Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 51
Found at i:3481787 original size:18 final size:17
Alignment explanation
Indices: 3481745--3481787 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
3481735 ATGAGCAAGT
3481745 TGAAGAAGAAGAAGATG
1 TGAAGAAGAAGAAGATG
* *
3481762 TAGTAGAAGAAGAAGGTG
1 T-GAAGAAGAAGAAGATG
3481780 ATGAAGAA
1 -TGAAGAA
3481788 TCTAAAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.35, T:0.14
Consensus pattern (17 bp):
TGAAGAAGAAGAAGATG
Found at i:3484061 original size:25 final size:27
Alignment explanation
Indices: 3484007--3484065 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
3483997 TAGTTATAAA
3484007 GAAGAAGAAAAAGAAATGAAGTTTGAAT
1 GAAGAAGAAAAAGAAA-GAAGTTTGAAT
*
3484035 GAAGAAGAAAGAAGACA-AAG-TTG-AT
1 GAAGAAGAAA-AAGAAAGAAGTTTGAAT
3484060 GAAGAA
1 GAAGAA
3484066 AATGAGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.28
26 3 0.10
27 3 0.10
28 10 0.34
29 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.27, T:0.14
Consensus pattern (27 bp):
GAAGAAGAAAAAGAAAGAAGTTTGAAT
Found at i:3489713 original size:20 final size:20
Alignment explanation
Indices: 3489688--3489729 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3489678 CTAAGAGCTT
3489688 ATTTAGAACCATATAGATGC
1 ATTTAGAACCATATAGATGC
* * *
3489708 ATTTAGGAGCATATAGTTGC
1 ATTTAGAACCATATAGATGC
3489728 AT
1 AT
3489730 GTGGTGGAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (20 bp):
ATTTAGAACCATATAGATGC
Found at i:3501231 original size:20 final size:20
Alignment explanation
Indices: 3501193--3501231 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3501183 TAATCCTATT
**
3501193 CACTGGTAATCTTTTATTCC
1 CACTGGTAATCTTACATTCC
3501213 CACTGGTAATCTTACATTC
1 CACTGGTAATCTTACATTC
3501232 TGTGAACCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (20 bp):
CACTGGTAATCTTACATTCC
Found at i:3505329 original size:31 final size:31
Alignment explanation
Indices: 3505244--3505329 Score: 100
Period size: 31 Copynumber: 2.8 Consensus size: 31
3505234 AAATTGAAAG
* * * *
3505244 TTTAAATATTAAAACAGATTAAAATTAATAA
1 TTTAGATACTAAAACAAATCAAAATTAATAA
* * * *
3505275 TTTAGGTACTAAAGCGAACCAAAATTAATAA
1 TTTAGATACTAAAACAAATCAAAATTAATAA
3505306 TTTAGATACTAAAACAAATCAAAA
1 TTTAGATACTAAAACAAATCAAAA
3505330 ATAGTTTAGT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.55, C:0.09, G:0.07, T:0.29
Consensus pattern (31 bp):
TTTAGATACTAAAACAAATCAAAATTAATAA
Found at i:3521757 original size:2 final size:2
Alignment explanation
Indices: 3521746--3521778 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
3521736 ATTTTTATCC
3521746 AT AT -T 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
3521779 TAAGTGGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3522077 original size:19 final size:19
Alignment explanation
Indices: 3522053--3522091 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3522043 ATTCTAAAAA
3522053 TAGAATTGACTTGTCAAAG
1 TAGAATTGACTTGTCAAAG
3522072 TAGAATTGACTTGTCAAAG
1 TAGAATTGACTTGTCAAAG
3522091 T
1 T
3522092 CCTAGCTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (19 bp):
TAGAATTGACTTGTCAAAG
Found at i:3522440 original size:20 final size:22
Alignment explanation
Indices: 3522410--3522463 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
3522400 TGTTTGTTAG
*
3522410 GGTACCGATACTGTAAG-GTAA
1 GGTATCGATACTGTAAGAGTAA
*
3522431 -GTATCGATAC--CAAGAGTAA
1 GGTATCGATACTGTAAGAGTAA
3522450 GGTATCGATACTGT
1 GGTATCGATACTGT
3522464 CACCACCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
18 3 0.12
19 4 0.15
20 19 0.73
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (22 bp):
GGTATCGATACTGTAAGAGTAA
Found at i:3525588 original size:47 final size:48
Alignment explanation
Indices: 3525519--3525617 Score: 137
Period size: 47 Copynumber: 2.1 Consensus size: 48
3525509 AATTCTGTTA
* * *
3525519 TGATATATGACTTGAATTCTGATCTGATAC-TGACATGGATTATGATT
1 TGATACATGACATGAATTCTGATCTGATACTTGACATGAATTATGATT
* * *
3525566 TGATACATGACATGGATTCTGATCTGATACTTGACTTGAATTATGTTT
1 TGATACATGACATGAATTCTGATCTGATACTTGACATGAATTATGATT
3525614 TGAT
1 TGAT
3525618 TTTTTATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
47 27 0.60
48 18 0.40
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.41
Consensus pattern (48 bp):
TGATACATGACATGAATTCTGATCTGATACTTGACATGAATTATGATT
Found at i:3525617 original size:24 final size:24
Alignment explanation
Indices: 3525506--3525607 Score: 100
Period size: 24 Copynumber: 4.3 Consensus size: 24
3525496 GATTTTCGAT
* *
3525506 TTGAATTCTGTTATGATA-TATGAC
1 TTGAATTCTGATCTGATACT-TGAC
3525530 TTGAATTCTGATCTGATAC-TGAC
1 TTGAATTCTGATCTGATACTTGAC
* * * * *
3525553 ATGGATTATGATTTGATACATGAC
1 TTGAATTCTGATCTGATACTTGAC
* *
3525577 ATGGATTCTGATCTGATACTTGAC
1 TTGAATTCTGATCTGATACTTGAC
3525601 TTGAATT
1 TTGAATT
3525608 ATGTTTTGAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.29
24 46 0.71
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (24 bp):
TTGAATTCTGATCTGATACTTGAC
Found at i:3526942 original size:3 final size:3
Alignment explanation
Indices: 3526934--3526967 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
3526924 TATGTGAATC
3526934 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3526968 ATTGAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3527769 original size:21 final size:22
Alignment explanation
Indices: 3527739--3527787 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3527729 GAAATTACTT
3527739 TAGCAAGGGTATCAATA-CACTG
1 TAGC-AGGGTATCAATACCACTG
* *
3527761 TAGCAGGGTATCGATACCCCTG
1 TAGCAGGGTATCAATACCACTG
3527783 TAGCA
1 TAGCA
3527788 TTTTGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.22
Consensus pattern (22 bp):
TAGCAGGGTATCAATACCACTG
Found at i:3531087 original size:24 final size:24
Alignment explanation
Indices: 3531056--3531140 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
3531046 ATATTTTATA
3531056 TATATTAACTCTAAAAAATAT-TTT
1 TATATTAACT-TAAAAAATATATTT
* **
3531080 TATATTAAATTATTAAATATATTT
1 TATATTAACTTAAAAAATATATTT
*
3531104 TATTATTAACTTAATTTAAATATATATAT
1 TA-TATTAACTTAA---AAA-ATATATTT
3531133 TATATTAA
1 TATATTAA
3531141 AATATTATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.17
24 14 0.29
25 9 0.19
28 8 0.17
29 9 0.19
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATTAACTTAAAAAATATATTT
Found at i:3531122 original size:27 final size:24
Alignment explanation
Indices: 3531071--3531147 Score: 84
Period size: 27 Copynumber: 3.0 Consensus size: 24
3531061 TAACTCTAAA
3531071 AAATAT-TTTTATATTAAATTATT
1 AAATATATTTTATATTAAATTATT
*
3531094 AAATATATTTTATTATTAACTTAATTT
1 AAATATATTTTA-TATTAAATT-A-TT
*
3531121 AAATATATATATTATATTAAAATATT
1 AAATATAT-T-TTATATTAAATTATT
3531147 A
1 A
3531148 TGAAATTAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 6 0.13
24 5 0.11
25 8 0.18
26 4 0.09
27 11 0.24
28 8 0.18
29 3 0.07
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
AAATATATTTTATATTAAATTATT
Found at i:3531215 original size:22 final size:21
Alignment explanation
Indices: 3531176--3531216 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3531166 TGAATATATT
3531176 TAATAATTTAAAATAATAATG
1 TAATAATTTAAAATAATAATG
3531197 TAATATATTTAATAA-AATAA
1 TAATA-ATTTAA-AATAATAA
3531217 GATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 11 0.61
23 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAATAATTTAAAATAATAATG
Found at i:3531260 original size:33 final size:30
Alignment explanation
Indices: 3531209--3531314 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 30
3531199 ATATATTTAA
*
3531209 TAAAATAAGATAAAATATATAATTTTGAAAAT
1 TAAAATAAAATAAAATATAT-ATTTT-AAAAT
3531241 TAAAATAATAATAAAATATAT-TTTTAAAAGT
1 TAAAATAA-AATAAAATATATATTTTAAAA-T
* * *
3531272 TTAGATAAAAATAAAATATATATTTTTAAAT
1 TAAAAT-AAAATAAAATATATATTTTAAAAT
*
3531303 AAAAATAAAATA
1 TAAAATAAAATA
3531315 TTTTTAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
30 10 0.16
31 25 0.40
32 17 0.27
33 11 0.17
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (30 bp):
TAAAATAAAATAAAATATATATTTTAAAAT
Found at i:3534741 original size:204 final size:204
Alignment explanation
Indices: 3534386--3534782 Score: 607
Period size: 204 Copynumber: 1.9 Consensus size: 204
3534376 ACTCATCTTA
* * *
3534386 TTGTCACGCCCTTAGAACTTCGACGTCTCGGAACGTGCGGCTTTAGTCGCATTCTCAGTAATTGC
1 TTGTCACGCCCTTAGAACTTCGACGCCACAGAACGTGCGGCTTTAGTCGCATTCTCAGTAATTGC
* * *
3534451 GGCTAAGTAAGCCTGAAAATATCCCAAACAAGGATGCTTAGAATCTCGACGGAAGCTAGACAAGA
66 GGCTAAGTAAGCATGAAAATATCCCAAACAAAGATGCTTAGAATCTCGACGAAAGCTAGACAAGA
* * * *
3534516 GAACTAGCACAAAATGGAAGATAAAAAAACTTTAAGAGAATAATGCTCTTATGATTTCTCAAAGT
131 GAACTAACACAAAAAGGAAGATAAAAAAACTTTAAGAGAACAACGCTCTTATGATTTCTCAAAGT
3534581 GAAGGAGTC
196 GAAGGAGTC
* * *
3534590 TTGTCACGCCCTTAGAACTTCGGCGCCACAGAACGTGCGG-TCTTAGTCGCCTTCTCAGTGATTG
1 TTGTCACGCCCTTAGAACTTCGACGCCACAGAACGTGCGGCT-TTAGTCGCATTCTCAGTAATTG
*
3534654 CGGCTAAGTAAGCATGAAAATATCCCAAGCAAAGATGCTTAGAATCTCGACGAAAGCTAGACAAG
65 CGGCTAAGTAAGCATGAAAATATCCCAAACAAAGATGCTTAGAATCTCGACGAAAGCTAGACAAG
* ** * *
3534719 AGAACTAACACAAAAAGGAAGATAAGAAAGTTTTGAGAGAACAACGCTTTTATGATTTCTCAAA
130 AGAACTAACACAAAAAGGAAGATAAAAAAACTTTAAGAGAACAACGCTCTTATGATTTCTCAAA
3534783 ACTTTATATA
Statistics
Matches: 173, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
203 1 0.01
204 172 0.99
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (204 bp):
TTGTCACGCCCTTAGAACTTCGACGCCACAGAACGTGCGGCTTTAGTCGCATTCTCAGTAATTGC
GGCTAAGTAAGCATGAAAATATCCCAAACAAAGATGCTTAGAATCTCGACGAAAGCTAGACAAGA
GAACTAACACAAAAAGGAAGATAAAAAAACTTTAAGAGAACAACGCTCTTATGATTTCTCAAAGT
GAAGGAGTC
Found at i:3535809 original size:12 final size:11
Alignment explanation
Indices: 3535784--3535835 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
3535774 GGTTCTCGTT
3535784 TTATTAATTTA
1 TTATTAATTTA
3535795 TTATTAATATTA
1 TTATTAAT-TTA
3535807 TTATT-ATTT-
1 TTATTAATTTA
* * *
3535816 TAACTATTTTA
1 TTATTAATTTA
3535827 TTATTAATT
1 TTATTAATT
3535836 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
9 3 0.09
10 5 0.16
11 16 0.50
12 8 0.25
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATTAATTTA
Found at i:3535812 original size:15 final size:15
Alignment explanation
Indices: 3535791--3535843 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
3535781 GTTTTATTAA
3535791 TTTATTATTAA-TAT
1 TTTATTATTAACTAT
3535805 TATTATTATTTTAACTAT
1 T-TTATTA--TTAACTAT
*
3535823 TTTATTATTAATTAT
1 TTTATTATTAACTAT
3535838 TTTATT
1 TTTATT
3535844 TTACAAATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 1 0.03
15 19 0.56
17 10 0.29
18 4 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATTATTAACTAT
Found at i:3537258 original size:24 final size:24
Alignment explanation
Indices: 3537220--3537271 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3537210 GAGAGGGCAG
* *
3537220 AAAAAAAAGAGAAAAATCGAA-GA
1 AAAAAAAAGAAAAAAAACGAACGA
3537243 AAAAAAACAGAAAAAAAACGAACGA
1 AAAAAAA-AGAAAAAAAACGAACGA
3537268 AAAA
1 AAAA
3537272 CAGAGAAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
24 12 0.48
25 6 0.24
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.02
Consensus pattern (24 bp):
AAAAAAAAGAAAAAAAACGAACGA
Found at i:3537261 original size:11 final size:11
Alignment explanation
Indices: 3537217--3537275 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
3537207 GGGGAGAGGG
3537217 CAGAAAAAAAA
1 CAGAAAAAAAA
* **
3537228 GAGAAAAATCGA
1 CAGAAAAA-AAA
3537240 -AGAAAAAAAA
1 CAGAAAAAAAA
3537250 CAGAAAAAAAA
1 CAGAAAAAAAA
*
3537261 C-GAACGAAAAA
1 CAGAA-AAAAAA
3537272 CAGA
1 CAGA
3537276 GAAAGCTCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
10 4 0.11
11 31 0.82
12 3 0.08
ACGTcount: A:0.73, C:0.10, G:0.15, T:0.02
Consensus pattern (11 bp):
CAGAAAAAAAA
Found at i:3537269 original size:14 final size:13
Alignment explanation
Indices: 3537226--3537271 Score: 51
Period size: 11 Copynumber: 3.6 Consensus size: 13
3537216 GCAGAAAAAA
* *
3537226 AAGAGAAAAATCG
1 AAGAAAAAAAACG
3537239 AAGAAAAAAAAC-
1 AAGAAAAAAAACG
3537251 -AGAAAAAAAACG
1 AAGAAAAAAAACG
3537263 AACGAAAAA
1 AA-GAAAAA
3537272 CAGAGAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 11 0.39
13 11 0.39
14 6 0.21
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAAACG
Found at i:3538477 original size:15 final size:15
Alignment explanation
Indices: 3538454--3538500 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
3538444 TATTTCATTC
*
3538454 TATTTTTTTATTTTG
1 TATTATTTTATTTTG
*
3538469 TATTATTTTATTTTA
1 TATTATTTTATTTTG
*
3538484 TTTTATTTTATTTTG
1 TATTATTTTATTTTG
3538499 TA
1 TA
3538501 AATAAATGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (15 bp):
TATTATTTTATTTTG
Found at i:3538479 original size:5 final size:5
Alignment explanation
Indices: 3538459--3538497 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
3538449 CATTCTATTT
* *
3538459 TTTTA TTTTG TATTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
3538498 GTAAATAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:3547681 original size:13 final size:13
Alignment explanation
Indices: 3547663--3547691 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
3547653 GTGAGGTATG
3547663 ATATATATATAAT
1 ATATATATATAAT
3547676 ATATATATATAAT
1 ATATATATATAAT
3547689 ATA
1 ATA
3547692 CTGTTGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATATATATATAAT
Found at i:3549589 original size:48 final size:48
Alignment explanation
Indices: 3549518--3549624 Score: 187
Period size: 48 Copynumber: 2.2 Consensus size: 48
3549508 GTTGAAACTA
3549518 AAAGACTTCCTCAACACAGAATTTGAGCTTAAAAATTTGGGGAATCTC
1 AAAGACTTCCTCAACACAGAATTTGAGCTTAAAAATTTGGGGAATCTC
* *
3549566 AAAGACTTCCTCAGCACAGAATTTGAGCTTAAAGATTTGGGGAATCTC
1 AAAGACTTCCTCAACACAGAATTTGAGCTTAAAAATTTGGGGAATCTC
*
3549614 AAATACTTCCT
1 AAAGACTTCCT
3549625 TGGCATGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 56 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (48 bp):
AAAGACTTCCTCAACACAGAATTTGAGCTTAAAAATTTGGGGAATCTC
Found at i:3559571 original size:107 final size:107
Alignment explanation
Indices: 3559407--3559635 Score: 354
Period size: 107 Copynumber: 2.1 Consensus size: 107
3559397 CTCCATTATG
*
3559407 TTTGGTATCGGTACCCCTTTTGGTACCGATATCATTTTTGCATTCTGAAATTTGAGCAATGTTGG
1 TTTGGTATCGGTACCCCTTTTGGTACCGATACCATTTTTGCATTCTGAAATTTGAGCAATGTTGG
* *
3559472 TAGTATCGATACTA-CATTGTGAGTATCAATACTTCTGATACC
66 TAGTATCAATACTATC-TTGTGAGTATCAATACTTCCGATACC
* * * *
3559514 TTTGGTATCGGTATCCC-TTTGGATATCGGTACCATTTTTGCATTCTGGAATTTGAGCAATGTTG
1 TTTGGTATCGGTACCCCTTTTGG-TACCGATACCATTTTTGCATTCTGAAATTTGAGCAATGTTG
*
3559578 GTAGTATCAATACTATCTTGTGAGTATCGATACTTCCGATACC
65 GTAGTATCAATACTATCTTGTGAGTATCAATACTTCCGATACC
3559621 TTTGGTATCGGTACC
1 TTTGGTATCGGTACC
3559636 ATATGAACAA
Statistics
Matches: 111, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
106 5 0.05
107 105 0.95
108 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (107 bp):
TTTGGTATCGGTACCCCTTTTGGTACCGATACCATTTTTGCATTCTGAAATTTGAGCAATGTTGG
TAGTATCAATACTATCTTGTGAGTATCAATACTTCCGATACC
Found at i:3562215 original size:19 final size:19
Alignment explanation
Indices: 3562191--3562240 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
3562181 ATGCAATTAA
3562191 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
3562210 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
* *
3562229 TGTAGCGATGCA
1 TGCATCGATGCA
3562241 CCTGCTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.30, C:0.16, G:0.32, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:3563602 original size:23 final size:23
Alignment explanation
Indices: 3563576--3563683 Score: 117
Period size: 23 Copynumber: 4.7 Consensus size: 23
3563566 CATCACAGCT
*
3563576 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
3563599 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* * *
3563622 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* * *
3563645 TATAATAATTGTACCGGAGTGCCG
1 CAT-ATAATTGCACCGGAGTGCCA
* *
3563669 CGTAGAATTGCACCG
1 CATATAATTGCACCG
3563684 TAGTTCCATA
Statistics
Matches: 68, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
23 51 0.75
24 17 0.25
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.23
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:3563666 original size:47 final size:47
Alignment explanation
Indices: 3563581--3563698 Score: 193
Period size: 47 Copynumber: 2.5 Consensus size: 47
3563571 CAGCTCATAT
* *
3563581 AATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
*
3563627 AATTGCACCGTAGTGCCATATAATAATTGTACCGGAGTGCCGCGTAG
1 AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
*
3563674 AATTGCACCGTAGTTCCATATAATA
1 AATTGCACCGTAGTGCCATATAATA
3563699 GTGTCTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 19 0.28
47 48 0.72
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (47 bp):
AATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
Found at i:3563841 original size:103 final size:103
Alignment explanation
Indices: 3563707--3563924 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
3563697 TAGTGTCTAT
* *
3563707 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3563772 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
3563810 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
3563875 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
3563913 AAGGACCACATA
1 AAGGACCACATA
3563925 GACCCTCGAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:3569419 original size:23 final size:23
Alignment explanation
Indices: 3569393--3569517 Score: 142
Period size: 23 Copynumber: 5.3 Consensus size: 23
3569383 CACCACAGCT
*
3569393 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
3569416 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGGAGTGCCA
* *
3569439 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
* *
3569462 TATAATAATTGCACCGGAGTGCCG
1 CAT-ATAATTGCACCGGAGTGCCA
* * *
3569486 CATAGAATTGTACCGTAGTGCCA
1 CATATAATTGCACCGGAGTGCCA
*
3569509 TATAATAAT
1 CAT-ATAAT
3569518 GTCCATAAGG
Statistics
Matches: 84, Mismatches: 16, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
23 61 0.73
24 23 0.27
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (23 bp):
CATATAATTGCACCGGAGTGCCA
Found at i:3569482 original size:47 final size:47
Alignment explanation
Indices: 3569393--3569517 Score: 207
Period size: 47 Copynumber: 2.7 Consensus size: 47
3569383 CACCACAGCT
* * *
3569393 CATATAATTGCACCGAAGTGCCACAT-ATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
3569439 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
1 CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
*
3569486 CATAGAATTGTACCGTAGTGCCATATAATAAT
1 CATAGAATTGCACCGTAGTGCCATATAATAAT
3569518 GTCCATAAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
46 23 0.31
47 51 0.69
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (47 bp):
CATAGAATTGCACCGTAGTGCCATATAATAATTGCACCGGAGTGCCG
Found at i:3569695 original size:103 final size:103
Alignment explanation
Indices: 3569527--3569741 Score: 385
Period size: 103 Copynumber: 2.1 Consensus size: 103
3569517 TGTCCATAAG
* *
3569527 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
3569592 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
*
3569630 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
* *
3569695 TTCACACATGTTCCAAAGAATACATATATGTCTCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
3569733 GACCACATA
1 GACCACATA
3569742 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 107 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:3577389 original size:19 final size:19
Alignment explanation
Indices: 3577365--3577412 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3577355 GTAATTAGTG
3577365 CATCGATGCATAAGGAGTA
1 CATCGATGCATAAGGAGTA
*
3577384 CATCGATGCATAAGGAGTG
1 CATCGATGCATAAGGAGTA
*
3577403 CAGCGATGCA
1 CATCGATGCA
3577413 CCTGCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (19 bp):
CATCGATGCATAAGGAGTA
Found at i:3578098 original size:38 final size:38
Alignment explanation
Indices: 3578045--3578121 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
3578035 TCGAGGGATT
* * *
3578045 ATCAGTGGTCTTTCGGGATATAGTGGTTCTTCGGAACA
1 ATCAGTGGTCATTCGGGACATAGTGGTCCTTCGGAACA
*
3578083 ATCAGTGGTCATTCGGGACATAGTGGTCCTTCGGGACA
1 ATCAGTGGTCATTCGGGACATAGTGGTCCTTCGGAACA
3578121 A
1 A
3578122 ATATTAGTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (38 bp):
ATCAGTGGTCATTCGGGACATAGTGGTCCTTCGGAACA
Found at i:3578119 original size:18 final size:18
Alignment explanation
Indices: 3578048--3578120 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
3578038 AGGGATTATC
* *
3578048 AGTGGTCTTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
* *
3578066 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
*
3578085 CAGTGGTCATTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
3578104 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
3578121 AATATTAGTG
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
18 28 0.62
19 4 0.09
20 13 0.29
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:3591624 original size:30 final size:30
Alignment explanation
Indices: 3591581--3591637 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3591571 TGGCGTTTAG
* * *
3591581 TTATTTTATGATAACAT-ATTAATATTATTA
1 TTATTTAACGATAA-ATAATTAAAATTATTA
3591611 TTATTTAACGATAAATAATTAAAATTA
1 TTATTTAACGATAAATAATTAAAATTA
3591638 AATATCATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 2 0.09
30 21 0.91
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (30 bp):
TTATTTAACGATAAATAATTAAAATTATTA
Found at i:3593958 original size:20 final size:20
Alignment explanation
Indices: 3593933--3594030 Score: 90
Period size: 20 Copynumber: 4.8 Consensus size: 20
3593923 CGCGAATTGG
*
3593933 GACTATCGCAATGCGATACT
1 GACTATCGCAACGCGATACT
* *
3593953 GACTATCGCAATGCGATAAT
1 GACTATCGCAACGCGATACT
* *
3593973 -ACAAAATCGCAACGAGATACT
1 GAC--TATCGCAACGCGATACT
* * *
3593994 GACTTTCGCAACGAGATTCT
1 GACTATCGCAACGCGATACT
*
3594014 GACTTTCGCAACGCGAT
1 GACTATCGCAACGCGAT
3594031 TTACATAGCG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
19 2 0.03
20 49 0.74
21 13 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
GACTATCGCAACGCGATACT
Found at i:3598978 original size:19 final size:19
Alignment explanation
Indices: 3598965--3599015 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
3598955 GAGCACACGA
3598965 CGACCTATGGAGCACTTGG
1 CGACCTATGGAGCACTTGG
3598984 CGACCTATGGAGCACTTGG
1 CGACCTATGGAGCACTTGG
3599003 CGACCTATGGAGC
1 CGACCTATGGAGC
3599016 TACAACAGCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.31, T:0.20
Consensus pattern (19 bp):
CGACCTATGGAGCACTTGG
Found at i:3600012 original size:140 final size:136
Alignment explanation
Indices: 3599850--3600325 Score: 455
Period size: 140 Copynumber: 3.4 Consensus size: 136
3599840 CCCTAAACTT
* * *
3599850 TTTAATTTA-GATGAATTGTTAATTTTGTCATCACATTTATGCCCGAGGTTCCATATTAATTATT
1 TTTAATTTAGGA-GAATT-TTAATTTGGTCATCGCATTTATGCCCGAGGTTCCATTTTAATTATT
3599914 CGATCCAATAAATTAATTAAAATTGATTAGGATTAATATTAGAGTC-TTCATTTTAGATTAATTT
64 CGATCCAATAAATT--TTAAAATTGATTAGGATTAATATTAGAG-CATTCATTTTAGATTAATTT
*
3599978 CATGTTTAG-TC
126 CA-CTTTAGTTC
* *
3599989 ATTTAATTTAGGAGAATTATTAATTTGGTCATCGCTTTTATGCCCAAGGTTCCATTTTAATTATT
1 -TTTAATTTAGGAGAATT-TTAATTTGGTCATCGCATTTATGCCCGAGGTTCCATTTTAATTATT
* * * * * * *
3600054 TGATCCATTACTATTTTAAAATTGGTTAAGATTAATAATTAGAGCTTTCATTTTAGATTGATTTC
64 CGATCCAATA-AATTTTAAAATTGATTAGGATTAAT-ATTAGAGCATTCATTTTAGATTAATTTC
*
3600119 ACTTTGGTTC
127 ACTTTAGTTC
* ** * * * *
3600129 TTTAATTTAGGTGAATTTTAA-TTGGTCCCCGTATTTATGTCCGAGG-TCCTATTTTGATTACTC
1 TTTAATTTAGGAGAATTTTAATTTGGTCATCGCATTTATGCCCGAGGTTCC-ATTTTAATTATTC
* *
3600192 GATCCAATAAATTGTTAAAATT-AGTTAGGATTAATATTAGAGCATTCATTTTAGGTTTATTTTC
65 GATCCAATAAATT-TTAAAATTGA-TTAGGATTAATATTAGAGCATTCATTTTA-GATTAATTTC
* *
3600256 ACCTTAGTCC
127 ACTTTAGTTC
* * * * ** * *
3600266 CTTAATTTA-GATTATTTTTATTTTATTCCTCATC-TTTATGCCCGAGGTTCCATTTTAATT
1 TTTAATTTAGGA-GAATTTTAATTTGGTCATC-GCATTTATGCCCGAGGTTCCATTTTAATT
3600326 TTAGAATCAA
Statistics
Matches: 276, Mismatches: 47, Indels: 28
0.79 0.13 0.08
Matches are distributed among these distances:
136 24 0.09
137 83 0.30
138 30 0.11
139 43 0.16
140 91 0.33
141 5 0.02
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (136 bp):
TTTAATTTAGGAGAATTTTAATTTGGTCATCGCATTTATGCCCGAGGTTCCATTTTAATTATTCG
ATCCAATAAATTTTAAAATTGATTAGGATTAATATTAGAGCATTCATTTTAGATTAATTTCACTT
TAGTTC
Found at i:3607526 original size:8 final size:8
Alignment explanation
Indices: 3607513--3607576 Score: 51
Period size: 8 Copynumber: 7.6 Consensus size: 8
3607503 AAATAAGGGA
3607513 AAAAAAAG
1 AAAAAAAG
*
3607521 AAAAAATG
1 AAAAAAAG
3607529 AAAAGACAAAG
1 -AAA-A-AAAG
*
3607540 AAAAAATG
1 AAAAAAAG
3607548 --AAAAAG
1 AAAAAAAG
3607554 AAAAAAAG
1 AAAAAAAG
3607562 AAAGAAAATG
1 AAA-AAAA-G
3607572 AAAAA
1 AAAAA
3607577 TAAATAAAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
6 5 0.11
8 19 0.42
9 10 0.22
10 8 0.18
11 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:3607551 original size:26 final size:24
Alignment explanation
Indices: 3607511--3607586 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 24
3607501 AAAAATAAGG
*
3607511 GAAAAAAAAGAAAAAATGAAAAGACAA
1 GAAAAAAATG-AAAAATGAAAA-A-AA
3607538 -AGAAAAAATGAAAAA-GAAAAAAA
1 GA-AAAAAATGAAAAATGAAAAAAA
3607561 GAAAGAAAATGAAAAAT-AAATAAAA
1 GAAA-AAAATGAAAAATGAAA-AAAA
3607586 G
1 G
3607587 GGGGTTCAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
23 4 0.09
24 16 0.37
25 10 0.23
26 6 0.14
27 7 0.16
ACGTcount: A:0.78, C:0.01, G:0.14, T:0.07
Consensus pattern (24 bp):
GAAAAAAATGAAAAATGAAAAAAA
Found at i:3607586 original size:33 final size:33
Alignment explanation
Indices: 3607514--3607580 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
3607504 AATAAGGGAA
*
3607514 AAAAAAGAAAAAATGAAAAGACAAAGAAAAAAT
1 AAAAAAGAAAAAAAGAAAAGACAAAGAAAAAAT
*
3607547 GAAAAAGAAAAAAAG-AAAGA-AAATG-AAAAAT
1 AAAAAAGAAAAAAAGAAAAGACAAA-GAAAAAAT
3607578 AAA
1 AAA
3607581 TAAAAGGGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
31 11 0.37
32 6 0.20
33 13 0.43
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (33 bp):
AAAAAAGAAAAAAAGAAAAGACAAAGAAAAAAT
Found at i:3609479 original size:20 final size:20
Alignment explanation
Indices: 3609454--3609515 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
3609444 AAAATTATTA
3609454 TATTTAT-TATTT-TAATACTT
1 TATTTATATATTTATAA-A-TT
3609474 TATTTATATATTTATAAATT
1 TATTTATATATTTATAAATT
3609494 TATTT-TAT-TGTATATAAATT
1 TATTTATATAT-T-TATAAATT
3609514 TA
1 TA
3609516 GGGAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.03
19 4 0.11
20 24 0.63
21 6 0.16
22 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
TATTTATATATTTATAAATT
Found at i:3611239 original size:133 final size:134
Alignment explanation
Indices: 3610953--3611290 Score: 367
Period size: 133 Copynumber: 2.5 Consensus size: 134
3610943 GAACACATTT
* * * *
3610953 TTCTTCTTTCAAGATTTGGTATTCCTGAAGAGCAGCGAAGCAAATTAAATTCGATTCAATCTTCC
1 TTCTTCTTTC-AGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCAAGTTCGATTCAATCTTCC
* * * * *
3611018 CTGAAGGGCAATAAAGTGGATCAAAATTTTCTCGAGTATGATCTCCCCGAAAGAGTAGTGGAGCA
65 CTGAAGAGCAACAAAGTGGATCAAAATTTCCTCGAGTATGATCTCCCCAAAAGAGTAGTAGAGCA
3611083 GATCC
130 GATCC
* * * * * * *
3611088 TTCTTCTTTCGGAATTGGTCTTTCTAAAGACCAGAGAAGAAAATCAAGTTCGATTCAATCTTTCC
1 TTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCAAGTTCGATTCAATCTTCCC
* * ** * * *
3611153 TGAAGAGCAGCGAAGTGGATCACGA-TTCCAT-GAGTTTGATCTCCCTAAAAGAGTAGTAGAGCG
66 TGAAGAGCAACAAAGTGGATCAAAATTTCC-TCGAGTATGATCTCCCCAAAAGAGTAGTAGAGCA
3611216 GATCC
130 GATCC
* * * * *
3611221 -TCTTTCTTTTAGATTTGGTCTTCCTGAAGAGAAGTGAAGCAAATCAAGTTCGGTTCAACCTTCC
1 TTC-TTCTTTCAGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCAAGTTCGATTCAATCTTCC
*
3611285 ATGAAG
65 CTGAAG
3611291 TGAATCCAAT
Statistics
Matches: 165, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
132 2 0.01
133 89 0.54
134 64 0.39
135 10 0.06
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (134 bp):
TTCTTCTTTCAGATTTGGTCTTCCTGAAGAGCAGAGAAGCAAATCAAGTTCGATTCAATCTTCCC
TGAAGAGCAACAAAGTGGATCAAAATTTCCTCGAGTATGATCTCCCCAAAAGAGTAGTAGAGCAG
ATCC
Found at i:3615277 original size:20 final size:20
Alignment explanation
Indices: 3615248--3615286 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3615238 AGAGCTCATA
*
3615248 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3615268 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3615287 GTGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3616159 original size:21 final size:20
Alignment explanation
Indices: 3616121--3616159 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3616111 TAATGGATGG
*
3616121 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
3616141 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
3616160 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.10, C:0.00, G:0.21, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:3622405 original size:31 final size:31
Alignment explanation
Indices: 3622370--3622540 Score: 274
Period size: 31 Copynumber: 5.5 Consensus size: 31
3622360 ATAGATTCCA
* *
3622370 AAGAACCTAGGTAAACA-TCCCATATGTCCCG
1 AAGAACATAGGTAAACAGT-CCATATGTCTCG
*
3622401 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCTCG
*
3622432 AAGAATATAGGTAAACCA-TCCATATGTCTCG
1 AAGAACATAGGTAAA-CAGTCCATATGTCTCG
3622463 AAGAACATAGGTAAACAGTCCATATGTCTCG
1 AAGAACATAGGTAAACAGTCCATATGTCTCG
3622494 AAGAACATAGGTAAACAGTCCATATGTCTCG
1 AAGAACATAGGTAAACAGTCCATATGTCTCG
3622525 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
3622541 CCTCGACTCT
Statistics
Matches: 133, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
30 2 0.02
31 128 0.96
32 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCTCG
Found at i:3623751 original size:3 final size:3
Alignment explanation
Indices: 3623743--3623767 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3623733 ATGCATCTCT
3623743 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
3623768 AACCATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:3629320 original size:19 final size:19
Alignment explanation
Indices: 3629296--3629336 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3629286 AAGGTCTCCA
3629296 GGAGCACACGGCGACCTAT
1 GGAGCACACGGCGACCTAT
** *
3629315 GGAGCACTTGGTGACCTAT
1 GGAGCACACGGCGACCTAT
3629334 GGA
1 GGA
3629337 AATGCAACAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.34, T:0.17
Consensus pattern (19 bp):
GGAGCACACGGCGACCTAT
Found at i:3636829 original size:181 final size:182
Alignment explanation
Indices: 3636482--3637152 Score: 1042
Period size: 182 Copynumber: 3.7 Consensus size: 182
3636472 TGTCGGTTTA
* * * * *
3636482 TGTCGATACTTTATAAAAATGTATCGATCCATATCAATATAACATGTAAAAATATGACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCG
* * * * * *
3636547 GTCTCAAAAAGACAAAAGCGGTAAAGTGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATA
66 GTCTCAAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
*
3636611 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTTGTGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTTGCGCCTATAAAG
* *
3636663 TGTCGATA-TTTATAACAATGTATCGATCTACAACGATATAACAGGTAAAAATATGACAAAATCA
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCG
*
3636727 GTCTCAAAAGGACAAAATCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCAAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* *
3636792 AGTATCGACATTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTTGCGCCTATAAAG
* *
3636844 TGTTGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCG
* * *
3636909 GTCTCGAAATGACAAAACCGGTATAGAGCTATCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCAAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* * * *
3636974 AGTATCGACACTTTGTAAATTTAAAAGATAAACAGTTTTTACGCCTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTTGCGCCTATAAAG
** *
3637026 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACATATAAAAATATGACAAAACCG
1 TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCG
* *
3637091 ATCTCGAAAGGA-AAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 GTCTCAAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
3637153 AGTACGCGTA
Statistics
Matches: 452, Mismatches: 36, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
180 102 0.23
181 118 0.26
182 232 0.51
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (182 bp):
TGTCGATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAATCG
GTCTCAAAAGGACAAAACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTTGCGCCTATAAAG
Found at i:3637150 original size:363 final size:362
Alignment explanation
Indices: 3636486--3637152 Score: 1068
Period size: 363 Copynumber: 1.8 Consensus size: 362
3636476 GGTTTATGTC
* * * *
3636486 GATACTTTATAAAAATGTATCGATCCATATCAATATAACATGTAAAAATATGACAAAATCGGTCT
1 GATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGTAAAAATATGACAAAACCGGTCT
* * *
3636551 CAAAAAGACAAAAGCGGTAAAGTGTTACCGGATATATTAAAAGTGTCGATACTTTATATAAGTAT
66 CAAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTAAAAGTGTCGATACTTTATATAAGTAT
* * **
3636616 CGACACTTTGTGAATTTAAAAGAGAAGCAGTTTTTGTGCCTATAAAGTGTCGATATTTATAACAA
131 CGACACTTTGTAAATTTAAAAGAGAAACAGTTTTTACGCCTATAAAGTGTCGATATTTATAACAA
* * * *
3636681 TGTATCGATCTACAACGATATAACAGGTAAAAATATGACAAAATCAGTCTCAAAAGGACAAAATC
196 TGTATCGATCCACAACGATATAACAGATAAAAATATGACAAAACCAGTCTCAAAAGGACAAAACC
3636746 GGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACATTTTGTGAA
261 GGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACATTTTGTGAA
3636811 TTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTT
326 TTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTT
* *
3636848 GATACTTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCGGTCT
1 GATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGTAAAAATATGACAAAACCGGTCT
* * * * *
3636913 CGAAATGACAAAACCGGTATAGAGCTATCGGATATATTGAAAGTGTCGATACTTTAATATAAGTA
66 CAAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGTA
*
3636978 TCGACACTTTGTAAATTTAAAAGATAAACAGTTTTTACGCCTATAAAGTGTCGATACTTTATAAC
130 TCGACACTTTGTAAATTTAAAAGAGAAACAGTTTTTACGCCTATAAAGTGTCGATA-TTTATAAC
* *
3637043 AATGTATCGATCCACAACGATATAACATATAAAAATATGACAAAACC-GATCTCGAAAGGA-AAA
194 AATGTATCGATCCACAACGATATAACAGATAAAAATATGACAAAACCAG-TCTCAAAAGGACAAA
3637106 ACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
258 ACCGGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
3637153 AGTACGCGTA
Statistics
Matches: 277, Mismatches: 25, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
362 106 0.38
363 110 0.40
364 61 0.22
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (362 bp):
GATACTTTATAAAAATGTATCGATCCACAACAATATAACAGGTAAAAATATGACAAAACCGGTCT
CAAAAAGACAAAACCGGTAAAGAGCTACCGGATATATTAAAAGTGTCGATACTTTATATAAGTAT
CGACACTTTGTAAATTTAAAAGAGAAACAGTTTTTACGCCTATAAAGTGTCGATATTTATAACAA
TGTATCGATCCACAACGATATAACAGATAAAAATATGACAAAACCAGTCTCAAAAGGACAAAACC
GGTATAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACATTTTGTGAA
TTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAGTGTT
Found at i:3639518 original size:21 final size:21
Alignment explanation
Indices: 3639492--3639535 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3639482 AAGACAATCA
3639492 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
3639513 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGACACTTGAG
3639534 AG
1 AG
3639536 GCAAAAGGGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGACACTTGAG
Found at i:3642749 original size:200 final size:198
Alignment explanation
Indices: 3642365--3643060 Score: 851
Period size: 200 Copynumber: 3.5 Consensus size: 198
3642355 ACCTAAATAT
* *
3642365 GTGTTGATACATTT-TCTAAAAGTATCGACCAAAAAAACATCGAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTAT-TAAAAGTATCGACC-AAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * *
3642429 AGGTAAATTAACAATGTAACCGGTATAAATATACCGG-TTAATTAGAAAATA-GTTCAACATAAT
64 AGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATG-TCCACATAAT
** *
3642492 GTATCGACACTTGTGGAATTTGTGTCGATACTTATTGTCCAGAATGAATACCCAAACGAGGTGCA
128 GTATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAAT-GCCAAACGAGGTGCA
3642557 CGCATAAA
191 CGCATAAA
*
3642565 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGA-CCAAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
3642630 GGTAAATTTACAATGTAACCGATATAAATATACCAGTTTTATGAGAAAATATG-CCAGCATAAAG
65 GGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATGTCCA-CATAATG
* * *
3642694 TATCGACACTTGTTAAATTTTTGTCGATACATTTTGTCCATAATGAATGCCAAACGGGGTGCACG
129 TATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACG
*
3642759 CATAGA
193 CATAAA
* * * *
3642765 GTGTCGATACATTTATTAAAACTATCGATCCCAAAAACATCGAAA-CGA-AGATTACAATGTGAT
1 GTGTCGATACATTTATTAAAAGTATCGA-CCAAAAAACATCGAAACCGATA-ATTATAATGTAAT
* * * *
3642828 AGGTAAATTTAGAATGT-ACC-ATGTATAAATATATCGGTTTTATAAGAAAATATGTCTAAATAA
64 AGGTAAATTTACAATGTAACCGA--TATAAATATACCGGTTTTATAAGAAAATATGTCCACATAA
** * * * * * *
3642891 TGTATTAACACTTTTTAAGTTTGTGTCGATATTTTTTTCCAGAATGAATGCCCAACGATGTGCAC
127 TGTATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCAC
3642956 GCATAAA
192 GCATAAA
*
3642963 GTGTCGATACA-TTA--AAATGTATC--CCAAAAAACATCGAAACCGATAATTATAATGTAATAG
1 GTGTCGATACATTTATTAAAAGTATCGACCAAAAAACATCGAAACCGATAATTATAATGTAATAG
* * *
3643023 GTAAATTTGCAATGTTACCGGTATAAATATACCGGTTT
66 GTAAATTTACAATGTAACCGATATAAATATACCGGTTT
3643061 ACTTAGAAAA
Statistics
Matches: 434, Mismatches: 48, Indels: 35
0.84 0.09 0.07
Matches are distributed among these distances:
192 15 0.03
193 45 0.10
194 4 0.01
195 7 0.02
197 4 0.01
198 49 0.11
199 87 0.20
200 158 0.36
201 62 0.14
202 3 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (198 bp):
GTGTCGATACATTTATTAAAAGTATCGACCAAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATAAGAAAATATGTCCACATAATGTA
TCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCAT
AAA
Found at i:3643754 original size:21 final size:22
Alignment explanation
Indices: 3643730--3643776 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
3643720 TGTTTTAATT
* *
3643730 TTAAAA-AATATAATTTTTGGA
1 TTAAAATAAGATAATTTTTAGA
*
3643751 TTAAAATCAGATAATTTTTAGA
1 TTAAAATAAGATAATTTTTAGA
3643773 TTAA
1 TTAA
3643777 TTTCAAGCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.43
Consensus pattern (22 bp):
TTAAAATAAGATAATTTTTAGA
Found at i:3645255 original size:105 final size:107
Alignment explanation
Indices: 3645051--3645264 Score: 339
Period size: 105 Copynumber: 2.0 Consensus size: 107
3645041 TCATTTTTAG
3645051 TCACGATGCTCTCATCCCGATTACAAATGTTACAGATATTATCGTAATTGTCACAGACGTAAATT
1 TCACGAT-CTCTCATCCCGATTACAAATGTTACAGATATTATCGTAATTGT-ACAGACGTAAATT
*
3645116 CTTTTTAAAATTTACATCACTTATTAAAATATAA-TA-ATTATA
64 CTTTTTAAAATTTACATCACTTATAAAAATATAATTATATTATA
3645158 TCACGAT-TCTCATCCCGATTACAAATGTTACAGATATTATCGTAATTGT-CAGACGTAAATTCT
1 TCACGATCTCTCATCCCGATTACAAATGTTACAGATATTATCGTAATTGTACAGACGTAAATTCT
3645221 TTTTAAAA-TTACATCACTTTATAAAATATAATAATTATATTATA
66 TTTTAAAATTTACATCAC-TTATAAAA-AT-ATAATTATATTATA
3645265 AAAATCATCT
Statistics
Matches: 101, Mismatches: 1, Indels: 10
0.90 0.01 0.09
Matches are distributed among these distances:
102 9 0.09
103 29 0.29
104 2 0.02
105 46 0.46
106 2 0.02
107 13 0.13
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (107 bp):
TCACGATCTCTCATCCCGATTACAAATGTTACAGATATTATCGTAATTGTACAGACGTAAATTCT
TTTTAAAATTTACATCACTTATAAAAATATAATTATATTATA
Found at i:3647778 original size:36 final size:36
Alignment explanation
Indices: 3647731--3647803 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
3647721 TCTGAAAGAA
*
3647731 TGTTGGATTCTGAGGTACAGAGCATCAATCTCTTAG
1 TGTTGGATTCTGAGGTAAAGAGCATCAATCTCTTAG
3647767 TGTTGGATTCTGAGGTAAAGAGCATCAATCTCTTAG
1 TGTTGGATTCTGAGGTAAAGAGCATCAATCTCTTAG
3647803 T
1 T
3647804 TTGAGGCAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (36 bp):
TGTTGGATTCTGAGGTAAAGAGCATCAATCTCTTAG
Found at i:3653893 original size:16 final size:19
Alignment explanation
Indices: 3653872--3653913 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3653862 CAACATTTCA
3653872 GTAATC-CTATT-CC-CTG
1 GTAATCTCTATTCCCACTG
*
3653888 GTAATCTTTATTCCCACTG
1 GTAATCTCTATTCCCACTG
3653907 GTAATCT
1 GTAATCT
3653914 TACATTCCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 6 0.27
17 4 0.18
18 2 0.09
19 10 0.45
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.40
Consensus pattern (19 bp):
GTAATCTCTATTCCCACTG
Found at i:3654386 original size:77 final size:77
Alignment explanation
Indices: 3654280--3654428 Score: 212
Period size: 77 Copynumber: 1.9 Consensus size: 77
3654270 GAAATACGGT
* *
3654280 TGCACCCAAGAATGTAATGATCCACTAAGAAA-TAAGTTGTGATAT-GAAATGTTAATATTTTTA
1 TGCACCCAAGAATGTAATGATCCAATAAGAAAGTAAGTTGCGATATAG-AATGTTAATATTTTTA
3654343 TTAATAAAATGGGA
65 TT-ATAAAATGGGA
* * * *
3654357 TGCACCCAAGAATGTTATGGTTCAATAAGAAAGTAAGTTGCGATCTAGAATGTTAATATTTTTAT
1 TGCACCCAAGAATGTAATGATCCAATAAGAAAGTAAGTTGCGATATAGAATGTTAATATTTTTAT
3654422 TATAAAA
66 TATAAAA
3654429 AATTGAAATT
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
77 34 0.53
78 29 0.45
79 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (77 bp):
TGCACCCAAGAATGTAATGATCCAATAAGAAAGTAAGTTGCGATATAGAATGTTAATATTTTTAT
TATAAAATGGGA
Found at i:3655436 original size:76 final size:75
Alignment explanation
Indices: 3655272--3655436 Score: 185
Period size: 75 Copynumber: 2.2 Consensus size: 75
3655262 TAACATTTTA
* * * *
3655272 GGCAC-ACCTATTTTATTATAAAAATATTAAGATTCGATATACAACCTGATTTCTTAATGAATCG
1 GGCACAACCTATTTTATAATAAAAATATTAACATTCGATATACAA-CTGATTTCTTAATGAACCA
*
3655336 TGATATTTTTG
65 TGATATTATTG
* *
3655347 GGCACAACCTATTTTATAATAAAAATATTAACATTAC-ATATTGCAA-T-ATGTTCTTACTGAAC
1 GGCACAACCTATTTTATAATAAAAATATTAACATT-CGATA-TACAACTGAT-TTCTTAATGAAC
3655409 CATGATATTATTG
63 CATGATATTATTG
*
3655422 GGCGCAACCGTATTT
1 GGCACAACC-TATTT
3655437 CTTATATATA
Statistics
Matches: 77, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
74 2 0.03
75 35 0.45
76 35 0.45
77 5 0.06
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (75 bp):
GGCACAACCTATTTTATAATAAAAATATTAACATTCGATATACAACTGATTTCTTAATGAACCAT
GATATTATTG
Found at i:3658143 original size:21 final size:21
Alignment explanation
Indices: 3658119--3658172 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
3658109 CGCAACCCAG
*
3658119 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAATTTCGCGTTGCGAT
*
3658140 TTTCCAATTTCGCGTTGCGGT
1 TTTCCAATTTCGCGTTGCGAT
3658161 TTTCCAATTTCG
1 TTTCCAATTTCG
3658173 TAACGCGAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.15, C:0.24, G:0.19, T:0.43
Consensus pattern (21 bp):
TTTCCAATTTCGCGTTGCGAT
Found at i:3658215 original size:20 final size:20
Alignment explanation
Indices: 3658190--3658277 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
3658180 AATCTGTAAA
3658190 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
3658210 TCGCAACGC-GATAGTCAAAT
1 TCGCAACACAGA-AGTCAAAT
* *
3658230 TCGTAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* * *
3658250 TCGCAACGCGGAATTTCAAAT
1 TCGCAACACAGAA-GTCAAAT
3658271 TCGCAAC
1 TCGCAAC
3658278 TGAATTTCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.04
20 40 0.71
21 14 0.25
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:3658284 original size:19 final size:19
Alignment explanation
Indices: 3658244--3658334 Score: 155
Period size: 19 Copynumber: 4.7 Consensus size: 19
3658234 AACACAAAAG
*
3658244 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAA--CTGAATT
3658265 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
3658284 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
3658303 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
3658322 TCAAATTCGCAAC
1 TCAAATTCGCAAC
3658335 ACGAATTTAG
Statistics
Matches: 69, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
19 57 0.83
21 12 0.17
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.29
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:3659102 original size:12 final size:12
Alignment explanation
Indices: 3659081--3659114 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3659071 ACCACATTTC
*
3659081 CAATACCAAACA
1 CAATATCAAACA
3659093 CAATATCAAACA
1 CAATATCAAACA
*
3659105 CAATCTCAAA
1 CAATATCAAA
3659115 ACCAACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:3659293 original size:24 final size:24
Alignment explanation
Indices: 3659235--3659281 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3659225 AGTCAGTATT
*
3659235 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
3659259 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
3659282 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:3659476 original size:3 final size:3
Alignment explanation
Indices: 3659468--3659498 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
3659458 ATATAACCCT
3659468 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3659499 TCCCCGAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3661583 original size:18 final size:18
Alignment explanation
Indices: 3661560--3661595 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3661550 AAGCAAAAGG
*
3661560 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
3661578 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
3661596 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:3661906 original size:20 final size:20
Alignment explanation
Indices: 3661881--3661930 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3661871 ATGTTGCGAT
3661881 CAACGCGAAAGGCAAATTCG
1 CAACGCGAAAGGCAAATTCG
* *
3661901 CAACGCGATAGTCAAATTCG
1 CAACGCGAAAGGCAAATTCG
3661921 CAACGCGAAA
1 CAACGCGAAA
3661931 TCGCAAACCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.26, G:0.22, T:0.12
Consensus pattern (20 bp):
CAACGCGAAAGGCAAATTCG
Found at i:3661962 original size:20 final size:20
Alignment explanation
Indices: 3661939--3661995 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3661929 AATCGCAAAC
*
3661939 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCATTG
3661959 CGAATTTGACTTTCGCATTG
1 CGAATTTGACTTTCGCATTG
*
3661979 CGAATTTGACTATCGCA
1 CGAATTTGACTTTCGCA
3661996 ACGCTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
CGAATTTGACTTTCGCATTG
Found at i:3662403 original size:39 final size:39
Alignment explanation
Indices: 3662360--3662446 Score: 165
Period size: 39 Copynumber: 2.2 Consensus size: 39
3662350 TCCGATGCTC
3662360 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
*
3662399 ATCAAAATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
3662438 ATCAAAATC
1 ATCAAAATC
3662447 TACAACTTGA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.47, C:0.21, G:0.15, T:0.17
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:3662669 original size:20 final size:20
Alignment explanation
Indices: 3662620--3662662 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3662610 ATGTTGCGAT
*
3662620 CAACGCGAAAGTCAAATTCG
1 CAACACGAAAGTCAAATTCG
3662640 CAACACGAAAGTCAAATTCG
1 CAACACGAAAGTCAAATTCG
3662660 CAA
1 CAA
3662663 ACCGAAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.26, G:0.16, T:0.14
Consensus pattern (20 bp):
CAACACGAAAGTCAAATTCG
Found at i:3666613 original size:13 final size:13
Alignment explanation
Indices: 3666595--3666626 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
3666585 GGGTTTCTTC
3666595 AACAAAAAGACAA
1 AACAAAAAGACAA
3666608 AACAAAAAGACAA
1 AACAAAAAGACAA
3666621 AACAAA
1 AACAAA
3666627 GACAAATACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.16, G:0.06, T:0.00
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:3666629 original size:11 final size:12
Alignment explanation
Indices: 3666599--3666632 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3666589 TTCTTCAACA
3666599 AAAAGACAAAAC
1 AAAAGACAAAAC
3666611 AAAAAGACAAAAC
1 -AAAAGACAAAAC
3666624 -AAAGACAAA
1 AAAAGACAAA
3666633 TACTAACTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
13 12 0.57
ACGTcount: A:0.76, C:0.15, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAGACAAAAC
Found at i:3667153 original size:20 final size:20
Alignment explanation
Indices: 3667104--3667157 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
3667094 CGATTTACAT
*
3667104 ATTCACGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
3667124 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
3667144 ATTCGCGTTGCGAA
1 ATTCGCGTTGCGAA
3667158 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.04
20 25 0.93
21 1 0.04
ACGTcount: A:0.28, C:0.15, G:0.30, T:0.28
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:3670917 original size:2 final size:2
Alignment explanation
Indices: 3670910--3670946 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3670900 TAGTTTTGAA
*
3670910 AT AT AT AT AT AT AT AT AT AT AT AT AG 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 A
3670947 GTTTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3671000 original size:35 final size:35
Alignment explanation
Indices: 3670936--3671119 Score: 152
Period size: 35 Copynumber: 5.3 Consensus size: 35
3670926 ATATATATAG
* * **
3670936 ATATATATATAGTTTTGAAAACATGTTTGAAATATTT
1 ATATATATATAGTTTTTAAAATAT-TTTGAAA-ATAA
*
3670973 ATATTTATATAGTTTTTAAAATA-TTTGAAAATAA
1 ATATATATATAGTTTTTAAAATATTTTGAAAATAA
*
3671007 ATATAAGATATAG-TTTTAAAATATTTTTGAAAATAA
1 ATAT-ATATATAGTTTTTAAAATA-TTTTGAAAATAA
*
3671043 ATAT-TATATAATTTTTAAAAATATTTTG--AA-AA
1 ATATATATATAGTTTTT-AAAATATTTTGAAAATAA
* *
3671075 ATATATAGT-T--TTTTAAAAAAATATTTTGAAAATAT
1 ATATATA-TATAGTTTT--TAAAATATTTTGAAAATAA
3671110 ATATATATAT
1 ATATATATAT
3671120 TATATAGTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 28
0.76 0.07 0.17
Matches are distributed among these distances:
31 4 0.03
32 17 0.14
33 5 0.04
34 25 0.20
35 31 0.25
36 21 0.17
37 20 0.16
ACGTcount: A:0.47, C:0.01, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATATATAGTTTTTAAAATATTTTGAAAATAA
Found at i:3671029 original size:34 final size:35
Alignment explanation
Indices: 3670979--3671169 Score: 130
Period size: 36 Copynumber: 5.4 Consensus size: 35
3670969 ATTTATATTT
3670979 ATATAGTTTTTAAAATA-TTTGAAAATAAATATAAG
1 ATATAG-TTTTAAAATATTTTGAAAATAAATATAAG
* *
3671014 ATATAGTTTTAAAATATTTTTGAAAATAAATATTAT
1 ATATAGTTTTAAAATA-TTTTGAAAATAAATATAAG
* *
3671050 ATA-ATTTTTAAAAATATTTTGAAAA-ATATAT-AG
1 ATATAGTTTT-AAAATATTTTGAAAATAAATATAAG
*
3671083 -T-T--TTTTAAAAAAATATTTTGAAAATATATATATATATT
1 ATATAGTTTT---AAAATATTTTGAAAATA-A-ATATA-A-G
* * * *
3671121 ATATAGTTTTGAAATCATTTTAAAAACT-TATATAAT
1 ATATAGTTTTAAAAT-ATTTTGAAAA-TAAATATAAG
3671157 ATATAGTTTTAAA
1 ATATAGTTTTAAA
3671170 TTTTTTTTTT
Statistics
Matches: 127, Mismatches: 11, Indels: 35
0.73 0.06 0.20
Matches are distributed among these distances:
30 4 0.03
32 17 0.13
33 2 0.02
34 15 0.12
35 24 0.19
36 38 0.30
37 2 0.02
38 5 0.04
39 5 0.04
40 10 0.08
41 1 0.01
42 4 0.03
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (35 bp):
ATATAGTTTTAAAATATTTTGAAAATAAATATAAG
Found at i:3672231 original size:3 final size:3
Alignment explanation
Indices: 3672223--3672267 Score: 83
Period size: 3 Copynumber: 15.3 Consensus size: 3
3672213 AAACCAAAGA
3672223 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3672268 TGTATACCAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 39 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3673565 original size:3 final size:3
Alignment explanation
Indices: 3673557--3673583 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3673547 AAATAAAGAT
3673557 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
3673584 AGGTAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3673614 original size:2 final size:2
Alignment explanation
Indices: 3673607--3673647 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3673597 AACAACAATA
3673607 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
3673648 ATTTTCCAAA
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:3673779 original size:102 final size:104
Alignment explanation
Indices: 3673672--3673926 Score: 265
Period size: 101 Copynumber: 2.4 Consensus size: 104
3673662 ACATATATAT
* * *
3673672 TTTTAAAAGTATTTTAAAATTATATATAT-TATAATTTTTTTTAAAA-TGTTTT-CAAAATTATA
1 TTTTAAAA-TATTTTAAAATTATATATATATATAATTTTTTTCAAAATTGTTTTAAAAAACTATA
* *
3673734 TAGTTTTCAAAAATGTTTTTAAAACTATATATTATATAAA-
65 TAGTTTTC-AAAATGTTTTAAAAACTATATAATATATAAAG
* * * * *
3673774 TTTTAAAATGATTTCAAATTTATA-ATATCTAT-A-TGTTTTCAAAATTTTTTTAAAAAACTATA
1 TTTTAAAAT-ATTTTAAAATTATATATATATATAATTTTTTTCAAAATTGTTTTAAAAAACTATA
*
3673836 TATTTTTCAAAATGTTTTAAAAACTATATAATATATAAATG
65 TAGTTTTCAAAATGTTTTAAAAACTATATAATATATAAA-G
*
3673877 TTTTCAAACATTTTTTCAAAATTATAT-TATATATATATATTTTTTCAAAA
1 TTTT-AAA-ATATTTT-AAAATTATATATATATATA-AT-TTTTTTCAAAA
3673927 ATCATTTACA
Statistics
Matches: 124, Mismatches: 15, Indels: 21
0.77 0.09 0.13
Matches are distributed among these distances:
100 9 0.07
101 40 0.32
102 38 0.31
103 4 0.03
104 6 0.05
105 16 0.13
107 1 0.01
109 10 0.08
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.49
Consensus pattern (104 bp):
TTTTAAAATATTTTAAAATTATATATATATATAATTTTTTTCAAAATTGTTTTAAAAAACTATAT
AGTTTTCAAAATGTTTTAAAAACTATATAATATATAAAG
Found at i:3673845 original size:30 final size:29
Alignment explanation
Indices: 3673803--3673865 Score: 92
Period size: 28 Copynumber: 2.1 Consensus size: 29
3673793 TTATAATATC
*
3673803 TATATGTTTTCAAAATTTTTTTAAAAAACTA
1 TATATGTTTTCAAAA-TGTTTT-AAAAACTA
3673834 TATAT-TTTTCAAAATGTTTTAAAAACTA
1 TATATGTTTTCAAAATGTTTTAAAAACTA
3673862 TATA
1 TATA
3673866 ATATATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
28 12 0.39
29 5 0.16
30 9 0.29
31 5 0.16
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (29 bp):
TATATGTTTTCAAAATGTTTTAAAAACTA
Found at i:3673899 original size:80 final size:80
Alignment explanation
Indices: 3673809--3673957 Score: 185
Period size: 80 Copynumber: 1.9 Consensus size: 80
3673799 TATCTATATG
* * **
3673809 TTTTCAAAATTTTTTTAAAAA-ACTATATATTTTTC-AAAATGTTTTAAAAACTATATAATATAT
1 TTTTCAAAATTATATTAAAAATA-TATAT-TTTTTCAAAAATCATTTAAAAACTATATAATATAT
3673872 AAATGTTTTCAAACATT
64 AAATGTTTTCAAACATT
* * * * *
3673889 TTTTCAAAATTATATTATATATATATATTTTTTCAAAAATCATTTACAAATTATATAATATATAG
1 TTTTCAAAATTATATTAAAAATATATATTTTTTCAAAAATCATTTAAAAACTATATAATATATAA
3673954 ATGT
66 ATGT
3673958 ATATATAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
79 6 0.10
80 51 0.88
81 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (80 bp):
TTTTCAAAATTATATTAAAAATATATATTTTTTCAAAAATCATTTAAAAACTATATAATATATAA
ATGTTTTCAAACATT
Found at i:3673922 original size:41 final size:39
Alignment explanation
Indices: 3673832--3673952 Score: 113
Period size: 41 Copynumber: 3.1 Consensus size: 39
3673822 TTTAAAAAAC
* *
3673832 TATATA-TTTTTCAAAATGTTTTAAAAACTATA-TA-ATA
1 TATATATTTTTTCAAAATCTTTT-AAAATTATATTATATA
* * *
3673869 TATAAATGTTTTCAAACATTTTTTCAAAATTATATTATATA
1 TATATATTTTTTCAAA-ATCTTTT-AAAATTATATTATATA
* *
3673910 TATATATTTTTTCAAAAATCATTTACAAATTATATAATATA
1 TATATATTTTTTC-AAAATCTTTTA-AAATTATATTATATA
3673951 TA
1 TA
3673953 GATGTATATA
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
37 5 0.07
38 8 0.12
39 14 0.21
40 3 0.04
41 35 0.51
42 3 0.04
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (39 bp):
TATATATTTTTTCAAAATCTTTTAAAATTATATTATATA
Found at i:3676529 original size:17 final size:18
Alignment explanation
Indices: 3676507--3676541 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3676497 AATTTGAGTA
*
3676507 TTAATATT-ATTATATTT
1 TTAATATTCAATATATTT
3676524 TTAATATTCAATATATTT
1 TTAATATTCAATATATTT
3676542 GTTATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (18 bp):
TTAATATTCAATATATTT
Found at i:3679139 original size:37 final size:37
Alignment explanation
Indices: 3679084--3679191 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
3679074 AACATAGCGT
*
3679084 TAGAGTTTTACTATGATTCAAACTCCTAAAAATATGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAAGA
*
3679121 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAAGA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATAAGA
*
3679158 TAGAGTTCTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
3679192 GGATCCAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTATGATTCAAACTCCTAAAAATAAGA
Found at i:3679800 original size:19 final size:18
Alignment explanation
Indices: 3679757--3679840 Score: 62
Period size: 19 Copynumber: 4.4 Consensus size: 18
3679747 AGATTATATA
* *
3679757 TATATATGTGTTATTTTT
1 TATATATGTTTTATTATT
3679775 TATTATATGTTTTATTAATT
1 TA-TATATGTTTTATT-ATT
* *
3679795 TATATATATATTTACTATT
1 TATATATGT-TTTATTATT
*
3679814 T-TTTATGTTTTTATTTATT
1 TATATATG-TTTTA-TTATT
3679833 ATATATAT
1 -TATATAT
3679841 ATTATTTTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
18 10 0.20
19 27 0.53
20 10 0.20
21 4 0.08
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.65
Consensus pattern (18 bp):
TATATATGTTTTATTATT
Found at i:3679831 original size:42 final size:42
Alignment explanation
Indices: 3679737--3679873 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 42
3679727 AGTATATATA
* * **
3679737 TTTATTTTTTAGATTATATATATATATGTGTTATTTTTTATTAT
1 TTTATTTATTA-ATT-TATATATATATTTACTATTTTTTATTAT
*
3679781 ATGT-TTTATTAATTTATATATATATTTACTATTTTTTATGT-T
1 -TTTATTTATTAATTTATATATATATTTACTATTTTTTAT-TAT
* *
3679823 TTTATTTATT-ATATATATATTATTTTTACT-TTTTATTATTAT
1 TTTATTTATTAATTTATATA-TATATTTACTATTTT-TTATTAT
3679865 TTTATTTAT
1 TTTATTTAT
3679874 ATATTTTTCT
Statistics
Matches: 79, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
41 15 0.19
42 52 0.66
43 4 0.05
44 6 0.08
45 2 0.03
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (42 bp):
TTTATTTATTAATTTATATATATATTTACTATTTTTTATTAT
Found at i:3679856 original size:39 final size:37
Alignment explanation
Indices: 3679780--3679877 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 37
3679770 TTTTTTATTA
*
3679780 TATGTTTTATTAATTTATATATATATTTACTATTTTT
1 TATGTTTTATTAATTTATATATATATTTACTACTTTT
* *
3679817 TATGTTTTTATTTATTATATATATATTATTT-TTACTTTT
1 TATG-TTTTATTAATT-TATATATA-TATTTACTACTTTT
* *
3679856 TAT-TATTATTTTATTTATATAT
1 TATGTTTTA-TTAATTTATATAT
3679878 TTTTCTTCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
37 15 0.28
38 16 0.30
39 17 0.32
40 5 0.09
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (37 bp):
TATGTTTTATTAATTTATATATATATTTACTACTTTT
Found at i:3679858 original size:24 final size:24
Alignment explanation
Indices: 3679821--3679871 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
3679811 ATTTTTTATG
3679821 TTTTTATTTATTA-TATATATATTA
1 TTTTTATTTATTATTAT-TATATTA
*
3679845 TTTTTACTTT-TTATTATTATTTTA
1 TTTTTA-TTTATTATTATTATATTA
3679869 TTT
1 TTT
3679872 ATATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTATTTATTATTATTATATTA
Found at i:3679865 original size:33 final size:32
Alignment explanation
Indices: 3679784--3679922 Score: 94
Period size: 33 Copynumber: 4.3 Consensus size: 32
3679774 TTATTATATG
*
3679784 TTTTATTAATTTATATATATATTTACTATTTTTTAT
1 TTTTATT-ATTTAT-TATATATATA-TA-TTTTTAT
*
3679820 GTTT-TTATTTATTATATATATATTATTTTTACT
1 TTTTATTATTTATTATATATATA-TATTTTTA-T
* * *
3679853 TTTTATTA-TTATTTTATTTATATATTTTTCT
1 TTTTATTATTTATTATATATATATATTTTTAT
* *
3679884 TCTTT-TTCTTTATT-TAT-TTTATA-TTTTAT
1 T-TTTATTATTTATTATATATATATATTTTTAT
*
3679913 TTAT-TTATTT
1 TTTTATTATTT
3679923 TACTTACTAT
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
28 7 0.08
29 6 0.07
30 5 0.06
31 7 0.08
32 21 0.24
33 27 0.31
34 9 0.10
35 2 0.02
36 3 0.03
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (32 bp):
TTTTATTATTTATTATATATATATATTTTTAT
Found at i:3679897 original size:35 final size:35
Alignment explanation
Indices: 3679784--3679907 Score: 105
Period size: 34 Copynumber: 3.5 Consensus size: 35
3679774 TTATTATATG
*
3679784 TTTTATTAATTTATATATATATTTACTATTTT--TTATGT
1 TTTTATTATTTTATATATATA-TTA-T-TTTTACTT-T-T
*
3679822 TTTTATT-TATTATATATATATTATTTTTACTTTT
1 TTTTATTATTTTATATATATATTATTTTTACTTTT
* *
3679856 TATTATTATTTTATTTATATATT-TTTCTT-CTTTT
1 TTTTATTATTTTATATATATATTATTT-TTACTTTT
3679890 TCTTTATTTATTTTATAT
1 T-TTTA-TTATTTTATAT
3679908 TTTATTTATT
Statistics
Matches: 73, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
34 20 0.27
35 20 0.27
36 15 0.21
37 11 0.15
38 7 0.10
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (35 bp):
TTTTATTATTTTATATATATATTATTTTTACTTTT
Found at i:3679914 original size:35 final size:33
Alignment explanation
Indices: 3679821--3679923 Score: 88
Period size: 34 Copynumber: 3.0 Consensus size: 33
3679811 ATTTTTTATG
*
3679821 TTTTTATTTATTATATATATATTA-TTTTTACTTT
1 TTTTTATTTATT-T-TATATTTTATTTTTTACTTT
* *
3679855 TTATTA-TTATTTTAT-TTATATATTTTTCTTCTTT
1 TTTTTATTTATTTTATATT-T-TATTTTT-TACTTT
3679889 TTCTTTATTTATTTTATATTTTATTTATTTA-TTT
1 TT-TTTATTTATTTTATATTTTATTT-TTTACTTT
3679923 T
1 T
3679924 ACTTACTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
30 1 0.02
31 4 0.07
32 3 0.05
33 9 0.16
34 16 0.29
35 9 0.16
36 12 0.21
37 2 0.04
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTTATTTATTTTATATTTTATTTTTTACTTT
Found at i:3679933 original size:20 final size:20
Alignment explanation
Indices: 3679892--3679934 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3679882 CTTCTTTTTC
**
3679892 TTTATTTATTTTATATTTTA
1 TTTATTTATTTTATATACTA
3679912 TTTATTTATTTTACT-TACTA
1 TTTATTTATTTTA-TATACTA
3679932 TTT
1 TTT
3679935 TATCTTTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTATTTATTTTATATACTA
Found at i:3679952 original size:32 final size:32
Alignment explanation
Indices: 3679898--3679969 Score: 74
Period size: 32 Copynumber: 2.2 Consensus size: 32
3679888 TTTCTTTATT
* *
3679898 TATTTTATATTTTATTTATTTATTTTA-CTTA
1 TATTTTATATTTGATTTATTTATCTTATCTTA
* * *
3679929 CTATTTTATCTTTGCTTTCTTTATCTTATCTTA
1 -TATTTTATATTTGATTTATTTATCTTATCTTA
*
3679962 TCTTTTAT
1 TATTTTAT
3679970 TTAATTTGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 29 0.88
33 4 0.12
ACGTcount: A:0.19, C:0.11, G:0.01, T:0.68
Consensus pattern (32 bp):
TATTTTATATTTGATTTATTTATCTTATCTTA
Found at i:3683086 original size:10 final size:10
Alignment explanation
Indices: 3683066--3683096 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
3683056 AGATTCAATC
3683066 AGAACAAAAAG
1 AGAA-AAAAAG
3683077 AGAAAAAAAG
1 AGAAAAAAAG
3683087 AGAAAAAAAG
1 AGAAAAAAAG
3683097 CAAAGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 16 0.80
11 4 0.20
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAG
Found at i:3684986 original size:19 final size:19
Alignment explanation
Indices: 3684962--3685024 Score: 117
Period size: 19 Copynumber: 3.3 Consensus size: 19
3684952 GAAGCCTGAG
3684962 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCTGAGCC
*
3684981 GAGCCGTTTGAGCTGAGTC
1 GAGCCGTTTGAGCTGAGCC
3685000 GAGCCGTTTGAGCTGAGCC
1 GAGCCGTTTGAGCTGAGCC
3685019 GAGCCG
1 GAGCCG
3685025 AGCCGCCTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.16, C:0.25, G:0.38, T:0.21
Consensus pattern (19 bp):
GAGCCGTTTGAGCTGAGCC
Found at i:3688416 original size:32 final size:32
Alignment explanation
Indices: 3688369--3688463 Score: 129
Period size: 32 Copynumber: 2.9 Consensus size: 32
3688359 TACAGGTATC
3688369 TTTGAAGATTCAACATCAGATGTTGGGGCATTT
1 TTTG-AGATTCAACATCAGATGTTGGGGCATTT
* * *
3688402 TTTGAGATTTAACATCAAATGTTGGGGTATTT
1 TTTGAGATTCAACATCAGATGTTGGGGCATTT
*
3688434 TTTGAGATTCAACATC-GAATATTGGGGCAT
1 TTTGAGATTCAACATCAG-ATGTTGGGGCAT
3688464 ATTTGGGAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
32 50 0.93
33 4 0.07
ACGTcount: A:0.28, C:0.11, G:0.23, T:0.38
Consensus pattern (32 bp):
TTTGAGATTCAACATCAGATGTTGGGGCATTT
Found at i:3689732 original size:37 final size:37
Alignment explanation
Indices: 3689682--3689790 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
3689672 CCAAGTTTTT
3689682 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTG
* *
3689719 TCTCTCTTTAGACAGTTTCCCTTGAAAC-AAATTTTG
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTG
* *
3689755 TCTCTCTTGGGATAGTTTCCCTTGAAACAAAATCTT
1 TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTT
3689791 TGAATATCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 32 0.49
37 33 0.51
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.39
Consensus pattern (37 bp):
TCTCTCTTGAGACAGTTTCCCTTGAAACAAAATCTTG
Found at i:3689772 original size:36 final size:36
Alignment explanation
Indices: 3689677--3689921 Score: 220
Period size: 36 Copynumber: 6.9 Consensus size: 36
3689667 AATTTCCAAG
*
3689677 TTTTTTCTCTCTTGAGACAGTTTCCCTTGAAACAAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
* *
3689714 TCTTGTCTCTCTTTAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
3689750 TTTTGTCTCTCTTGGGATAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
3689786 ------ATCT-TTGA-ATATCTTTTCCTTAAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
* * * * *
3689815 TTTCGTCTCCCTTGAGACAGTTT-CTTTTAGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGA-AAC-AAA
**
3689852 TTTTGTCTCTCTTGAGACAGTTTCTTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
3689888 TTTTGTCACTCTTGAGACAGTTTCTCTTGAAACA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
3689922 CAAAAAAACC
Statistics
Matches: 170, Mismatches: 26, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
28 3 0.02
29 17 0.10
30 3 0.02
35 6 0.04
36 79 0.46
37 58 0.34
38 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:3690123 original size:83 final size:84
Alignment explanation
Indices: 3689984--3690239 Score: 286
Period size: 83 Copynumber: 3.1 Consensus size: 84
3689974 CTCTTGAAAC
*
3689984 ACAAAG-CCTTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGG
1 ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGG
* *
3690048 CTAGAAGGGTTATCTGTCA
66 CAAGAAGGGTTATCAGTCA
* *
3690067 ACAAAGACCTTCGAGTTCGACTACGCTCAGCTTTAA-GGCACATCATTTGCAGCATAACTCAAGG
1 ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGG
3690131 CAAGAAGGGTTATCAGTCA
66 CAAGAAGGGTTATCAGTCA
* * * * * * * * * * *
3690150 TCAAAGACCTTTGATTTTGATTACATTCAACTT--AGAGACAAATCAAATTTACAGCATAGCTCA
1 ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAG-GGCACATC--ATTTGCAGCATAACTCA
* * *
3690213 AGGCAAGAAGGGCTATCTGCCA
63 AGGCAAGAAGGGTTATCAGTCA
3690235 ACAAA
1 ACAAA
3690240 ATTGTCGAGT
Statistics
Matches: 147, Mismatches: 21, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
81 1 0.01
83 82 0.56
84 26 0.18
85 38 0.26
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.25
Consensus pattern (84 bp):
ACAAAGACCTTCGAGTTCGACTACACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGG
CAAGAAGGGTTATCAGTCA
Found at i:3690773 original size:37 final size:37
Alignment explanation
Indices: 3690732--3690843 Score: 206
Period size: 37 Copynumber: 3.0 Consensus size: 37
3690722 AACATAGCGT
3690732 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
3690769 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
* *
3690806 TAGAGTTCTACTATGATTCAAACTCCTAAAAATAGGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
3690843 T
1 T
3690844 CCATAAGAAT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 73 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.30
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATAGGA
Found at i:3691448 original size:33 final size:31
Alignment explanation
Indices: 3691406--3691499 Score: 84
Period size: 33 Copynumber: 2.9 Consensus size: 31
3691396 TGTTATTTTT
* *
3691406 TATTATATGTTTTATTAATTATATATATTTAC
1 TATTTTATGTTTTATTAATTAT-TATATATAC
* * *
3691438 TATTTTTATGTTTGTTTTATTTATTATATATAT
1 TA-TTTTATGTTT-TATTAATTATTATATATAC
3691471 TATTTTACT-TTTTATT-ATTATTTATATAT
1 TATTTTA-TGTTTTATTAATTA-TTATATAT
3691500 TTTTTTCTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
30 3 0.06
31 11 0.22
32 10 0.20
33 19 0.37
34 8 0.16
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.66
Consensus pattern (31 bp):
TATTTTATGTTTTATTAATTATTATATATAC
Found at i:3691483 original size:39 final size:39
Alignment explanation
Indices: 3691385--3691488 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 39
3691375 TTTAGATTAC
*
3691385 ATATATATATATGTTATTTTTTATTATATGTTTTATTAATT
1 ATATATAT-TATATTA-TTTTTATTATATGTTTTATTAATT
* *
3691426 ATATATATT-TACTATTTTTATGT-T-TGTTTTATTTATT
1 ATATATATTATATTATTTTTAT-TATATGTTTTATTAATT
*
3691463 ATATATATTATTTTACTTTTTATTAT
1 ATATATATTATATTA-TTTTTATTAT
3691489 TATTTATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
37 21 0.39
38 12 0.22
39 12 0.22
40 1 0.02
41 8 0.15
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (39 bp):
ATATATATTATATTATTTTTATTATATGTTTTATTAATT
Found at i:3691496 original size:31 final size:32
Alignment explanation
Indices: 3691454--3691537 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
3691444 TATGTTTGTT
3691454 TTATTTA-TTATATATATTATTT-TACTTTTTA
1 TTATTTATTTATATAT-TTATTTCTACTTTTTA
* * *
3691485 TTA-TTATTTATATATTTTTTTCTTCTTTTTC
1 TTATTTATTTATATATTTATTTCTACTTTTTA
3691516 TTATTTATTT-TATATTTTATTT
1 TTATTTATTTATATA-TTTATTT
3691538 ATTTATTTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
30 8 0.18
31 25 0.56
32 12 0.27
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (32 bp):
TTATTTATTTATATATTTATTTCTACTTTTTA
Found at i:3691543 original size:24 final size:23
Alignment explanation
Indices: 3691457--3691545 Score: 65
Period size: 24 Copynumber: 3.7 Consensus size: 23
3691447 GTTTGTTTTA
*
3691457 TTTA-TTATATATATTATTTTACTT
1 TTTATTTATTTAT-TTATTTTA-TT
*
3691481 TTTATTATTATTTATATATTTT-TT
1 TTTA-T-TTATTTATTTATTTTATT
* *
3691505 TCTTCTTTTTCTTATTTATTTTATAT
1 T-TTATTTAT-TTATTTATTTTAT-T
3691531 TTTATTTATTTATTT
1 TTTATTTATTTATTT
3691546 TACTTACTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
23 3 0.06
24 24 0.47
25 9 0.18
26 8 0.16
27 7 0.14
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTATTTATTTATTTATTTTATT
Found at i:3691575 original size:32 final size:31
Alignment explanation
Indices: 3691480--3691579 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 31
3691470 TTATTTTACT
3691480 TTTTA-TTATTATTTATATATTTTTTTCTTCT-
1 TTTTACTTATTATTT-TATATTTTTTTCTT-TA
*
3691511 TTTT-CTTATTTATTTTATATTTTATTTATTTA
1 TTTTACTTA-TTATTTTATATTTT-TTTCTTTA
* *
3691543 TTTTACTTACTATTTTATCTTTGTTTTCTTTA
1 TTTTACTTATTATTTTATATTT-TTTTCTTTA
3691575 TTTTA
1 TTTTA
3691580 TCATATTTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
31 16 0.27
32 38 0.64
33 5 0.08
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTTACTTATTATTTTATATTTTTTTCTTTA
Found at i:3692608 original size:20 final size:20
Alignment explanation
Indices: 3692573--3692647 Score: 123
Period size: 20 Copynumber: 3.7 Consensus size: 20
3692563 TTTGGTTCAC
3692573 GGAATGTAAGGATTATCAGTG
1 GGAATGTAA-GATTATCAGTG
3692594 GGAATGTAAGATTATCAGTG
1 GGAATGTAAGATTATCAGTG
* *
3692614 AGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTATCAGTG
3692634 GGAATGTAAGATTA
1 GGAATGTAAGATTA
3692648 CCAGGAATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 42 0.82
21 9 0.18
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.28
Consensus pattern (20 bp):
GGAATGTAAGATTATCAGTG
Found at i:3693523 original size:13 final size:13
Alignment explanation
Indices: 3693505--3693545 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
3693495 ATCCTTAAAT
3693505 TAATTTATTTTAA
1 TAATTTATTTTAA
3693518 TAATTTATTTTAA
1 TAATTTATTTTAA
**
3693531 TTTTTTATATTTAA
1 TAATTTAT-TTTAA
3693545 T
1 T
3693546 TTATTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TAATTTATTTTAA
Found at i:3693613 original size:24 final size:23
Alignment explanation
Indices: 3693573--3693618 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
3693563 AATTGTTTAC
3693573 ATTTTATATTTTTAATTAATAAA
1 ATTTTATATTTTTAATTAATAAA
3693596 ATTTT-TATTTTTGAAATTAATAA
1 ATTTTATATTTTT--AATTAATAA
3693619 GTCCTCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.33
23 5 0.24
24 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
ATTTTATATTTTTAATTAATAAA
Found at i:3695063 original size:161 final size:161
Alignment explanation
Indices: 3694798--3695120 Score: 628
Period size: 161 Copynumber: 2.0 Consensus size: 161
3694788 GCGCTCTACC
3694798 AACTGAGCTAGACGGGCAATTCAAAATCTCATATCAATAATAGCTTACCCTTATTCCCATATGTA
1 AACTGAGCTAGACGGGCAATTCAAAATCTCATATCAATAATAGCTTACCCTTATTCCCATATGTA
*
3694863 ATGGGATAAGGGAAATGTAGGATAGTAGGCTGCCCCCAAAACCAGGTTGAGAGTATCTTCCGTGG
66 ATGGGATAAGGGAAAGGTAGGATAGTAGGCTGCCCCCAAAACCAGGTTGAGAGTATCTTCCGTGG
3694928 GAGACCTCCGAATTATGAATTACCCACCGTA
131 GAGACCTCCGAATTATGAATTACCCACCGTA
3694959 AACTGAGCTAGACGGGCAATTCAAAATCTCATATCAATAATAGCTTACCCTTATTCCCATATGTA
1 AACTGAGCTAGACGGGCAATTCAAAATCTCATATCAATAATAGCTTACCCTTATTCCCATATGTA
*
3695024 ATGGGATAAGGGAAAGGTAGGATAGTAGGCTGCCCCCAAAACTAGGTTGAGAGTATCTTCCGTGG
66 ATGGGATAAGGGAAAGGTAGGATAGTAGGCTGCCCCCAAAACCAGGTTGAGAGTATCTTCCGTGG
3695089 GAGACCTCCGAATTATGAATTACCCACCGTA
131 GAGACCTCCGAATTATGAATTACCCACCGTA
3695120 A
1 A
3695121 GACGGTATCC
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
161 160 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (161 bp):
AACTGAGCTAGACGGGCAATTCAAAATCTCATATCAATAATAGCTTACCCTTATTCCCATATGTA
ATGGGATAAGGGAAAGGTAGGATAGTAGGCTGCCCCCAAAACCAGGTTGAGAGTATCTTCCGTGG
GAGACCTCCGAATTATGAATTACCCACCGTA
Found at i:3695309 original size:24 final size:24
Alignment explanation
Indices: 3695276--3695321 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3695266 CATGATATGA
*
3695276 TAATATTTTTTTGTATTTTTTACG
1 TAATAATTTTTTGTATTTTTTACG
*
3695300 TAATAATTTTTTTTATTTTTTA
1 TAATAATTTTTTGTATTTTTTA
3695322 AAAATTAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
TAATAATTTTTTGTATTTTTTACG
Found at i:3695663 original size:11 final size:11
Alignment explanation
Indices: 3695649--3695687 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
3695639 CTCGAGCTTG
3695649 ATTCAAGCTCA
1 ATTCAAGCTCA
**
3695660 ATTCAAATTCA
1 ATTCAAGCTCA
3695671 ATTCAAGCTCA
1 ATTCAAGCTCA
3695682 ATTCAA
1 ATTCAA
3695688 ACTCGAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (11 bp):
ATTCAAGCTCA
Found at i:3697514 original size:7 final size:7
Alignment explanation
Indices: 3697502--3697582 Score: 64
Period size: 7 Copynumber: 11.7 Consensus size: 7
3697492 AATTTAGGGT
3697502 TTTATGG
1 TTTATGG
3697509 TTTATGG
1 TTTATGG
3697516 -TTATGG
1 TTTATGG
3697522 TTTA-GG
1 TTTATGG
*
3697528 ATTTATGA
1 -TTTATGG
*
3697536 TTTATGA
1 TTTATGG
3697543 TTTATGG
1 TTTATGG
3697550 TTTA-GAG
1 TTTATG-G
3697557 TTTA-GG
1 TTTATGG
3697563 ATTTA-GAG
1 -TTTATG-G
*
3697571 TTTAGGG
1 TTTATGG
3697578 TTTAT
1 TTTAT
3697583 TATAAGGACA
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
6 10 0.16
7 51 0.80
8 3 0.05
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (7 bp):
TTTATGG
Found at i:3697526 original size:28 final size:29
Alignment explanation
Indices: 3697494--3697581 Score: 85
Period size: 28 Copynumber: 3.1 Consensus size: 29
3697484 ATAAGTTCAA
*
3697494 TTTAGGGTTTTATGGTTTATG-GTTATGG
1 TTTAGGGTTTTATGATTTATGAGTTATGG
* *
3697522 TTTA-GGATTTATGATTTATGATTTATGG
1 TTTAGGGTTTTATGATTTATGAGTTATGG
* * *
3697550 TTTAGAG-TTTAGGATTTA-GAGTTTAGGG
1 TTTAGGGTTTTATGATTTATGAG-TTATGG
3697578 TTTA
1 TTTA
3697582 TTATAAGGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 16 0.32
28 33 0.66
29 1 0.02
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (29 bp):
TTTAGGGTTTTATGATTTATGAGTTATGG
Found at i:3698942 original size:56 final size:56
Alignment explanation
Indices: 3698868--3699078 Score: 280
Period size: 57 Copynumber: 3.7 Consensus size: 56
3698858 TCCCTCACGG
** * * *
3698868 TAAAAAAAAACCTAAGAATTTGAAACTATCAAGTTCAAATTTAATAAAATAAAATT
1 TAAAAAATTACCTCAGAATTTGAAACTTTCAAATTCAAATTTAATAAAATAAAATT
* *
3698924 TAAAAAATTACCTCAGAATTTGAAACTTTCAAGTTGAAATTTAATAAACATAAAATT
1 TAAAAAATTACCTCAGAATTTGAAACTTTCAAATTCAAATTTAATAAA-ATAAAATT
* *
3698981 TTAAAAATTACCTCAGAATTTGAAACTTTCAAATTCAGATTTAAT-AAATATAAATT
1 TAAAAAATTACCTCAGAATTTGAAACTTTCAAATTCAAATTTAATAAAATA-AAATT
* * *
3699037 TAAAGGAATTACGTCAGAATTTGAAACTTTCAAATTAAAATT
1 TAAA-AAATTACCTCAGAATTTGAAACTTTCAAATTCAAATT
3699079 ACAAAATATA
Statistics
Matches: 138, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
55 3 0.02
56 53 0.38
57 82 0.59
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (56 bp):
TAAAAAATTACCTCAGAATTTGAAACTTTCAAATTCAAATTTAATAAAATAAAATT
Found at i:3699945 original size:3 final size:3
Alignment explanation
Indices: 3699939--3699970 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3699929 CTTCATTCTT
3699939 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3699971 GGTATCAGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3703574 original size:16 final size:16
Alignment explanation
Indices: 3703547--3703591 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
3703537 ACTGATTTAA
3703547 AAATAT-TTTTAAGAT
1 AAATATATTTTAAGAT
3703562 AAATATATTTT-A-AT
1 AAATATATTTTAAGAT
3703576 AATATATAATTTTAAG
1 AA-ATAT-ATTTTAAG
3703592 TGAATTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 4 0.16
15 11 0.44
16 9 0.36
17 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (16 bp):
AAATATATTTTAAGAT
Found at i:3704144 original size:18 final size:19
Alignment explanation
Indices: 3704111--3704146 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3704101 GCGATGTTTT
*
3704111 ATTTTTACAATTATATTTA
1 ATTTTTACAATAATATTTA
3704130 ATTTTTA-AATAATATTT
1 ATTTTTACAATAATATTT
3704147 TTCATATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTACAATAATATTTA
Done.