTTCCT
1 T-TTTTTCCTTTTT-CT
*
2563665 TTTTTTCCTTTTTCC
1 TTTTTTCCTTTTTCT
*
2563680 TTTTTTCCTTTTTCG
1 TTTTTTCCTTTTTCT
*
2563695 TTTTTTCGTTTTT-T
1 TTTTTTCCTTTTTCT
*
2563709 TTTTCTT--TTTTCCT
1 TTTT-TTCCTTTTTCT
2563723 TTTTTTC
1 TTTTTTC
2563730 AAGTATAATA
Statistics
Matches: 71, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
13 6 0.08
14 9 0.13
15 30 0.42
16 24 0.34
17 2 0.03
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTTTCCTTTTTCT
Found at i:2563661 original size:23 final size:24
Alignment explanation
Indices: 2563632--2563692 Score: 106
Period size: 23 Copynumber: 2.6 Consensus size: 24
2563622 CTTTATTCTT
*
2563632 CTTTTTTCCTTTTTTTTCTTTTTC
1 CTTTTTTCCTTTTTTTCCTTTTTC
2563656 C-TTTTTCCTTTTTTTCCTTTTTC
1 CTTTTTTCCTTTTTTTCCTTTTTC
2563679 CTTTTTTCCTTTTT
1 CTTTTTTCCTTTTT
2563693 CGTTTTTTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 22 0.63
24 13 0.37
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (24 bp):
CTTTTTTCCTTTTTTTCCTTTTTC
Found at i:2568138 original size:46 final size:49
Alignment explanation
Indices: 2568071--2568161 Score: 125
Period size: 46 Copynumber: 1.9 Consensus size: 49
2568061 AGGTATAAAT
* * * *
2568071 CCTAACCTCATGCTTTCTAGTT-TCATGC-TTTGTT-TGGAAAAATTAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCATTTGTTCAGGAAAAATTAA
2568117 CCTAACCGCATGATTTCTAGTTCGCATGCATTTGTTCAGGAAAAA
1 CCTAACCGCATGATTTCTAGTTCGCATGCATTTGTTCAGGAAAAA
2568162 GAAAATAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 20 0.53
47 5 0.13
48 6 0.16
49 7 0.18
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (49 bp):
CCTAACCGCATGATTTCTAGTTCGCATGCATTTGTTCAGGAAAAATTAA
Found at i:2569025 original size:193 final size:196
Alignment explanation
Indices: 2568687--2569077 Score: 761
Period size: 193 Copynumber: 2.0 Consensus size: 196
2568677 AATAATAAGG
2568687 ATATATAAAAATTTGAAAAGAAAGAATTAAAAATTAAATATATGAATTTTTAATTTTCTAATTGA
1 ATATATAAAAATTTGAAAAGAAAGAATTAAAAATTAAATATATGAATTTTTAATTTTCTAATTGA
2568752 TAGAGACAATTAATAATTGGTTTTAAAGTTTGACCGGTCCCCAGCGGAGTCGCCAAGCTGTCGCA
66 TAGAGACAATTAATAATTGGTTTTAAAGTTTGACCGGTCCCCAGCGGAGTCGCCAAGCTGTCGCA
2568817 ACCGGTTTTCGCCCGGCACGAATTTTTTTTTTACTTGGCGGGAAAAATAAAATGAATAAATAAAT
131 ACCGGTTTTCGCCCGGCACGAATTTTTTTTTTACTTGGCGGGAAAAATAAAATGAATAAATAAAT
2568882 A
196 A
2568883 ATATAT-AAAATTTGAAAAGAAAGAATTAAAAATT-AA-ATATGAATTTTTAATTTTCTAATTGA
1 ATATATAAAAATTTGAAAAGAAAGAATTAAAAATTAAATATATGAATTTTTAATTTTCTAATTGA
2568945 TAGAGACAATTAATAATTGGTTTTAAAGTTTGACCGGTCCCCAGCGGAGTCGCCAAGCTGTCGCA
66 TAGAGACAATTAATAATTGGTTTTAAAGTTTGACCGGTCCCCAGCGGAGTCGCCAAGCTGTCGCA
2569010 ACCGGTTTTCGCCCGGCACGAATTTTTTTTTTACTTGGCGGGAAAAATAAAATGAATAAATAAAT
131 ACCGGTTTTCGCCCGGCACGAATTTTTTTTTTACTTGGCGGGAAAAATAAAATGAATAAATAAAT
2569075 A
196 A
2569076 AT
1 AT
2569078 TTTGATTTAA
Statistics
Matches: 195, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
193 159 0.82
194 2 0.01
195 28 0.14
196 6 0.03
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (196 bp):
ATATATAAAAATTTGAAAAGAAAGAATTAAAAATTAAATATATGAATTTTTAATTTTCTAATTGA
TAGAGACAATTAATAATTGGTTTTAAAGTTTGACCGGTCCCCAGCGGAGTCGCCAAGCTGTCGCA
ACCGGTTTTCGCCCGGCACGAATTTTTTTTTTACTTGGCGGGAAAAATAAAATGAATAAATAAAT
A
Found at i:2569676 original size:12 final size:12
Alignment explanation
Indices: 2569659--2569720 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
2569649 TAAGGCTAAG
2569659 ATAAAAATAATA
1 ATAAAAATAATA
2569671 AT-AAAATAATA
1 ATAAAAATAATA
* *
2569682 ATTAAAGTAATA
1 ATAAAAATAATA
*
2569694 ATTAAAAT-ATA
1 ATAAAAATAATA
* *
2569705 TTAAAATTAATA
1 ATAAAAATAATA
2569717 ATAA
1 ATAA
2569721 TATTACAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
11 19 0.45
12 23 0.55
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (12 bp):
ATAAAAATAATA
Found at i:2569949 original size:14 final size:14
Alignment explanation
Indices: 2569916--2569951 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
2569906 TTGGGAAAGT
*
2569916 ATTAAAATAAAACA
1 ATTAAATTAAAACA
2569930 ATTTAAATTAAAACA
1 A-TTAAATTAAAACA
2569945 ATTAAAT
1 ATTAAAT
2569952 CATATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAATTAAAACA
Found at i:2571199 original size:3 final size:3
Alignment explanation
Indices: 2571191--2571252 Score: 99
Period size: 3 Copynumber: 20.3 Consensus size: 3
2571181 ATTTTTTATT
2571191 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA-A TAA
2571237 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
2571253 GAAAAAAATT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.04
3 48 0.86
4 6 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2574512 original size:2 final size:2
Alignment explanation
Indices: 2574500--2574563 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
2574490 TTAGCTTAAG
*
2574500 AT AT CT AT AT AT AT AT AT AT AT A- 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
2574541 AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
2574564 CAATTGGCTA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2582603 original size:20 final size:20
Alignment explanation
Indices: 2582578--2582616 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2582568 ATGCGTCGAT
2582578 GCACTGTAGCACTATTCACA
1 GCACTGTAGCACTATTCACA
2582598 GCACTGTAGCACTATTCAC
1 GCACTGTAGCACTATTCAC
2582617 GGTAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
GCACTGTAGCACTATTCACA
Found at i:2584291 original size:32 final size:34
Alignment explanation
Indices: 2584222--2584314 Score: 90
Period size: 32 Copynumber: 2.9 Consensus size: 34
2584212 TTCGCATCAG
2584222 GATGTTGAATC-CACAAAGATGCCCCAATAATCT
1 GATGTTGAATCTCACAAAGATGCCCCAATAATCT
* *
2584255 -ATGTTGAATCTCTA-AAA-ATGCCCCAA-CATTT
1 GATGTTGAATCTC-ACAAAGATGCCCCAATAATCT
* *
2584286 GATGTTAAATCT-TCAAAGATGTCCCCAAT
1 GATGTTGAATCTCACAAAGATG-CCCCAAT
2584315 GTTCCTCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
31 6 0.12
32 32 0.65
33 10 0.20
34 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (34 bp):
GATGTTGAATCTCACAAAGATGCCCCAATAATCT
Found at i:2585378 original size:23 final size:24
Alignment explanation
Indices: 2585344--2585396 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
2585334 TTCCTTTGTT
*
2585344 TTTGTTTCTCTT-TTTTATTTTCTC
1 TTTGTTTCTCTTATCTT-TTTTCTC
*
2585368 TTTGTTT-TCTTATCTTTTTTCTT
1 TTTGTTTCTCTTATCTTTTTTCTC
2585391 TTTGTT
1 TTTGTT
2585397 CTGATTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 16 0.62
24 10 0.38
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (24 bp):
TTTGTTTCTCTTATCTTTTTTCTC
Found at i:2588723 original size:23 final size:23
Alignment explanation
Indices: 2588692--2588735 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
2588682 AAATGTATAT
* *
2588692 ATATATATATATATATAATAGTA
1 ATATATATAGATAAATAATAGTA
*
2588715 ATATGTATAGATAAATAATAG
1 ATATATATAGATAAATAATAG
2588736 ATAGAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (23 bp):
ATATATATAGATAAATAATAGTA
Found at i:2588870 original size:14 final size:15
Alignment explanation
Indices: 2588822--2588878 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 15
2588812 AAATGTTTTA
2588822 AAAATATTAATAA-ATT
1 AAAATA-TAATAATA-T
* *
2588838 AAAA-A-AATAAAAC
1 AAAATATAATAATAT
2588851 AAAATATAA-AATAT
1 AAAATATAATAATAT
2588865 AAAATATAATAATA
1 AAAATATAATAATA
2588879 ATAATGAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
13 9 0.26
14 14 0.41
15 7 0.21
16 4 0.12
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAATATAATAATAT
Found at i:2588921 original size:23 final size:23
Alignment explanation
Indices: 2588865--2588921 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
2588855 TATAAAATAT
* *
2588865 AAAATATAATAATAATAATGAAG
1 AAAATATAATAATAATAAGGAAA
* *
2588888 AATATATAATAATAGTAAGGAAA
1 AAAATATAATAATAATAAGGAAA
*
2588911 AAAATAAAATA
1 AAAATATAATA
2588922 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (23 bp):
AAAATATAATAATAATAAGGAAA
Found at i:2589303 original size:37 final size:36
Alignment explanation
Indices: 2589262--2589373 Score: 152
Period size: 37 Copynumber: 3.0 Consensus size: 36
2589252 ATGTTTATGG
*
2589262 ATCTTATTTTTATGAGTTTGAATCATAATAAAACTCT
1 ATCTTATTTTTA-GAGTTTGAATCATAGTAAAACTCT
*
2589299 ATCTTATTTTTAGAAATTTGAATCATAGTAAAACTCT
1 ATCTTATTTTTAG-AGTTTGAATCATAGTAAAACTCT
* * *
2589336 ATCATATTTTTAGGAGTTTGAATCTTAGTAAAATTCT
1 ATCTTATTTTTA-GAGTTTGAATCATAGTAAAACTCT
2589373 A
1 A
2589374 ATATTATATT
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
36 1 0.01
37 65 0.97
38 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.45
Consensus pattern (36 bp):
ATCTTATTTTTAGAGTTTGAATCATAGTAAAACTCT
Found at i:2589990 original size:21 final size:21
Alignment explanation
Indices: 2589972--2590013 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2589962 ATTACGATTT
*
2589972 TCCAAATTCGCAATGCGATAG
1 TCCAAAATCGCAATGCGATAG
*
2589993 TCCAAAATCGCATTGCGATAG
1 TCCAAAATCGCAATGCGATAG
2590014 CACTGTTCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
TCCAAAATCGCAATGCGATAG
Found at i:2590029 original size:21 final size:21
Alignment explanation
Indices: 2590005--2590097 Score: 159
Period size: 21 Copynumber: 4.4 Consensus size: 21
2589995 CAAAATCGCA
2590005 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
2590026 TTGCGATAGCACTGTTCACCG
1 TTGCGATAGCACTGTTCACCG
*
2590047 TTGCGATAGCACTGTTTACCG
1 TTGCGATAGCACTGTTCACCG
*
2590068 TTGCGATAGCACTGTTCACCA
1 TTGCGATAGCACTGTTCACCG
*
2590089 TTACGATAG
1 TTGCGATAG
2590098 TGATCAAAAT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 68 1.00
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.30
Consensus pattern (21 bp):
TTGCGATAGCACTGTTCACCG
Found at i:2590783 original size:21 final size:21
Alignment explanation
Indices: 2590759--2590812 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
2590749 GAACAGTGCT
*
2590759 ATCGCATTGCGAATTCGGAAA
1 ATCGCAATGCGAATTCGGAAA
* *
2590780 ATCGCAACGCGAATTTGGAAA
1 ATCGCAATGCGAATTCGGAAA
2590801 ATCGCAATGCGA
1 ATCGCAATGCGA
2590813 TAGTCAGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
ATCGCAATGCGAATTCGGAAA
Found at i:2591454 original size:3 final size:3
Alignment explanation
Indices: 2591432--2591487 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
2591422 TCTACAAAAA
* *
2591432 TAT TAT TTT TA- TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2591478 TAT TAT TAT T
1 TAT TAT TAT T
2591488 GTTGTTGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2593052 original size:59 final size:60
Alignment explanation
Indices: 2592914--2593066 Score: 222
Period size: 59 Copynumber: 2.6 Consensus size: 60
2592904 TGTAATTACC
* * * *
2592914 ATTTTAGTTCTTTAAATTTTTATTTTTGT-TATTTTAGTCTTTTAAATTTCTATTTTTGCT
1 ATTTTAGTCCTTTAAATTTCTATTTTT-TCTATTTGAGTCCTTTAAATTTCTATTTTTGCT
2592974 ATTTTAGTCCTTTAAATTTCTATTTTTTCTATTTGAGTCCTTTAAA-TT-TATGTTTTGCT
1 ATTTTAGTCCTTTAAATTTCTATTTTTTCTATTTGAGTCCTTTAAATTTCTAT-TTTTGCT
*
2593033 ATTTTAGTCCTTTAAATTTCTATTTTTGCTATTT
1 ATTTTAGTCCTTTAAATTTCTATTTTTTCTATTT
2593067 TAGCCTCTCA
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
58 3 0.03
59 43 0.50
60 40 0.47
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.63
Consensus pattern (60 bp):
ATTTTAGTCCTTTAAATTTCTATTTTTTCTATTTGAGTCCTTTAAATTTCTATTTTTGCT
Found at i:2593083 original size:30 final size:30
Alignment explanation
Indices: 2592914--2593069 Score: 235
Period size: 30 Copynumber: 5.2 Consensus size: 30
2592904 TGTAATTACC
* * *
2592914 ATTTTAGTTCTTTAAATTTTTATTTTTGTT
1 ATTTTAGTCCTTTAAATTTCTATTTTTGCT
*
2592944 ATTTTAGTCTTTTAAATTTCTATTTTTGCT
1 ATTTTAGTCCTTTAAATTTCTATTTTTGCT
*
2592974 ATTTTAGTCCTTTAAATTTCTATTTTTTCT
1 ATTTTAGTCCTTTAAATTTCTATTTTTGCT
*
2593004 ATTTGAGTCCTTTAAA-TT-TATGTTTTGCT
1 ATTTTAGTCCTTTAAATTTCTAT-TTTTGCT
2593033 ATTTTAGTCCTTTAAATTTCTATTTTTGCT
1 ATTTTAGTCCTTTAAATTTCTATTTTTGCT
2593063 ATTTTAG
1 ATTTTAG
2593070 CCTCTCAAGT
Statistics
Matches: 114, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
28 3 0.03
29 23 0.20
30 85 0.75
31 3 0.03
ACGTcount: A:0.21, C:0.10, G:0.08, T:0.62
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAATTTCTATTTTTGCT
Found at i:2593096 original size:89 final size:89
Alignment explanation
Indices: 2592914--2593096 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 89
2592904 TGTAATTACC
* * * *
2592914 ATTTTAGTTCTTTAAATTTTTATTTTTGTTATTTTAGTCTTTTAAATTTCTATTTTTGCTATTTT
1 ATTTGAGTCCTTTAAA-TTTTATTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTTT
* *
2592979 AGTCCTTTAAATTTCTATTTTTTCT
65 AGTCCTTCAAATTTCTATTGTTTCT
2593004 ATTTGAGTCCTTTAAA-TTTATGTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTTT
1 ATTTGAGTCCTTTAAATTTTAT-TTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTTT
* *
2593068 AG-CCTCTCAAGTTTCTGTTAGTTT-T
65 AGTCCT-TCAAATTTCTATT-GTTTCT
2593093 ATTT
1 ATTT
2593097 TGGTCCCTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
88 8 0.10
89 57 0.70
90 17 0.21
ACGTcount: A:0.20, C:0.11, G:0.08, T:0.61
Consensus pattern (89 bp):
ATTTGAGTCCTTTAAATTTTATTTTTGCTATTTTAGTCCTTTAAATTTCTATTTTTGCTATTTTA
GTCCTTCAAATTTCTATTGTTTCT
Found at i:2594921 original size:32 final size:32
Alignment explanation
Indices: 2594885--2594946 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
2594875 TCTTACCTGT
2594885 ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
* *
2594917 ACTAATTTATTTCTTTTCTTTTGTTTGTGT
1 ACTAACTAATTTCTTTTCTTTTGTTTGTGT
2594947 CATTTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (32 bp):
ACTAACTAATTTCTTTTCTTTTGTTTGTGTAC
Found at i:2597593 original size:2 final size:2
Alignment explanation
Indices: 2597586--2597664 Score: 140
Period size: 2 Copynumber: 39.5 Consensus size: 2
2597576 TATGCCCAGA
2597586 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
* *
2597628 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2597665 CAATAAAGTT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2599615 original size:131 final size:131
Alignment explanation
Indices: 2599376--2599728 Score: 372
Period size: 131 Copynumber: 2.7 Consensus size: 131
2599366 CTTGAAACAA
* * * * *
2599376 ATCCCTAAAGATGGCCAATCGTCATCATCGCGTAGGAACTGTGTCATCCACCGACCAGAGCTCCT
1 ATCCCTAAAGATGGCCAATCATCATCATCACGAAGGAACCGTGTCATCCACCGACCAGACCTCCT
* * *
2599441 AATCACGTAGGAGTCGTGTCACCCGTAGATAATCAGCCATCCTCATCACGTAGGAACCGTGTTAT
66 AATCACATAGGAGCCGTGTCACCCCTAGATAATCAGCCATCCTCATCACGTAGGAACCGTGTTAT
2599506 C
131 C
* * *
2599507 ATCCCTAAAGATGG-TATATCATCCTCATCACGAAGGAACCGTGTCATCCACCGACCAGACCTCT
1 ATCCCTAAAGATGGCCA-ATCATCATCATCACGAAGGAACCGTGTCATCCACCGACCAGACCTCC
* * **
2599571 TCATCACATAGGAGCCGTGTCACCCCTAGATAA-CTAGCCGTCCTCATCGGGTAGGAACCGTGTT
65 TAATCACATAGGAGCCGTGTCACCCCTAGATAATC-AGCCATCCTCATCACGTAGGAACCGTGTT
2599635 ATC
129 ATC
* * * * * * * * * * *
2599638 ACTGTTCCTATAGATGGCCAGTTATCCTCATCGCGTAGGAACCATGTTATCCACCGACAAGATCT
1 A---TCCCTAAAGATGGCCAATCATCATCATCACGAAGGAACCGTGTCATCCACCGACCAGACCT
* *
2599703 CCTCATCACGAT--GAGTCGTGTCACCC
63 CCTAATCAC-ATAGGAGCCGTGTCACCC
2599729 TTAAACGACC
Statistics
Matches: 187, Mismatches: 28, Indels: 12
0.82 0.12 0.05
Matches are distributed among these distances:
130 2 0.01
131 113 0.60
133 13 0.07
134 56 0.30
135 3 0.02
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.24
Consensus pattern (131 bp):
ATCCCTAAAGATGGCCAATCATCATCATCACGAAGGAACCGTGTCATCCACCGACCAGACCTCCT
AATCACATAGGAGCCGTGTCACCCCTAGATAATCAGCCATCCTCATCACGTAGGAACCGTGTTAT
C
Found at i:2599929 original size:3 final size:3
Alignment explanation
Indices: 2599912--2599989 Score: 131
Period size: 3 Copynumber: 26.3 Consensus size: 3
2599902 CCTACAAAAA
* *
2599912 TAT TAT TTT TA- TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2599959 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2599990 GATACATTAC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.31, C:0.00, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2601490 original size:30 final size:30
Alignment explanation
Indices: 2601454--2601558 Score: 156
Period size: 30 Copynumber: 3.5 Consensus size: 30
2601444 TTTGCAATTA
** *
2601454 CTATTTTAACCCTTTAAAATTTTGTTTTTG
1 CTATTTTAGTCCTTTAAATTTTTGTTTTTG
* * *
2601484 CTATTTTAGTCTTTTAAATTTTTATTTTTT
1 CTATTTTAGTCCTTTAAATTTTTGTTTTTG
2601514 CTATTTTAGTCCTTTAAATTTTTGTTTTTG
1 CTATTTTAGTCCTTTAAATTTTTGTTTTTG
2601544 CTATTTTAGTCCTTT
1 CTATTTTAGTCCTTT
2601559 TTTTATATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 66 1.00
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (30 bp):
CTATTTTAGTCCTTTAAATTTTTGTTTTTG
Found at i:2601568 original size:49 final size:48
Alignment explanation
Indices: 2601508--2601606 Score: 162
Period size: 49 Copynumber: 2.0 Consensus size: 48
2601498 TAAATTTTTA
* *
2601508 TTTTTTCTATTTTAGTCCTTTAAATTTTTGTTTTTGCTATTTTAGTCCT
1 TTTTTTATATTTTAGTCCTTTAAATTTATGTTTTTGCTATTTTAG-CCT
*
2601557 TTTTTTATATTTTAGTCCTTTAAATTTATGTTTTTTCTATTTTAGCCT
1 TTTTTTATATTTTAGTCCTTTAAATTTATGTTTTTGCTATTTTAGCCT
2601605 TT
1 TT
2601607 CAAGTTTCTG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 5 0.11
49 42 0.89
ACGTcount: A:0.16, C:0.11, G:0.07, T:0.66
Consensus pattern (48 bp):
TTTTTTATATTTTAGTCCTTTAAATTTATGTTTTTGCTATTTTAGCCT
Found at i:2601628 original size:30 final size:30
Alignment explanation
Indices: 2601564--2601640 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
2601554 CCTTTTTTTA
*
2601564 TATTTTAGTCCTTTAAATTTATGTTTTTTC
1 TATTTTAGTCCTTTAAATTTATGTTGTTTC
* *
2601594 TATTTTAG-CCTTTCAAGTTTCTGTTAGTTT-
1 TATTTTAGTCCTTT-AAATTTATGTT-GTTTC
* *
2601624 TATTTTGGTCCCTTAAA
1 TATTTTAGTCCTTTAAA
2601641 ATCATCAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 5 0.13
30 26 0.68
31 7 0.18
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.57
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAATTTATGTTGTTTC
Found at i:2603110 original size:2 final size:2
Alignment explanation
Indices: 2603103--2603135 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2603093 GTTTCTGATA
2603103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2603136 ATTCAAGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2609197 original size:21 final size:21
Alignment explanation
Indices: 2609171--2609228 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
2609161 ATTATCCAAT
*
2609171 AAACTT-AACATCCATAACGAC
1 AAACTTGAA-ATCCATAACAAC
*
2609192 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
2609213 AAACTTGAAATTCATA
1 AAACTTGAAATCCATA
2609229 TAATAAATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:2611698 original size:41 final size:41
Alignment explanation
Indices: 2611665--2611861 Score: 238
Period size: 40 Copynumber: 4.9 Consensus size: 41
2611655 TTTAGCAGTA
* * *
2611665 TTTGTATAAAAACGCCGCTAAAGTACAAGTCTTTGGCGGCG
1 TTTGTATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCG
* * **
2611706 TTTGTATAGAAACGCAACTAAAGTATGAGTATTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCG
* *
2611747 TTTGTGCTTAAAACGCCAC-AAAGTACAA-TATTTAGCGGCG
1 TTTGT-ATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCG
* * * *
2611787 TTTATATAAAAACACTACTAAAGTACAA-TATTTAGAGGCG
1 TTTGTATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCG
*
2611827 TTTATATAAAAACGCCACTAAAGTACAAGTATTTA
1 TTTGTATAAAAACGCCACTAAAGTACAAGTATTTA
2611862 CTGACGTTTG
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
39 9 0.07
40 62 0.47
41 52 0.39
42 9 0.07
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (41 bp):
TTTGTATAAAAACGCCACTAAAGTACAAGTATTTAGCGGCG
Found at i:2619832 original size:31 final size:33
Alignment explanation
Indices: 2619763--2619835 Score: 89
Period size: 32 Copynumber: 2.2 Consensus size: 33
2619753 TATATTTATA
* *
2619763 TATTTTATTTTTGATCAAAATAAGTACCTAAAGT
1 TATTTTATTTTTGATAAAAATAAGTACC-AAAGG
2619797 TATTTT-TTTTTG-TAAAAATAAGTATCC-AAGG
1 TATTTTATTTTTGATAAAAATAAGTA-CCAAAGG
2619828 TATTTTAT
1 TATTTTAT
2619836 GTCAAAATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 9 0.26
32 12 0.34
33 8 0.23
34 6 0.17
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (33 bp):
TATTTTATTTTTGATAAAAATAAGTACCAAAGG
Found at i:2619935 original size:29 final size:28
Alignment explanation
Indices: 2619851--2619940 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 28
2619841 AATATGTATC
* * *
2619851 TATTTTAATAAAATAAACTTTAGATACT
1 TATTTTAATAAAATATACTTTAAATATT
* *
2619879 TATGTTGACA-AAAATATAATTTTAAATATT
1 TAT-TTTA-ATAAAATAT-ACTTTAAATATT
2619909 TATTTTAATTAAAATATACTTTAAATAATT
1 TATTTTAA-TAAAATATACTTTAAAT-ATT
2619939 TA
1 TA
2619941 AACTTTTCAT
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.08
29 20 0.41
30 25 0.51
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (28 bp):
TATTTTAATAAAATATACTTTAAATATT
Found at i:2620703 original size:2 final size:2
Alignment explanation
Indices: 2620696--2620721 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2620686 TTGTTAGTTG
2620696 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2620722 TGTTTAACAG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2624285 original size:2 final size:2
Alignment explanation
Indices: 2624240--2624276 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2624230 AGCATGTAAC
2624240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2624277 TCGTATATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2625415 original size:16 final size:17
Alignment explanation
Indices: 2625378--2625440 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 17
2625368 ACTAAAAACT
2625378 ATAATTATAAAATAGATAAA
1 ATAATTA-AAAAT--ATAAA
2625398 ATAATTAAAAAT-TAAA
1 ATAATTAAAAATATAAA
*
2625414 ATATTATAAAAATAATAAA
1 ATAAT-TAAAAAT-ATAAA
*
2625433 ATACTTAA
1 ATAATTAA
2625441 GTCTAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
16 8 0.21
17 7 0.18
18 3 0.08
19 13 0.34
20 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
ATAATTAAAAATATAAA
Found at i:2625941 original size:8 final size:7
Alignment explanation
Indices: 2625905--2625940 Score: 54
Period size: 7 Copynumber: 4.9 Consensus size: 7
2625895 TTTTGATTTT
2625905 TTTTAAA
1 TTTTAAA
2625912 TTTTAAA
1 TTTTAAA
2625919 TTTTAAA
1 TTTTAAA
2625926 TATTTAATA
1 T-TTTAA-A
2625935 TTTTAA
1 TTTTAA
2625941 TGTAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 15 0.56
8 10 0.37
9 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (7 bp):
TTTTAAA
Found at i:2625955 original size:17 final size:17
Alignment explanation
Indices: 2625933--2625966 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2625923 AAATATTTAA
*
2625933 TATTTTAATGTAATTTT
1 TATTTTAATATAATTTT
*
2625950 TATTTTTATATAATTTT
1 TATTTTAATATAATTTT
2625967 CTCTGAGATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TATTTTAATATAATTTT
Found at i:2627132 original size:12 final size:12
Alignment explanation
Indices: 2627115--2627157 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
2627105 TTATTAAAAA
2627115 TAAAGAAAACTT
1 TAAAGAAAACTT
*
2627127 TAAAGAAAA--A
1 TAAAGAAAACTT
2627137 TAAAGAAAACTT
1 TAAAGAAAACTT
2627149 TAAAGAAAA
1 TAAAGAAAA
2627158 ATAAAGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (12 bp):
TAAAGAAAACTT
Found at i:2627140 original size:10 final size:10
Alignment explanation
Indices: 2627110--2627168 Score: 64
Period size: 10 Copynumber: 5.5 Consensus size: 10
2627100 TAGCATTATT
2627110 AAAAATAAAG
1 AAAAATAAAG
*
2627120 AAAACTTTAAAG
1 AAAA--ATAAAG
2627132 AAAAATAAAG
1 AAAAATAAAG
*
2627142 AAAACTTTAAAG
1 AAAA--ATAAAG
2627154 AAAAATAAAG
1 AAAAATAAAG
2627164 AAAAA
1 AAAAA
2627169 ACTTTTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 23 0.56
12 18 0.44
ACGTcount: A:0.73, C:0.03, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:2627180 original size:23 final size:22
Alignment explanation
Indices: 2627110--2627167 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
2627100 TAGCATTATT
2627110 AAAAATAAAGAAAACTTTAAAG
1 AAAAATAAAGAAAACTTTAAAG
2627132 AAAAATAAAGAAAACTTTAAAG
1 AAAAATAAAGAAAACTTTAAAG
2627154 AAAAATAAAGAAAA
1 AAAAATAAAGAAAA
2627168 AACTTTTATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.72, C:0.03, G:0.09, T:0.16
Consensus pattern (22 bp):
AAAAATAAAGAAAACTTTAAAG
Found at i:2628627 original size:32 final size:32
Alignment explanation
Indices: 2628546--2628633 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 32
2628536 TCTTGAAAAT
2628546 AAATAGTA-ATATATATAATATGATATAAATTTGA
1 AAATAGTATATATATAT-ATAT--TATAAATTTGA
* **
2628580 AAATA-TATA-A-GTATATATTATAGTTTTGA
1 AAATAGTATATATATATATATTATAAATTTGA
2628609 AAATAGTATATATATATATATTATA
1 AAATAGTATATATATATATATTATA
2628634 TTATATCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
29 14 0.30
30 4 0.09
31 5 0.11
32 14 0.30
33 3 0.07
34 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (32 bp):
AAATAGTATATATATATATATTATAAATTTGA
Found at i:2628645 original size:73 final size:73
Alignment explanation
Indices: 2628524--2628712 Score: 175
Period size: 73 Copynumber: 2.7 Consensus size: 73
2628514 ACAGTATTTT
* * *
2628524 TATA-ATATATAGTCTTGAAAAT-AAATAGTA--ATAT-ATATA--ATATGATATAAATTTGA-A
1 TATATATATATAGTTTTAAAAATAAAATAGTAGTATATAATATATTATATCATAT-AATTTGAGA
2628581 AATATATAA
65 AATATATAA
* * * *
2628590 GTATATAT-TATAGTTTTGAAAATAGTATATA-TA-TATATATTATATTATATCATATAATTTTA
1 -TATATATATATAGTTTTAAAAATA--AAATAGTAGTATATAATATATTATATCATATAATTTGA
* *
2628652 GAAGTATATTA
63 GAAATATATAA
*
2628663 TATATGTATATAGTTTTAAAAATAAAATAGTAGTATATAATATATTATAT
1 TATATATATATAGTTTTAAAAATAAAATAGTAGTATATAATATATTATAT
2628713 AGATTTTAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
67 18 0.18
68 2 0.02
69 2 0.02
70 8 0.08
71 8 0.08
72 14 0.14
73 47 0.47
ACGTcount: A:0.48, C:0.01, G:0.08, T:0.43
Consensus pattern (73 bp):
TATATATATATAGTTTTAAAAATAAAATAGTAGTATATAATATATTATATCATATAATTTGAGAA
ATATATAA
Found at i:2628905 original size:17 final size:17
Alignment explanation
Indices: 2628880--2628913 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2628870 TTTTGTTTAA
2628880 TATTATCATGATTAATT
1 TATTATCATGATTAATT
* *
2628897 TATTTTCATTATTAATT
1 TATTATCATGATTAATT
2628914 CAGGTTAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
TATTATCATGATTAATT
Found at i:2630729 original size:223 final size:222
Alignment explanation
Indices: 2630340--2630913 Score: 907
Period size: 223 Copynumber: 2.6 Consensus size: 222
2630330 TTGTCAGTTT
* * * *
2630340 GTGTCGATACTTTATAAAAATATATTGATACATAACAATATAACAAGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGATAAAAC
* * * * *
2630405 CGGTCTATAAATGACAAAATAGATAAAGCGTTACTGGATATATTGAAAGTGTCGATACTTTATAA
65 CGGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAA
* *
2630470 AAATATATCTATCCATAACAATATAACAGGTAAAAAAAATGAC-AATCGATCTATAAATGACAAA
130 AAATATATCGATCCATAACAATATAACAGGT--AAAAAATGACAAACCGATCTATAAATGACAAA
*
2630534 ACAAGTAAAGCGCTACCGGATATATTGAAA
193 ACAAGTAAAGCGCTACAGGATATATTGAAA
2630564 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
2630629 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
* *
2630694 AATGTATCGATCCATAACAATATAACAGTTAAAAAATGACAAAACCGATCTATAAATGACAAAAC
131 AATATATCGATCCATAACAATATAACAGGTAAAAAATGAC-AAACCGATCTATAAATGACAAAAC
* * *
2630759 AGGTAAAGCGCTACAGGATATGTTGATA
195 AAGTAAAGCGCTACAGGATATATTGAAA
*
2630787 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
* * * *
2630852 GGTCTATAAATGACAAAACATGTAAAATGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTAT
2630914 TATAAGTATC
Statistics
Matches: 326, Mismatches: 22, Indels: 5
0.92 0.06 0.01
Matches are distributed among these distances:
221 10 0.03
223 272 0.83
224 44 0.13
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.26
Consensus pattern (222 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATATATCGATCCATAACAATATAACAGGTAAAAAATGACAAACCGATCTATAAATGACAAAACA
AGTAAAGCGCTACAGGATATATTGAAA
Found at i:2630849 original size:20 final size:20
Alignment explanation
Indices: 2630824--2630878 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
2630814 ATCCATAACA
2630824 ATAAAACAGGTAAAAAAATG
1 ATAAAACAGGTAAAAAAATG
* ** *
2630844 ATAAAACCGGTCTATAAATG
1 ATAAAACAGGTAAAAAAATG
* *
2630864 ACAAAACATGTAAAA
1 ATAAAACAGGTAAAA
2630879 TGCTACCGGA
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.58, C:0.11, G:0.13, T:0.18
Consensus pattern (20 bp):
ATAAAACAGGTAAAAAAATG
Found at i:2630923 original size:111 final size:112
Alignment explanation
Indices: 2630340--2630913 Score: 866
Period size: 111 Copynumber: 5.1 Consensus size: 112
2630330 TTGTCAGTTT
* * * *
2630340 GTGTCGATACTTTATAAAAATATATTGATACATAACAATATAACAAGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGATAAAAC
* * * *
2630405 CGGTCTATAAATGACAAAATAGATAAAGCGTTACTGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
2630453 GTGTCGATACTTTATAAAAATATATCTATCCATAACAATATAACAGGTAAAAAAA--ATGACAAT
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGAT-AAAAC
* *
2630516 CGATCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
2630564 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
*
2630629 GGTCTATAAATGACAAAACAGGTAAAACGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
2630676 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA-GTTAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
* * * *
2630740 GATCTATAAATGACAAAACAGGTAAAGCGCTACAGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
2630787 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
* ** * *
2630852 GGTCTATAAATGACAAAACATGTAAAATGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
2630899 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
2630914 TATAAGTATC
Statistics
Matches: 423, Mismatches: 34, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
110 2 0.00
111 201 0.48
112 174 0.41
113 46 0.11
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGATAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:2631006 original size:182 final size:182
Alignment explanation
Indices: 2630786--2631239 Score: 721
Period size: 182 Copynumber: 2.5 Consensus size: 182
2630776 ATATGTTGAT
* * * *
2630786 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAACAGGTAAAAAAATGATAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* ** * *
2630851 CGGTCTATAAATGACAAAACATGTAAA-ATGCTACCGGATATGTTGATAGTGTCGATACTTTATT
66 CGATCTCGAAATGACAAAACAGGTAAAGA-GCTACCAGATATGTTGATAGTGTCGATACTTTATT
* * * *
2630915 ATAAGTATCAACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAA
130 ACAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
* *
2630968 AGTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACAGGTAAAATTATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
* *
2631033 CGATCTCGAAATGATAAAACCGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
66 CGATCTCGAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
*
2631098 CAAGTATCGACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
131 CAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
2631150 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
*
2631215 CGATCTCGAAATGACAAAACCGGTA
66 CGATCTCGAAATGACAAAACAGGTA
2631240 GTAAAAAAGT
Statistics
Matches: 250, Mismatches: 21, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
182 249 1.00
183 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAT
CGATCTCGAAATGACAAAACAGGTAAAGAGCTACCAGATATGTTGATAGTGTCGATACTTTATTA
CAAGTATCAACACTTTTAGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
Found at i:2637468 original size:18 final size:18
Alignment explanation
Indices: 2637441--2637480 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2637431 TGCATCTTAC
*
2637441 ATTTGTATTT-TACATTTT
1 ATTTGCATTTGTA-ATTTT
2637459 ATTTGCATTTGTAATTTT
1 ATTTGCATTTGTAATTTT
2637477 ATTT
1 ATTT
2637481 CATGCGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (18 bp):
ATTTGCATTTGTAATTTT
Found at i:2652873 original size:11 final size:10
Alignment explanation
Indices: 2652854--2652883 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2652844 TTGCCTGAAG
2652854 AAGAAAAAAA
1 AAGAAAAAAA
2652864 AAGAAAAAAA
1 AAGAAAAAAA
2652874 AAGAAAAAAA
1 AAGAAAAAAA
2652884 GATAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:2652882 original size:18 final size:18
Alignment explanation
Indices: 2652859--2652899 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2652849 TGAAGAAGAA
*
2652859 AAAAAAAGAAAAAAAAAG
1 AAAAAAAGAAAAAAAAAC
* *
2652877 AAAAAAAGATAAATAAAC
1 AAAAAAAGAAAAAAAAAC
2652895 AAAAA
1 AAAAA
2652900 TATAATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.85, C:0.02, G:0.07, T:0.05
Consensus pattern (18 bp):
AAAAAAAGAAAAAAAAAC
Found at i:2654855 original size:23 final size:22
Alignment explanation
Indices: 2654813--2654855 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
2654803 ATATATTATA
*
2654813 TATTATATCATTTTTCATTTTT
1 TATTATATCATATTTCATTTTT
2654835 TATTATTATCATGATTT-ATTT
1 TATTA-TATCAT-ATTTCATTT
2654856 ATTTTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 5 0.28
23 10 0.56
24 3 0.17
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (22 bp):
TATTATATCATATTTCATTTTT
Found at i:2657965 original size:179 final size:184
Alignment explanation
Indices: 2657772--2658136 Score: 695
Period size: 179 Copynumber: 2.0 Consensus size: 184
2657762 TAGAAATATT
2657772 AATTCCATAATTTAGAATAGTGAAATTTGACATGGATTACTGGAATTAAGACCGATTTTCCATTT
1 AATTCCATAATTTAGAATAGTGAAATTTGACATGGATTACTGGAATTAAGACCGATTTTCCATTT
2657837 TAAGCCAAAATTGTGAAATTAGGTGACT-AAATTGCAATTTTTGAAAGTTGCAT-GGAAAAGGTG
66 TAAGCCAAAATTGTGAAATTAGGTGACTAAAATTGCAATTTTTGAAAGTTGCATGGGAAAAGGTG
2657900 G-AATTCAAAA-TTTTTTGTTAATGTTTGAATTTGAA-TTGGATATTAAATTGG
131 GAAATTCAAAATTTTTTTGTTAATGTTTGAATTTGAATTTGGATATTAAATTGG
2657951 AATTCCATAATTTAGAATAGTGAAATTTGACATGGATTACTGGAATTAAGACCGATTTTCCATTT
1 AATTCCATAATTTAGAATAGTGAAATTTGACATGGATTACTGGAATTAAGACCGATTTTCCATTT
2658016 TAAGCCAAAATTGTGAAATTAGGTGACTAAAATTGCAATTTTTGAAAGTTGCATGGGAAAAGGTG
66 TAAGCCAAAATTGTGAAATTAGGTGACTAAAATTGCAATTTTTGAAAGTTGCATGGGAAAAGGTG
2658081 GAAATTCAAAATTTTTTTGTTAATGTTTGAATTTGAATTTGGATATTAAATTGG
131 GAAATTCAAAATTTTTTTGTTAATGTTTGAATTTGAATTTGGATATTAAATTGG
2658135 AA
1 AA
2658137 GATATTATGG
Statistics
Matches: 181, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
179 93 0.51
180 25 0.14
181 11 0.06
182 9 0.05
183 25 0.14
184 18 0.10
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.37
Consensus pattern (184 bp):
AATTCCATAATTTAGAATAGTGAAATTTGACATGGATTACTGGAATTAAGACCGATTTTCCATTT
TAAGCCAAAATTGTGAAATTAGGTGACTAAAATTGCAATTTTTGAAAGTTGCATGGGAAAAGGTG
GAAATTCAAAATTTTTTTGTTAATGTTTGAATTTGAATTTGGATATTAAATTGG
Found at i:2659421 original size:21 final size:19
Alignment explanation
Indices: 2659370--2659423 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
2659360 AATAGTGGGA
*
2659370 AAAGACAGAAAAAAGAGAG
1 AAAGAGAGAAAAAAGAGAG
*
2659389 AAAGAGAGAAAAAAGGGAGG
1 AAAGAGAGAAAAAAGAGA-G
*
2659409 AAAGA-AGATAAAAGA
1 AAAGAGAGAAAAAAGA
2659424 ATCATCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.67, C:0.02, G:0.30, T:0.02
Consensus pattern (19 bp):
AAAGAGAGAAAAAAGAGAG
Found at i:2659605 original size:21 final size:21
Alignment explanation
Indices: 2659580--2659626 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2659570 CAAGGAAAAT
*
2659580 AATCTTGAATAGATTTTCCTA
1 AATCTTGAATAGATTTTCCAA
2659601 AATCTTGAATAGATTTTCCAA
1 AATCTTGAATAGATTTTCCAA
2659622 AATCT
1 AATCT
2659627 AACATTCCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (21 bp):
AATCTTGAATAGATTTTCCAA
Found at i:2662833 original size:296 final size:297
Alignment explanation
Indices: 2662297--2662864 Score: 870
Period size: 296 Copynumber: 1.9 Consensus size: 297
2662287 TGATGGAGGT
* * *
2662297 CTGCAGTGGCGGTGACCTTAAGAAGAGGCATAATGCAAAGTGAAAGCAAGAGATGTTATTCGCGA
1 CTGCAGTGGCGGTGACCTTAAGAAGAGGCATAATGCAAAGTGAAAGAAAGAGATGTTATTCACAA
*
2662362 TCAGGTCCACAAGACGGCTCATCACATACATGATTTGGAAAAAAGAAGCTGAGTATTCAGCCAGT
66 TCAGGTCCACAAGACAGCTCATCACATACATGATTTGGAAAAAAGAAGCTGAGTATTCAGCCAGT
* * * *
2662427 GACCAGAGAAATAAGAAGACTTGTCAACCTGCTAAAAGTTGTCCAGAGTTTAAAATATCTAGCTC
131 GACCAGAGAAATAAGAAGAATTGTCAACCTGCTAAAAGTTATCCAAAGTTTAAAAAATCTAGCTC
* * * *
2662492 AAGTGTGCATTTAAAATGTTTTTAACCTCATTGTAGTATCACTTTTGTCCCAATGAAGGCTATTT
196 AAGTATACATTTAAAATGTTTTCAACCTCATTGTAGTAACACTTTTGTCCCAATGAAGGCTATTT
2662557 ATTATGACATGCTCCATTTAATCTGTTTGATGAAGAC
261 ATTATGACATGCTCCATTTAATCTGTTTGATGAAGAC
** * *
2662594 CTGCAGTGGTTGTGTCCTTAAGAAGAGGCCTAATGCAAAGTGAAAGAAAGAGATGTTATTCACAA
1 CTGCAGTGGCGGTGACCTTAAGAAGAGGCATAATGCAAAGTGAAAGAAAGAGATGTTATTCACAA
* * * *
2662659 TCAGGTCCACAAGACAGCTCATCACATGCATGATTTGG-CAAAAGAAGCT-ATGTATTTAGCTAG
66 TCAGGTCCACAAGACAGCTCATCACATACATGATTTGGAAAAAAGAAGCTGA-GTATTCAGCCAG
* * * *
2662722 TGACTAGAGAAGTAAGAAGAATTGTCAACTTGCTAAAATTTATCCAAAGTTTAAAAAATCTAGCT
130 TGACCAGAGAAATAAGAAGAATTGTCAACCTGCTAAAAGTTATCCAAAGTTTAAAAAATCTAGCT
* *
2662787 CAAGTATACCTTTAAAATGTTTTCGACCTCATTGTAGTAACACTTTTGTCCCAATGAAGGCTATT
195 CAAGTATACATTTAAAATGTTTTCAACCTCATTGTAGTAACACTTTTGTCCCAATGAAGGCTATT
*
2662852 TATTATGGCATGC
260 TATTATGACATGC
2662865 ACTTTTGGGA
Statistics
Matches: 243, Mismatches: 27, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
295 1 0.00
296 148 0.61
297 94 0.39
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (297 bp):
CTGCAGTGGCGGTGACCTTAAGAAGAGGCATAATGCAAAGTGAAAGAAAGAGATGTTATTCACAA
TCAGGTCCACAAGACAGCTCATCACATACATGATTTGGAAAAAAGAAGCTGAGTATTCAGCCAGT
GACCAGAGAAATAAGAAGAATTGTCAACCTGCTAAAAGTTATCCAAAGTTTAAAAAATCTAGCTC
AAGTATACATTTAAAATGTTTTCAACCTCATTGTAGTAACACTTTTGTCCCAATGAAGGCTATTT
ATTATGACATGCTCCATTTAATCTGTTTGATGAAGAC
Found at i:2665980 original size:134 final size:133
Alignment explanation
Indices: 2665748--2666160 Score: 488
Period size: 134 Copynumber: 3.1 Consensus size: 133
2665738 GCGATTTATT
* ** *
2665748 TTAACTCAACAACGAGGAGCTACTTCCTAGTTTA-GACTTCGAGCTAGATTTCAACTTCATGACG
1 TTAACTCAACAATGAGGAGCTACTTCCTAGTACATGACTTTGAGCTAGATTTCAACTTCATGACG
* * * * * *
2665812 AATGATATCATGCTCAAGTCATCCGAGACCGACTCAACTTCACAACGAATGAGTCATCCACAATT
66 AA-GATATCATGCTCAAATCATTCAAGATCGACTCAACTTCATAACGAATGAGTCATCCAAAATT
2665877 TAGC
130 TAGC
* * * * *
2665881 TTAACTCAATAATGAGGAACTACTTCCCAGTCCATGACTTTGAGCTAGATTTCAACTTCATGATG
1 TTAACTCAACAATGAGGAGCTACTTCCTAGTACATGACTTTGAGCTAGATTTCAACTTCATGACG
* * * * * *
2665946 AAGAATACCATGCTCAATTCATTCAAGATCGACTCAACTTCATGACGAAGGAGTTATCCATAATT
66 AAG-ATATCATGCTCAAATCATTCAAGATCGACTCAACTTCATAACGAATGAGTCATCCAAAATT
2666011 TAGC
130 TAGC
* * * *
2666015 TTAACTTAACAATGAGTAGCTACTTCCTAGTACATGA-TTTCGAGCTAGATTTTAACTTCACGAC
1 TTAACTCAACAATGAGGAGCTACTTCCTAGTACATGACTTT-GAGCTAGATTTCAACTTCATGAC
* * ** * *
2666079 GAAGGATATCGTGCTCAAATAATTTTAGATCGACTCAACTTCATAATGAATGAGTCATCAAAAAT
65 GAA-GATATCATGCTCAAATCATTCAAGATCGACTCAACTTCATAACGAATGAGTCATCCAAAAT
*
2666144 TTAGT
129 TTAGC
2666149 TTAACTCAACAA
1 TTAACTCAACAA
2666161 GGATGAGATA
Statistics
Matches: 235, Mismatches: 41, Indels: 7
0.83 0.14 0.02
Matches are distributed among these distances:
133 32 0.14
134 202 0.86
135 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (133 bp):
TTAACTCAACAATGAGGAGCTACTTCCTAGTACATGACTTTGAGCTAGATTTCAACTTCATGACG
AAGATATCATGCTCAAATCATTCAAGATCGACTCAACTTCATAACGAATGAGTCATCCAAAATTT
AGC
Found at i:2667240 original size:21 final size:21
Alignment explanation
Indices: 2667214--2667261 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
2667204 TCTAGGACAT
*
2667214 GAAAAAAGAGGGAAAA-AGAGG
1 GAAAAAAG-GGAAAAATAGAGG
2667235 GAAAAAAGGGAAAAATAGAGG
1 GAAAAAAGGGAAAAATAGAGG
2667256 GAAAAA
1 GAAAAA
2667262 GATAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (21 bp):
GAAAAAAGGGAAAAATAGAGG
Found at i:2667249 original size:9 final size:10
Alignment explanation
Indices: 2667216--2667263 Score: 71
Period size: 10 Copynumber: 4.7 Consensus size: 10
2667206 TAGGACATGA
2667216 AAAAAGAGGG
1 AAAAAGAGGG
2667226 AAAAAGAGGG
1 AAAAAGAGGG
2667236 AAAAA-AGGG
1 AAAAAGAGGG
2667245 AAAAATAGAGGG
1 -AAAA-AGAGGG
2667257 AAAAAGA
1 AAAAAGA
2667264 TAAAAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.11
10 22 0.63
11 5 0.14
12 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (10 bp):
AAAAAGAGGG
Found at i:2667268 original size:20 final size:20
Alignment explanation
Indices: 2667214--2667276 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
2667204 TCTAGGACAT
*
2667214 GAAAAAAGAGGGAAAAAGAGG
1 GAAAAAAGA-GAAAAAAGAGG
*
2667235 GAAAAAAGGGAAAAATAGAGG
1 GAAAAAAGAGAAAAA-AGAGG
* *
2667256 GAAAAAGATAAAAAAAAGAGG
1 GAAAAA-AGAGAAAAAAGAGG
2667277 AAGAGAGAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 5 0.14
21 24 0.69
22 6 0.17
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (20 bp):
GAAAAAAGAGAAAAAAGAGG
Found at i:2674342 original size:13 final size:13
Alignment explanation
Indices: 2674324--2674348 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2674314 TTATCATTTT
2674324 AAAAACACACTTA
1 AAAAACACACTTA
2674337 AAAAACACACTT
1 AAAAACACACTT
2674349 CTCCCCCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAACACACTTA
Found at i:2676020 original size:20 final size:20
Alignment explanation
Indices: 2675991--2676028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
2675981 CCCCTTCAAA
*
2675991 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2676011 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2676029 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:2679724 original size:21 final size:20
Alignment explanation
Indices: 2679682--2679725 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
2679672 TCAAAAGAAG
*
2679682 TTTTAAGATCATCAATTTTC
1 TTTTAAGATCATCAATTATC
2679702 TTTTAATGATCATC-ATTGATC
1 TTTTAA-GATCATCAATT-ATC
2679723 TTT
1 TTT
2679726 GAAAGTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTTAAGATCATCAATTATC
Found at i:2679879 original size:22 final size:21
Alignment explanation
Indices: 2679837--2679876 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2679827 GAGTTTGTTT
*
2679837 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
2679858 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
2679877 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:2682484 original size:31 final size:32
Alignment explanation
Indices: 2682431--2682501 Score: 110
Period size: 31 Copynumber: 2.2 Consensus size: 32
2682421 GGCTTGAGAA
*
2682431 CCTACTCAAGAAAGTTTCTCGGGGCCTCA-AGG
1 CCTACCCAAGAAAGTTTCTCGGGGCCTCAGA-G
2682463 CCTACCCAAGAAAG-TTCTCGGGGCCTCAGAG
1 CCTACCCAAGAAAGTTTCTCGGGGCCTCAGAG
2682494 CCTACCCA
1 CCTACCCA
2682502 GGGGTACCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
31 23 0.62
32 14 0.38
ACGTcount: A:0.25, C:0.34, G:0.23, T:0.18
Consensus pattern (32 bp):
CCTACCCAAGAAAGTTTCTCGGGGCCTCAGAG
Found at i:2690673 original size:20 final size:21
Alignment explanation
Indices: 2690627--2690673 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
2690617 ATTTCAATGC
*
2690627 TGAAATTTAAAGTTAGAATGT
1 TGAAATTTAAAGTTAGAAAGT
*
2690648 TG-AATTTAAGGTTAGAAAG-
1 TGAAATTTAAAGTTAGAAAGT
2690667 TGAAATT
1 TGAAATT
2690674 CGGACCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.21, T:0.36
Consensus pattern (21 bp):
TGAAATTTAAAGTTAGAAAGT
Found at i:2691358 original size:25 final size:25
Alignment explanation
Indices: 2691311--2691358 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2691301 AAGTATGATT
*
2691311 TATAATTTTAATTATAGATTATTTA
1 TATAATTTTAATTATAAATTATTTA
*
2691336 TATAATTTTTA-TATAAATGTATT
1 TATAATTTTAATTATAAAT-TATT
2691359 ATGGATGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
TATAATTTTAATTATAAATTATTTA
Found at i:2705636 original size:34 final size:34
Alignment explanation
Indices: 2705593--2705664 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
2705583 TTATTTTTAT
* *
2705593 TCATATTTTATAGGTTGTAAAGAATGAATGTTTC
1 TCATATTTTATAGGTTGTAAAGAACGAAAGTTTC
*
2705627 TCATATTTTATAGGTTGTAAGGAACGAAAGTTTC
1 TCATATTTTATAGGTTGTAAAGAACGAAAGTTTC
2705661 TCAT
1 TCAT
2705665 GGATGGATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.08, G:0.18, T:0.42
Consensus pattern (34 bp):
TCATATTTTATAGGTTGTAAAGAACGAAAGTTTC
Found at i:2706484 original size:45 final size:45
Alignment explanation
Indices: 2706267--2706485 Score: 242
Period size: 45 Copynumber: 4.9 Consensus size: 45
2706257 AACATACCAT
* * *
2706267 CTTTTCTGTTGATAATGCGCCCATATGCATTTCAACTATAGTATA
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * **
2706312 CTTTTATATTGATGATGTACCCATATACAACTCAAC-CATAGTATA
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTC-TAGTATA
* * *
2706357 CTTTTCTATTGATAATGTACCCATATACATTTCAACTCTAGCATA
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* * * * * *
2706402 CTTTTCTAATGATACTTCACCCATATGTAGTTCAACTCCAGTATA
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATA
* *
2706447 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCT
1 CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCT
2706486 GGCATCATTT
Statistics
Matches: 141, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
45 140 0.99
46 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.39
Consensus pattern (45 bp):
CTTTTCTATTGATAATGCACCCATATGCATTTCAACTCTAGTATA
Found at i:2706513 original size:90 final size:89
Alignment explanation
Indices: 2706275--2706518 Score: 217
Period size: 90 Copynumber: 2.7 Consensus size: 89
2706265 ATCTTTTCTG
* * * * * * * *
2706275 TTGATAATGCGCCCATATGCATTTCAACTATAGTATAC-TTTTATATTGATGATGTACCCATATA
1 TTGATAATGCACCCATATACATTTCAACTCTAGCATACATTTCA-A-TGATAATGCACCCATATG
* ** * *
2706339 CAACTCAAC-CATAGTATACTTTTCTA
64 TAGTTCAACTC-CAGTATACTTTTATA
* * * *
2706365 TTGATAATGTACCCATATACATTTCAACTCTAGCATACTTTTCTAATGATACTTCACCCATATGT
1 TTGATAATGCACCCATATACATTTCAACTCTAGCATACATTTC-AATGATAATGCACCCATATGT
*
2706430 AGTTCAACTCCAGTATACTTTTATG
65 AGTTCAACTCCAGTATACTTTTATA
* *
2706455 TTGATAATGCACCCATATGCATTTCAACTCTGGCAT-CATTTC-ATGCCAATAATGCACCCATAT
1 TTGATAATGCACCCATATACATTTCAACTCTAGCATACATTTCAATG---ATAATGCACCCATAT
2706518 G
63 G
2706519 CATTATTCTT
Statistics
Matches: 125, Mismatches: 23, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
87 3 0.02
89 5 0.04
90 111 0.89
91 5 0.04
92 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (89 bp):
TTGATAATGCACCCATATACATTTCAACTCTAGCATACATTTCAATGATAATGCACCCATATGTA
GTTCAACTCCAGTATACTTTTATA
Found at i:2707069 original size:22 final size:22
Alignment explanation
Indices: 2707012--2707074 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 22
2707002 ATTTCTAGCC
2707012 CTTA-GGTATCGATAC-CCCTA
1 CTTAGGGTATCGATACTCCCTA
* **
2707032 CTTATGGTATTAATACTACCCTA
1 CTTAGGGTATCGATACT-CCCTA
2707055 -TTAGGGTATCGATACTCCCT
1 CTTAGGGTATCGATACTCCCT
2707075 TAATGTATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.11
21 13 0.37
22 13 0.37
23 5 0.14
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.35
Consensus pattern (22 bp):
CTTAGGGTATCGATACTCCCTA
Found at i:2707156 original size:21 final size:19
Alignment explanation
Indices: 2707111--2707184 Score: 62
Period size: 21 Copynumber: 3.8 Consensus size: 19
2707101 CGATATAGCC
*
2707111 TGGTATCGATAGCCTCA-CCA
1 TGGTATCGATA-CC-CATCTA
2707131 TGGTATCGATACCCTATGCTA
1 TGGTATCGATACCC-AT-CTA
* * *
2707152 TGGTACCAATACCCCTCTA
1 TGGTATCGATACCCATCTA
2707171 -GGTATCGATACCCA
1 TGGTATCGATACCCA
2707185 AATTAGATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
18 12 0.27
19 6 0.14
20 12 0.27
21 14 0.32
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (19 bp):
TGGTATCGATACCCATCTA
Found at i:2714647 original size:16 final size:16
Alignment explanation
Indices: 2714626--2714656 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2714616 AAAACACACT
2714626 CCACACGTTAAACCCC
1 CCACACGTTAAACCCC
2714642 CCACACGTTAAACCC
1 CCACACGTTAAACCC
2714657 GTCAGTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.48, G:0.06, T:0.13
Consensus pattern (16 bp):
CCACACGTTAAACCCC
Found at i:2719483 original size:2 final size:2
Alignment explanation
Indices: 2719476--2719536 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
2719466 TTTCAAAAAC
2719476 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
2719518 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2719537 GTTTTTGAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2719576 original size:37 final size:37
Alignment explanation
Indices: 2719520--2719830 Score: 452
Period size: 37 Copynumber: 8.4 Consensus size: 37
2719510 ATATATATAT
*
2719520 ATATATATATATATATAGTTTTTGAAAATATTTTGAAA
1 ATATATATA-ATATATAGTTTTTGAAAACATTTTGAAA
* *
2719558 ATATATATAATATATAGTTTTTCAAAACA-TTT-CAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
2719593 ATATATAT-ATAATATAGTTTTTGAAAACATTTTGAATA
1 ATATATATAAT-ATATAGTTTTTGAAAACATTTTGAA-A
* *
2719631 TATATATATAATATATAGTTTTAGAAAATATTTTGAAAA
1 -ATATATATAATATATAGTTTTTGAAAACATTTTG-AAA
* *
2719670 ATATATATAATATATAGTTTATGAAAATATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
2719707 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
2719744 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
*
2719781 ATATATAT-ATAATATAATTTTTG-AAACATTTTGAAA
1 ATATATATAAT-ATATAGTTTTTGAAAACATTTTGAAA
*
2719817 ATATATATTATATA
1 ATATATATAATATA
2719831 AAATATTTAT
Statistics
Matches: 252, Mismatches: 12, Indels: 20
0.89 0.04 0.07
Matches are distributed among these distances:
34 2 0.01
35 27 0.11
36 32 0.13
37 115 0.46
38 42 0.17
39 30 0.12
40 4 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAA
Found at i:2719711 original size:112 final size:112
Alignment explanation
Indices: 2719516--2719830 Score: 473
Period size: 112 Copynumber: 2.8 Consensus size: 112
2719506 ATATATATAT
2719516 ATATATATATATATATATATAGTTTTTGAAAATATTTTG-AAAATATATATAATATATAGTTTTT
1 ATATATATATATA-ATATATAGTTTTTGAAAATATTTTGAAAAATATATATAATATATAGTTTTT
* *
2719580 CAAAACA-TTTCAAATATATATATAATATAGTTTTTGAAAACATTTTGA
65 GAAAACATTTTGAAA-ATATATATAATATAGTTTTTGAAAACATTTTGA
* *
2719628 ATATATATATATAATATATAGTTTTAGAAAATATTTTGAAAAATATATATAATATATAGTTTATG
1 ATATATATATATAATATATAGTTTTTGAAAATATTTTGAAAAATATATATAATATATAGTTTTTG
*
2719693 AAAATATTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGA
66 AAAACATTTTGAAAATATATAT-A-ATATAGTTTTTGAAAACATTTTGA
*
2719742 A-A-ATATATATAATATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATA-A-TTTTT
1 ATATATATATATAATATATAGTTTTTGAAAATATTTTGAAAA-ATATATATAATATATAGTTTTT
*
2719803 G-AAACATTTTGAAAATATATATTATATA
65 GAAAACATTTTGAAAATATATATAATATA
2719831 AAATATTTAT
Statistics
Matches: 188, Mismatches: 10, Indels: 14
0.89 0.05 0.07
Matches are distributed among these distances:
108 5 0.03
110 20 0.11
111 29 0.15
112 87 0.46
113 22 0.12
114 25 0.13
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (112 bp):
ATATATATATATAATATATAGTTTTTGAAAATATTTTGAAAAATATATATAATATATAGTTTTTG
AAAACATTTTGAAAATATATATAATATAGTTTTTGAAAACATTTTGA
Found at i:2719841 original size:149 final size:152
Alignment explanation
Indices: 2719516--2719830 Score: 491
Period size: 149 Copynumber: 2.1 Consensus size: 152
2719506 ATATATATAT
*
2719516 ATATATATATATATATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTTTTC
1 ATATATAT-TATATATATATAGTTTATGAAAATATTTTGAAAATATATATAATATATAGTTTTTC
* *
2719581 AAAACATTTCAAATATATATATAATATAGTTTTTGAAAACATTTTGAATATATATATATAATATA
65 AAAACATTTAAAATATATATATAATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATA
*
2719646 TAGTTTTAGAAAATATTTTGAAA
130 TAGTTTTAGAAAACATTTTGAAA
*
2719669 A-ATATA-TATA-ATATATAGTTTATGAAAATATTTTGAAAATATATATAATATATAGTTTTTGA
1 ATATATATTATATATATATAGTTTATGAAAATATTTTGAAAATATATATAATATATAGTTTTTCA
2719731 AAACATTTTGAAAATATATATA-ATATATAGTTTTTGAAAACATTTTGAAAATATATATATAATA
66 AAACA-TTT-AAAATATATATATA-ATATAGTTTTTGAAAACATTTTGAAAATATATATATAATA
*
2719795 TA-A-TTTTTG-AAACATTTTGAAA
128 TATAGTTTTAGAAAACATTTTGAAA
2719817 ATATATATTATATA
1 ATATATATTATATA
2719831 AAATATTTAT
Statistics
Matches: 150, Mismatches: 6, Indels: 14
0.88 0.04 0.08
Matches are distributed among these distances:
148 13 0.09
149 65 0.43
150 13 0.09
151 53 0.35
152 5 0.03
153 1 0.01
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (152 bp):
ATATATATTATATATATATAGTTTATGAAAATATTTTGAAAATATATATAATATATAGTTTTTCA
AAACATTTAAAATATATATATAATATAGTTTTTGAAAACATTTTGAAAATATATATATAATATAT
AGTTTTAGAAAACATTTTGAAA
Found at i:2719855 original size:5 final size:5
Alignment explanation
Indices: 2719842--2719919 Score: 51
Period size: 5 Copynumber: 16.2 Consensus size: 5
2719832 AATATTTATG
* * *
2719842 TATTA TATTT TATTAT T-TAT TA-TT TATTA TATTAT TA-TT TATTT TATTTT
1 TATTT TATTT TATT-T TATTT TATTT TATTT TATT-T TATTT TATTT TA-TTT
*
2719892 TATTT TA-TT TATTT T-CTT T-TTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT TATTT T
2719920 GGTCCAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
4 18 0.31
5 31 0.53
6 9 0.16
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:2719876 original size:15 final size:15
Alignment explanation
Indices: 2719850--2719896 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
2719840 TGTATTATAT
2719850 TTTATTAT-TTATTA
1 TTTATTATATTATTA
2719864 TTTATTATATTATTA
1 TTTATTATATTATTA
* *
2719879 TTTATTTTATTTTTA
1 TTTATTATATTATTA
2719894 TTT
1 TTT
2719897 TATTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 8 0.27
15 22 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTATTATATTATTA
Found at i:2719899 original size:20 final size:21
Alignment explanation
Indices: 2719834--2719917 Score: 79
Period size: 20 Copynumber: 4.0 Consensus size: 21
2719824 TTATATAAAA
2719834 TATTTATGTATTATATTTTATTAT
1 TATTTAT-T-TTAT-TTTTATTAT
*
2719858 T-TATTA-TTTA-TTATATTAT
1 TAT-TTATTTTATTTTTATTAT
2719877 TATTTATTTTATTTTTATT-T
1 TATTTATTTTATTTTTATTAT
*
2719897 TATTTATTTTCTTTTT-TTAT
1 TATTTATTTTATTTTTATTAT
2719917 T
1 T
2719918 TTGGTCCAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
19 14 0.27
20 23 0.44
21 9 0.17
22 1 0.02
23 1 0.02
24 4 0.08
ACGTcount: A:0.24, C:0.01, G:0.01, T:0.74
Consensus pattern (21 bp):
TATTTATTTTATTTTTATTAT
Found at i:2719902 original size:15 final size:15
Alignment explanation
Indices: 2719847--2719919 Score: 66
Period size: 15 Copynumber: 5.0 Consensus size: 15
2719837 TTATGTATTA
2719847 TATTTTA-TTATTTAT
1 TATTTTATTTATTT-T
*
2719862 TA-TTTATTATATTAT
1 TATTTTATT-TATTTT
2719877 TA-TTTATTTTATTTT
1 TATTTTA-TTTATTTT
2719892 TATTTTATTTA-TTT
1 TATTTTATTTATTTT
*
2719906 TCTTTT-TTTATTTT
1 TATTTTATTTATTTT
2719920 GGTCCAAATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
13 4 0.08
14 15 0.30
15 21 0.42
16 10 0.20
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTATTTATTTT
Found at i:2728758 original size:4 final size:4
Alignment explanation
Indices: 2728751--2728806 Score: 67
Period size: 4 Copynumber: 13.0 Consensus size: 4
2728741 AACAACAATA
*
2728751 AAAT AAAT AAAT AAAT AAAAGT GAAAT AAAAT AAAT AAAT AGAT AAAT
1 AAAT AAAT AAAT AAAT -AAA-T -AAAT -AAAT AAAT AAAT AAAT AAAT
2728799 AAAT AAAT
1 AAAT AAAT
2728807 TAAAAACATT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 34 0.74
5 8 0.17
6 4 0.09
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2728912 original size:37 final size:37
Alignment explanation
Indices: 2728907--2729029 Score: 173
Period size: 37 Copynumber: 3.3 Consensus size: 37
2728897 ACTATATAAT
2728907 ATATATATTT--AAAAACTAATTTTCAAAACTATATA
1 ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
*
2728942 ATATATATGTTTTTCAAAAA-T-GTTTTCAAAACTATATA
1 ATATATA--TTTTT-AAAAACTAATTTTCAAAACTATATA
2728980 ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
1 ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
2729017 ATATATATGTTTT
1 ATATATAT-TTTT
2729030 TCAAAAATGT
Statistics
Matches: 78, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
35 12 0.15
36 6 0.08
37 27 0.35
38 27 0.35
39 1 0.01
40 5 0.06
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
ATATATATTTTTAAAAACTAATTTTCAAAACTATATA
Found at i:2728968 original size:112 final size:109
Alignment explanation
Indices: 2728806--2729024 Score: 332
Period size: 112 Copynumber: 2.0 Consensus size: 109
2728796 AATAAATAAA
* * * *
2728806 TTAAAAACATTTTTTAAAACTATACAATATATGTTTTAAAAAATAATTTTCAAAACCATATAATC
1 TTAAAAACAATTTTCAAAACTATAAAATATATGTTTTAAAAAATAATTTTCAAAACCATATAATA
2728871 TATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
66 TATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
* * *
2728915 TTAAAAACTAATTTTCAAAACTATATAATATATATGTTTTTCAAAAAT-GTTTTCAAAACTATAT
1 TTAAAAAC-AATTTTCAAAACTATA-AA-ATATATG-TTTTAAAAAATAATTTTCAAAACCATAT
2728979 AATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATAT
62 AATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATAT
2729025 GTTTTTCAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
109 8 0.08
110 14 0.14
111 1 0.01
112 66 0.67
113 10 0.10
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (109 bp):
TTAAAAACAATTTTCAAAACTATAAAATATATGTTTTAAAAAATAATTTTCAAAACCATATAATA
TATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
Found at i:2728983 original size:75 final size:74
Alignment explanation
Indices: 2728816--2729223 Score: 365
Period size: 75 Copynumber: 5.4 Consensus size: 74
2728806 TTAAAAACAT
* * * * * *
2728816 TTTTTAAAACTATACAATATATGT-TTTAAAAAATAATTTTCAAAACCATATAATCTATA-TTTT
1 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATTTTT
*
2728879 T-AAAAACTAA
66 TCAAAAA-T-G
2728889 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
1 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATAT-TTT
2728954 TTCAAAAATG
65 TTCAAAAATG
*
2728964 TTTTCAAAACTATATAATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
1 TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATAT-TTT
2729029 TTCAAAAATG
65 TTCAAAAATG
* *
2729039 TTTTTAAAAATTATATATTATATATATATATATATATTTTAAA--AAGTTTTCAAAA-TGATATA
1 -TTTTCAAAACTATATA--ATATATATAT-T-TA-A----AAACTAA-TTTTCAAAACT-ATATA
2729101 ATATATA--TTTTCAAAAATG
54 ATATATATTTTTTCAAAAATG
* * ** * *
2729120 TTTTTCAAAGACTATATATTATATAT-TTTCAAAAC--ATTTAAAAAACCCATATATTATATAAT
1 -TTTTCAAA-ACTATATAATATATATATTTAAAAACTAATTTTCAAAA-CTATATAATATAT-AT
2729182 TTTTTC-AAAATG
62 TTTTTCAAAAATG
* * * *
2729194 ATTTC-AATCCATATAATATATATATATAAA
1 TTTTCAAAACTATATAATATATATATTTAAA
2729224 TAAAAATGGA
Statistics
Matches: 286, Mismatches: 25, Indels: 49
0.79 0.07 0.14
Matches are distributed among these distances:
71 20 0.07
72 20 0.07
73 26 0.09
74 38 0.13
75 79 0.28
76 21 0.07
77 6 0.02
78 10 0.03
79 2 0.01
80 9 0.03
81 21 0.07
82 7 0.02
83 3 0.01
84 21 0.07
85 3 0.01
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.43
Consensus pattern (74 bp):
TTTTCAAAACTATATAATATATATATTTAAAAACTAATTTTCAAAACTATATAATATATATTTTT
TCAAAAATG
Found at i:2729061 original size:112 final size:110
Alignment explanation
Indices: 2728806--2729178 Score: 330
Period size: 112 Copynumber: 3.3 Consensus size: 110
2728796 AATAAATAAA
* * *
2728806 TTAAAAAC-ATTTTTTAAAACTATACAATATATGTTTTAAAAAATAATTTTCAAAACCATATAAT
1 TTAAAAACTATTTTTAAAAACTATATATTATATGTTTTAAAAAATAATTTTCAAAACCATATAAT
*
2728870 CTATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
66 ATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
* * * * *
2728915 TTAAAAACTAATTTTCAAAACTATATAATATATATGTTTTTCAAAAAT-GTTTTCAAAACTATAT
1 TTAAAAACTATTTTTAAAAACTATAT-AT-TATATG-TTTTAAAAAATAATTTTCAAAACCATAT
*
2728979 AATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATGTTT
63 AATATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATA--TAT
* * *
2729029 TTCAAAAA-TGTTTTTAAAAATTATATATTATATATATATATATATATTTTAAA-AAGTTTTCAA
1 TT-AAAAACTATTTTTAAAAACTATATATTATATGT-T-T-TA-A-A----AAATAA-TTTTCAA
** * ** *
2729092 AATGATATAATATATATTTTCAAAAA-TGTTTTTCAAAGACTATATATTATATAT-T
55 AACCATATAATATATATTTTTAAAAACTAATTTTCAAA-ACTATATAATATATATAT
* * *
2729147 TTCAAAAC-A-TTTAAAAAACCCATATATTATAT
1 TTAAAAACTATTTTTAAAAA-CTATATATTATAT
2729179 AATTTTTTCA
Statistics
Matches: 216, Mismatches: 27, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
109 8 0.04
110 14 0.06
111 2 0.01
112 70 0.32
113 13 0.06
114 19 0.09
115 6 0.03
116 9 0.04
117 15 0.07
118 3 0.01
119 1 0.00
120 12 0.06
121 44 0.20
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (110 bp):
TTAAAAACTATTTTTAAAAACTATATATTATATGTTTTAAAAAATAATTTTCAAAACCATATAAT
ATATATTTTTAAAAACTAATTTTCAAAACTATATAATATATATAT
Found at i:2729105 original size:35 final size:35
Alignment explanation
Indices: 2729060--2729153 Score: 97
Period size: 35 Copynumber: 2.7 Consensus size: 35
2729050 TATATATTAT
2729060 ATATATATATATATATTTTAAAAA-G-TTTTCAAAATG
1 ATATA-ATATATATATTTTAAAAATGTTTTTC-AAA-G
*
2729096 ATATAATATATAT-TTTCAAAAATGTTTTTCAAAG
1 ATATAATATATATATTTTAAAAATGTTTTTCAAAG
*
2729130 ACTAT-ATATTATATATTTTCAAAA
1 A-TATAATA-TATATATTTTAAAAA
2729154 CATTTAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
34 13 0.26
35 20 0.40
36 17 0.34
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (35 bp):
ATATAATATATATATTTTAAAAATGTTTTTCAAAG
Found at i:2729108 original size:45 final size:47
Alignment explanation
Indices: 2729011--2729108 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 47
2729001 TTTTCAAAAC
* * *
2729011 TATATA-ATATATATGTTTTTCAAAAATGTTTTTAAAAATTATATAT
1 TATATATATATATATATTTTTCAAAAATGTTTTTAAAAATGATATAA
*
2729057 TATATATATATATATATATTTT-AAAAA-G-TTTTCAAAATGATATAA
1 TATATATATATATATAT-TTTTCAAAAATGTTTTTAAAAATGATATAA
2729102 TATATAT
1 TATATAT
2729109 TTTCAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
45 21 0.46
46 7 0.15
47 14 0.30
48 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (47 bp):
TATATATATATATATATTTTTCAAAAATGTTTTTAAAAATGATATAA
Found at i:2729137 original size:37 final size:33
Alignment explanation
Indices: 2729060--2729153 Score: 118
Period size: 37 Copynumber: 2.7 Consensus size: 33
2729050 TATATATTAT
2729060 ATATATATATATATATTTT-AAAAAGTTTTCAAA
1 ATATATA-ATATATATTTTCAAAAAGTTTTCAAA
2729093 ATGATATAATATATATTTTCAAAAATGTTTTTCAAA
1 AT-ATATAATATATATTTTCAAAAA-G-TTTTCAAA
*
2729129 GACTATATATTATATATTTTCAAAA
1 -A-TATATAATATATATTTTCAAAA
2729154 CATTTAAAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 8
0.86 0.02 0.13
Matches are distributed among these distances:
33 13 0.24
34 10 0.19
35 1 0.02
36 8 0.15
37 21 0.39
38 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (33 bp):
ATATATAATATATATTTTCAAAAAGTTTTCAAA
Found at i:2730027 original size:84 final size:82
Alignment explanation
Indices: 2729804--2730399 Score: 536
Period size: 84 Copynumber: 7.2 Consensus size: 82
2729794 CCTTGCCTTG
* * * *
2729804 AGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGTGACA
1 AGCTATGCTGCAAATGATATGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTG-CA
* * * *
2729869 GATAACCATTCT-AACCATG
64 GATAACCCTTCTCGA-CTTA
* * * * * *
2729888 AGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTTTGC
1 AGCTATGCTGCAAATGATATGCCCTCG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG--TGC
*
2729953 AGATAGCCCTTCTCGACTTA
63 AGATAACCCTTCTCGACTTA
* * * * * * **
2729973 AGCTATACTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTATTGGCA
1 AGCTATGCTGCAAATGATATGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGT-GCA
* * *
2730038 GACAAACCTTCTAGACTTA
64 GATAACCCTTCTCGACTTA
* * * * * *
2730057 TGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTGACAG
1 AGCTATGCTGCAAATGATATGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG-CAG
* * *
2730122 ATAACCCTTCTAGCCTTG
65 ATAACCCTTCTCGACTTA
* ** * * **
2730140 AGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-GCAG
1 AGCTATGCTGCAAATGATATGCCCTCG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAG
*
2730203 ATAGCCCTTCTCGACTTA
65 ATAACCCTTCTCGACTTA
* * *
2730221 AGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAA
1 AGCTATGCTGCAAATGATATGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GCA
*
2730286 GATAACCCTTCTCGACTTG
64 GATAACCCTTCTCGACTTA
* * * * * * *
2730305 AGTTATGTTGTAAATGATATGCCCTCGAAGCTGAACGTAATCCAACTCGAGGGTCTTT-G-GCAG
1 AGCTATGCTGCAAATGATATGCCCTCG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAG
*
2730368 ATAGCCCTTCTCGACTTA
65 ATAACCCTTCTCGACTTA
*
2730386 AGCTATACTGCAAA
1 AGCTATGCTGCAAA
2730400 AGGCTTGTAT
Statistics
Matches: 411, Mismatches: 88, Indels: 29
0.78 0.17 0.05
Matches are distributed among these distances:
80 26 0.06
81 69 0.17
82 2 0.00
83 42 0.10
84 184 0.45
85 85 0.21
86 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (82 bp):
AGCTATGCTGCAAATGATATGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGCAGA
TAACCCTTCTCGACTTA
Found at i:2730074 original size:169 final size:165
Alignment explanation
Indices: 2729800--2730362 Score: 562
Period size: 169 Copynumber: 3.4 Consensus size: 165
2729790 CCCTCCTTGC
* *
2729800 CTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGT
1 CTTGAGCTATGCTGTAAATGATGTGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT--T
* * * * * * * * *
2729865 GACAGATAACCATTCTA-AC-CATGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAA
64 GGCAGAAAACC-TTCTAGACTTAT--GTTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
* *
2729928 TCGAACTCGAGGGTCTTTGGTTTGCAGATAGCCCTTCTCGA
125 TCGAACTCGAAGGTCTTTGGTTTGCAGATAACCCTTCTCGA
* * * * * * *
2729969 CTTAAGCTATACTGCAAATGATGTGTCGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTATT
1 CTTGAGCTATGCTGTAAATGATGTGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-T-TT
* *
2730034 GGCAGACAAACCTTCTAGACTTATGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTG
64 GGCAGA-AAACCTTCTAGACTTATGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCG
* *
2730099 AACTCGAAGGTCTTTGG--TGACAGATAACCCTTCTAGC
128 AACTCGAAGGTCTTTGGTTTG-CAGATAACCCTTCTCGA
* * * * * **
2730136 CTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC--TTTG
1 CTTGAGCTATGCTGTAAATGATGTGCCCTCG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTTG
** * * *
2730199 GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
65 GCAGA-AAACCTTCTAGACTTATGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGA
* *
2730264 ACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGA
129 ACTCGAAGGTCTTTGGTTTGCAGATAACCCTTCTCGA
* * * * * * *
2730301 CTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAACGTAATCCAACTCGAGGGTCTTT
1 CTTGAGCTATGCTGTAAATGATGTGCCCTCG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTT
2730363 GGCAGATAGC
Statistics
Matches: 328, Mismatches: 55, Indels: 24
0.81 0.14 0.06
Matches are distributed among these distances:
164 76 0.23
165 68 0.21
166 3 0.01
167 37 0.11
168 54 0.16
169 80 0.24
170 7 0.02
171 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (165 bp):
CTTGAGCTATGCTGTAAATGATGTGCCCTCGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTTGG
CAGAAAACCTTCTAGACTTATGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGTTTGCAGATAACCCTTCTCGA
Found at i:2730322 original size:248 final size:250
Alignment explanation
Indices: 2729800--2730364 Score: 771
Period size: 248 Copynumber: 2.3 Consensus size: 250
2729790 CCCTCCTTGC
* * * *
2729800 CTTGAGCTATGCTGTAAATGATGTGCCCTGGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGGT
1 CTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT
2729865 GACAGATAACCATTCTAACCATGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATC
65 GACAGATAACCATTCTAACCATGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATC
*
2729930 GAACTCGAGGGTCTTTGGTTTGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGT
130 GAACTCGAGGGTCTTTGG--TGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGT
* *
2729995 CGTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTATTGGCAGACAAACCTTCTAGA
193 CCTTGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTATTGGAAGACAAACCTTCTAGA
* * *
2730053 CTT-ATGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGT
1 CTTGA-GTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
* * * * *
2730117 GACAGATAACCCTTCTAGCCTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATC
65 GACAGATAACCATTCTAACCATGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATC
* *
2730182 GAACTCGGGGGTCTTT-G-GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CC
130 GAACTCGAGGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGTCC
* * * * *
2730244 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT-TGGTTGGAAGATAACCCTTCTCGA
195 TT-GAGCTGAGCGTAGTCGAACTCAAAGGTCTTGT-ATTGGAAGACAAACCTTCTAGA
* * * * * * *
2730301 CTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAACGTAATCCAACTCGAGGGTCTTTGG
1 CTTGAGTTATGCTGTAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
2730365 CAGATAGCCC
Statistics
Matches: 275, Mismatches: 32, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
247 4 0.01
248 107 0.39
249 32 0.12
251 1 0.00
252 82 0.30
253 49 0.18
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (250 bp):
CTTGAGTTATGCTGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
ACAGATAACCATTCTAACCATGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCG
AACTCGAGGGTCTTTGGTGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATATGTCCT
TGAGCTGAGCGTAGTCGAACTCAAAGGTCTTGTATTGGAAGACAAACCTTCTAGA
Found at i:2730367 original size:165 final size:164
Alignment explanation
Indices: 2729800--2730399 Score: 614
Period size: 165 Copynumber: 3.6 Consensus size: 164
2729790 CCCTCCTTGC
* * * * **
2729800 CTTGAGCTATGCTGTAAATGATGTGCCCT-GGAGCTGAGCGTAGTCGAACTCGAATGTCTTTTGG
1 CTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGGTC-TTT-G
* * * * * * * * * * * *
2729864 TGACAGATAACCATTCT-AACCATGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAA
64 -G-CAGATAGCCCTTCTCGA-CTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAG
* * *
2729928 TCGAACTCGAGGGTCTTTGGTTTGCAGATAGCCCTTCTCGA
125 TCGAACTCGAAGGTCTTTGG-TTGAAGATAACCCTTCTCGA
* * * * * * * * * * *
2729969 CTTAAGCTATACTGCAAATGATGTGTCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGTCTTGTAT
1 CTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGGTC---T-T
* ** * * * * *
2730033 TGGCAGACAAACCTTCTAGACTTATGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTT
62 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTC
* *
2730098 GAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGC
127 GAACTCGAAGGTCTTTGGTTGA-AGATAACCCTTCTCGA
* * *
2730136 CTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGGC
1 CTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGC
2730201 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAAC
66 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAAC
2730266 TCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGA
131 TCGAAGGTCTTTGGTT-GAAGATAACCCTTCTCGA
* * *
2730301 CTTGAGTTATGTTGTAAATGATATGCCCTCGAAGCTGAACGTAATCCAACTCGAGGGTCTTTGGC
1 CTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGC
*
2730366 AGATAGCCCTTCTCGACTTAAGCTATACTGCAAA
66 AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAA
2730400 AGGCTTGTAT
Statistics
Matches: 363, Mismatches: 59, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
164 76 0.21
165 108 0.30
166 4 0.01
167 35 0.10
168 54 0.15
169 79 0.22
170 3 0.01
171 2 0.01
172 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (164 bp):
CTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAGGGTCTTTGGC
AGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAAC
TCGAAGGTCTTTGGTTGAAGATAACCCTTCTCGA
Found at i:2736845 original size:4 final size:4
Alignment explanation
Indices: 2736838--2736890 Score: 63
Period size: 4 Copynumber: 13.0 Consensus size: 4
2736828 ACAATAAAAC
* *
2736838 AAAT AAAT AAAT AAAT -AAT AAAT GAAAT AAAAT AAAT ATAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AAAT AAAT AAAT
2736887 AAAT
1 AAAT
2736891 TAAAAACCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
3 3 0.07
4 33 0.75
5 8 0.18
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Done.