Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 19
Found at i:2589912 original size:27 final size:27
Alignment explanation
Indices: 2589882--2589964 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
2589872 ATGGAAAAGA
2589882 ACAAGACACCAACATACAGAAACTACT
1 ACAAGACACCAACATACAGAAACTACT
* * * ** **
2589909 ACAA-ATAACAAGCACATGGAAA--AGA
1 ACAAGACACCAA-CATACAGAAACTACT
2589934 ACAAGACACCAACATACAGAAACTACT
1 ACAAGACACCAACATACAGAAACTACT
2589961 ACAA
1 ACAA
2589965 ATAACAAGCA
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
25 12 0.32
26 10 0.26
27 16 0.42
ACGTcount: A:0.55, C:0.25, G:0.10, T:0.10
Consensus pattern (27 bp):
ACAAGACACCAACATACAGAAACTACT
Found at i:2589946 original size:52 final size:52
Alignment explanation
Indices: 2589868--2589974 Score: 214
Period size: 52 Copynumber: 2.1 Consensus size: 52
2589858 CCAAAGAAGT
2589868 GCACATGGAAAAGAACAAGACACCAACATACAGAAACTACTACAAATAACAA
1 GCACATGGAAAAGAACAAGACACCAACATACAGAAACTACTACAAATAACAA
2589920 GCACATGGAAAAGAACAAGACACCAACATACAGAAACTACTACAAATAACAA
1 GCACATGGAAAAGAACAAGACACCAACATACAGAAACTACTACAAATAACAA
2589972 GCA
1 GCA
2589975 AAACCTCAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (52 bp):
GCACATGGAAAAGAACAAGACACCAACATACAGAAACTACTACAAATAACAA
Found at i:2589955 original size:25 final size:25
Alignment explanation
Indices: 2589875--2589955 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
2589865 AGTGCACATG
2589875 GAAAAGAACAAGACACCAACATACA
1 GAAAAGAACAAGACACCAACATACA
** * * * **
2589900 GAAACTACTACAA-ATAACAAGCACATG
1 GAAA--AGAACAAGACACCAA-CATACA
2589927 GAAAAGAACAAGACACCAACATACA
1 GAAAAGAACAAGACACCAACATACA
2589952 GAAA
1 GAAA
2589956 CTACTACAAA
Statistics
Matches: 38, Mismatches: 14, Indels: 8
0.63 0.23 0.13
Matches are distributed among these distances:
25 16 0.42
26 10 0.26
27 12 0.32
ACGTcount: A:0.58, C:0.22, G:0.12, T:0.07
Consensus pattern (25 bp):
GAAAAGAACAAGACACCAACATACA
Found at i:2591437 original size:38 final size:38
Alignment explanation
Indices: 2591342--2591437 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
2591332 TGCAGGGAAC
** *
2591342 AAGGGCATGAAAGAAGATGCCTTTAAATTGATTCAAAT
1 AAGGGCATGAAAGAAGATATCTTTAAATCGATTCAAAT
*
2591380 AAGGGCATGAAAGAAGATATCTTTGAATCGATTCAAAT
1 AAGGGCATGAAAGAAGATATCTTTAAATCGATTCAAAT
*
2591418 AAGGACATGAAAGAAGATAT
1 AAGGGCATGAAAGAAGATAT
2591438 GTGGATGAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 53 1.00
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (38 bp):
AAGGGCATGAAAGAAGATATCTTTAAATCGATTCAAAT
Found at i:2592328 original size:12 final size:13
Alignment explanation
Indices: 2592304--2592328 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2592294 TTATTTTACA
2592304 AAAAATTATTTTT
1 AAAAATTATTTTT
2592317 AAAAATTATTTT
1 AAAAATTATTTT
2592329 CAATGAAATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAAAATTATTTTT
Found at i:2592615 original size:97 final size:98
Alignment explanation
Indices: 2592496--2592685 Score: 283
Period size: 101 Copynumber: 1.9 Consensus size: 98
2592486 CAACCAAACA
* * *
2592496 TAACGTAGAGCATGTCATAGG-CATTCAATAAGTAAAATTATATAATTATAAACGTCAATCCTCA
1 TAACGTAGAGCATGCCACAGGTCATTCAATAAGTAAAATTATATAATTATAAACGTAAATCCTCA
2592560 CATAACGACTTATATACTCAATTCAATCAAGCC
66 CATAACGACTTATATACTCAATTCAATCAAGCC
* * *
2592593 TAACGTAGAGCATGCCACAGGCATTCATTCAATAAGTACAATTATATAGTTATAAATGTAAATCC
1 TAACGTAGAGCATGCCACAGG---TCATTCAATAAGTAAAATTATATAATTATAAACGTAAATCC
*
2592658 TCACATAACGACTTATATACTGAATTCA
63 TCACATAACGACTTATATACTCAATTCA
2592686 CTCTATTGGA
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
97 19 0.23
101 63 0.77
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.29
Consensus pattern (98 bp):
TAACGTAGAGCATGCCACAGGTCATTCAATAAGTAAAATTATATAATTATAAACGTAAATCCTCA
CATAACGACTTATATACTCAATTCAATCAAGCC
Found at i:2597334 original size:170 final size:170
Alignment explanation
Indices: 2597052--2597388 Score: 629
Period size: 170 Copynumber: 2.0 Consensus size: 170
2597042 ACTCGGAGCT
*
2597052 TCTCGATACGAAAGAAACCAGCAACCTCATAATACCACAAGCAAGAATTCACACCAGACAACAAA
1 TCTCGATACGAAAGAAACCAACAACCTCATAATACCACAAGCAAGAATTCACACCAGACAACAAA
*
2597117 ATACATACTCCATGACACCATTATTCAACAAGAACAACCCAACTATCTAATCTGAATAATCGCAT
66 ATACATACTCCATGACACCATCATTCAACAAGAACAACCCAACTATCTAATCTGAATAATCGCAT
2597182 CCGGGCTAGAAATGAAATCTTGCATCGAAGCAATGAAATC
131 CCGGGCTAGAAATGAAATCTTGCATCGAAGCAATGAAATC
*
2597222 TCTCGATATGAAAGAAACCAACAACCTCATAATACCACAAGCAAGAATTCACACCAGACAACAAA
1 TCTCGATACGAAAGAAACCAACAACCTCATAATACCACAAGCAAGAATTCACACCAGACAACAAA
* *
2597287 ATACATACTCCATGACACCATCATTCAACAAGAACAACCTAACTATCTAATCTGAATAATTGCAT
66 ATACATACTCCATGACACCATCATTCAACAAGAACAACCCAACTATCTAATCTGAATAATCGCAT
2597352 CCGGGCTAGAAATGAAATCTTGCATCGAAGCAATGAA
131 CCGGGCTAGAAATGAAATCTTGCATCGAAGCAATGAA
2597389 CTTAGGACTA
Statistics
Matches: 162, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
170 162 1.00
ACGTcount: A:0.43, C:0.26, G:0.12, T:0.19
Consensus pattern (170 bp):
TCTCGATACGAAAGAAACCAACAACCTCATAATACCACAAGCAAGAATTCACACCAGACAACAAA
ATACATACTCCATGACACCATCATTCAACAAGAACAACCCAACTATCTAATCTGAATAATCGCAT
CCGGGCTAGAAATGAAATCTTGCATCGAAGCAATGAAATC
Found at i:2599423 original size:20 final size:21
Alignment explanation
Indices: 2599395--2599446 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
2599385 AATATTCTGG
2599395 AGATGTGTGGAACCTTATGGA
1 AGATGTGTGGAACCTTATGGA
2599416 AGAT-TGTGGAACCTTATGGA
1 AGATGTGTGGAACCTTATGGA
*
2599436 AGA-GTATGGAA
1 AGATGTGTGGAA
2599447 GAATATGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.33, C:0.08, G:0.33, T:0.27
Consensus pattern (21 bp):
AGATGTGTGGAACCTTATGGA
Found at i:2604140 original size:20 final size:20
Alignment explanation
Indices: 2604097--2604141 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2604087 TAGAGATGTG
* *
2604097 TGGAACCTTATGCACGAATG
1 TGGAACCTTATGCAAGAATA
* *
2604117 TGGAACCTTATGGAAGAGTA
1 TGGAACCTTATGCAAGAATA
2604137 TGGAA
1 TGGAA
2604142 GAATATGGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.24
Consensus pattern (20 bp):
TGGAACCTTATGCAAGAATA
Found at i:2604920 original size:2 final size:2
Alignment explanation
Indices: 2604915--2604940 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2604905 ATCATTTAAG
2604915 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
2604941 CGAGAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2605119 original size:118 final size:116
Alignment explanation
Indices: 2604997--2605236 Score: 381
Period size: 118 Copynumber: 2.1 Consensus size: 116
2604987 TGTCTAAAAT
* * *
2604997 AATCTAGATATTTATAATATTTAATATTTTGTCTAGAATTATATATAGAATAATTTATATATTTA
1 AATCTAGATATTTATAATATTTAATATTTTGTCTAGAATTATATATAAAAGAATTTAGATATTTA
* * *
2605062 TAAGGTTAAATGGTTAAGATGTTGACATGTATCAATAATCTAATGACTACTCA
66 TAAGATTAAATAGTTAAGAT-TTGACATGTATC-ATAATCTAATGACTACTAA
*
2605115 AATCTAGATATTTGTAATATTTAATATTTTGTCTAGAATTATATATAAAAGAATTTAGATATTTA
1 AATCTAGATATTTATAATATTTAATATTTTGTCTAGAATTATATATAAAAGAATTTAGATATTTA
* *
2605180 TAAGATTAAATAGTTAAGATTTGACATGTGTCATAATCTAATGATTACTAA
66 TAAGATTAAATAGTTAAGATTTGACATGTATCATAATCTAATGACTACTAA
2605231 AATCTA
1 AATCTA
2605237 ATAGCTATAC
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
116 23 0.20
117 11 0.10
118 79 0.70
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (116 bp):
AATCTAGATATTTATAATATTTAATATTTTGTCTAGAATTATATATAAAAGAATTTAGATATTTA
TAAGATTAAATAGTTAAGATTTGACATGTATCATAATCTAATGACTACTAA
Found at i:2605696 original size:30 final size:30
Alignment explanation
Indices: 2605588--2605682 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
2605578 CATCTTGAGA
*
2605588 TGACGTGACAGACTCACATGGCACTAGTGC
1 TGACGCGACAGACTCACATGGCACTAGTGC
2605618 TGACGCGACAGACTCACATGGCACTAGTGC
1 TGACGCGACAGACTCACATGGCACTAGTGC
*
2605648 TGACGCGACAGACTCACATGGCACTAATGC
1 TGACGCGACAGACTCACATGGCACTAGTGC
2605678 TGACG
1 TGACG
2605683 TGTCAGTGCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.27, C:0.28, G:0.26, T:0.18
Consensus pattern (30 bp):
TGACGCGACAGACTCACATGGCACTAGTGC
Found at i:2606925 original size:30 final size:30
Alignment explanation
Indices: 2606891--2606962 Score: 126
Period size: 30 Copynumber: 2.4 Consensus size: 30
2606881 TATGTGACAT
2606891 TGCCACATCATCATTAGTGCCATGCGAGTC
1 TGCCACATCATCATTAGTGCCATGCGAGTC
*
2606921 TGCCACATCATCATTAGTGCCATGTGAGTC
1 TGCCACATCATCATTAGTGCCATGCGAGTC
*
2606951 TACCACATCATC
1 TGCCACATCATC
2606963 TCAAGGCATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.28
Consensus pattern (30 bp):
TGCCACATCATCATTAGTGCCATGCGAGTC
Found at i:2608236 original size:42 final size:41
Alignment explanation
Indices: 2608190--2608284 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
2608180 TGGTGAAAGA
*
2608190 GATCAATCCTTTAGGGGAAGGGACCGATCCTTTTAATCGAGG
1 GATCAATCCTTT-GGGGAAGGGACCGATCCATTTAATCGAGG
* * ** *
2608232 GATCAATCCATTTGGTGAAGGGATCGATCCATTTCCTTGAGG
1 GATCAATCC-TTTGGGGAAGGGACCGATCCATTTAATCGAGG
*
2608274 GATCGATCCTT
1 GATCAATCCTT
2608285 ACGTGAAGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 2 0.04
42 40 0.89
43 3 0.07
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.29
Consensus pattern (41 bp):
GATCAATCCTTTGGGGAAGGGACCGATCCATTTAATCGAGG
Found at i:2608274 original size:21 final size:20
Alignment explanation
Indices: 2608228--2608282 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2608218 CCTTTTAATC
* *
2608228 GAGGGATCAATCCATTTGGT
1 GAGGGATCGATCCATTTCGT
*
2608248 GAAGGGATCGATCCATTTCCTT
1 G-AGGGATCGATCCATTT-CGT
2608270 GAGGGATCGATCC
1 GAGGGATCGATCC
2608283 TTACGTGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.90
22 2 0.07
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (20 bp):
GAGGGATCGATCCATTTCGT
Found at i:2618474 original size:20 final size:21
Alignment explanation
Indices: 2618428--2618488 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2618418 TTCCCCTGTG
2618428 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2618451 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2618471 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2618489 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:2624620 original size:23 final size:21
Alignment explanation
Indices: 2624578--2624624 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 21
2624568 TTTTCAAGTC
2624578 TTTTATCTTTTATTTATCTTG
1 TTTTATCTTTTATTTATCTTG
*
2624599 TTTTAATCTTATTTTTTATCTTG
1 TTTT-ATCTT-TTATTTATCTTG
2624622 TTT
1 TTT
2624625 CCAGGACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 5 0.22
23 14 0.61
ACGTcount: A:0.15, C:0.09, G:0.04, T:0.72
Consensus pattern (21 bp):
TTTTATCTTTTATTTATCTTG
Found at i:2628786 original size:18 final size:19
Alignment explanation
Indices: 2628763--2628809 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
2628753 ATGCAATTAT
**
2628763 TATCGATAC-TGAGGTGGG
1 TATCGATACATGAGGAAGG
2628781 TATCGATACTATGAGGAAGG
1 TATCGATAC-ATGAGGAAGG
2628801 TATCGATAC
1 TATCGATAC
2628810 CATTAATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.28
Consensus pattern (19 bp):
TATCGATACATGAGGAAGG
Found at i:2628858 original size:19 final size:21
Alignment explanation
Indices: 2628834--2628884 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
2628824 TGCAGAAATG
*
2628834 GTATCGATACCTTA-ATAG-A
1 GTATCGATACCATAGATAGAA
2628853 GTATCGATACCATAGTATAGAA
1 GTATCGATACCATAG-ATAGAA
2628875 GTATCGATAC
1 GTATCGATAC
2628885 TAAGAGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.46
21 4 0.14
22 11 0.39
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (21 bp):
GTATCGATACCATAGATAGAA
Found at i:2629385 original size:54 final size:54
Alignment explanation
Indices: 2629320--2629703 Score: 603
Period size: 54 Copynumber: 7.2 Consensus size: 54
2629310 AATGACATTA
* * *
2629320 TGTGTGCAAACTAAGAATTTCATAATAAGTTTATGATTTTTCGTATGGGTACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
* * * *
2629374 TGTGTGTAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGACACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
* *
2629428 TGTGTGCAAACTAAGAAATTCATAACAAGTTTATGAATTTCCGTATGGGCACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
*
2629482 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
* * * *
2629536 TGTGTGCAAACTAATAAATTCATAATAAGTTTATAAATTTTTGTATGGACACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
* *
2629590 TGTGTGCAAACTAAGAAATTCATAATAATTTTATGAATTTTTGTATGGGCACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
2629644 TGTGTGCAAACTAAGAAATTC---ATAAGTTTATGAATTTTCGTATGGGCACTG
1 TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
2629695 TGTGTGCAA
1 TGTGTGCAA
2629704 TCAACGTAAA
Statistics
Matches: 309, Mismatches: 21, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
51 37 0.12
54 272 0.88
ACGTcount: A:0.33, C:0.11, G:0.20, T:0.36
Consensus pattern (54 bp):
TGTGTGCAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTG
Found at i:2633489 original size:3 final size:3
Alignment explanation
Indices: 2633481--2633547 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
2633471 TTTTATCCCG
* *
2633481 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TGA TTA TTA TTA TTA GTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
*
2633527 TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
2633548 AAAAATAACA
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 54 0.95
4 3 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2648340 original size:19 final size:19
Alignment explanation
Indices: 2648316--2648370 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
2648306 AAGCCAAGAG
2648316 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAGT
2648335 CATGTATTTTCATTAAAGT
1 CATGTATTTTCATTAAAGT
2648354 CATGTATTTTCATTAAA
1 CATGTATTTTCATTAAA
2648371 AAAATCATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAGT
Found at i:2656748 original size:15 final size:17
Alignment explanation
Indices: 2656723--2656755 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2656713 CAATTATCTA
2656723 TTTTACTTTATTT-TTG
1 TTTTACTTTATTTATTG
2656739 TTTT-CTTTATTTATTG
1 TTTTACTTTATTTATTG
2656755 T
1 T
2656756 AGGCATGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (17 bp):
TTTTACTTTATTTATTG
Found at i:2659481 original size:20 final size:21
Alignment explanation
Indices: 2659451--2659489 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2659441 GAATAGTGAA
2659451 TAGTGAGGGTATCAGTACCTG
1 TAGTGAGGGTATCAGTACCTG
*
2659472 TAGT-AGGGTATCGGTACC
1 TAGTGAGGGTATCAGTACC
2659490 CCTTAAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.23, C:0.15, G:0.33, T:0.28
Consensus pattern (21 bp):
TAGTGAGGGTATCAGTACCTG
Found at i:2669806 original size:2 final size:2
Alignment explanation
Indices: 2669733--2669791 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
2669723 AATTCAAATC
2669733 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
* *
2669775 AT CAA AT AT AC AT AT AT
1 AT -AT AT AT AT AT AT AT
2669792 TAACTCTAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2674855 original size:19 final size:21
Alignment explanation
Indices: 2674831--2674881 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
2674821 AGCCAAGAGA
*
2674831 ATGTATTTTCATT-A-AAGTC
1 ATGTATTTTCATTAACAAATC
2674850 ATGTATTTTCATTAACAAATC
1 ATGTATTTTCATTAACAAATC
2674871 ATGTATTTTCA
1 ATGTATTTTCA
2674882 AAGGTATTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.45
20 1 0.03
21 15 0.52
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (21 bp):
ATGTATTTTCATTAACAAATC
Found at i:2684917 original size:21 final size:21
Alignment explanation
Indices: 2684809--2684917 Score: 66
Period size: 21 Copynumber: 5.2 Consensus size: 21
2684799 ATAAAAACTA
*
2684809 TAAACCTTAAACACTAAAT-T
1 TAAACCTTAAACACAAAATCT
* *
2684829 ATAAACCTTAAACTATAAAA-CA
1 -TAAACCTTAAAC-ACAAAATCT
* * * *
2684851 CAAACCATAAACATC-ATATCC
1 TAAACCTTAAACA-CAAAATCT
*
2684872 TAAACCATAAATGCA-AAAATC-
1 TAAACCTTAAA--CACAAAATCT
2684893 TAAACCTTAAACACAAAATCT
1 TAAACCTTAAACACAAAATCT
2684914 TAAA
1 TAAA
2684918 TTGGAAACCA
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.03
20 9 0.13
21 47 0.69
22 8 0.12
23 2 0.03
ACGTcount: A:0.54, C:0.22, G:0.01, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAACACAAAATCT
Found at i:2685296 original size:15 final size:15
Alignment explanation
Indices: 2685248--2685290 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2685238 TAGAAAATAC
2685248 AATAACATTAAA-TAA
1 AATAACA-TAAATTAA
* *
2685263 AACACCATAAATTAA
1 AATAACATAAATTAA
2685278 AATAACATAAATT
1 AATAACATAAATT
2685291 CCAATACCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAACATAAATTAA
Found at i:2687746 original size:102 final size:102
Alignment explanation
Indices: 2687481--2687730 Score: 274
Period size: 102 Copynumber: 2.5 Consensus size: 102
2687471 ATTTTGATTA
* * * * * * * *
2687481 TGAGGTCAAACAAGTT-GACAGATTAATGTCTTCCCCTTGAACTCGAAGGCAT-GCTACCATATG
1 TGAGATCAAAGAAGTTGGA-AGATGAATGCCTTTCCCTTGAACTTGAAGGCATACCT-TCATATG
* * * * * *
2687544 GGTT-TTGAACGAATTGTTGTGTCAATGGAATTTTGATGT
64 GGTTCTT-AATGCACTATTGTGTCAATGAAATTTCGATGT
* **
2687583 TGAGGTTGAAGAAGTTGGAAGATGAATGCCTTTCCCTTGAACTTGAAGGCATACCTTCATATGGG
1 TGAGATCAAAGAAGTTGGAAGATGAATGCCTTTCCCTTGAACTTGAAGGCATACCTTCATATGGG
*
2687648 TTCTTAATGCACTATTGTGTCGATGAAATTTCGATGT
66 TTCTTAATGCACTATTGTGTCAATGAAATTTCGATGT
2687685 TGAGATCAAAGAAGTTGGAAGATGAATGCC-TTCCCATTGAACTTGA
1 TGAGATCAAAGAAGTTGGAAGATGAATGCCTTTCCC-TTGAACTTGA
2687731 TGGGATTTTT
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
101 5 0.04
102 114 0.91
103 6 0.05
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (102 bp):
TGAGATCAAAGAAGTTGGAAGATGAATGCCTTTCCCTTGAACTTGAAGGCATACCTTCATATGGG
TTCTTAATGCACTATTGTGTCAATGAAATTTCGATGT
Found at i:2689040 original size:20 final size:20
Alignment explanation
Indices: 2688973--2689042 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 20
2688963 ATATCTAGAG
*
2688973 TTAATTAAATATATGTTTTAA
1 TTAATTAAATATA-GATTTAA
2688994 -TAATTCCAAATATTTA-ATTTCAA
1 TTAATT--AAATA--TAGATTT-AA
2689017 TTAATTAAATATAGATTTAA
1 TTAATTAAATATAGATTTAA
2689037 TTAATT
1 TTAATT
2689043 TGAAATAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
20 15 0.37
21 4 0.10
22 13 0.32
23 2 0.05
24 7 0.17
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (20 bp):
TTAATTAAATATAGATTTAA
Found at i:2689122 original size:90 final size:89
Alignment explanation
Indices: 2689004--2689180 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
2688994 TAATTCCAAA
* * *
2689004 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCTTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAA-CCATAATATGAT
*
2689069 TAGGGTAACTTAGATATAAAAGGAT
65 TAGAGTAACTTAGATATAAAAGGAT
2689094 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
* *
2689159 AGAGTAACTTGGCTATAAAAGG
66 AGAGTAACTTAGATATAAAAGG
2689181 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 31 0.38
90 50 0.62
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCATAATATGATT
AGAGTAACTTAGATATAAAAGGAT
Found at i:2690336 original size:23 final size:23
Alignment explanation
Indices: 2690305--2690360 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
2690295 ACCGGTCATA
*
2690305 ACCCGACCCGACCTGACCCATTT
1 ACCCGACCCGACCTGACCCATTG
* *
2690328 ACCCTACCCGACCTGACCCGTTG
1 ACCCGACCCGACCTGACCCATTG
2690351 ACCCGACCCG
1 ACCCGACCCG
2690361 TTGACCGTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.20, C:0.50, G:0.16, T:0.14
Consensus pattern (23 bp):
ACCCGACCCGACCTGACCCATTG
Found at i:2690353 original size:13 final size:13
Alignment explanation
Indices: 2690337--2690366 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2690327 TACCCTACCC
*
2690337 GACCTGACCCGTT
1 GACCCGACCCGTT
2690350 GACCCGACCCGTT
1 GACCCGACCCGTT
2690363 GACC
1 GACC
2690367 GTTGACCGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2692937 original size:24 final size:24
Alignment explanation
Indices: 2692806--2692920 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
2692796 TCGATTTGAT
2692806 TTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
2692830 TTCTGATATGATA-TCTGACATGGA
1 TTCTGATATGATACT-TGACATGGA
* * * *
2692854 TTTTGGTCTGATACTTGACTTGGA
1 TTCTGATATGATACTTGACATGGA
*
2692878 TTCTGATATGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
2692902 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
2692921 GTGAATTATG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
23 1 0.01
24 78 0.98
25 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:2695968 original size:17 final size:18
Alignment explanation
Indices: 2695946--2695981 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2695936 TTTTACAGAC
2695946 ATATTGATATG-ATAAAA
1 ATATTGATATGCATAAAA
*
2695963 ATATTGATGTGCATAAAA
1 ATATTGATATGCATAAAA
2695981 A
1 A
2695982 ATGTTAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (18 bp):
ATATTGATATGCATAAAA
Found at i:2697606 original size:48 final size:48
Alignment explanation
Indices: 2697554--2697685 Score: 158
Period size: 48 Copynumber: 2.8 Consensus size: 48
2697544 TTTATTTGAT
*
2697554 TTCTGATATGATACTTGACATGGATTCTGATATGATA-TCTAACATGGA
1 TTCTGATATGATACTTGACATGAATTCTGATATGATACT-TAACATGGA
* * * * *
2697602 TTCTGATTTGATACTTGACTTGAATTCTGATGTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGAATTCTGATATGATACTTAACATGGA
* * * *
2697650 TTTTGATATGATACTTGACGTGAATTATGATTTGAT
1 TTCTGATATGATACTTGACATGAATTCTGATATGAT
2697686 TTTTGATATA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 71 0.99
49 1 0.01
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (48 bp):
TTCTGATATGATACTTGACATGAATTCTGATATGATACTTAACATGGA
Found at i:2697680 original size:24 final size:24
Alignment explanation
Indices: 2697554--2697668 Score: 151
Period size: 24 Copynumber: 4.8 Consensus size: 24
2697544 TTTATTTGAT
2697554 TTCTGATATGATACTTGACATGGA
1 TTCTGATATGATACTTGACATGGA
*
2697578 TTCTGATATGATA-TCTAACATGGA
1 TTCTGATATGATACT-TGACATGGA
* * *
2697602 TTCTGATTTGATACTTGACTTGAA
1 TTCTGATATGATACTTGACATGGA
* *
2697626 TTCTGATGTGATACTTGACCTGGA
1 TTCTGATATGATACTTGACATGGA
*
2697650 TTTTGATATGATACTTGAC
1 TTCTGATATGATACTTGAC
2697669 GTGAATTATG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
23 1 0.01
24 77 0.97
25 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (24 bp):
TTCTGATATGATACTTGACATGGA
Found at i:2697681 original size:72 final size:72
Alignment explanation
Indices: 2697549--2697685 Score: 186
Period size: 72 Copynumber: 1.9 Consensus size: 72
2697539 GATTTTTTAT
* * *
2697549 TTGATTTCTGATATGATACTTGACATGGATTCTGATATGATATCTAACATGGATTCTGATTTGAT
1 TTGAATTCTGATATGATACTTGACATGGATTCTGATATGATATCTAACATGAATTATGATTTGAT
2697614 ACTTGAC
66 ACTTGAC
* * * * *
2697621 TTGAATTCTGATGTGATACTTGACCTGGATTTTGATATGATA-CTTGACGTGAATTATGATTTGA
1 TTGAATTCTGATATGATACTTGACATGGATTCTGATATGATATC-TAACATGAATTATGATTTGA
2697685 T
65 T
2697686 TTTTGATATA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 1 0.02
72 55 0.98
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (72 bp):
TTGAATTCTGATATGATACTTGACATGGATTCTGATATGATATCTAACATGAATTATGATTTGAT
ACTTGAC
Found at i:2697691 original size:24 final size:24
Alignment explanation
Indices: 2697605--2697685 Score: 99
Period size: 24 Copynumber: 3.4 Consensus size: 24
2697595 ACATGGATTC
* *
2697605 TGATTTGATACTTGACTTGAATTC
1 TGATTTGATACTTGACCTGAATTA
* * *
2697629 TGATGTGATACTTGACCTGGATTT
1 TGATTTGATACTTGACCTGAATTA
* *
2697653 TGATATGATACTTGACGTGAATTA
1 TGATTTGATACTTGACCTGAATTA
2697677 TGATTTGAT
1 TGATTTGAT
2697686 TTTTGATATA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (24 bp):
TGATTTGATACTTGACCTGAATTA
Found at i:2701269 original size:95 final size:95
Alignment explanation
Indices: 2701144--2701367 Score: 276
Period size: 95 Copynumber: 2.4 Consensus size: 95
2701134 ATACCAACGA
* * *
2701144 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAAACATTGAATCTAAAATTAGTATCG
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGG-AAACATCGAACCTAAAATGAGTATCG
* *
2701209 ATA-CAGGAA-GGGGTATTTGTACCATAGTAT
65 ATACCA-AAAGGGGGTATTAGTACCATAGTAT
* * *
2701239 GGTAGTATCGATACTATGGTAAGGGTATCGATACCAGGTAACATCGAACCTAAAATGGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATGAGTATCGA
2701304 TACCAAAAGGGGGTATTAGTACCATAGTAT
66 TACCAAAAGGGGGTATTAGTACCATAGTAT
* * * *
2701334 -ATAAGTAACGGTACCATGGT-AGTAGTATCGATAC
1 GGT-AGTATCGATACCATGGTAAG-GGTATCGATAC
2701368 TATGGAACTT
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
94 29 0.26
95 83 0.74
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATGAGTATCGA
TACCAAAAGGGGGTATTAGTACCATAGTAT
Found at i:2703306 original size:29 final size:29
Alignment explanation
Indices: 2703229--2703336 Score: 123
Period size: 29 Copynumber: 3.8 Consensus size: 29
2703219 ATCACCTTTA
*
2703229 TTAAAAATAATTACCAAAATATCATTGTT
1 TTAAAAATAATTACCAAAATGTCATTGTT
* *
2703258 TT-TAAATAATTCCCAAAATGTCATTGTT
1 TTAAAAATAATTACCAAAATGTCATTGTT
* *
2703286 TTAAAAATATTTACCAGAATGTCACTAT-TT
1 TTAAAAATAATTACCAAAATGTCA-T-TGTT
*
2703316 TTAAAAA-AATTCCCAAAATGT
1 TTAAAAATAATTACCAAAATGT
2703337 TACCTTTTCA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
28 25 0.38
29 30 0.45
30 10 0.15
31 1 0.02
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.38
Consensus pattern (29 bp):
TTAAAAATAATTACCAAAATGTCATTGTT
Found at i:2703354 original size:28 final size:28
Alignment explanation
Indices: 2703214--2703372 Score: 106
Period size: 28 Copynumber: 5.5 Consensus size: 28
2703204 AAAAATTACA
* *
2703214 AAAATATCACCTTTATTAAAAATAATTACC
1 AAAATGTCACC-TT-TTAAAAATAATTCCC
* * **
2703244 AAAATATCA-TTGTTTTTAAATAATTCCC
1 AAAATGTCACCT-TTTAAAAATAATTCCC
** * *
2703272 AAAATGTCATTGTTTTAAAAATATTTACC
1 AAAATGTCA-CCTTTTAAAAATAATTCCC
* *
2703301 AGAATGTCACTATTTTTAAAAA-AATTCCC
1 AAAATGTCAC--CTTTTAAAAATAATTCCC
* * *
2703330 AAAATGTTACCTTTTCAAAATAATTCTC
1 AAAATGTCACCTTTTAAAAATAATTCCC
*
2703358 AAAATGTTACCTTTT
1 AAAATGTCACCTTTT
2703373 TGGATCTGGT
Statistics
Matches: 103, Mismatches: 20, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
27 8 0.08
28 42 0.41
29 34 0.33
30 19 0.18
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.39
Consensus pattern (28 bp):
AAAATGTCACCTTTTAAAAATAATTCCC
Found at i:2703364 original size:57 final size:57
Alignment explanation
Indices: 2703229--2703364 Score: 150
Period size: 57 Copynumber: 2.4 Consensus size: 57
2703219 ATCACCTTTA
* * * * **
2703229 TTAAAAATAATTACCAAAATATCATTGTTTTTAAATAATTCCCAAAATGTCATTGTT
1 TTAAAAATAATTACCAAAATGTCACTATTTTTAAAAAATTCCCAAAATGTCATCCTT
* * *
2703286 TTAAAAATATTTACCAGAATGTCACTATTTTTAAAAAAATTCCCAAAATGTTA-CCTT
1 TTAAAAATAATTACCAAAATGTCACTATTTTT-AAAAAATTCCCAAAATGTCATCCTT
*
2703343 TTCAAAATAATT-CTCAAAATGT
1 TTAAAAATAATTAC-CAAAATGT
2703365 TACCTTTTTG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
56 1 0.02
57 46 0.71
58 18 0.28
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (57 bp):
TTAAAAATAATTACCAAAATGTCACTATTTTTAAAAAATTCCCAAAATGTCATCCTT
Found at i:2703453 original size:19 final size:19
Alignment explanation
Indices: 2703385--2703446 Score: 106
Period size: 19 Copynumber: 3.3 Consensus size: 19
2703375 GATCTGGTCG
2703385 GGTCAGACCGGTTCGGATC
1 GGTCAGACCGGTTCGGATC
*
2703404 GGTCAGACCGATTCGGATC
1 GGTCAGACCGGTTCGGATC
*
2703423 GGTCAGACCGGTTTGGATC
1 GGTCAGACCGGTTCGGATC
2703442 GGTCA
1 GGTCA
2703447 AGCCGGTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.23
Consensus pattern (19 bp):
GGTCAGACCGGTTCGGATC
Found at i:2709668 original size:75 final size:75
Alignment explanation
Indices: 2709485--2709689 Score: 244
Period size: 74 Copynumber: 2.8 Consensus size: 75
2709475 CAAAGCCAAA
* * **
2709485 AATTCCA-TATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACTC-ATT-CCCCCTGAATG
1 AATTCCAGTA-TGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAAC-CGATTCCCCCCTAAACA
2709547 GTTTGGCTCCGAG
63 GTTTGGCTCCGAG
*
2709560 ATTTCCAG-ATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
2709624 CT-GTTCCGAG
66 -TGGCTCCGAG
* *
2709634 AATTCCAGTATGCTCGGAGGGAACCGA-TCACCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGTATGCTCGGAGGGAACCGATTC-CCCCATAGGAGGAACCGATTCCCCCCT
2709690 GTTCAACGGT
Statistics
Matches: 115, Mismatches: 9, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
72 1 0.01
73 19 0.17
74 64 0.56
75 31 0.27
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.21
Consensus pattern (75 bp):
AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:2710408 original size:14 final size:16
Alignment explanation
Indices: 2710377--2710409 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
2710367 GTCATTCGAT
2710377 TAACTCAACAAGTATC
1 TAACTCAACAAGTATC
2710393 TAAC-CAACAA-TATC
1 TAACTCAACAAGTATC
2710407 TAA
1 TAA
2710410 AATGGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 6 0.35
16 4 0.24
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.24
Consensus pattern (16 bp):
TAACTCAACAAGTATC
Found at i:2711856 original size:86 final size:86
Alignment explanation
Indices: 2711670--2711932 Score: 234
Period size: 86 Copynumber: 3.0 Consensus size: 86
2711660 CATATTCAAA
* * * * *
2711670 AATTACAAAAATATCACCT-TTATTA-AAAATAATTACCAAAATATCATCGTTTTACAAATAATT
1 AATTACAAAAATGT-AACTATT-TTACAAAATAATTCCCAAAATATCA-CATTTTAAAAATAATT
*
2711733 CCCAAAATGTCATCATTTAAAAAT
63 ACCAAAATGTCATCATTTAAAAAT
* * * *
2711757 AATTACCAGAATGTCACTATTTTAC-AAATAATTCCCAAAATGTCACCATTTTAAAAATAATTAC
1 AATTACAAAAATGTAACTATTTTACAAAATAATTCCCAAAATATCA-CATTTTAAAAATAATTAC
* **
2711821 CAGAATGTCATTGTTTTAAAAA-
65 CAAAATGTCA-TCATTTAAAAAT
* * *
2711843 AATT-CAAAAAATGTAACTTTTTTTCAAAATAATTCCCAAAATATCACATTTTTCAAAATAATT-
1 AATTAC-AAAAATGTAACTATTTTACAAAATAATTCCCAAAATATCACA-TTTTAAAAATAATTA
*
2711906 CTCGAAATGTCA-CATTTATCAAAAT
64 C-CAAAATGTCATCATTTA--AAAAT
2711931 AA
1 AA
2711933 ATCCCAAAAT
Statistics
Matches: 141, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
85 5 0.04
86 68 0.48
87 66 0.47
88 2 0.01
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (86 bp):
AATTACAAAAATGTAACTATTTTACAAAATAATTCCCAAAATATCACATTTTAAAAATAATTACC
AAAATGTCATCATTTAAAAAT
Found at i:2711928 original size:58 final size:58
Alignment explanation
Indices: 2711677--2711976 Score: 254
Period size: 58 Copynumber: 5.2 Consensus size: 58
2711667 AAAAATTACA
* * * * *
2711677 AAAATATCACCTTTATTAAAAATAATTACCAAAATATCATCGTTTTAC-AAATAATTCCC
1 AAAATGTCACATTTA-TCAAAATAATTACCAAAATATCA-CATTTTTCAAAATAATTCCC
* * *
2711736 AAAATGTCATCATTTA--AAAATAATTACCAGAATGTCACTATTTTAC-AAATAATTCCC
1 AAAATGTCA-CATTTATCAAAATAATTACCAAAATATCAC-ATTTTTCAAAATAATTCCC
* * * * * **
2711793 AAAATGTCACCATTT-TAAAAATAATTACCAGAATGT--CATTGTTTTAAAAAAATTCAA
1 AAAATGTCA-CATTTATCAAAATAATTACCAAAATATCACATT-TTTCAAAATAATTCCC
* * * * *
2711850 AAAATGTAACTTTTTTTCAAAATAATTCCCAAAATATCACATTTTTCAAAATAATTCTC
1 AAAATGTCAC-ATTTATCAAAATAATTACCAAAATATCACATTTTTCAAAATAATTCCC
* * * * **
2711909 GAAATGTCACATTTATCAAAATAAATCCCAAAATATCACCTTTTTCAAAATAATTATC
1 AAAATGTCACATTTATCAAAATAATTACCAAAATATCACATTTTTCAAAATAATTCCC
2711967 AAAATGTCAC
1 AAAATGTCAC
2711977 CGGGTCAGGT
Statistics
Matches: 202, Mismatches: 29, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
55 3 0.01
56 5 0.02
57 69 0.34
58 88 0.44
59 28 0.14
60 9 0.04
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATGTCACATTTATCAAAATAATTACCAAAATATCACATTTTTCAAAATAATTCCC
Found at i:2711977 original size:29 final size:29
Alignment explanation
Indices: 2711670--2711977 Score: 218
Period size: 29 Copynumber: 10.6 Consensus size: 29
2711660 CATATTCAAA
* * *
2711670 AATTACAAAAATATCACCTTTATTAAAAAT
1 AATTACCAAAATGTCACCTTT-TTCAAAAT
* * *
2711700 AATTACCAAAATATCATCGTTTT-ACAAAT
1 AATTACCAAAATGTCACCTTTTTCA-AAAT
* * * *
2711729 AATTCCCAAAATGTCATC-ATTTAAAAAT
1 AATTACCAAAATGTCACCTTTTTCAAAAT
*
2711757 AATTACCAGAATGTCA-CTATTTT-ACAAAT
1 AATTACCAAAATGTCACCT-TTTTCA-AAAT
* * *
2711786 AATTCCCAAAATGTCACCATTTTAAAAAT
1 AATTACCAAAATGTCACCTTTTTCAAAAT
* * *
2711815 AATTACCAGAATGTCA--TTGTTTTAAAAA
1 AATTACCAAAATGTCACCTT-TTTCAAAAT
* * *
2711843 AATT-CAAAAAATGTAACTTTTTTTCAAAAT
1 AATTAC-CAAAATGTCAC-CTTTTTCAAAAT
* * *
2711873 AATTCCCAAAATATCACATTTTTCAAAAT
1 AATTACCAAAATGTCACCTTTTTCAAAAT
* * *
2711902 AATT-CTCGAAATGTCACATTTATCAAAAT
1 AATTAC-CAAAATGTCACCTTTTTCAAAAT
* * *
2711931 AAATCCCAAAATATCACCTTTTTCAAAAT
1 AATTACCAAAATGTCACCTTTTTCAAAAT
*
2711960 AATTATCAAAATGTCACC
1 AATTACCAAAATGTCACC
2711978 GGGTCAGGTC
Statistics
Matches: 225, Mismatches: 38, Indels: 31
0.77 0.13 0.11
Matches are distributed among these distances:
27 3 0.01
28 42 0.19
29 137 0.61
30 40 0.18
31 3 0.01
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.34
Consensus pattern (29 bp):
AATTACCAAAATGTCACCTTTTTCAAAAT
Found at i:2712036 original size:20 final size:20
Alignment explanation
Indices: 2712011--2712060 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
2712001 AGTCAACGGG
*
2712011 TCGGGTCGGTTCAGACCTGT
1 TCGGGTCGGTTCAGACCAGT
*
2712031 TCGGGTCGGGTCAGACCAGT
1 TCGGGTCGGTTCAGACCAGT
*
2712051 TCGGATCGGT
1 TCGGGTCGGT
2712061 CATACTGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.38, T:0.26
Consensus pattern (20 bp):
TCGGGTCGGTTCAGACCAGT
Found at i:2713050 original size:56 final size:57
Alignment explanation
Indices: 2712964--2713411 Score: 601
Period size: 56 Copynumber: 8.0 Consensus size: 57
2712954 CCTAAATATG
* * * *
2712964 AAAACCAC-AGAATTCATCATGAGTTGATGAATAACCGCACAGGGTATTATGTATGC
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* *
2713020 AAAACCACGA-AATTCGTCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGT
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* *
2713076 AAAACCAC-AGAATTCATCATGAGTTGATGAATAACTGTATAGGGCACTATGTGTGC
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* * *
2713132 GAAACCACGA-AATTCATCATGAGTTGATGAATAACCGTACATGGCACTATCTGTGC
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* * *
2713188 AAAACCA-TAGAATTCATCATGAGTTGATGAATAGCCGTACAGGGCACTATGTGTGT
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* * * *
2713244 AAATCCACG-GAATTCATCATAAGTTGATGAATAACCATACAGAGCACTATGTGTGC
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* *
2713300 AAAACCAC-AGAATTCATCATGAGTTGATGAATAACCGTACATGGCACTATGTGTGT
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
* * * *
2713356 AAATCCACGA-CATTCATCATGAGTTGATGAATAATCGTATA-GG-ATCTATGTGTGC
1 AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCA-CTATGTGTGC
2713411 A
1 A
2713412 TCTTAATAAA
Statistics
Matches: 345, Mismatches: 39, Indels: 17
0.86 0.10 0.04
Matches are distributed among these distances:
54 1 0.00
55 14 0.04
56 327 0.95
57 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (57 bp):
AAAACCACGAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTGC
Found at i:2718127 original size:20 final size:20
Alignment explanation
Indices: 2718102--2718155 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
2718092 CACTATGGTA
2718102 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
2718122 GTATCGATACCATGGTAAGG
1 GTATCGATACCATGGTAAGG
2718142 GTATCGATACCATG
1 GTATCGATACCATG
2718156 TAACATTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATGGTAAGG
Found at i:2718197 original size:115 final size:114
Alignment explanation
Indices: 2718004--2718246 Score: 296
Period size: 115 Copynumber: 2.1 Consensus size: 114
2717994 TACCAGCGAG
* * *
2718004 GTAGTATCGATACCATAGTAAGGGTATCGATACCAGTAAAACATCAAATCTAAAATTGGTATCGA
1 GTAGTATCGATACCATAGTAAGGGTATCGATACCAGT-AAACATCAAACCTAAAATGGGCATCGA
* * *
2718069 TACCGGAAAGGGTATCGGTACCACACTATGGTAGTATC-GATACCATGGTAA
65 TACCGAAAAGGGTATCGGTACCACACTATAGAAGTATCAG-TACCATGGT-A
* * **
2718120 G-GGTATCGATACCATGGTAAGGGTATCGATACCATGT-AACATTGAACCTAAAATGGGCATCGA
1 GTAGTATCGATACCATAGTAAGGGTATCGATACCA-GTAAACATCAAACCTAAAATGGGCATCGA
* *
2718183 TACC-AAAAGGGGGTATCGGTACCATAGTATAGAAGTATCAGTACCATGGTA
65 TACCGAAAA--GGGTATCGGTACCACACTATAGAAGTATCAGTACCATGGTA
2718234 GTAGTATCGATAC
1 GTAGTATCGATAC
2718247 TATTGAACTT
Statistics
Matches: 109, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
113 3 0.03
114 27 0.25
115 75 0.69
116 4 0.04
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (114 bp):
GTAGTATCGATACCATAGTAAGGGTATCGATACCAGTAAACATCAAACCTAAAATGGGCATCGAT
ACCGAAAAGGGTATCGGTACCACACTATAGAAGTATCAGTACCATGGTA
Found at i:2718682 original size:56 final size:57
Alignment explanation
Indices: 2718580--2718696 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 57
2718570 CTAAATGTAC
* * *
2718580 AAAACCACGGAATTCATCATGAGCTGATGAATAATCGTACATGGCACTATGTGTGCA
1 AAAACCACAGAATTCATCATGAGCTGATGAATAATCCTACAGGGCACTATGTGTGCA
* **
2718637 AAAACCACAGAATTCATGATGATTTGATGAATAA-CCTACAGGGCACTATGTGTGCA
1 AAAACCACAGAATTCATCATGAGCTGATGAATAATCCTACAGGGCACTATGTGTGCA
2718693 AAAA
1 AAAA
2718697 GTTAAGGATA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
56 24 0.44
57 30 0.56
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (57 bp):
AAAACCACAGAATTCATCATGAGCTGATGAATAATCCTACAGGGCACTATGTGTGCA
Found at i:2718926 original size:283 final size:284
Alignment explanation
Indices: 2718411--2718979 Score: 1115
Period size: 283 Copynumber: 2.0 Consensus size: 284
2718401 CTGAGACAAC
2718411 AAAGTTAAGGATAAAGGTGCAGTACCAAAACAATCAACCTTACGTTTTGGATACTTAGCGAAGAA
1 AAAGTTAAGGATAAAGGTGCAGTACCAAAACAATCAACCTTACGTTTTGGATACTTAGCGAAGAA
2718476 AGTCAGGTGAGTTCATTTATTAGGTACCTCTATATGTTATACTAGTCATAGAGTATGATTGCTTA
66 AGTCAGGTGAGTTCATTTATTAGGTACCTCTATATGTTATACTAGTCATAGAGTATGATTGCTTA
2718541 ATATATGTATGGTGATTACCAAATAGGCACTAAATGTACAAAACCACGGAATTCATCATGAGCTG
131 ATATATGTATGGTGATTACCAAATAGGCACTAAATGTACAAAACCACGGAATTCATCATGAGCTG
2718606 ATGAATAATCGTACATGGCACTATGTGTGCAAAAACCACAGAATTCATGATGATTTGATGAATAA
196 ATGAATAATCGTACATGGCACTATGTGTGCAAAAACCACAGAATTCATGATGATTTGATGAATAA
2718671 CC-TACAGGGCACTATGTGTGCAA
261 CCGTACAGGGCACTATGTGTGCAA
2718694 AAAGTTAAGGATAAAGGTGCAGTACCAAAACAATCAACCTTACGTTTTGGATACTTAGCGAAGAA
1 AAAGTTAAGGATAAAGGTGCAGTACCAAAACAATCAACCTTACGTTTTGGATACTTAGCGAAGAA
2718759 AGTCAGGTGAGTTCATTTATTAGGTACCTCTATATGTTATACTAGTCATAGAAGTATGATTGCTT
66 AGTCAGGTGAGTTCATTTATTAGGTACCTCTATATGTTATACTAGTCATAG-AGTATGATTGCTT
2718824 AATATATGTATGGTGATTACCAAATAGGCACTAAATGTACAAAACCACGGAATTCATCATGAGCT
130 AATATATGTATGGTGATTACCAAATAGGCACTAAATGTACAAAACCACGGAATTCATCATGAGCT
2718889 GATGAATAATCGTACATGGCACTATGTGTGC-AAAACCACAGAATTCATGATGATTTGATGAATA
195 GATGAATAATCGTACATGGCACTATGTGTGCAAAAACCACAGAATTCATGATGATTTGATGAATA
2718953 ACCGTACAGGGCACTATGTGTGCAA
260 ACCGTACAGGGCACTATGTGTGCAA
2718978 AA
1 AA
2718980 CCACGAAATT
Statistics
Matches: 284, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
283 152 0.54
284 132 0.46
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.28
Consensus pattern (284 bp):
AAAGTTAAGGATAAAGGTGCAGTACCAAAACAATCAACCTTACGTTTTGGATACTTAGCGAAGAA
AGTCAGGTGAGTTCATTTATTAGGTACCTCTATATGTTATACTAGTCATAGAGTATGATTGCTTA
ATATATGTATGGTGATTACCAAATAGGCACTAAATGTACAAAACCACGGAATTCATCATGAGCTG
ATGAATAATCGTACATGGCACTATGTGTGCAAAAACCACAGAATTCATGATGATTTGATGAATAA
CCGTACAGGGCACTATGTGTGCAA
Found at i:2718936 original size:56 final size:56
Alignment explanation
Indices: 2718863--2719121 Score: 421
Period size: 56 Copynumber: 4.6 Consensus size: 56
2718853 ACTAAATGTA
* * * *
2718863 CAAAACCACGGAATTCATCATGAGCTGATGAATAATCGTACATGGCACTATGTGTG
1 CAAAACCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTG
* *
2718919 CAAAACCACAGAATTCATGATGATTTGATGAATAACCGTACAGGGCACTATGTGTG
1 CAAAACCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTG
* * *
2718975 CAAAACCAC-GAAATTCATTATGAGTTGTTGAATAACCATACAGGGCACTATGTGTG
1 CAAAACCACAG-AATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTG
2719031 CAAAACCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTG
1 CAAAACCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTG
2719087 CAAAACCACAGAATTCATCATGAGTTGATGAATAA
1 CAAAACCACAGAATTCATCATGAGTTGATGAATAA
2719122 ACGTCATTCA
Statistics
Matches: 188, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
55 1 0.01
56 186 0.99
57 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.25
Consensus pattern (56 bp):
CAAAACCACAGAATTCATCATGAGTTGATGAATAACCGTACAGGGCACTATGTGTG
Found at i:2720787 original size:22 final size:22
Alignment explanation
Indices: 2720760--2720813 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
2720750 AATGTCAAGA
2720760 AAAAACTGAAGGTTTAGAAGTG
1 AAAAACTGAAGGTTTAGAAGTG
2720782 AAAAACTGAAGGTTTAGAAGTG
1 AAAAACTGAAGGTTTAGAAGTG
2720804 AAAAACTGAA
1 AAAAACTGAA
2720814 TTTTTTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.50, C:0.06, G:0.24, T:0.20
Consensus pattern (22 bp):
AAAAACTGAAGGTTTAGAAGTG
Found at i:2721098 original size:13 final size:13
Alignment explanation
Indices: 2721082--2721106 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2721072 AACATCATAT
2721082 TAAATATAAAAAC
1 TAAATATAAAAAC
2721095 TAAATATAAAAA
1 TAAATATAAAAA
2721107 ATATAACATT
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:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATATAAAAAC
Found at i:2724204 original size:2 final size:2
Alignment explanation
Indices: 2724197--2724254 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
2724187 TGGTTATTAG
2724197 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
2724239 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
2724255 TGAAATAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2731007 original size:15 final size:15
Alignment explanation
Indices: 2730987--2731019 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
2730977 CTTCTTATTC
2730987 TCAATGGCAATAATT
1 TCAATGGCAATAATT
2731002 TCAATGGCAATAATT
1 TCAATGGCAATAATT
2731017 TCA
1 TCA
2731020 TTTGACGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (15 bp):
TCAATGGCAATAATT
Found at i:2739399 original size:6 final size:6
Alignment explanation
Indices: 2739346--2739385 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
2739336 TATATCATTG
* * *
2739346 AAATTG AAATTG AAACTA AAATTA AAATTA AAATTA AAAT
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAAT
2739386 CAAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:2739616 original size:22 final size:22
Alignment explanation
Indices: 2739591--2739641 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2739581 AAATAATGGA
*
2739591 AATAAGCTAAGCAATCATGTTC
1 AATAAGCTAAGCAACCATGTTC
*
2739613 AATAAGCTAATCAACCATGTTC
1 AATAAGCTAAGCAACCATGTTC
2739635 ACATAAG
1 A-ATAAG
2739642 TGGAAAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.25
Consensus pattern (22 bp):
AATAAGCTAAGCAACCATGTTC
Found at i:2740627 original size:62 final size:62
Alignment explanation
Indices: 2740530--2740656 Score: 254
Period size: 62 Copynumber: 2.0 Consensus size: 62
2740520 CGTCATGCAT
2740530 AAACGACATCTTGACTCATATTTTCCCGAGTTTTCCATTCAAGGGCTTACTCAAGATTCCCA
1 AAACGACATCTTGACTCATATTTTCCCGAGTTTTCCATTCAAGGGCTTACTCAAGATTCCCA
2740592 AAACGACATCTTGACTCATATTTTCCCGAGTTTTCCATTCAAGGGCTTACTCAAGATTCCCA
1 AAACGACATCTTGACTCATATTTTCCCGAGTTTTCCATTCAAGGGCTTACTCAAGATTCCCA
2740654 AAA
1 AAA
2740657 ATTAACCATG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (62 bp):
AAACGACATCTTGACTCATATTTTCCCGAGTTTTCCATTCAAGGGCTTACTCAAGATTCCCA
Found at i:2740870 original size:94 final size:94
Alignment explanation
Indices: 2740760--2740937 Score: 347
Period size: 94 Copynumber: 1.9 Consensus size: 94
2740750 AATCCATACT
2740760 TATATATATATATCATTCCTCATTACATAAGAATCAATTCCTATGATATTGTCTCTATTATGCTG
1 TATATATATATATCATTCCTCATTACATAAGAATCAATTCCTATGATATTGTCTCTATTATGCTG
*
2740825 ATGCACTACTGATACATTATATATATAAA
66 ATGCACTAATGATACATTATATATATAAA
2740854 TATATATATATATCATTCCTCATTACATAAGAATCAATTCCTATGATATTGTCTCTATTATGCTG
1 TATATATATATATCATTCCTCATTACATAAGAATCAATTCCTATGATATTGTCTCTATTATGCTG
2740919 ATGCACTAATGATACATTA
66 ATGCACTAATGATACATTA
2740938 CTGAAGAATA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 83 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (94 bp):
TATATATATATATCATTCCTCATTACATAAGAATCAATTCCTATGATATTGTCTCTATTATGCTG
ATGCACTAATGATACATTATATATATAAA
Found at i:2741964 original size:100 final size:97
Alignment explanation
Indices: 2741791--2742789 Score: 633
Period size: 98 Copynumber: 10.2 Consensus size: 97
2741781 GAGGCACAAC
* ** * **
2741791 TTATTATAATATAAACT-TTTAAAATATTATAAGATAAACAGTTCAAAAAAAATCAAGGTGCAAC
1 TTATTATAATATAAA-TGGTTAAAGCATTATAACATAAATGGTT-AAAAAAAATCAA-G-GCAAC
*
2741855 CTATTACGTTACCATCAAAATTTGATTTGTTATAGG
62 CTATTACGTTACCATCAAAATTGGATTTGTTATAGG
* * *
2741891 TTATTATAGTATAAATGTTTAGAAGCAATATAACATAAATGGTTAAAAAAAATCAAGGCATAGCC
1 TTATTATAATATAAATGGTTA-AAGCATTATAACATAAATGGTTAAAAAAAATCAAGGCA-A-CC
*
2741956 TATTACGTTACCATGAAAATTGGATTTGTTATAGG
63 TATTACGTTACCATCAAAATTGGATTTGTTATAGG
* * * *
2741991 TT-TTAATAATATAAACGGTTAAA-TATTTATAACTTAATTGGTTAAAAAAAATCAAGGTGCAAC
1 TTATT-ATAATATAAATGGTTAAAGCA-TTATAACATAAATGGTTAAAAAAAATCAA-G-GCAAC
* * * *** ** *
2742054 CTATTACGTTACCCTTACAATCAAATTTAATATAGA
62 CTATTACGTTACCATCAAAATTGGATTTGTTATAGG
*
2742090 TTATTATAATATAAATGATTAAAGCATTATAACATAAATGGTT--AAAAAATCAAGGCACAACCT
1 TTATTATAATATAAATGGTTAAAGCATTATAACATAAATGGTTAAAAAAAATCAAGG--CAACCT
** ** * *
2742153 ATTGTGTTACCATTGAAACTGGTTTTGTTATAGG
64 ATTACGTTACCATCAAAATTGGATTTGTTATAGG
* * * * *
2742187 TTATTATAATATAAAAGGTTAAAAGCATTATAACATAAATGATTCACAAAAGTCAAGGCGCAACC
1 TTATTATAATATAAATGGTT-AAAGCATTATAACATAAATGGTTAAAAAAAATCAA-G-GCAACC
* *
2742252 TATTATGTTACCATCAAAATTGGATTAGTTATA-G
63 TATTACGTTACCATCAAAATTGGATTTGTTATAGG
* ** *
2742286 TTTTTAATAATAT-TTTCGGTTAAAG-ACTTATAACATAACAT--TTCAAAAAAATCAAGGTGCA
1 TTATT-ATAATATAAAT-GGTTAAAGCA-TTATAACATAA-ATGGTTAAAAAAAATCAA-G-GCA
* * **
2742347 ACCTATTA-TTTACCCTTGCAATAA--GG-TTTAATATAGG
60 ACCTATTACGTTA-CCAT-CAA-AATTGGATTTGTTATAGG
*** * * *** * * *
2742384 TTATTATAATATAAGCAGTTAAAGAATTATAACTTACCCGGTTAAAGAGAA-GAAGGTGCAACCT
1 TTATTATAATATAAATGGTTAAAGCATTATAACATAAATGGTTAAAAAAAATCAA-G-GCAACCT
* * ** *
2742448 ATTACGTTACCCT-AGCAACCGTATTTGTTATAGG
64 ATTACGTTACCATCA-AAATTGGATTTGTTATAGG
* * * ***
2742482 TTGTTATAATATAAACGGTTAAAGC-TAATAACATAAA-CAAT-AAAAAAATCAAGGTGCAACCT
1 TTATTATAATATAAATGGTTAAAGCATTATAACATAAATGGTTAAAAAAAATCAA-G-GCAACCT
* * *
2742544 AATACGTTACCATCGAAACTGGATTTGTTATAGG
64 ATTACGTTACCATCAAAATTGGATTTGTTATAGG
* * * * * * *
2742578 TAATTATAAAATAAATGGTTAAAAGCATTAAAACATAAAAGATT-CAAAAAATCAAGGCGCATCC
1 TTATTATAATATAAATGGTT-AAAGCATTATAACATAAATGGTTAAAAAAAATCAA-G-GCAACC
* * * *
2742642 TACTACGTTACTATCAAAACTCGATTTGTTATAGG
63 TATTACGTTACCATCAAAATTGGATTTGTTATAGG
* * * * * *
2742677 TT-TTAATAACAT-AATCGATTAAAG-ACTTATAACTTAACTAGTT-AAAAAAATTAAGACGCAA
1 TTATT-ATAATATAAAT-GGTTAAAGCA-TTATAACATAAATGGTTAAAAAAAATCAAG--GCAA
* ** ***
2742738 CCTATTACATTACCATCGGAATCAAATTTGTTATAGG
61 CCTATTACGTTACCATCAAAATTGGATTTGTTATAGG
*
2742775 TTATTGTAATATAAA
1 TTATTATAATATAAA
2742790 CAATTAAACC
Statistics
Matches: 711, Mismatches: 143, Indels: 91
0.75 0.15 0.10
Matches are distributed among these distances:
95 9 0.01
96 57 0.08
97 122 0.17
98 181 0.25
99 181 0.25
100 140 0.20
101 20 0.03
102 1 0.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (97 bp):
TTATTATAATATAAATGGTTAAAGCATTATAACATAAATGGTTAAAAAAAATCAAGGCAACCTAT
TACGTTACCATCAAAATTGGATTTGTTATAGG
Found at i:2742118 original size:23 final size:23
Alignment explanation
Indices: 2742092--2742135 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
2742082 AATATAGATT
*
2742092 ATTATAATATAAATGATTAAAGC
1 ATTATAACATAAATGATTAAAGC
*
2742115 ATTATAACATAAATGGTTAAA
1 ATTATAACATAAATGATTAAA
2742136 AAATCAAGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.34
Consensus pattern (23 bp):
ATTATAACATAAATGATTAAAGC
Found at i:2742669 original size:99 final size:96
Alignment explanation
Indices: 2741836--2742790 Score: 313
Period size: 99 Copynumber: 9.7 Consensus size: 96
2741826 AAACAGTTCA
* * * * * **
2741836 AAAAAAATCAAGGTGCAACCTATTACGTTACCATCAAAATTTGATTTGTTATAGGTTATTATAGT
1 AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATTATAAA
* * * ***
2741901 ATAAATGTTTAGAAGCAATATAACATAAATGGTT
66 ATAAACGGTTA-AAGCTA-ATAACATAAA-CAAT
** * * * * * *
2741935 AAAAAAAATCAAGGCATAGCCTATTACGTTACCATGAAAATTGGATTTGTTATAGGT-TTTAATA
1 -AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATT-ATA
* ** * * ****
2741999 ATATAAACGGTTAAATATTTATAACTTAATTGGTT
64 AAATAAACGGTTAAA-GCTAATAACATAA-ACAAT
* * * * * * ** * *
2742034 AAAAAAAATCAAGGTGCAACCTATTACGTTACCCTTACAA-TCAAATTTAATATAGATTATTATA
1 -AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTC-GATTTGTTATAGGTAATTATA
* * * * ***
2742098 ATATAAATGATTAAAGCATTATAACATAAATGGT
64 AAATAAACGGTTAAAGC-TAATAACATAAACAAT
* * * ** ** * * * *
2742132 TAAAAAATCAAGGCACAACCTATTGTGTTACCATTGAAACTGGTTTTGTTATAGGTTATTATAAT
1 AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATTATAAA
* * * *
2742197 ATAAAAGGTTAAAAGCATTATAACATAAATGATT
66 ATAAACGGTT-AAAGC-TAATAACATAAA-CAAT
* * * * * * * **
2742231 CACAAAAGTCAAGGCGCAACCTATTATGTTACCATCAAAATTGGATTAGTTATA-GTTTTTAATA
1 -AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATT-ATA
* *** * *
2742295 ATATTTTCGGTTAAAGACTTATAACAT-AACATTT
64 AAATAAACGGTTAAAG-CTAATAACATAAACA-AT
* * * * * ** *
2742329 CAAAAAAATCAAGGTGCAACCTATTA-TTTACCCTTGCAATAA---GGTTTAATATAGGTTATTA
1 -AAAAAAATCAAGGCGCAACCTAATACGTTA-CCAT-CAA-AACTCGATTTGTTATAGGTAATTA
* * * * * * ** **
2742390 TAATATAAGCAGTTAAAGAATTATAACTTACCCGGTT
62 TAAAATAAACGGTTAAAG-CTAATAACATAAAC-AAT
* * * * * * **
2742427 AAAGAGAA-GAAGGTGCAACCTATTACGTTACCCT-AGCAAC-CGTATTTGTTATAGGTTGTTAT
1 AAA-AAAATCAAGGCGCAACCTAATACGTTACCATCA-AAACTCG-ATTTGTTATAGGTAATTAT
*
2742489 AATATAAACGGTTAAAGCTAATAACATAAACAAT
63 AAAATAAACGGTTAAAGCTAATAACATAAACAAT
* * *
2742523 AAAAAAATCAAGGTGCAACCTAATACGTTACCATCGAAACTGGATTTGTTATAGGTAATTATAAA
1 AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATTATAAA
*
2742588 ATAAATGGTTAAAAGCATTAA-AACATAAA-AGATT
66 ATAAACGGTT-AAAGC--TAATAACATAAACA-A-T
* * * * *
2742622 CAAAAAATCAAGGCGCATCCTACTACGTTACTATCAAAACTCGATTTGTTATAGGT-TTTAATAA
1 AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATT-ATAA
* * * * * *
2742686 CATAATCGATTAAAGACTTATAAC-TTAACTAGTT
65 AATAAACGGTTAAAG-CTAATAACATAAAC-A-AT
* * * * ** * * *
2742720 AAAAAAATTAAGACGCAACCTATTACATTACCATCGGAA-TCAAATTTGTTATAGGTTATTGTAA
1 AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTC-GATTTGTTATAGGTAATTATAA
*
2742784 TATAAAC
65 AATAAAC
2742791 AATTAAACCG
Statistics
Matches: 666, Mismatches: 149, Indels: 82
0.74 0.17 0.09
Matches are distributed among these distances:
95 6 0.01
96 58 0.09
97 138 0.21
98 166 0.25
99 176 0.26
100 122 0.18
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (96 bp):
AAAAAAATCAAGGCGCAACCTAATACGTTACCATCAAAACTCGATTTGTTATAGGTAATTATAAA
ATAAACGGTTAAAGCTAATAACATAAACAAT
Found at i:2742775 original size:391 final size:393
Alignment explanation
Indices: 2741838--2742797 Score: 994
Period size: 391 Copynumber: 2.4 Consensus size: 393
2741828 ACAGTTCAAA
* * * * * **
2741838 AAAAATCAAGGTGCAACCTATTACGTTACCATCAAAATTTGATTTGTTATAGGTTATT-ATAGTA
1 AAAAATCAAGGCGCAACCTACTACGTTACCATCAAAACTCGATTAGTTATAGGTT-TTAATAACA
* * *
2741902 TAAAT-GTTTAGAAG-CAATATAACATAA-ATGGTTAAAAAAAATCAAG--GCATAGCCTATTAC
65 T-AATCGATTA-AAGAC-TTATAACATAACA--GTTCAAAAAAATCAAGACGCA-A-CCTATTA-
* * ** * * *
2741962 GTTACCAT-GAAAATTGGATTTGTTATAGGTT-TTAATAATATAAACGGTTAAATATTTATAACT
122 ATTACCATCG-CAATAAGATTTGTTATAGGTTATT-ATAATATAAACAGTTAAAGAATTATAACT
** *
2742025 TAATTGGTTAAAAAAAATCAAGGTGCAACCTATTACGTTACCCTTACAATCAAATTTAATATAGA
185 TAACCGGTTAAAAAAAATCAAGGTGCAACCTATTACGTTACCCTTACAACCAAATTTAATATAGA
* * *** * *
2742090 TTATTATAATATAAATGATTAAAGCATTATAACATAAATGGTTAAAAAATCAAGGCACAACCTAT
250 TTATTATAATATAAACGATTAAAGCATAATAACATAAACAATAAAAAAATCAAGGCACAACCTAA
** * * * * *
2742155 TGTGTTACCATTGAAACTGGTTTTGTTATAGGTTATTATAATATAAAAGGTTAAAAGCATTATAA
315 TACGTTACCATCGAAACTGGATTTGTTATAGGTAATTATAAAATAAAAGGTTAAAAGCATTAAAA
*
2742220 CATAAATGATTCAC
380 CATAAAAGATTCAC
* * * * * * *
2742234 AAAAGTCAAGGCGCAACCTATTATGTTACCATCAAAATTGGATTAGTTATAGTTTTTAATAATAT
1 AAAAATCAAGGCGCAACCTACTACGTTACCATCAAAACTCGATTAGTTATAGGTTTTAATAACAT
** * * ** * * *
2742299 TTTCGGTTAAAGACTTATAACATAACATTTCAAAAAAATCAAGGTGCAACCTATTATTTACCCTT
66 AATCGATTAAAGACTTATAACATAACAGTTCAAAAAAATCAAGACGCAACCTATTAATTACCATC
* ** * *
2742364 GCAATAAGGTTTAATATAGGTTATTATAATATAAGCAGTTAAAGAATTATAACTTACCCGGTTAA
131 GCAATAAGATTTGTTATAGGTTATTATAATATAAACAGTTAAAGAATTATAACTTAACCGGTTAA
* * * ** ** * *
2742429 AGAGAA-GAAGGTGCAACCTATTACGTTACCC-TAGCAACCGTATTTGTTATAGGTTGTTATAAT
196 AAAAAATCAAGGTGCAACCTATTACGTTACCCTTA-CAACCAAATTTAATATAGATTATTATAAT
* **
2742492 ATAAACGGTTAAAGC-TAATAACATAAACAATAAAAAAATCAAGGTGCAACCTAATACGTTACCA
260 ATAAACGATTAAAGCATAATAACATAAACAATAAAAAAATCAAGGCACAACCTAATACGTTACCA
*
2742556 TCGAAACTGGATTTGTTATAGGTAATTATAAAATAAATGGTTAAAAGCATTAAAACATAAAAGAT
325 TCGAAACTGGATTTGTTATAGGTAATTATAAAATAAAAGGTTAAAAGCATTAAAACATAAAAGAT
2742621 TCA-
390 TCAC
* * *
2742624 AAAAATCAAGGCGCATCCTACTACGTTACTATCAAAACTCGATTTGTTATAGGTTTTAATAACAT
1 AAAAATCAAGGCGCAACCTACTACGTTACCATCAAAACTCGATTAGTTATAGGTTTTAATAACAT
* *
2742689 AATCGATTAAAGACTTATAACTTAACTAGTT-AAAAAAATTAAGACGCAACCTATTACATTACCA
66 AATCGATTAAAGACTTATAACATAAC-AGTTCAAAAAAATCAAGACGCAACCTATTA-ATTACCA
* * *
2742753 TCGGAATCAA-ATTTGTTATAGGTTATTGTAATATAAACAATTAAA
129 TCGCAAT-AAGATTTGTTATAGGTTATTATAATATAAACAGTTAAA
2742798 CCGTATTACT
Statistics
Matches: 467, Mismatches: 85, Indels: 29
0.80 0.15 0.05
Matches are distributed among these distances:
390 99 0.21
391 144 0.31
392 61 0.13
393 58 0.12
394 24 0.05
395 17 0.04
396 64 0.14
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (393 bp):
AAAAATCAAGGCGCAACCTACTACGTTACCATCAAAACTCGATTAGTTATAGGTTTTAATAACAT
AATCGATTAAAGACTTATAACATAACAGTTCAAAAAAATCAAGACGCAACCTATTAATTACCATC
GCAATAAGATTTGTTATAGGTTATTATAATATAAACAGTTAAAGAATTATAACTTAACCGGTTAA
AAAAAATCAAGGTGCAACCTATTACGTTACCCTTACAACCAAATTTAATATAGATTATTATAATA
TAAACGATTAAAGCATAATAACATAAACAATAAAAAAATCAAGGCACAACCTAATACGTTACCAT
CGAAACTGGATTTGTTATAGGTAATTATAAAATAAAAGGTTAAAAGCATTAAAACATAAAAGATT
CAC
Found at i:2745251 original size:19 final size:19
Alignment explanation
Indices: 2745227--2745263 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2745217 GCTCAACTCG
2745227 GTTCAGTCTAACTGGACCA
1 GTTCAGTCTAACTGGACCA
*
2745246 GTTCAGTCTGACTGGACC
1 GTTCAGTCTAACTGGACC
2745264 GATTTCAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (19 bp):
GTTCAGTCTAACTGGACCA
Found at i:2750135 original size:18 final size:17
Alignment explanation
Indices: 2750090--2750137 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2750080 TGTCTAAAGG
2750090 TTTATTTTTTATTTATTC
1 TTTATTTTTTA-TTATTC
* * *
2750108 TTTCTCTTTTATTATTAT
1 TTTATTTTTTATTATT-C
2750126 TTTATTTTTTAT
1 TTTATTTTTTAT
2750138 AAATACCATA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 5 0.21
18 19 0.79
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (17 bp):
TTTATTTTTTATTATTC
Found at i:2750244 original size:42 final size:42
Alignment explanation
Indices: 2750185--2750265 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
2750175 AGATGGCCCG
* * *
2750185 AATCATCTTGCTTGAAAGCCTAACTGATGACCCGAAGGATTT
1 AATCATCATGCTCGAAAGCCTAACAGATGACCCGAAGGATTT
* * *
2750227 AATCATCATGCTCGAAAGGCTTACAGATGGCCCGAAGGA
1 AATCATCATGCTCGAAAGCCTAACAGATGACCCGAAGGA
2750266 CTTACCAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.23
Consensus pattern (42 bp):
AATCATCATGCTCGAAAGCCTAACAGATGACCCGAAGGATTT
Found at i:2752304 original size:28 final size:28
Alignment explanation
Indices: 2752269--2752519 Score: 202
Period size: 28 Copynumber: 8.3 Consensus size: 28
2752259 CCTAAACTTG
2752269 AACCCGACCTGAATATCACACTTAAAAAA
1 AACCCGACCTGAATATCACACTT-AAAAA
2752298 ATCCGACCCGACCCT-AATATCACACTTAAAAA
1 A----ACCCGA-CCTGAATATCACACTTAAAAA
*
2752330 AACCCGACCTAAATATCACACTTAAAAA
1 AACCCGACCTGAATATCACACTTAAAAA
**
2752358 AGA-CCGACCCAAATATCACACTTAAAAAAA
1 A-ACCCGACCTGAATATCACACTT--AAAAA
2752388 CACGACCCGACCTGAATATCACACTTAAAAA
1 -A--ACCCGACCTGAATATCACACTTAAAAA
* ** *
2752419 GATTCGACCCGAATATCACACTTAAAAA
1 AACCCGACCTGAATATCACACTTAAAAA
2752447 ACCCGACCCGACCCT-AATATCACACTTAAAAAA
1 A----ACCCGA-CCTGAATATCACACTT-AAAAA
* *
2752480 ATCCGACCCGACCCGAATATCAAACTTAAAAA
1 A----ACCCGACCTGAATATCACACTTAAAAA
2752512 AACCCGAC
1 AACCCGAC
2752520 TCGACCTGAC
Statistics
Matches: 189, Mismatches: 14, Indels: 39
0.78 0.06 0.16
Matches are distributed among these distances:
27 3 0.02
28 74 0.39
29 2 0.01
30 5 0.03
31 6 0.03
32 32 0.17
33 64 0.34
34 3 0.02
ACGTcount: A:0.45, C:0.31, G:0.08, T:0.16
Consensus pattern (28 bp):
AACCCGACCTGAATATCACACTTAAAAA
Found at i:2752307 original size:33 final size:32
Alignment explanation
Indices: 2752270--2752528 Score: 278
Period size: 33 Copynumber: 8.3 Consensus size: 32
2752260 CTAAACTTGA
2752270 ACCCGACCTGAATATCACACTTAAAAAAATCCG
1 ACCCGACCTGAATATCACACTTAAAAAAA-CCG
2752303 ACCCGACCCT-AATATCACACTT-AAAAAA---
1 ACCCGA-CCTGAATATCACACTTAAAAAAACCG
*
2752331 ACCCGACCTAAATATCACACTTAAAAAAGACCG
1 ACCCGACCTGAATATCACACTTAAAAAA-ACCG
2752364 ACCC-A----AATATCACACTTAAAAAAACACG
1 ACCCGACCTGAATATCACACTTAAAAAAAC-CG
2752392 ACCCGACCTGAATATCACACTT--AAAAA--G
1 ACCCGACCTGAATATCACACTTAAAAAAACCG
** * *
2752420 ATTCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCTGAATATCACACTTAAAAAAACCG
2752452 ACCCGACCCT-AATATCACACTTAAAAAAATCCG
1 ACCCGA-CCTGAATATCACACTTAAAAAAA-CCG
* *
2752485 ACCCGACCCGAATATCAAACTTAAAAAAACCCG
1 ACCCGACCTGAATATCACACTTAAAAAAA-CCG
*
2752518 ACTCGACCTGA
1 ACCCGACCTGA
2752529 CCCGATCCCA
Statistics
Matches: 193, Mismatches: 13, Indels: 40
0.78 0.05 0.16
Matches are distributed among these distances:
27 5 0.03
28 62 0.32
29 6 0.03
30 5 0.03
31 5 0.03
32 32 0.17
33 75 0.39
34 3 0.02
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (32 bp):
ACCCGACCTGAATATCACACTTAAAAAAACCG
Found at i:2752365 original size:61 final size:57
Alignment explanation
Indices: 2752269--2752519 Score: 267
Period size: 61 Copynumber: 4.1 Consensus size: 57
2752259 CCTAAACTTG
2752269 AACCCGACCTGAATATCACACTTAAAAAAATCCGACCCGACCCTAATATCACACTTAAAAA
1 AACCCGACCTGAATATCACACTTAAAAAAATCCGACCCGA----AATATCACACTTAAAAA
*
2752330 AACCCGACCTAAATATCACACTTAAAAAAGA-CCGACCC-AAATATCACACTTAAAAAAA
1 AACCCGACCTGAATATCACACTTAAAAAA-ATCCGACCCGAAATATCACACTT--AAAAA
* *
2752388 CACGACCCGACCTGAATATCACACTTAAAAAGATTCGACCCG-AATATCACACTTAAAAA
1 -A--ACCCGACCTGAATATCACACTTAAAAAAATCCGACCCGAAATATCACACTTAAAAA
*
2752447 ACCCGACCCGACCCT-AATATCACACTTAAAAAAATCCGACCCGACCCGAATATCAAACTTAAAA
1 A----ACCCGA-CCTGAATATCACACTTAAAAAAATCCGACCCGA----AATATCACACTTAAAA
2752511 A
57 A
2752512 AACCCGAC
1 AACCCGAC
2752520 TCGACCTGAC
Statistics
Matches: 167, Mismatches: 7, Indels: 33
0.81 0.03 0.16
Matches are distributed among these distances:
56 12 0.07
58 6 0.04
59 6 0.04
60 37 0.22
61 88 0.53
62 1 0.01
65 17 0.10
ACGTcount: A:0.45, C:0.31, G:0.08, T:0.16
Consensus pattern (57 bp):
AACCCGACCTGAATATCACACTTAAAAAAATCCGACCCGAAATATCACACTTAAAAA
Found at i:2753874 original size:31 final size:31
Alignment explanation
Indices: 2753839--2753939 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
2753829 TGCTTTGTTG
2753839 TTTTATTTCCTGGTTTTTTACTGTTCGCCCT
1 TTTTATTTCCTGGTTTTTTACTGTTCGCCCT
** * *
2753870 TTTTATTTTTGTGGTTCCTTTTGCT-TT-G--TT
1 TTTTA-TTTCCTGGTT--TTTTACTGTTCGCCCT
2753900 GTTTTATTTCCTGGTTTTTTACTGTTCGCCCT
1 -TTTTATTTCCTGGTTTTTTACTGTTCGCCCT
2753932 TTTTATTT
1 TTTTATTT
2753940 TTGTTGTGGT
Statistics
Matches: 54, Mismatches: 8, Indels: 16
0.69 0.10 0.21
Matches are distributed among these distances:
28 6 0.11
29 2 0.04
30 10 0.19
31 18 0.33
32 10 0.19
33 2 0.04
34 6 0.11
ACGTcount: A:0.06, C:0.17, G:0.14, T:0.63
Consensus pattern (31 bp):
TTTTATTTCCTGGTTTTTTACTGTTCGCCCT
Found at i:2753899 original size:62 final size:62
Alignment explanation
Indices: 2753826--2753943 Score: 236
Period size: 62 Copynumber: 1.9 Consensus size: 62
2753816 CGAATCTCCT
2753826 TTTTGCTTTGTTGTTTTATTTCCTGGTTTTTTACTGTTCGCCCTTTTTATTTTTGTGGTTCC
1 TTTTGCTTTGTTGTTTTATTTCCTGGTTTTTTACTGTTCGCCCTTTTTATTTTTGTGGTTCC
2753888 TTTTGCTTTGTTGTTTTATTTCCTGGTTTTTTACTGTTCGCCCTTTTTATTTTTGT
1 TTTTGCTTTGTTGTTTTATTTCCTGGTTTTTTACTGTTCGCCCTTTTTATTTTTGT
2753944 TGTGGTTGTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 56 1.00
ACGTcount: A:0.05, C:0.15, G:0.15, T:0.64
Consensus pattern (62 bp):
TTTTGCTTTGTTGTTTTATTTCCTGGTTTTTTACTGTTCGCCCTTTTTATTTTTGTGGTTCC
Found at i:2755870 original size:36 final size:36
Alignment explanation
Indices: 2755826--2755923 Score: 126
Period size: 36 Copynumber: 2.7 Consensus size: 36
2755816 ATTTTATTTC
*
2755826 AAGAGAAACAATTTCAAGTGAGATAAAA-CATGTTCT
1 AAGAGAAACAATTTCAAGTGAGATAAAATC-CGTTCT
* * *
2755862 AAGGGAAACAATCTCAAGTGAGATAAAATCCGTTTT
1 AAGAGAAACAATTTCAAGTGAGATAAAATCCGTTCT
* *
2755898 AAGAAAAATAATTTCAAGTGAGATAA
1 AAGAGAAACAATTTCAAGTGAGATAA
2755924 CATCTTGAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 52 0.98
37 1 0.02
ACGTcount: A:0.48, C:0.10, G:0.17, T:0.24
Consensus pattern (36 bp):
AAGAGAAACAATTTCAAGTGAGATAAAATCCGTTCT
Found at i:2756047 original size:20 final size:20
Alignment explanation
Indices: 2756024--2756086 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
2756014 GTTGAACAAG
2756024 TTCTTCTCATTCGGAACTTA
1 TTCTTCTCATTCGGAACTTA
* *
2756044 TTCTCCCTCA-TCGG-A-TGA
1 TTCT-TCTCATTCGGAACTTA
* *
2756062 GTTCTTCTCATTTGGAACTTT
1 -TTCTTCTCATTCGGAACTTA
2756083 TTCT
1 TTCT
2756087 CTTTCATCAG
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
18 6 0.19
19 8 0.25
20 13 0.41
21 5 0.16
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.46
Consensus pattern (20 bp):
TTCTTCTCATTCGGAACTTA
Found at i:2756079 original size:39 final size:39
Alignment explanation
Indices: 2756022--2756112 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
2756012 AGGTTGAACA
*
2756022 AGTTCTTCTCATTCGGAACTTATTCTCCCTCATCGGAT-G
1 AGTTCTTCTCATTCGGAACTTATTCTCCCTCATCAG-TCG
* * **
2756061 AGTTCTTCTCATTTGGAACTTTTTCTCTTTCATCAGTCG
1 AGTTCTTCTCATTCGGAACTTATTCTCCCTCATCAGTCG
2756100 AGTTCTTCTCATT
1 AGTTCTTCTCATT
2756113 ATGAACCCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.02
39 45 0.98
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.45
Consensus pattern (39 bp):
AGTTCTTCTCATTCGGAACTTATTCTCCCTCATCAGTCG
Found at i:2756272 original size:116 final size:116
Alignment explanation
Indices: 2756099--2756335 Score: 260
Period size: 116 Copynumber: 2.0 Consensus size: 116
2756089 TTCATCAGTC
* * ** ** *
2756099 GAGTTCTTCTCATTATGAACCCTTTCATTGGAAATTTTGATCCACCTCTTTCCATGATGGACGAA
1 GAGTTCTTATCATTAGGAACCCTTTCATTAAAAAGGTTGATCCACCTATTTCCATGATGGACGAA
* * * * * *
2756164 ACAAGGTTGAATAAGTTCTTCTCATTAGGAATTTCTTCTCCCCCATTGGGT
66 ACAAGATTAAACAAGTTATTCTCATTAGGAACTTCTTCTCCCCCATTGGAT
* ** **
2756215 GAGTTCTTATCATTAGGAACCC-TTCAATTAAAAAGGTTGATCCTCCTATTTTTATGATGGATTA
1 GAGTTCTTATCATTAGGAACCCTTTC-ATTAAAAAGGTTGATCCACCTATTTCCATGATGGACGA
* * * *
2756279 ACCATGATTAAACAAGTTATTCTCATTAGGAACTTCTTCTCTCTCATTGGAT
65 AACAAGATTAAACAAGTTATTCTCATTAGGAACTTCTTCTCCCCCATTGGAT
2756331 GAGTT
1 GAGTT
2756336 ATTCTCTTTA
Statistics
Matches: 98, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
115 3 0.03
116 95 0.97
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (116 bp):
GAGTTCTTATCATTAGGAACCCTTTCATTAAAAAGGTTGATCCACCTATTTCCATGATGGACGAA
ACAAGATTAAACAAGTTATTCTCATTAGGAACTTCTTCTCCCCCATTGGAT
Found at i:2757485 original size:37 final size:38
Alignment explanation
Indices: 2757443--2757520 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 38
2757433 TTTTACCTAA
*
2757443 ACCTTAGGCATTATTGCCTTTATTG-CTCATCATCCTC
1 ACCTTAGGCATTATCGCCTTTATTGACTCATCATCCTC
*
2757480 ACCTTAGGCATTATCGTCTTTATTGCACTCATCATCCTC
1 ACCTTAGGCATTATCGCCTTTATTG-ACTCATCATCCTC
2757519 AC
1 AC
2757521 TTTTAACTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 23 0.62
39 14 0.38
ACGTcount: A:0.21, C:0.31, G:0.10, T:0.38
Consensus pattern (38 bp):
ACCTTAGGCATTATCGCCTTTATTGACTCATCATCCTC
Found at i:2769002 original size:29 final size:31
Alignment explanation
Indices: 2768959--2769017 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 31
2768949 TTTTGGTTAG
* *
2768959 TGACCAAAATGTAAA-TTTTG-AAAGTTTAA
1 TGACCAAAATATAAAGTTTGGAAAAGTTTAA
*
2768988 TGACTAAAATATAAAGTTTGGAAAAGTTTA
1 TGACCAAAATATAAAGTTTGGAAAAGTTTA
2769018 GGAACTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 13 0.52
30 4 0.16
31 8 0.32
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.34
Consensus pattern (31 bp):
TGACCAAAATATAAAGTTTGGAAAAGTTTAA
Found at i:2775577 original size:20 final size:20
Alignment explanation
Indices: 2775542--2775598 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
2775532 GCCACTTTTG
*
2775542 GTATCGATAC-CAAGGGTGA
1 GTATCGATACTCAAGGGTCA
2775561 GTATCGATACTCAAGGGTCA
1 GTATCGATACTCAAGGGTCA
* * *
2775581 GTACCGATGCTGAAGGGT
1 GTATCGATACTCAAGGGT
2775599 ATAGTATTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 10 0.30
20 23 0.70
ACGTcount: A:0.28, C:0.18, G:0.32, T:0.23
Consensus pattern (20 bp):
GTATCGATACTCAAGGGTCA
Found at i:2778801 original size:18 final size:18
Alignment explanation
Indices: 2778780--2778814 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2778770 CCGACCTGTT
2778780 AACCCGACCCGTTGACCC
1 AACCCGACCCGTTGACCC
* *
2778798 AACCCGATCTGTTGACC
1 AACCCGACCCGTTGACC
2778815 TGACCCGTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.23, C:0.43, G:0.17, T:0.17
Consensus pattern (18 bp):
AACCCGACCCGTTGACCC
Found at i:2778810 original size:31 final size:31
Alignment explanation
Indices: 2778763--2778827 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2778753 ACCCGTCACA
*
2778763 ACCCGACCCGACCTGTTAACCCGACCCGTTG
1 ACCCAACCCGACCTGTTAACCCGACCCGTTG
* * *
2778794 ACCCAACCCGATCTGTTGACCTGACCCGTTG
1 ACCCAACCCGACCTGTTAACCCGACCCGTTG
2778825 ACC
1 ACC
2778828 GACGTTGACC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.20, C:0.43, G:0.18, T:0.18
Consensus pattern (31 bp):
ACCCAACCCGACCTGTTAACCCGACCCGTTG
Found at i:2791457 original size:21 final size:21
Alignment explanation
Indices: 2791433--2791504 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 21
2791423 GTATCGCAAT
2791433 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
2791454 TCGCGTTACGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
2791474 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
2791495 TCGCGTTGCG
1 TCGCGTTGCG
2791505 GTTTTCCATT
Statistics
Matches: 38, Mismatches: 12, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.37
21 24 0.63
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:2791489 original size:41 final size:41
Alignment explanation
Indices: 2791432--2791522 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
2791422 AGTATCGCAA
2791432 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
* *
2791473 TTCGCGTTGCGATAGTTGAAAATCGCGTTGCGGTTTTCCAT
1 TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
2791514 TTCGCGTTG
1 TTCGCGTTG
2791523 GGAATGGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTTGAAAATCGCGTTACGATTTTCCAT
Found at i:2791520 original size:20 final size:20
Alignment explanation
Indices: 2791454--2791522 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
2791444 TAGTTGAAAA
*
2791454 TCGCGTTACGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
2791474 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
*
2791495 TCGCGTTGCGGTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
2791515 TCGCGTTG
1 TCGCGTTG
2791523 GGAATGGTAT
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 22 0.61
21 14 0.39
ACGTcount: A:0.14, C:0.22, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2791960 original size:21 final size:21
Alignment explanation
Indices: 2791934--2791985 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
2791924 AATGGAAAAC
2791934 CGCAACGCGATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
*
2791955 CGCAACGCAATTTTCAACTAT
1 CGCAACGCGATTTTCAACTAT
2791976 CGCAACGCGA
1 CGCAACGCGA
2791986 AATGCAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (21 bp):
CGCAACGCGATTTTCAACTAT
Found at i:2791962 original size:41 final size:41
Alignment explanation
Indices: 2791704--2791940 Score: 420
Period size: 41 Copynumber: 5.8 Consensus size: 41
2791694 CATTTTTAAA
*
2791704 ACTATCGCAACGCGAAATGGAAAATCACAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
2791745 ACTATCGCAACGCGAAATGGAAAATCGCAATGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
2791786 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
* *
2791827 ACTATCGCAACGCGAAATGGAAAACCGCAATGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
2791868 ATTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
*
2791909 ACTATCGCAACGCGAAATGGAAAACCGCAACG
1 ACTATCGCAACGCGAAATGGAAAATCGCAACG
2791941 CGATTTTCAA
Statistics
Matches: 186, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 186 1.00
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.15
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGACACTGTAG
Found at i:2792758 original size:16 final size:17
Alignment explanation
Indices: 2792720--2792765 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 17
2792710 TGTTTATGAG
2792720 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
2792738 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
2792754 GGAATTGGAATC
1 GGAATTGGAATC
2792766 CAATTCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 13 0.46
18 15 0.54
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:2801001 original size:9 final size:11
Alignment explanation
Indices: 2800974--2801017 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
2800964 AAAGGGGGAG
2800974 AAGTGTGTTTT
1 AAGTGTGTTTT
2800985 AAGTGTGTTTT
1 AAGTGTGTTTT
*
2800996 AGGTGTGTTTT
1 AAGTGTGTTTT
2801007 AAGTGTGTTTT
1 AAGTGTGTTTT
2801018 TAAATGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.55
Consensus pattern (11 bp):
AAGTGTGTTTT
Found at i:2808859 original size:2 final size:2
Alignment explanation
Indices: 2808854--2808888 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2808844 TAGAGAGATC
2808854 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 T
2808889 TTTGATTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2809018 original size:2 final size:2
Alignment explanation
Indices: 2809011--2809035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2809001 ATAATAACTT
2809011 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 T
2809036 TGCTTCCGAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2810084 original size:60 final size:60
Alignment explanation
Indices: 2809975--2810102 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
2809965 TAAAGTATAC
* *
2809975 AAATGATCCCTCGACTATAGGACATTGGTTTGTTGAGTCCTATGACTATTAAAAGTTATG
1 AAATGATCCCTCGACTATAGGACATTGCTTTGTTGAGTCCTATCACTATTAAAAGTTATG
* * * * * * **
2810035 AAATGGTCCCTTGATTATAGGACATTGCTTTGTTTAGTTC-ATCACCTATTGAAAGTTACA
1 AAATGATCCCTCGACTATAGGACATTGCTTTGTTGAGTCCTATCA-CTATTAAAAGTTATG
2810095 AAATGATC
1 AAATGATC
2810103 ACCCAACTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 3 0.05
60 53 0.95
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (60 bp):
AAATGATCCCTCGACTATAGGACATTGCTTTGTTGAGTCCTATCACTATTAAAAGTTATG
Found at i:2810560 original size:5 final size:5
Alignment explanation
Indices: 2810550--2810576 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2810540 GTGGTGGAAA
2810550 GAAGT GAAGT GAAGT GAAGT GAAGT GA
1 GAAGT GAAGT GAAGT GAAGT GAAGT GA
2810577 GAATCCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (5 bp):
GAAGT
Found at i:2831062 original size:29 final size:30
Alignment explanation
Indices: 2830968--2831068 Score: 98
Period size: 31 Copynumber: 3.3 Consensus size: 30
2830958 AAACCATATA
* * *
2830968 ATATATATATATTCAAAAATTGTTTTAAAACT
1 ATATAT-TATTTTTAAAAA-TGTTTCAAAACT
* **
2831000 A-ATATATATTTTTAAAAATATTTTCAATTCT
1 ATATAT-TATTTTTAAAAAT-GTTTCAAAACT
2831031 ATATATTATTTTT-AAAATGTTTCAAAACT
1 ATATATTATTTTTAAAAATGTTTCAAAACT
2831060 ATATATTAT
1 ATATATTAT
2831069 ATAAGTTTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
29 17 0.29
30 6 0.10
31 30 0.52
32 5 0.09
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.49
Consensus pattern (30 bp):
ATATATTATTTTTAAAAATGTTTCAAAACT
Found at i:2831082 original size:24 final size:25
Alignment explanation
Indices: 2831050--2831106 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
2831040 TTTTAAAATG
2831050 TTTCAAAACTATATATTATATA-AGT
1 TTTC-AAACTATATATTATATATAGT
*
2831075 TTTCAAACTATATATTATATATATT
1 TTTCAAACTATATATTATATATAGT
2831100 TTTCAAA
1 TTTCAAA
2831107 ATGTTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (25 bp):
TTTCAAACTATATATTATATATAGT
Found at i:2831171 original size:39 final size:38
Alignment explanation
Indices: 2831074--2831306 Score: 177
Period size: 37 Copynumber: 6.2 Consensus size: 38
2831064 ATTATATAAG
* * *
2831074 TTTTCAAACTATATATTATATATATTTTTC-AAAAT-G
1 TTTTCAAAATATATAATATATATATTTTTCAAAAATCA
*
2831110 TTTTAAAAACTATATTATATATATATATTTTTTCAAAAATCA
1 TTTTCAAAA-TATA-TA-ATATATATA-TTTTTCAAAAATCA
* *
2831152 TTTGCAAAATATATAATATATATA-TTTTCAGAAATCA
1 TTTTCAAAATATATAATATATATATTTTTCAAAAATCA
* *
2831189 TTTTCAAAGCTATAT-A-ATATATATTTTT-AAAAACTGA
1 TTTTCAAA-ATATATAATATATATATTTTTCAAAAA-TCA
* *
2831226 TTTTTAAAA-AGTAT-AT-TATAT-GTTTTCAAAAATCA
1 TTTTCAAAATA-TATAATATATATATTTTTCAAAAATCA
* * *
2831261 TTTTCTAAAACAT-T-ATATGTTATATTTTTGAAAAAT-A
1 TTTTC-AAAATATATAATAT-ATATATTTTTCAAAAATCA
2831298 TTTTCAAAA
1 TTTTCAAAA
2831307 ATTGTACTAT
Statistics
Matches: 161, Mismatches: 19, Indels: 34
0.75 0.09 0.16
Matches are distributed among these distances:
35 14 0.09
36 42 0.26
37 47 0.29
38 17 0.11
39 17 0.11
40 8 0.05
41 9 0.06
42 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (38 bp):
TTTTCAAAATATATAATATATATATTTTTCAAAAATCA
Found at i:2831241 original size:38 final size:37
Alignment explanation
Indices: 2831085--2831307 Score: 144
Period size: 38 Copynumber: 6.0 Consensus size: 37
2831075 TTTCAAACTA
* * *
2831085 TATATTATATATATTTTTC-AAAAT-GTTTTAAAAACTA
1 TATATAATATATATTTTTCAAAAATCATTTTAAAAA--G
**
2831122 TATTATATATATATATTTTTTCAAAAATCATTTGCAAAA-
1 TA-TATA-ATATATA-TTTTTCAAAAATCATTTTAAAAAG
* *
2831161 TATATAATATATATATTTTCAGAAATCATTTT-CAAAG
1 TATATAATATATAT-TTTTCAAAAATCATTTTAAAAAG
*
2831198 CTATATAATATATATTTTT-AAAAACTGATTTTTAAAAAG
1 -TATATAATATATATTTTTCAAAAA-TCA-TTTTAAAAAG
* *
2831237 TATAT--TATAT-GTTTTCAAAAATCATTTTCTAAAACAT
1 TATATAATATATATTTTTCAAAAATCA-TTT-TAAAA-AG
* *
2831274 TATAT-GT-TATATTTTTGAAAAAT-ATTTTCAAAAA
1 TATATAATATATATTTTTCAAAAATCATTTT-AAAAA
2831308 TTGTACTATA
Statistics
Matches: 154, Mismatches: 15, Indels: 36
0.75 0.07 0.18
Matches are distributed among these distances:
35 12 0.08
36 30 0.19
37 40 0.26
38 41 0.27
39 13 0.08
40 6 0.04
41 5 0.03
42 7 0.05
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (37 bp):
TATATAATATATATTTTTCAAAAATCATTTTAAAAAG
Found at i:2831246 original size:36 final size:34
Alignment explanation
Indices: 2831201--2831307 Score: 99
Period size: 36 Copynumber: 3.0 Consensus size: 34
2831191 TTCAAAGCTA
*
2831201 TATAATATATATTTTTAAAAACTGATTTTTAAAAAG
1 TATATTATATATTTTTAAAAA-T-ATTTTTAAAAAG
* * *
2831237 TATATTATATGTTTTCAAAAATCATTTTCTAAAACAT
1 TATATTATATATTTTTAAAAAT-ATTTT-TAAAA-AG
*
2831274 TATATGT-TATATTTTTGAAAAATATTTTCAAAAA
1 TATAT-TATATATTTTT-AAAAATATTTTTAAAAA
2831308 TTGTACTATA
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
35 7 0.12
36 27 0.46
37 18 0.31
38 7 0.12
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
TATATTATATATTTTTAAAAATATTTTTAAAAAG
Found at i:2831301 original size:72 final size:72
Alignment explanation
Indices: 2831125--2831307 Score: 173
Period size: 72 Copynumber: 2.5 Consensus size: 72
2831115 AAAACTATAT
* * *
2831125 TATAT-ATATATATTTTTTCAAAAA-TCATTTGCAAAATA-TATAATATATATATTTTCAGAAAT
1 TATATAATATATA-TTTTT-AAAAACTGATTTTCAAAA-AGTAT-AT-TATATATTTTCAAAAAT
*
2831187 CATTTTCAAAGC
61 CATTTTCAAAAC
* *
2831199 TATATAATATATATTTTTAAAAACTGATTTTTAAAAAGTATATTATATGTTTTCAAAAATCATTT
1 TATATAATATATATTTTTAAAAACTGATTTTCAAAAAGTATATTATATATTTTCAAAAATCATTT
2831264 TCTAAAAC
66 TC-AAAAC
*
2831272 -AT-TATATGTTATATTTTTGAAAAA-T-ATTTTCAAAAA
1 TATATA-AT-ATATATTTTT-AAAAACTGATTTTCAAAAA
2831308 TTGTACTATA
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
71 2 0.02
72 36 0.38
73 22 0.23
74 27 0.29
75 7 0.07
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (72 bp):
TATATAATATATATTTTTAAAAACTGATTTTCAAAAAGTATATTATATATTTTCAAAAATCATTT
TCAAAAC
Found at i:2831328 original size:2 final size:2
Alignment explanation
Indices: 2831321--2831361 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2831311 TACTATATTA
2831321 AT AT AT AT 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 AT AT AT AT A
2831362 AAATAAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2831956 original size:184 final size:183
Alignment explanation
Indices: 2831646--2832105 Score: 622
Period size: 184 Copynumber: 2.5 Consensus size: 183
2831636 TTAAAATATT
* ** * * *
2831646 TATCGATGCATAACAATATATA-AGGTAAAAATATGGGAAAA-CCGATTCA-ATATGACAAAACC
1 TATCGATACATAACAATATA-ACAGGTAAAAATATGACAAAATCGGTTTCATA-ATGACAAAATC
** * * *
2831708 GGAAAAG-CACTACCGGATATGTTGAAGGTATCGATTCCATTCAAATAAGTATTGACACTTTTGG
64 GGTGAAGTGA-TACCGGATATGTTGAAGGTATAGATTCCATTCAAATAAGTATAGACACTTTTGG
* *
2831772 AATTTAAAAGAAAAGCAGTAATAACGCCTATAAAGTATCAATACTTTATAAACATG
128 AATTTAAAAGAAAAACAATAATAACGCCTATAAAGTATCAATACTTTATAAACATG
* *
2831828 TATCGATACATAATAATATAACAGGTAAAAATATGACAAACTCGGTTTCATAATGACAAAATCGG
1 TATCGATACATAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATAATGACAAAATCGG
*
2831893 TGAAGTGATACCGGATATGTTGAATGGTATAGATTCCATTCAAATAAGTATAGACATTTTTGGAA
66 TGAAGTGATACCGGATATGTTGAA-GGTATAGATTCCATTCAAATAAGTATAGACACTTTTGGAA
**
2831958 TTTAAAAGAAAAACAATAATAACGCCTATAAAGTATCGGTACTTTATAAACATG
130 TTTAAAAGAAAAACAATAATAACGCCTATAAAGTATCAATACTTTATAAACATG
* *
2832012 TATCGATACATGACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATAATGACAAAATTGG
1 TATCGATACATAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATAATGACAAAATCGG
* * * * * *
2832077 TAAAGCGCTATCAGATATGTTAAAGGTAT
66 TGAAGTGATACCGGATATGTTGAAGGTAT
2832106 CGATACTTTA
Statistics
Matches: 245, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
181 1 0.00
182 34 0.14
183 42 0.17
184 168 0.69
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (183 bp):
TATCGATACATAACAATATAACAGGTAAAAATATGACAAAATCGGTTTCATAATGACAAAATCGG
TGAAGTGATACCGGATATGTTGAAGGTATAGATTCCATTCAAATAAGTATAGACACTTTTGGAAT
TTAAAAGAAAAACAATAATAACGCCTATAAAGTATCAATACTTTATAAACATG
Found at i:2837079 original size:45 final size:45
Alignment explanation
Indices: 2837030--2837285 Score: 275
Period size: 45 Copynumber: 5.7 Consensus size: 45
2837020 ATTCTAACAT
* * *
2837030 CTTTTCTATTAATAATGCAGCCATATGCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* * * *
2837075 CTTTTATGTTGATAATGTACCCATATACATTTCAACCATTA-TATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTA-TAGTATA
* * * * *
2837120 C-TTTCTGTTGATAATGTACCCATATACATGTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* *
2837164 ATTTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGTATA
1 CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* * *
2837209 CCTTTTCTGTTGATAATGCACCCATATGCATTTCATCTATGGCAT-
1 -CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
* ***
2837254 CCTTTCATGCCAATAATGCACCCATATGCATT
1 CTTTTC-TGTTGATAATGCACCCATATGCATT
2837286 ATTCTTTTAT
Statistics
Matches: 180, Mismatches: 26, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
43 2 0.01
44 40 0.22
45 97 0.54
46 41 0.23
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGCACCCATATGCATTTCAACTATAGTATA
Found at i:2837154 original size:89 final size:91
Alignment explanation
Indices: 2837030--2837285 Score: 259
Period size: 89 Copynumber: 2.8 Consensus size: 91
2837020 ATTCTAACAT
* * * * * * * *
2837030 CTTTTCTATTAATAATGCAGCCATATGCATTTCAACTATAGTATACTTTTATGTTGATAATGTAC
1 CTTTTCTGTTGATAATGCACCCATATACATGTCAACTATAGCATAATTTTATGTTGATAATGCAC
2837095 CCATATACATTTCAAC-CATTA-TATA-
66 CCATATACATTTCAACTC--TAGTATAC
* * *
2837120 C-TTTCTGTTGATAATGTACCCATATACATGTCAACTCTAGCATAATTTTCTGTTGATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATGTCAACTATAGCATAATTTTATGTTGATAATGCAC
*
2837184 CCATATGCATTTCAACTCTAGTATAC
66 CCATATACATTTCAACTCTAGTATAC
* * * * ** * ***
2837210 CTTTTCTGTTGATAATGCACCCATATGCATTTCATCTATGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTCTGTTGATAATGCACCCATATACATGTCAACTATAGCATAATTTTATGTTGATAATGCAC
*
2837275 CCATATGCATT
66 CCATATACATT
2837286 ATTCTTTTAT
Statistics
Matches: 137, Mismatches: 25, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
88 2 0.01
89 71 0.52
90 3 0.02
91 61 0.45
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (91 bp):
CTTTTCTGTTGATAATGCACCCATATACATGTCAACTATAGCATAATTTTATGTTGATAATGCAC
CCATATACATTTCAACTCTAGTATAC
Found at i:2837342 original size:79 final size:79
Alignment explanation
Indices: 2837210--2837373 Score: 265
Period size: 79 Copynumber: 2.1 Consensus size: 79
2837200 TCTAGTATAC
* * * * *
2837210 CTTTTCTGTTGATAATGCACCCATATGCATTTCATCTATGGCATCCTTTCATGCCAATAATGCAC
1 CTTTTATGTTGACAATGCACCCATATACATTTCAACTATGGCATCCTTCCATGCCAATAATGCAC
2837275 CCATATGCATTATT
66 CCATATGCATTATT
* *
2837289 CTTTTATGTTGACAATGTACCCATATACATTTCAACTTTGGCATCCTTCCATGCCAATAATGCAC
1 CTTTTATGTTGACAATGCACCCATATACATTTCAACTATGGCATCCTTCCATGCCAATAATGCAC
2837354 CCATATGCATTATT
66 CCATATGCATTATT
2837368 CTTTTA
1 CTTTTA
2837374 CATTCGTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (79 bp):
CTTTTATGTTGACAATGCACCCATATACATTTCAACTATGGCATCCTTCCATGCCAATAATGCAC
CCATATGCATTATT
Found at i:2837903 original size:74 final size:74
Alignment explanation
Indices: 2837794--2837938 Score: 188
Period size: 74 Copynumber: 2.0 Consensus size: 74
2837784 GATATTACCC
* * *
2837794 TATTAGGGTATCGATACCCCTTAATGTATCAATACCGAAATTAGATTCG-A-TATAGCCTGGTAT
1 TATTAGGGTACCGATACCCCTTAAGGTATCAATACCCAAATTAGATTCGAAGTATA--CTGGTAT
2837857 CGATACCCCTA
64 CGATACCCCTA
* * *
2837868 TATTATGGTACCGATACCCCTCT-AGGTATCGATACCCAAATTAGATTCGAAGTTTACTGGTATC
1 TATTAGGGTACCGATACCCCT-TAAGGTATCAATACCCAAATTAGATTCGAAGTATACTGGTATC
2837932 GATACCC
65 GATACCC
2837939 TTACCATGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
74 57 0.92
75 2 0.03
76 3 0.05
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.31
Consensus pattern (74 bp):
TATTAGGGTACCGATACCCCTTAAGGTATCAATACCCAAATTAGATTCGAAGTATACTGGTATCG
ATACCCCTA
Found at i:2839126 original size:17 final size:17
Alignment explanation
Indices: 2839101--2839140 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2839091 GTATGTTGTT
*
2839101 CATTAAAGCATGCATTG
1 CATTTAAGCATGCATTG
* *
2839118 CATTTAAGCATGTATTT
1 CATTTAAGCATGCATTG
2839135 CATTTA
1 CATTTA
2839141 GGGAAGTAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATTTAAGCATGCATTG
Found at i:2839219 original size:18 final size:18
Alignment explanation
Indices: 2839196--2839241 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
2839186 ATCCATGCAT
*
2839196 TTAGTTCGTTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
2839214 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
2839232 TTATTTCATT
1 TTAGTTCATT
2839242 AATCAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:2844991 original size:14 final size:14
Alignment explanation
Indices: 2844972--2845007 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2844962 CCTATAATGT
*
2844972 CTGCTGAAGAGAAC
1 CTGCTGAAGAAAAC
2844986 CTGCTGAAGAAAAC
1 CTGCTGAAGAAAAC
*
2845000 CTACTGAA
1 CTGCTGAA
2845008 TGATAGGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (14 bp):
CTGCTGAAGAAAAC
Found at i:2848177 original size:58 final size:58
Alignment explanation
Indices: 2848102--2848422 Score: 360
Period size: 58 Copynumber: 5.5 Consensus size: 58
2848092 ATGGCACTTT
* *
2848102 GTGTGCTAAAATGATAAGGAAACCATACTGAGTGTATAGATTTCCATATGGAGCGCTGA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
* *
2848161 GTGTGCTAAATGATAAGAAAATCATACTGAGTGTATAGATTTCCATATGGAGCATTGA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
*
2848219 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTTCATATGGAGCACTGA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
* * *** * * *
2848277 GCGTGCTAAATGATAAGGAAATCATATTGAAAATAT-GAATTTCCAGATAGG-GCATTTTA
1 GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAG-ATTTCCATAT-GGAGCA-CTGA
* * * * * ** *
2848336 -TGTGCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAA
1 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
* *
2848394 GGGTGCTACAAAGATAAGGAAATCATACT
1 GTGTGCTA-AATGATAAGGAAATCATACT
2848423 AATGGTGTGG
Statistics
Matches: 223, Mismatches: 31, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
57 1 0.00
58 152 0.68
59 69 0.31
60 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (58 bp):
GTGTGCTAAATGATAAGGAAATCATACTGAGTGTATAGATTTCCATATGGAGCACTGA
Found at i:2848252 original size:30 final size:30
Alignment explanation
Indices: 2848157--2848252 Score: 76
Period size: 30 Copynumber: 3.3 Consensus size: 30
2848147 ATATGGAGCG
*
2848157 CTGAGTGTGCTAAATGATAAGAAAATCATA
1 CTGAGTGTGCTAAATGATAAGGAAATCATA
* * * * *
2848187 CTGAGTGT-ATAGATTTCCATATGG--AGCAT-
1 CTGAGTGTGCTA-A-AT-GATAAGGAAATCATA
2848216 -TGAGTGTGCTAAATGATAAGGAAATCATA
1 CTGAGTGTGCTAAATGATAAGGAAATCATA
2848245 CTGAGTGT
1 CTGAGTGT
2848253 ATAGATTTTC
Statistics
Matches: 47, Mismatches: 11, Indels: 16
0.64 0.15 0.22
Matches are distributed among these distances:
26 5 0.11
27 1 0.02
28 12 0.26
29 4 0.09
30 20 0.43
31 1 0.02
32 4 0.09
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.30
Consensus pattern (30 bp):
CTGAGTGTGCTAAATGATAAGGAAATCATA
Found at i:2848378 original size:59 final size:59
Alignment explanation
Indices: 2848102--2848571 Score: 304
Period size: 58 Copynumber: 8.0 Consensus size: 59
2848092 ATGGCACTTT
* * * **
2848102 GTGTGCTAAAATGATAAGGAAACCATACTGAGTGTATAGATTTCCATAT-GGAGCGCTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCATTGA
* * *
2848161 GTGTGCT-AAATGATAAGAAAATCATACTGAGTGTATAGATTTCCATAT-GGAGCATTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCATTGA
* * * *
2848219 GTGTGCT-AAATGATAAGGAAATCATACTGAGTGTATAGATTTTCATAT-GGAGCACTGA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGG-GCATTGA
* * *** * *
2848277 GCGTGCT-AAATGATAAGGAAATCATATTGAAAATATGAATTTCCAGATAGGGCATTTTA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCA-TTGA
* * * ** * *
2848336 -TGTGCTAAAAAGGTAAGGGAATCATACTGAGTGTATGGATTTCCAGATAAAGCACTAA
1 GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCATTGA
* * * * ** *
2848394 GGGTGCTACAAA-GATAAGGAAATCATACT-AATGGTGTGGATTTTCACTTAGGGCATTTCA
1 GTGTGCTA-AAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCAGATAGGGCA-TTGA
* ** * * ** *
2848454 -TGTGCTAAAATGGTAACAAAATCATACTAAAG-GTATGAATTT-TTGAATAGGGCACTT-C
1 GTGTGCTAAAATGATAAGGAAATCATACT-GAGTGTATGGATTTCCAG-ATAGGGCA-TTGA
* * * * * *
2848512 GTGTGCTAAAATGA-AAGGGGAAGCATACTAAGAGTAT-GATTTTCCAGATAGAGCACTGA
1 GTGTGCTAAAATGATAA-GGAAATCATACTGAGTGTATGGA-TTTCCAGATAGGGCATTGA
2848571 G
1 G
2848572 AGTACTAATA
Statistics
Matches: 327, Mismatches: 67, Indels: 34
0.76 0.16 0.08
Matches are distributed among these distances:
58 163 0.50
59 157 0.48
60 6 0.02
61 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (59 bp):
GTGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAGGGCATTGA
Found at i:2848714 original size:45 final size:45
Alignment explanation
Indices: 2848659--2848801 Score: 241
Period size: 45 Copynumber: 3.2 Consensus size: 45
2848649 AAATGAGGTT
* *
2848659 AATGGCAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATA
1 AATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGAATA
2848704 AATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGAATA
1 AATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGAATA
* *
2848749 AATGGTATGTATGTTGGTAAAATAAGCTTACGAGCTTATGGGATA
1 AATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGAATA
*
2848794 GATGGTAA
1 AATGGTAA
2848802 ATTTATTGAT
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 92 1.00
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (45 bp):
AATGGTAAGTATGTTGGTAAAATAAGCTTACGAGCTTATGGAATA
Found at i:2857473 original size:37 final size:37
Alignment explanation
Indices: 2857423--2857514 Score: 116
Period size: 36 Copynumber: 2.5 Consensus size: 37
2857413 TTCGTCTTAT
* *
2857423 TAGGATTCAAACTCCTAAAAATAAGATAGAA-TTTTGC
1 TAGGATTCAAACTCCTAAAAATAAGATA-AAGTTCTAC
*
2857460 TAGGATTCAAACTCCT-AAAATATGATAAAGTTCTAC
1 TAGGATTCAAACTCCTAAAAATAAGATAAAGTTCTAC
* *
2857496 TATGATTTAAACTCCTAAA
1 TAGGATTCAAACTCCTAAA
2857515 GATAGGATCC
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
35 2 0.04
36 28 0.58
37 18 0.38
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAAGATAAAGTTCTAC
Found at i:2858338 original size:4 final size:4
Alignment explanation
Indices: 2858325--2858384 Score: 63
Period size: 4 Copynumber: 15.2 Consensus size: 4
2858315 TATATTTTAA
*
2858325 TATT TCATT TATT TATT TATT TATT TATT TATT T-TT CTTTT TATT T-TT
1 TATT T-ATT TATT TATT TATT TATT TATT TATT TATT -TATT TATT TATT
*
2858373 T-TT TACT TATT T
1 TATT TATT TATT T
2858385 TTATTCTTCA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
3 8 0.16
4 35 0.71
5 6 0.12
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (4 bp):
TATT
Found at i:2858345 original size:25 final size:25
Alignment explanation
Indices: 2858283--2858371 Score: 60
Period size: 25 Copynumber: 3.6 Consensus size: 25
2858273 GTTATGATTA
*
2858283 TTATTT-TTCTATTTTACTCATTTAT
1 TTATTTATT-TATTTTAATCATTTAT
* * *
2858308 ATATATATATATTTTAAT-ATTTCAT
1 TTATTTATTTATTTTAATCATTT-AT
* *
2858333 TTATTTATTTA-TTTATTTATTTAT
1 TTATTTATTTATTTTAATCATTTAT
*
2858357 TT-TTCTTTTTATTTT
1 TTATT-TATTTATTTT
2858372 TTTTTACTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
23 2 0.04
24 18 0.36
25 29 0.58
26 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (25 bp):
TTATTTATTTATTTTAATCATTTAT
Found at i:2858382 original size:26 final size:28
Alignment explanation
Indices: 2858336--2858405 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 28
2858326 ATTTCATTTA
* *
2858336 TTTATTTATTTATTTATTTATTTTTCTT-
1 TTTATTT-TTTATTTACTTATTTTTATTC
2858364 TTTATTTTTT-TTTACTTATTTTTATTC
1 TTTATTTTTTATTTACTTATTTTTATTC
*
2858391 TTCATTTTTTCATTT
1 TTTATTTTTT-ATTT
2858406 TTTTCCCTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
26 14 0.39
27 12 0.33
28 7 0.19
29 3 0.08
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (28 bp):
TTTATTTTTTATTTACTTATTTTTATTC
Found at i:2858385 original size:12 final size:11
Alignment explanation
Indices: 2858333--2858409 Score: 50
Period size: 12 Copynumber: 6.7 Consensus size: 11
2858323 AATATTTCAT
*
2858333 TTATTTATTTA
1 TTATTTTTTTA
*
2858344 TTTATTTATTTA
1 -TTATTTTTTTA
*
2858356 TTTTTCTTTTTA
1 TTATT-TTTTTA
2858368 TT-TTTTTTTA
1 TTATTTTTTTA
*
2858378 CTTATTTTTATTC
1 -TTATTTTT-TTA
*
2858391 TTCATTTTTTCA
1 TT-ATTTTTTTA
2858403 TT-TTTTT
1 TTATTTTT
2858410 CCCTCTAACA
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 11 0.20
11 8 0.15
12 28 0.51
13 8 0.15
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATTTTTTTA
Done.