Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold361
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: 329584
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:3654 original size:26 final size:26
Alignment explanation
Indices: 3601--3650 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
3591 CTTTTGAGTT
*
3601 TCAAGTTTCAAACCAATATCTGTAAC
1 TCAAGTTTCAAACCAACATCTGTAAC
*
3627 TCAAGTTTC-ACCCAACATCTGTAA
1 TCAAGTTTCAAACCAACATCTGTAA
3651 ACTCCACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.36, C:0.26, G:0.08, T:0.30
Consensus pattern (26 bp):
TCAAGTTTCAAACCAACATCTGTAAC
Found at i:6822 original size:20 final size:21
Alignment explanation
Indices: 6799--6845 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
6789 AAAAACATTA
6799 ATTATATAAATATT-TAAAAT
1 ATTATATAAATATTATAAAAT
* *
6819 ATTATATTATTATTACTAAAAT
1 ATTATATAAATATTA-TAAAAT
6841 ATTAT
1 ATTAT
6846 TTCTATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 12 0.52
22 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATATAAATATTATAAAAT
Found at i:8842 original size:18 final size:20
Alignment explanation
Indices: 8805--8843 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
8795 CTCCTAAAAA
*
8805 ATATGTATTTATATTTAATT
1 ATATGTATTTATATTAAATT
8825 ATAT-TATTT-TATTAAATT
1 ATATGTATTTATATTAAATT
8843 A
1 A
8844 AAAAAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
ATATGTATTTATATTAAATT
Found at i:12142 original size:70 final size:70
Alignment explanation
Indices: 12023--12164 Score: 212
Period size: 70 Copynumber: 2.0 Consensus size: 70
12013 TACACACAAG
* * * *
12023 GAGGTTTGGAGAAGCATTGTGAACACAGGGGGGAGGAGGGATGCTAAGGAGAAAAACAATCATTC
1 GAGGTTTAGAGAAGCATTGTGAACACAGAGGGGAGGAGGGATGCAAAGGAGAAAAACAATCATGC
12088 TCCTA
66 TCCTA
* * *
12093 GAGGTTTAGAGAAGCTTTGTGAACACAGAGGGGAGGAGGGGTGCAAAGGAGAGAAACAATCATGC
1 GAGGTTTAGAGAAGCATTGTGAACACAGAGGGGAGGAGGGATGCAAAGGAGAAAAACAATCATGC
*
12158 TTCTA
66 TCCTA
12163 GA
1 GA
12165 TTTATAAGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.35, C:0.12, G:0.35, T:0.18
Consensus pattern (70 bp):
GAGGTTTAGAGAAGCATTGTGAACACAGAGGGGAGGAGGGATGCAAAGGAGAAAAACAATCATGC
TCCTA
Found at i:13890 original size:26 final size:26
Alignment explanation
Indices: 13839--13890 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
13829 TACATAAAAT
* *
13839 TAAAAATTAAAAATTTATTTGAGTAA
1 TAAAAATTAAAAACTTATCTGAGTAA
*
13865 TAAAAATATATAAACTTATCTG-GTAA
1 TAAAAAT-TAAAAACTTATCTGAGTAA
13891 GTGTTAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.37
Consensus pattern (26 bp):
TAAAAATTAAAAACTTATCTGAGTAA
Found at i:13921 original size:3 final size:3
Alignment explanation
Indices: 13909--13947 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
13899 GTTAGGGGTT
13909 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
13948 ACTTTTATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:14382 original size:24 final size:22
Alignment explanation
Indices: 14352--14403 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
14342 ATCTAATAAA
14352 AATATTAATTTAAGAGTATATTAAT
1 AATATT-ATTT-AGA-TATATTAAT
*
14377 -ATATTATTTATATATATTAAT
1 AATATTATTTAGATATATTAAT
14398 AATATT
1 AATATT
14404 TAAAATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 9 0.36
22 7 0.28
23 4 0.16
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
AATATTATTTAGATATATTAAT
Found at i:15798 original size:36 final size:35
Alignment explanation
Indices: 15751--15854 Score: 120
Period size: 37 Copynumber: 2.9 Consensus size: 35
15741 AATAAATCAT
* *
15751 TAAAAAT-TATTAAAATAATTTTTATATTAAATAA
1 TAAAAATGTATTAAAATTATATTTATATTAAATAA
* *
15785 TAAAATATGTATTAAAATTATATTAATTTTAAATAA
1 TAAAA-ATGTATTAAAATTATATTTATATTAAATAA
* *
15821 TAAATAAAAGTATTAAAATTCTATTTATATTAAA
1 T-AA-AAATGTATTAAAATTATATTTATATTAAA
15855 AATTAATAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
34 5 0.09
35 2 0.03
36 24 0.41
37 25 0.43
38 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (35 bp):
TAAAAATGTATTAAAATTATATTTATATTAAATAA
Found at i:15854 original size:37 final size:37
Alignment explanation
Indices: 15753--15865 Score: 131
Period size: 36 Copynumber: 3.1 Consensus size: 37
15743 TAAATCATTA
* * *
15753 AAAATTATTAAAATAATTTTTATATTAAATAATAAA-
1 AAAAGTATTAAAATTATATTTATATTAAATAATAAAT
* * * *
15789 ATATGTATTAAAATTATATTAATTTTAAATAATAAAT
1 AAAAGTATTAAAATTATATTTATATTAAATAATAAAT
* *
15826 AAAAGTATTAAAATTCTATTTATATTAAA-AATTAAT
1 AAAAGTATTAAAATTATATTTATATTAAATAATAAAT
15862 AAAA
1 AAAA
15866 TAAACTAAGA
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
36 39 0.62
37 24 0.38
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (37 bp):
AAAAGTATTAAAATTATATTTATATTAAATAATAAAT
Found at i:16326 original size:17 final size:15
Alignment explanation
Indices: 16304--16337 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
16294 TCTAAAATTT
16304 TAAAATTCAAAAATAAA
1 TAAAATT-AAAAA-AAA
16321 TAAAATTAAAAAAAA
1 TAAAATTAAAAAAAA
16336 TA
1 TA
16338 GTGTAGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 5 0.29
17 7 0.41
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (15 bp):
TAAAATTAAAAAAAA
Found at i:16751 original size:16 final size:17
Alignment explanation
Indices: 16730--16762 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
16720 ATCAAAGCAC
16730 TATACAATAA-AATTTT
1 TATACAATAATAATTTT
16746 TATACAATAATAATTTT
1 TATACAATAATAATTTT
16763 GAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
TATACAATAATAATTTT
Found at i:16918 original size:34 final size:35
Alignment explanation
Indices: 16879--16956 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 35
16869 AATAACTTCA
16879 AAAATTATTATTTATTTGCATGAAATATTTGCGT-
1 AAAATTATTATTTATTTGCATGAAATATTTGCGTC
*
16913 AAAATTATTATTTATTTGCATGAGATATTTGCGTC
1 AAAATTATTATTTATTTGCATGAAATATTTGCGTC
*
16948 AAAGTTATT
1 AAAATTATT
16957 TTCAAAAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 33 0.80
35 8 0.20
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.46
Consensus pattern (35 bp):
AAAATTATTATTTATTTGCATGAAATATTTGCGTC
Found at i:26760 original size:3 final size:3
Alignment explanation
Indices: 26741--26774 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
26731 ATATCTTTTA
*
26741 AAT AAA AAT AGAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
26775 TATTATTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:29354 original size:28 final size:27
Alignment explanation
Indices: 29323--29411 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 27
29313 TAAAGTTTTT
29323 TTTATTCATATTCTTTTAAAAAATTATA
1 TTTATTCATA-TCTTTTAAAAAATTATA
* *
29351 TTTATCGTTAATAAT-TTTTAAAATATTATA
1 TTTA---TTCAT-ATCTTTTAAAAAATTATA
* *
29381 TTTTTATTCTTAACTTTT-AAAAATTATA
1 --TTTATTCATATCTTTTAAAAAATTATA
29409 TTT
1 TTT
29412 TATTTTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 16
0.69 0.09 0.23
Matches are distributed among these distances:
26 3 0.06
28 14 0.29
29 7 0.15
30 14 0.29
31 5 0.10
32 5 0.10
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (27 bp):
TTTATTCATATCTTTTAAAAAATTATA
Found at i:29403 original size:59 final size:60
Alignment explanation
Indices: 29321--29442 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 60
29311 AGTAAAGTTT
* *
29321 TTTTTATTCATATTCTTTTAAAAAATTATA-TTTATCGTTAATAA-TTTTTAAAATATTATA
1 TTTTTATTCATATACTTTT-AAAAATTATATTTTATCGTTAATAACATTTTAAAA-ATTATA
* ** *
29381 TTTTTATTCTTA-ACTTTTAAAAATTATATTTTATTTTTTATAACATTTTAAAAATTATA
1 TTTTTATTCATATACTTTTAAAAATTATATTTTATCGTTAATAACATTTTAAAAATTATA
29440 TTT
1 TTT
29443 GCCATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
58 10 0.19
59 25 0.46
60 19 0.35
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (60 bp):
TTTTTATTCATATACTTTTAAAAATTATATTTTATCGTTAATAACATTTTAAAAATTATA
Found at i:29404 original size:30 final size:28
Alignment explanation
Indices: 29321--29442 Score: 109
Period size: 30 Copynumber: 4.1 Consensus size: 28
29311 AGTAAAGTTT
*
29321 TTTTTATTCATATTCTTTTAAAAAATTATA
1 TTTTTATTCATA-ACTTTT-AAAAATTATA
** * *
29351 TTTATCGTTAATAATTTTTAAAATATTATA
1 TTT-TTATTCATAACTTTTAAAA-ATTATA
*
29381 TTTTTATTCTTAACTTTTAAAAATTATA
1 TTTTTATTCATAACTTTTAAAAATTATA
* *
29409 TTTTATTTTTTATAACATTTTAAAAATTATA
1 -TTT-TTATTCATAAC-TTTTAAAAATTATA
29440 TTT
1 TTT
29443 GCCATATATA
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
28 6 0.08
29 21 0.28
30 27 0.36
31 20 0.27
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTTTATTCATAACTTTTAAAAATTATA
Found at i:29771 original size:20 final size:20
Alignment explanation
Indices: 29746--29813 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
29736 AAATTTAGTA
29746 ATTTTAAATTCCCATGTGTT
1 ATTTTAAATTCCCATGTGTT
* *
29766 ATTTTAGATTCCCACGTGTT
1 ATTTTAAATTCCCATGTGTT
**
29786 -TCTCGGCAAATTCCCATGTGTT
1 AT-T--TTAAATTCCCATGTGTT
29808 ATTTTA
1 ATTTTA
29814 GACTTTATCG
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
19 1 0.03
20 20 0.56
22 14 0.39
23 1 0.03
ACGTcount: A:0.22, C:0.19, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTTTAAATTCCCATGTGTT
Found at i:30468 original size:43 final size:43
Alignment explanation
Indices: 30420--30505 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
30410 AGATGACTTA
*
30420 AATTTTACTTTTTATGATTTTGTCACTTGATTTTTTTAAAAGT
1 AATTTTACTTTTTATGATTTTGTCACTTGATTTTTTAAAAAGT
**
30463 AATTTTGTTTTTTATGATTTTGTCACTTGATTTTTTAAAAAGT
1 AATTTTACTTTTTATGATTTTGTCACTTGATTTTTTAAAAAGT
30506 TAAAATTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (43 bp):
AATTTTACTTTTTATGATTTTGTCACTTGATTTTTTAAAAAGT
Found at i:30911 original size:22 final size:22
Alignment explanation
Indices: 30885--30954 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 22
30875 ATTATATTAA
30885 AAATATAATTATTTTAATATAT
1 AAATATAATTATTTTAATATAT
** *
30907 AAATATACA-TATTAAAATATTT
1 AAATATA-ATTATTTTAATATAT
30929 AAATAAATAATTACTATTTAATATAT
1 AAAT--ATAATTA-T-TTTAATATAT
30955 TTGAAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
22 21 0.58
23 2 0.06
24 5 0.14
25 1 0.03
26 7 0.19
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATATAATTATTTTAATATAT
Found at i:34148 original size:29 final size:28
Alignment explanation
Indices: 34115--34189 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
34105 ATACAAATAT
*
34115 TAATATATTTTTATTTTTTATTAAATTGA
1 TAATATATTTTTATATTTTATTAAATT-A
* *
34144 TAATA-ATATTTTATATTTTATTATATTT
1 TAATATAT-TTTTATATTTTATTAAATTA
*
34172 TAATTATTTTTTTATATT
1 TAA-TATATTTTTATATT
34190 ATTTAATATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.13
29 33 0.85
30 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (28 bp):
TAATATATTTTTATATTTTATTAAATTA
Found at i:34196 original size:21 final size:19
Alignment explanation
Indices: 34149--34189 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
34139 ATTGATAATA
34149 ATATTTT-A-TATTTTATT
1 ATATTTTAATTATTTTATT
*
34166 ATATTTTAATTATTTTTTT
1 ATATTTTAATTATTTTATT
34185 ATATT
1 ATATT
34190 ATTTAATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 1 0.05
19 13 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATATTTTAATTATTTTATT
Found at i:34206 original size:27 final size:26
Alignment explanation
Indices: 34176--34237 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
34166 ATATTTTAAT
* * *
34176 TATTTTTTTATATTATTTAATATATCA
1 TATTTTATCATATTA-TGAATATATCA
*
34203 TATTTATATCATATTATGATTATATCA
1 TATTT-TATCATATTATGAATATATCA
34230 TATTTTAT
1 TATTTTAT
34238 AATCATGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 3 0.10
27 19 0.63
28 8 0.27
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.60
Consensus pattern (26 bp):
TATTTTATCATATTATGAATATATCA
Found at i:38407 original size:18 final size:18
Alignment explanation
Indices: 38384--38423 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
38374 CAGTTTTTCC
38384 TTTTTGTTCATTGCTTTT
1 TTTTTGTTCATTGCTTTT
38402 TTTTTGTTCATTGCTTTT
1 TTTTTGTTCATTGCTTTT
38420 TTTT
1 TTTT
38424 AGATCCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.75
Consensus pattern (18 bp):
TTTTTGTTCATTGCTTTT
Found at i:38662 original size:3 final size:3
Alignment explanation
Indices: 38654--38690 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
38644 ATTCGCTCTC
38654 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38691 ACTTTTTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:45999 original size:23 final size:23
Alignment explanation
Indices: 45973--46031 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
45963 TTTATTTATT
*
45973 ATTTTATTTTGAATTATTTTAAA
1 ATTTTATTTTGAATTATCTTAAA
* * *
45996 ATTTCATATTAAATTATCTTAAA
1 ATTTTATTTTGAATTATCTTAAA
46019 ATTTCGTATTTTG
1 ATTT--TATTTTG
46032 TTAATAAGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
23 23 0.85
25 4 0.15
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (23 bp):
ATTTTATTTTGAATTATCTTAAA
Found at i:46233 original size:72 final size:72
Alignment explanation
Indices: 46116--46256 Score: 212
Period size: 72 Copynumber: 2.0 Consensus size: 72
46106 CAACTAGTAT
* * * *
46116 GTCATGGTTCAAGCATACAGTTTCTTTATTTATTAGAATTTCTCACAGTGAAACCGACTATAACA
1 GTCATGGTTCAACCATACAGTTTCTTTATTTACTAGAATTTCTCACAGTAAAACCGACGATAACA
46181 ATCTGAC
66 ATCTGAC
* *
46188 GTCATTGTTCAACCATACAG-TTCATTTATTTACTAGAATTTCTCACAGTAAAACCGACGGTAAC
1 GTCATGGTTCAACCATACAGTTTC-TTTATTTACTAGAATTTCTCACAGTAAAACCGACGATAAC
46252 AATCT
65 AATCT
46257 AACAGCCTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
71 3 0.05
72 59 0.95
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.34
Consensus pattern (72 bp):
GTCATGGTTCAACCATACAGTTTCTTTATTTACTAGAATTTCTCACAGTAAAACCGACGATAACA
ATCTGAC
Found at i:47205 original size:25 final size:26
Alignment explanation
Indices: 47168--47217 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
47158 CACCATCCCT
47168 TCTTTTCCAACCAACTCTCATCTCAA
1 TCTTTTCCAACCAACTCTCATCTCAA
*
47194 TCTTTTCC-ACCAACTCTTATCTCA
1 TCTTTTCCAACCAACTCTCATCTCA
47218 TCTCTCTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (26 bp):
TCTTTTCCAACCAACTCTCATCTCAA
Found at i:47575 original size:2 final size:2
Alignment explanation
Indices: 47568--47605 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47558 TGCTTGTGGG
47568 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
47606 GTGTGTGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48078 original size:14 final size:14
Alignment explanation
Indices: 48059--48096 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
48049 TTATTTTTTA
*
48059 TATAATATAAATTG
1 TATAATATAAAATG
48073 TATAATATATAAATG
1 TATAATATA-AAATG
48088 TA-AATATAA
1 TATAATATAA
48097 TATAAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 15 0.68
15 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (14 bp):
TATAATATAAAATG
Found at i:48208 original size:14 final size:14
Alignment explanation
Indices: 48189--48224 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
48179 ATATTGTCTT
48189 ATAATTTTTTAAAG
1 ATAATTTTTTAAAG
*
48203 ATAA-TTATTAAAG
1 ATAATTTTTTAAAG
48216 ATAATTTTT
1 ATAATTTTT
48225 CGTTCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (14 bp):
ATAATTTTTTAAAG
Found at i:48714 original size:2 final size:2
Alignment explanation
Indices: 48658--48703 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
48648 CTTAAGAGAT
*
48658 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
48700 TA TA
1 TA TA
48704 CACGCATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:51178 original size:19 final size:19
Alignment explanation
Indices: 51139--51178 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51129 ATCAAGAAAC
* * *
51139 TAAATTAAAATTATAGTTA
1 TAAAATAAAATTAAAGATA
51158 TAAAATAAAATTAAAGATA
1 TAAAATAAAATTAAAGATA
51177 TA
1 TA
51179 TAAGTCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAAAATAAAATTAAAGATA
Found at i:51316 original size:17 final size:17
Alignment explanation
Indices: 51296--51333 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
51286 TTAACTTAAT
51296 ATTT-TTTAAACAAAATA
1 ATTTATTTAAA-AAAATA
*
51313 ATTTATTTAAAAAAATT
1 ATTTATTTAAAAAAATA
51330 ATTT
1 ATTT
51334 CTAATTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTTATTTAAAAAAATA
Found at i:52682 original size:2 final size:2
Alignment explanation
Indices: 52677--52717 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
52667 ATATATATAT
*
52677 AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
52718 TGCACATTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:54519 original size:8 final size:8
Alignment explanation
Indices: 54506--54551 Score: 57
Period size: 8 Copynumber: 6.4 Consensus size: 8
54496 ATTTATAATT
54506 ATTATTTA
1 ATTATTTA
54514 ATTATTTA
1 ATTATTTA
54522 ATTATTT-
1 ATTATTTA
54529 A-T-TTT-
1 ATTATTTA
54534 ATTATTTA
1 ATTATTTA
54542 ATT-TTTA
1 ATTATTTA
54549 ATT
1 ATT
54552 TAATTCGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.11
6 2 0.06
7 11 0.31
8 18 0.51
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTATTTA
Found at i:54532 original size:20 final size:20
Alignment explanation
Indices: 54492--54556 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
54482 AAACGTGTTT
*
54492 TTTAATT-TATAATTA-TTA
1 TTTAATTATTTAATTATTTA
54510 TTTAATTATTTAATTATTTA
1 TTTAATTATTTAATTATTTA
*
54530 TTTTATTATTTAATT-TTTAA
1 TTTAATTATTTAATTATTT-A
54550 TTTAATT
1 TTTAATT
54557 CGTCTTATAT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 24 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTAATTATTTAATTATTTA
Found at i:55715 original size:2 final size:2
Alignment explanation
Indices: 55662--55697 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
55652 CCTAGCATTC
55662 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
55698 CATACTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58253 original size:2 final size:2
Alignment explanation
Indices: 58246--58289 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
58236 AGTTGGTTTG
* *
58246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58288 AT
1 AT
58290 TTTATGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59601 original size:24 final size:24
Alignment explanation
Indices: 59568--59613 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
59558 AAGTAAAATT
*
59568 AAAAATTTATCATATAT-TTTATA
1 AAAAATTTATAATATATATTTATA
59591 AAAAATATTATAATATATATTTA
1 AAAAAT-TTATAATATATATTTA
59614 AAATGATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 10 0.50
25 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
AAAAATTTATAATATATATTTATA
Found at i:59724 original size:6 final size:6
Alignment explanation
Indices: 59713--59755 Score: 70
Period size: 6 Copynumber: 7.2 Consensus size: 6
59703 ACTATGATGG
59713 ATAAAA ATAAAA ATAAAA AT-AAA ATAAAA ATAAAA ACTAAAA A
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA A-TAAAA A
59756 AAGGAGGCTG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.14
6 24 0.69
7 6 0.17
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:59736 original size:11 final size:11
Alignment explanation
Indices: 59713--59747 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
59703 ACTATGATGG
59713 ATAAAAATAAAA
1 ATAAAAAT-AAA
59725 ATAAAAATAAA
1 ATAAAAATAAA
59736 ATAAAAATAAA
1 ATAAAAATAAA
59747 A
1 A
59748 ACTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
ATAAAAATAAA
Found at i:59738 original size:17 final size:18
Alignment explanation
Indices: 59716--59754 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
59706 ATGATGGATA
59716 AAAATAAAAATAAAAA-T
1 AAAATAAAAATAAAAACT
59733 AAAATAAAAATAAAAACT
1 AAAATAAAAATAAAAACT
59751 AAAA
1 AAAA
59755 AAAGGAGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (18 bp):
AAAATAAAAATAAAAACT
Found at i:64923 original size:2 final size:2
Alignment explanation
Indices: 64916--64957 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
64906 ATATGGATGA
* *
64916 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG GG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
64958 TTGGAGCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:65130 original size:2 final size:2
Alignment explanation
Indices: 65123--65156 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
65113 CTTCTAATAC
65123 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
65157 TAGAGAGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74857 original size:6 final size:6
Alignment explanation
Indices: 74846--74896 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
74836 GATAAGCCGA
* *
74846 GCTTAG GCTTAG GCTTGG GCTTGG GCTTGG GCTTGG GCTTGG GCTTGG
1 GCTTGG GCTTGG GCTTGG GCTTGG GCTTGG GCTTGG GCTTGG GCTTGG
74894 GCT
1 GCT
74897 AATGGTCAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.04, C:0.18, G:0.45, T:0.33
Consensus pattern (6 bp):
GCTTGG
Found at i:77461 original size:58 final size:58
Alignment explanation
Indices: 77399--77508 Score: 148
Period size: 58 Copynumber: 1.9 Consensus size: 58
77389 AAATGACCTA
* * ** *
77399 AAAATGCATGAAATTACGTAATGATCCCTAAGTCATGGAAAATAACTAAAATAACATT
1 AAAATGCATGAAATGACATAAAAATCCCTAAATCATGGAAAATAACTAAAATAACATT
* * *
77457 AAAATGCATGGAATGATATAAAAATTCCTAAATCATGGAAAATAACTAAAAT
1 AAAATGCATGAAATGACATAAAAATCCCTAAATCATGGAAAATAACTAAAAT
77509 TACAAACAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 44 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (58 bp):
AAAATGCATGAAATGACATAAAAATCCCTAAATCATGGAAAATAACTAAAATAACATT
Found at i:79318 original size:10 final size:10
Alignment explanation
Indices: 79303--79341 Score: 69
Period size: 10 Copynumber: 3.9 Consensus size: 10
79293 AACTTTTCCT
*
79303 AAAACCAAAA
1 AAAACCTAAA
79313 AAAACCTAAA
1 AAAACCTAAA
79323 AAAACCTAAA
1 AAAACCTAAA
79333 AAAACCTAA
1 AAAACCTAA
79342 CATTATATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.72, C:0.21, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAACCTAAA
Found at i:79666 original size:19 final size:20
Alignment explanation
Indices: 79642--79689 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
79632 TAGAATTAGG
79642 TCTCTATAATGT-CTTAACT
1 TCTCTATAATGTCCTTAACT
** *
79661 TCTCTAATGGTTTCCTTAACT
1 TCTCT-ATAATGTCCTTAACT
79682 TCTCTATA
1 TCTCTATA
79690 TCTATCGGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 5 0.22
20 6 0.26
21 12 0.52
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (20 bp):
TCTCTATAATGTCCTTAACT
Found at i:82123 original size:152 final size:152
Alignment explanation
Indices: 81747--82255 Score: 580
Period size: 152 Copynumber: 3.3 Consensus size: 152
81737 AATTACCATA
* * * * *
81747 AAATCAATTTTGAAAAATTTAATTTATTTTATGAGTTTTAGAATTTTTTTTGTTACCAAGTTATA
1 AAATCAGTTTTGAAAAATTCAATTCATTTTATGAG-TTTAGAA-TTTTTTTGTTATCAAGTTACA
* * * *
81812 GAGTTTTCTACTCCGTAAATTTCTCCTATAGGATTTTTGTAAGTTTATAAATTTCAAAATTCTTC
64 GAGTTTTCTACTCCGTAAGTTTCTCTTATAGGATTTTTCTAAGTTTATAATTTTCAAAATTCTTC
*
81877 AAATATTATTGTTTGTTTCATATT
129 AAATATTATTGTTTATTTCATATT
* * *
81901 AAATCAGTTTTGAAAAATTCAATTCATTTTATGAGTTGTA-TATTTTCTTGTGATCAAGTTACAG
1 AAATCAGTTTTGAAAAATTCAATTCATTTTATGAGTT-TAGAATTTTTTTGTTATCAAGTTACAG
*
81965 AGTTTTCTGCTCCGTAAGTTTCTCTTATAGGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCA
65 AGTTTTCTACTCCGTAAGTTTCTCTTATAGGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCA
82030 AATATTATTGTTTATTTCATATT
130 AATATTATTGTTTATTTCATATT
* * *
82053 AAATTAGTTTTGAAAAATTCAATTCATTTTATGAGTTATAG-ATTTTTTTGTTTTCAAATTAC-G
1 AAATCAGTTTTGAAAAATTCAATTCATTTTATGAGTT-TAGAATTTTTTTGTTATCAAGTTACAG
* * * * * * * * * * *
82116 GGATTTTCTATTCCATAAGTTT-TTTTGGTTGGATTTTTCTCAA-TTCAAAATTTTTAAAATACA
65 AG-TTTTCTACTCCGTAAGTTTCTCTT-ATAGGATTTTTCT-AAGTTTATAATTTTCAAAATTCT
* * * * *
82179 TCAAATATTTTTATTAAATTCATAGT
127 TCAAATATTATTGTTTATTTCATATT
* * *
82205 AAATCAGTTTT-AGAGAATTCAATTTATTTTATGAGTTTCGAATTTTTTTGT
1 AAATCAGTTTTGA-AAAATTCAATTCATTTTATGAGTTTAGAATTTTTTTGT
82256 ATTTATTAAT
Statistics
Matches: 307, Mismatches: 41, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
151 8 0.03
152 260 0.85
153 5 0.02
154 34 0.11
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (152 bp):
AAATCAGTTTTGAAAAATTCAATTCATTTTATGAGTTTAGAATTTTTTTGTTATCAAGTTACAGA
GTTTTCTACTCCGTAAGTTTCTCTTATAGGATTTTTCTAAGTTTATAATTTTCAAAATTCTTCAA
ATATTATTGTTTATTTCATATT
Found at i:92799 original size:13 final size:13
Alignment explanation
Indices: 92781--92811 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
92771 ACATTTCTTC
92781 ATGTATCGATACA
1 ATGTATCGATACA
92794 ATGTATCGATACA
1 ATGTATCGATACA
*
92807 TTGTA
1 ATGTA
92812 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:92799 original size:33 final size:33
Alignment explanation
Indices: 92761--92827 Score: 102
Period size: 33 Copynumber: 2.0 Consensus size: 33
92751 GTTACAAGCT
92761 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
92794 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGTACCATGTATCGATACA
92827 A
1 A
92828 ATAACGATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:95331 original size:13 final size:13
Alignment explanation
Indices: 95313--95337 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95303 TAGTACCCAA
95313 TGTATCGATACAG
1 TGTATCGATACAG
95326 TGTATCGATACA
1 TGTATCGATACA
95338 AGGAATGTTG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:95351 original size:20 final size:20
Alignment explanation
Indices: 95326--95377 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
95316 ATCGATACAG
95326 TGTATCGATACAAGGAATGT
1 TGTATCGATACAAGGAATGT
95346 TGTATCGATACAAGGAATGT
1 TGTATCGATACAAGGAATGT
95366 TGTATCGATACA
1 TGTATCGATACA
95378 TCTGGGTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAGGAATGT
Found at i:99301 original size:21 final size:21
Alignment explanation
Indices: 99275--99314 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
99265 ATGCAAGTTT
* *
99275 TTATTTTTCTTAGCTAATTCA
1 TTATTTTTATTAGCCAATTCA
99296 TTATTTTTATTAGCCAATT
1 TTATTTTTATTAGCCAATT
99315 TTTTAATATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTTTATTAGCCAATTCA
Found at i:101540 original size:20 final size:20
Alignment explanation
Indices: 101515--101567 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
101505 GTTACAAGCT
* **
101515 ATGTATCGATACATTTTTTC
1 ATGTATCGATACATTATACC
*
101535 ATGTATTGATACATTATACC
1 ATGTATCGATACATTATACC
101555 ATGTATCGATACA
1 ATGTATCGATACA
101568 AATAGTGATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTATACC
Found at i:108195 original size:29 final size:29
Alignment explanation
Indices: 108111--108214 Score: 84
Period size: 29 Copynumber: 3.6 Consensus size: 29
108101 CTAACTATCA
* *
108111 GTTTCACTTAAGACATCTATTT-GACTATTG
1 GTTTCACCTAAGTCAT-T-TTTCGACTATTG
* * * * *
108141 GTTTCACCAAAGTTATCTTCCAACTATTG
1 GTTTCACCTAAGTCATTTTTCGACTATTG
*
108170 GTTTCACCTAAGTCATTTTTCGACTAATG
1 GTTTCACCTAAGTCATTTTTCGACTATTG
* **
108199 ATTTTGCCTAAGTCAT
1 GTTTCACCTAAGTCAT
108215 CTGGCCTACT
Statistics
Matches: 57, Mismatches: 16, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
28 2 0.04
29 43 0.75
30 12 0.21
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.41
Consensus pattern (29 bp):
GTTTCACCTAAGTCATTTTTCGACTATTG
Found at i:108737 original size:19 final size:21
Alignment explanation
Indices: 108686--108739 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
108676 TTTCAACAAT
108686 TTGTATCGATACAAATAGTAA
1 TTGTATCGATACAAATAGTAA
* ** *
108707 ATGTATTTATACATA-AGT-A
1 TTGTATCGATACAAATAGTAA
108726 TTGTATCGATACAA
1 TTGTATCGATACAA
108740 TGTATCGCTA
Statistics
Matches: 25, Mismatches: 8, Indels: 2
0.71 0.23 0.06
Matches are distributed among these distances:
19 11 0.44
20 3 0.12
21 11 0.44
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (21 bp):
TTGTATCGATACAAATAGTAA
Found at i:108808 original size:13 final size:13
Alignment explanation
Indices: 108790--108817 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
108780 CATTATTCAA
108790 TGTATCGATAAAT
1 TGTATCGATAAAT
108803 TGTATCGATAAAT
1 TGTATCGATAAAT
108816 TG
1 TG
108818 ATCTTTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATAAAT
Found at i:112594 original size:32 final size:32
Alignment explanation
Indices: 112533--112741 Score: 134
Period size: 32 Copynumber: 6.4 Consensus size: 32
112523 ATCAAAGTTG
* * * *
112533 TATCCTTTTGAACAAGGTAAAGATTTGAACTTA
1 TATCCTTCTAAAC-AGGTCAAGAATTGAACTTA
* * *
112566 CATCCTTCTAAATAGGTCAAGAATTGAACTTG
1 TATCCTTCTAAACAGGTCAAGAATTGAACTTA
* * * * *
112598 TATCCTTCTTAACAAGTTAAAGAGTTAAAACTGTA
1 TATCCTTCTAAAC-AGGTCAAGAATT-GAACT-TA
*
112633 CA-CC-TCTAAACAGGTCAAGAATTGAACTTA
1 TATCCTTCTAAACAGGTCAAGAATTGAACTTA
* * * * * *
112663 TATCTTTCTGAACAAGTTAAAAAGTTGAACCTA
1 TATCCTTCTAAACAGGTCAAGAA-TTGAACTTA
* * ** *
112696 TATCCTTCTAAATAGGTCAATAATCAAACTTG
1 TATCCTTCTAAACAGGTCAAGAATTGAACTTA
*
112728 TATCCTTTTAAACA
1 TATCCTTCTAAACA
112742 AGCTAGGAAG
Statistics
Matches: 130, Mismatches: 40, Indels: 13
0.71 0.22 0.07
Matches are distributed among these distances:
30 3 0.02
31 5 0.04
32 65 0.50
33 49 0.38
34 6 0.05
35 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
TATCCTTCTAAACAGGTCAAGAATTGAACTTA
Found at i:112757 original size:65 final size:64
Alignment explanation
Indices: 112523--112964 Score: 230
Period size: 65 Copynumber: 6.8 Consensus size: 64
112513 TCCTTTTAAG
* * * * *
112523 ATCAAAGTTGTATCCTTTTGAACAAGGTAAAGATTTGAACTTACATCCTTCTAAATAGGTCAAGA
1 ATCAAACTTGTATCCTTTTGAACAAGTTAAA-AGTTGAACCTATATCCTTCTAAATAGGTCAAGA
** * * * * *
112588 ATTGAACTTGTATCCTTCTT-AACAAGTTAAAGAGTTAAAACTGTA-CACCTCTAAACAGGTCAA
1 ATCAAACTTGTATCCTT-TTGAACAAGTTAAA-AGTTGAACCTATATC-CTTCTAAATAGGTCAA
112651 GA
63 GA
** * *
112653 ATTGAACTTATAT-CTTTCTGAACAAGTTAAAAAGTTGAACCTATATCCTTCTAAATAGGTCAAT
1 ATCAAACTTGTATCCTTT-TGAACAAGTT-AAAAGTTGAACCTATATCCTTCTAAATAGGTCAAG
112717 A
64 A
* * * * * * ** * * *
112718 ATCAAACTTGTATCCTTTTAAACAAGCTAGGAAGCTGAACATGTATAGTTTTGAATAGGTTAAGA
1 ATCAAACTTGTATCCTTTTGAACAAGTTA-AAAGTTGAACCTATATCCTTCTAAATAGGTCAAGA
* * * * ** * * ** * **
112783 GTCTAACTTATATCCTTTTGAAAAAGTTAAAAGGTCAAACTTGTATGTTTCAAAATAGGTTGAGA
1 ATCAAACTTGTATCCTTTTGAACAAGTTAAAA-GTTGAACCTATATCCTTCTAAATAGGTCAAGA
* * * * * **** * *
112848 GTTAAGCTTGTATCCTTTTGAATAAGTCAAAGAACCAAACTTATATCTTTCTAAATAGGTCAA-A
1 ATCAAACTTGTATCCTTTTGAACAAGTTAAA-AGTTGAACCTATATCCTTCTAAATAGGTCAAGA
** * * * *
112912 AGTGGAA-TTGTTTTCCTTTTAAACAAGTCAAAAGTTGAACCTA-ATTCTTCTAA
1 A-TCAAACTTG-TATCCTTTTGAACAAGTTAAAAGTTGAACCTATATCCTTCTAA
112965 GTGAGTCAAG
Statistics
Matches: 287, Mismatches: 78, Indels: 26
0.73 0.20 0.07
Matches are distributed among these distances:
63 9 0.03
64 18 0.06
65 249 0.87
66 11 0.04
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (64 bp):
ATCAAACTTGTATCCTTTTGAACAAGTTAAAAGTTGAACCTATATCCTTCTAAATAGGTCAAGA
Found at i:112802 original size:32 final size:32
Alignment explanation
Indices: 112766--112871 Score: 90
Period size: 32 Copynumber: 3.3 Consensus size: 32
112756 ACATGTATAG
*
112766 TTTTGAATAGGTTAAGAGTCTAACTTATATCC
1 TTTTGAATAGGTTAAGAGTCTAACTTGTATCC
* * * * *
112798 TTTTGAAAAAGTTAAAAGGTCAAACTTGTAT-G
1 TTTTGAATAGGTTAAGA-GTCTAACTTGTATCC
** *
112830 TTTCAAAATAGGTTGAGAGT-TAAGCTTGTATCC
1 TTT-TGAATAGGTTAAGAGTCTAA-CTTGTATCC
112863 TTTTGAATA
1 TTTTGAATA
112872 AGTCAAAGAA
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
31 2 0.04
32 30 0.56
33 22 0.41
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (32 bp):
TTTTGAATAGGTTAAGAGTCTAACTTGTATCC
Found at i:115661 original size:133 final size:133
Alignment explanation
Indices: 115440--115705 Score: 390
Period size: 133 Copynumber: 2.0 Consensus size: 133
115430 AAAACGAAAA
* * * * *
115440 AAGTTTAGGGATTAAATAGTAAATTTTGGTTTTTAAAGGTAAAATCATCATTTTAGTCATTTTTA
1 AAGTTTAGAGAATAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATAATTTTAGTCATTTTTA
* * * * * *
115505 AAGATTTTTATTGATCCTATGGCCTTTCATAGGGGTGTAGAAATTTTTAAAATTTTTTGTATCCT
66 AAGATTTTTATTGATCCTATGGCCTTTCATAGAGGTATAAAAATTTTCAAAACTTTTCGTATCCT
115570 CTC
131 CTC
115573 AAGTTTAGAGAATAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATAATTTTAGTCATTTTTA
1 AAGTTTAGAGAATAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATAATTTTAGTCATTTTTA
* * *
115638 AAGATTTTTATT-ATTCCTTTGGCCTTTCGTAGAGGTATAAAAATTTTCAAGACTTTTCGTATCC
66 AAGATTTTTATTGA-TCCTATGGCCTTTCATAGAGGTATAAAAATTTTCAAAACTTTTCGTATCC
115702 TCTC
130 TCTC
115706 GATTTTTCAT
Statistics
Matches: 118, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
132 1 0.01
133 117 0.99
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (133 bp):
AAGTTTAGAGAATAAATAGCAAATTTTAGTTTTTAAAGGTAAAATCATAATTTTAGTCATTTTTA
AAGATTTTTATTGATCCTATGGCCTTTCATAGAGGTATAAAAATTTTCAAAACTTTTCGTATCCT
CTC
Found at i:116262 original size:156 final size:154
Alignment explanation
Indices: 116076--116798 Score: 685
Period size: 156 Copynumber: 4.6 Consensus size: 154
116066 TTGAATCTAA
** *
116076 GTCATCACTAGGTCATTTTTATGCCAAAGGTATGAATTGAGGATAGGTTCATCCTTTTTCATATC
1 GTCATCACTAGGTCGCTTTTATGCCAAAGGTATGAATTCAGGATAGGTTCATCCTTTTTCATATC
* * ***
116141 ATTTTCATGTCTTTTAGGGTTAACGAGATACTTTCATG-TCGAAGGTATACTCCAACAACATTTT
66 ATTTTCATGTCTTTTAGGGTTACCGAGATACTTTCATGCT-GAAAGTATAC-CCAAGGGCATTTT
*
116205 AGTAATTTTACTATAACTGAGTCCTAG
129 AGTAATTTT-CTAGAACTGAGTCCTAG
* * * *
116232 GTCATCACTAGGTCGCTTTTATGCTAAAGGTGTGCATTCACGATAGGTTCATCCTTTTTCATATC
1 GTCATCACTAGGTCGCTTTTATGCCAAAGGTATGAATTCAGGATAGGTTCATCCTTTTTCATATC
* * * *
116297 ATTTTCATGTCTTTTAAGGTTATCG-GAATACTTTCATGCTGAAAGTATACCTTAAGGGTATTTT
66 ATTTTCATGTCTTTTAGGGTTACCGAG-ATACTTTCATGCTGAAAGTATACC-CAAGGGCATTTT
* *
116361 AGTAATTTTCTTATAACTAAGTCCTAG
129 AGTAATTTTC-TAGAACTGAGTCCTAG
* * * * * * * * *
116388 TTTATCATTGGGTCGCTTTTATGTCAAAGGTATGCATTTAGGATAGGTTAATCCTTTTTTATATC
1 GTCATCACTAGGTCGCTTTTATGCCAAAGGTATGAATTCAGGATAGGTTCATCCTTTTTCATATC
* * * *
116453 ATTTTCATGTCTTTTAGGATT-CCGAGATACTTTGATGCTGAAAGTATATTCTAAGGGCATTTTA
66 ATTTTCATGTCTTTTAGGGTTACCGAGATACTTTCATGCTGAAAGTATA-CCCAAGGGCATTTTA
* * *
116517 GTAATTTCTCTAGAATTGAGTCCCAA
130 GTAATTT-TCTAGAACTGAGTCCTAG
* * * * * ** *
116543 GTCATTACTAGGTTGCTTTTATGCCAAATGTATGCATTTCA-GATAAGTTTGTCCTTTGTCATAT
1 GTCATCACTAGGTCGCTTTTATGCCAAAGGTATG-AATTCAGGATAGGTTCATCCTTTTTCATAT
* * * *
116607 CATTTTCATGTCTTTTAGGATTAGCGAGATATTTTTTCAT-C-G-AAGATATACCCTAAGGGTAT
65 CATTTTCATGTCTTTTAGGGTTACCGAGATA--CTTTCATGCTGAAAG-TATACCC-AAGGGCAT
116669 TTTAGTAATTTTCCCTAGAA-TAGAGTCCTAG
126 TTTAGTAATTTT--CTAGAACT-GAGTCCTAG
* * * * * * *
116700 AAT-ATCA-TCAAGTCGCTTTTATGCCGAAGGTGT-ATATTTAGGATAGATTTATCCTTTTTCAT
1 -GTCATCACT-AGGTCGCTTTTATGCCAAAGGTATGA-ATTCAGGATAGGTTCATCCTTTTTCAT
* * *
116762 ATAATTTTCATGTCTTTTACGGTTACCGGGATACTTT
63 ATCATTTTCATGTCTTTTAGGGTTACCGAGATACTTT
116799 TACGTTAAAA
Statistics
Matches: 466, Mismatches: 81, Indels: 41
0.79 0.14 0.07
Matches are distributed among these distances:
155 131 0.28
156 247 0.53
157 82 0.18
158 6 0.01
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (154 bp):
GTCATCACTAGGTCGCTTTTATGCCAAAGGTATGAATTCAGGATAGGTTCATCCTTTTTCATATC
ATTTTCATGTCTTTTAGGGTTACCGAGATACTTTCATGCTGAAAGTATACCCAAGGGCATTTTAG
TAATTTTCTAGAACTGAGTCCTAG
Found at i:116619 original size:311 final size:312
Alignment explanation
Indices: 116092--116798 Score: 842
Period size: 311 Copynumber: 2.3 Consensus size: 312
116082 ACTAGGTCAT
* *
116092 TTTTATGCCAAAGGTATGAATTGAGGATAGGTTCATCCTTTTTCATATCATTTTCATGTCTTTTA
1 TTTTATGCCAAAGGTATGAATTTAGGATAGGTTAATCCTTTTTCATATCATTTTCATGTCTTTTA
* * *
116157 GGGTTAACGAGATACTTTCATGTCGAAGGTATACTCCAACAACATTTTAGTAATTTTACTATAAC
66 -GGTTACCGAGATACTTTCATGTCGAAAGTATACTCCAACAACATTTTAGTAATTTTACTAGAAC
* * * * *
116222 TGAGTCCTAGGTCATCACTAGGTCGCTTTTATGCTAAAGGTGTGCATTCACGATAGGTTCATCCT
130 TGAGTCCCAAGTCATCACTAGGTCGCTTTTATGCCAAAGGTATGCATTCACGATAAGTTCATCCT
* *
116287 TTTTCATATCATTTTCATGTCTTTTAAGG-TTATCG-GA-ATACTTTCATGCTGAA-AGTATACC
195 TTGTCATATCATTTTCATGTCTTTT-AGGATTAGCGAGATATACTTTCAT-C-GAAGA-TATACC
* * * ** ***
116348 TTAAGGGTATTTTAGTAATTTT-CTTATAACTA-AGTCCTAGTTTATCATTGGGTCGC
256 CTAAGGGTATTTTAGTAATTTTCCCTAGAA-TAGAGTCCTAGAATATCATCAAGTCGC
* * *
116404 TTTTATGTCAAAGGTATGCATTTAGGATAGGTTAATCCTTTTTTATATCATTTTCATGTCTTTTA
1 TTTTATGCCAAAGGTATGAATTTAGGATAGGTTAATCCTTTTTCATATCATTTTCATGTCTTTTA
* * * ***
116469 GGATT-CCGAGATACTTTGATG-CTGAAAGTATATTCTAAGGGCATTTTAGTAATTTCT-CTAGA
66 GG-TTACCGAGATACTTTCATGTC-GAAAGTATACTCCAACAACATTTTAGTAATTT-TACTAGA
* * * * **
116531 ATTGAGTCCCAAGTCATTACTAGGTTGCTTTTATGCCAAATGTATGCATTTCA-GATAAGTTTGT
128 ACTGAGTCCCAAGTCATCACTAGGTCGCTTTTATGCCAAAGGTATGCA-TTCACGATAAGTTCAT
**
116595 CCTTTGTCATATCATTTTCATGTCTTTTAGGATTAGCGAGATATTTTTTCATCGAAGATATACCC
192 CCTTTGTCATATCATTTTCATGTCTTTTAGGATTAGCGAGATATACTTTCATCGAAGATATACCC
116660 TAAGGGTATTTTAGTAATTTTCCCTAGAATAGAGTCCTAGAATATCATCAAGTCGC
257 TAAGGGTATTTTAGTAATTTTCCCTAGAATAGAGTCCTAGAATATCATCAAGTCGC
* * * * *
116716 TTTTATGCCGAAGGTGT-ATATTTAGGATAGATTTATCCTTTTTCATATAATTTTCATGTCTTTT
1 TTTTATGCCAAAGGTATGA-ATTTAGGATAGGTTAATCCTTTTTCATATCATTTTCATGTCTTTT
*
116780 ACGGTTACCGGGATACTTT
65 A-GGTTACCGAGATACTTT
116799 TACGTTAAAA
Statistics
Matches: 336, Mismatches: 46, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
310 4 0.01
311 158 0.47
312 153 0.46
313 21 0.06
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (312 bp):
TTTTATGCCAAAGGTATGAATTTAGGATAGGTTAATCCTTTTTCATATCATTTTCATGTCTTTTA
GGTTACCGAGATACTTTCATGTCGAAAGTATACTCCAACAACATTTTAGTAATTTTACTAGAACT
GAGTCCCAAGTCATCACTAGGTCGCTTTTATGCCAAAGGTATGCATTCACGATAAGTTCATCCTT
TGTCATATCATTTTCATGTCTTTTAGGATTAGCGAGATATACTTTCATCGAAGATATACCCTAAG
GGTATTTTAGTAATTTTCCCTAGAATAGAGTCCTAGAATATCATCAAGTCGC
Found at i:117411 original size:155 final size:154
Alignment explanation
Indices: 116830--117418 Score: 602
Period size: 155 Copynumber: 3.8 Consensus size: 154
116820 TCATCAACAA
* * *
116830 GATGTTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCTATTTATGATCATTTTTAAGTT
1 GATGCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCATCCTATTTATGATCATTTTTAAGTC
* * * * *
116895 CTTTAGGGTTA-CAGAGATACTTTCATATTGAACGCATACCTAAAGGCATTTTTGTAATTTCTTA
66 CTTTAGGGTTATC-GAGATACTTTCATATCGAAAGTATACCTAGAGACATTTTTGTAATTTCTTA
* * *
116959 AAATTGAGTCTTAGGTAGTCACCAT
130 AAATTGAGTCCTAGGTAGTCACTAG
* * ** * ** *
116984 G-TCACTTTTATGCCAAAAGCCTACATATAGGATAGGTTTGTCC-ATTTTATGATC-TTTTCATA
1 GAT-GCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCATCCTA-TTTATGATCATTTTTA-A
* * * * * ** **
117046 -TCCTTTAAGGTTACCGAGATACTTTTATATC-AAAGTTATACCTTTGGGGTATTTTCATAATTT
63 GTCCTTTAGGGTTATCGAGATACTTTCATATCGAAAG-TATACC-TAGAGACATTTTTGTAATTT
117109 CTTAAAATTGAGTCCTAGGTAGTCA-TCAG
126 CTTAAAATTGAGTCCTAGGTAGTCACT-AG
* * * * * * *
117138 GATTCTTTTGTGCTAAATGTG-AGCATTTAGCATAGTTTCATCCCATTTATGATCATTTTTAAGT
1 GATGCTTTTATGCCAAAGGTGTA-CATTTAGGATAGGTTCATCCTATTTATGATCATTTTTAAGT
* * * * * *
117202 CCTTTAGGGTTATCGAGATACTTTCATGTCTAAGGTATACCTAGGGATATTTTTGTAATTTTTTA
65 CCTTTAGGGTTATCGAGATACTTTCATATCGAAAGTATACCTAGAGACATTTTTGTAATTTCTTA
* *
117267 AGAATCGAGTCCTAGGTTGTCACTAG
130 A-AATTGAGTCCTAGGTAGTCACTAG
* * *
117293 GATGGTTTTATGTCAAAGGTGTATATTTAGGATAGGTTCATCCTATTTATGATCATTTTTAAGTC
1 GATGCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCATCCTATTTATGATCATTTTTAAGTC
117358 CTTTAGGGTTATCGAGATACTTTCATATCGAAAGTATACCTTAGAGACA-TTTTGATAATTT
66 CTTTAGGGTTATCGAGATACTTTCATATCGAAAGTATACC-TAGAGACATTTTTG-TAATTT
117419 TGTATTATAA
Statistics
Matches: 353, Mismatches: 64, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
152 3 0.01
153 38 0.11
154 140 0.40
155 155 0.44
156 17 0.05
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.41
Consensus pattern (154 bp):
GATGCTTTTATGCCAAAGGTGTACATTTAGGATAGGTTCATCCTATTTATGATCATTTTTAAGTC
CTTTAGGGTTATCGAGATACTTTCATATCGAAAGTATACCTAGAGACATTTTTGTAATTTCTTAA
AATTGAGTCCTAGGTAGTCACTAG
Found at i:119090 original size:41 final size:41
Alignment explanation
Indices: 119044--119121 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
119034 CATTTTTTCC
* *
119044 CAGATGTATTGATACATCTTTCAATGTATCAATACATTACT
1 CAGATGCATCGATACATCTTTCAATGTATCAATACATTACT
* *
119085 CAGATGCATCGATACATTTTTCAATGTATCGATACAT
1 CAGATGCATCGATACATCTTTCAATGTATCAATACAT
119122 GTATGAATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (41 bp):
CAGATGCATCGATACATCTTTCAATGTATCAATACATTACT
Found at i:119163 original size:20 final size:20
Alignment explanation
Indices: 119047--119164 Score: 107
Period size: 20 Copynumber: 5.8 Consensus size: 20
119037 TTTTTCCCAG
*
119047 ATGTATTGATACA-TCTTTCA
1 ATGTATCGATACATTC-TTCA
*
119067 ATGTATCAATACATTAC-TCA
1 ATGTATCGATACATT-CTTCA
* *
119087 GATGCATCGATACATTTTTCA
1 -ATGTATCGATACATTCTTCA
* *
119108 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTCA
*
119128 ATGTATCAATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
119148 ATATATCGATACATTCT
1 ATGTATCGATACATTCT
119165 GTTTTTTTAC
Statistics
Matches: 79, Mismatches: 13, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.01
20 59 0.75
21 18 0.23
22 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:124255 original size:32 final size:30
Alignment explanation
Indices: 124219--124277 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
124209 GAAATCAAAT
124219 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
124251 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
124278 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:124577 original size:13 final size:13
Alignment explanation
Indices: 124559--124584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
124549 ATATTTTATG
124559 TGTATCGATACAT
1 TGTATCGATACAT
124572 TGTATCGATACAT
1 TGTATCGATACAT
124585 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:124596 original size:19 final size:19
Alignment explanation
Indices: 124538--124602 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 19
124528 TACAAGCCAA
124538 TGTATCGATACATATTTTATG
1 TGTATCGATACATA-TTT-TG
124559 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
124572 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
124591 TGTATCGATACA
1 TGTATCGATACA
124603 AGTTTGGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
15 1 0.03
18 1 0.03
19 13 0.34
21 11 0.29
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:124598 original size:32 final size:34
Alignment explanation
Indices: 124538--124602 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 34
124528 TACAAGCCAA
124538 TGTATCGATACATATTTTATGTGTATCGATACAT
1 TGTATCGATACATATTTTATGTGTATCGATACAT
124572 TGTATCGATACATA-TTT-TGTGTATCGATACA
1 TGTATCGATACATATTTTATGTGTATCGATACA
124603 AGTTTGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 14 0.45
33 3 0.10
34 14 0.45
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (34 bp):
TGTATCGATACATATTTTATGTGTATCGATACAT
Found at i:127118 original size:13 final size:13
Alignment explanation
Indices: 127100--127124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127090 ATAATCCCCC
127100 TGTATCGATACAG
1 TGTATCGATACAG
127113 TGTATCGATACA
1 TGTATCGATACA
127125 AAGAAAAATG
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:129225 original size:15 final size:15
Alignment explanation
Indices: 129205--129235 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
129195 ATTTCGTTTG
*
129205 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
129220 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
129235 G
1 G
129236 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:133000 original size:32 final size:30
Alignment explanation
Indices: 132964--133022 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
132954 AAAATCAAAT
132964 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
132996 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
133023 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:134501 original size:20 final size:20
Alignment explanation
Indices: 134478--134552 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
134468 AAAAAGACAG
*
134478 AATGTATCGATACAAT-AAA
1 AATGTATCGATACATTCAAA
* *
134497 GAATGTAGCGATACATTCATA
1 -AATGTATCGATACATTCAAA
* *
134518 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTCAAA
134538 AATGTATCGATACAT
1 AATGTATCGATACAT
134553 CTGGGTACTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:135503 original size:28 final size:28
Alignment explanation
Indices: 135392--136149 Score: 824
Period size: 28 Copynumber: 26.4 Consensus size: 28
135382 CTAATTTGTT
* *
135392 TGGGCTTTGAAAAGAGTTGCCACCGACTCGTG
1 TGGGCTTTG-AAAG-GGTGCCACTGACT--TG
* *
135424 TGGGCTTTGAAAAGAGTTCCACT-AGCTTG
1 TGGGCTTTG-AAAGGGTGCCACTGA-CTTG
*
135453 TGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
135482 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * * * *
135510 TAGGCTTCGAAAAGATACCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
** *
135538 TGGGCTTTGAAAAAAGTGTCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
135567 TGGGCTTTGAAAGGGTGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
135595 TAGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
*
135624 TGGGCTTTGAAAGGGTGCCACTAACTTGCG
1 TGGGCTTTGAAAGGGTGCCACTGACTT--G
*
135654 TGGGCTTTGAAAGGGTGCCACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
135682 TGGGCTTTGAAAGAGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
135710 TGGGTTTTGAAAGGGTGCCATTGA-TTCG
1 TGGGCTTTGAAAGGGTGCCACTGACTT-G
*
135738 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * *
135766 TGAGCTTTGAAAAGAGTTGCCAAC-GACTCG
1 TGGGCTTTG-AAAG-GGTGCC-ACTGACTTG
* *
135796 TGGGCTTTGAAAGGATGCCCCTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* ** *
135824 TGGGCTTTGAAAAGAGTTATCA-TCGACTCGTA
1 TGGGCTTTG-AAAG-GGTGCCACT-GACT--TG
* * *
135856 TGGGCTTTGAAAAGATGCCACTGACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
135884 TGGGCTTTGAAAAGAGTGCCACTGACTTG
1 TGGGCTTTG-AAAGGGTGCCACTGACTTG
135913 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
135941 TGGGCTTTGAAAGGGTGCTACTAACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* *
135969 TGGGCTTTCAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
* * * *
135997 TGGGCTTTGAAAAAAGTTACCACCGA-TTCG
1 TGGGCTTTG--AAAGGGTGCCACTGACTT-G
* * * *
136027 TGGGCTTTGAAATGATGCCACTAACTTA
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
*
136055 TGGGCTTTGAAAGGATGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
136083 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
136111 TGGGCTTTGAAAGGGTGCCACTGACTTG
1 TGGGCTTTGAAAGGGTGCCACTGACTTG
136139 TGGGCTTTGAA
1 TGGGCTTTGAA
136150 GAGATGAACG
Statistics
Matches: 624, Mismatches: 79, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
27 3 0.00
28 372 0.60
29 128 0.21
30 84 0.13
31 13 0.02
32 24 0.04
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TGGGCTTTGAAAGGGTGCCACTGACTTG
Found at i:135614 original size:114 final size:113
Alignment explanation
Indices: 135392--136149 Score: 884
Period size: 114 Copynumber: 6.6 Consensus size: 113
135382 CTAATTTGTT
* * *
135392 TGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGTTCCACT-AGCTTGTGG
1 TGGGCTTTG-AAAG-GATGCCACTGACT--TGTGGGCTTTGAAAAGAGTGCCACTGA-CTTGTGG
* *
135456 GCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTG
61 GCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG
* * * * * * *
135510 TAGGCTTCGAAAAGATACCACTAACTTGTGGGCTTTGAAAAAAGTGTCACTGACTTGTGGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* *
135575 GAAAGGGTGCCACTGACTTATAGGCTTTGAAAAGAGTGCCACTGACTTG
66 GAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTG
* * * *
135624 TGGGCTTTGAAAGGGTGCCACTAACTTGCGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCT
1 TGGGCTTTGAAAGGATGCCACTGACTT--GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCT
* * * *
135688 TTGAAAGAGTGCCACTGACTTGTGGGTTTTGAAAGGGTGCCATTGA-TTCG
64 TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT-G
* *
135738 TGGGCTTTGAAAGGATGCCACTGACTTGTGAGCTTTGAAAAGAGTTGCCAAC-GACTCGTGGGCT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCC-ACTGACTTGTGGGCT
* * ** *
135802 TTGAAAGGATGCCCCTGACTTGTGGGCTTTGAAAAGAGTTATCA-TCGACTCGTA
64 TTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGAG-TGCCACT-GACT--TG
* *
135856 TGGGCTTTGAAAAGATGCCACTGACTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
* * *
135921 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCTACTAACTTG
66 GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG
* * * *
135969 TGGGCTTTCAAAGGATGCCACTGACTTGTGGGCTTTGAAAAAAGTTACCACCGA-TTCGTGGGCT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTT-GTGGGCT
* * * *
136033 TTGAAATGATGCCACTAACTTATGGGCTTTGAAAG-GATGCCACTGACTTG
64 TTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTG
* *
136083 TGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTT
1 TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
136147 GAA
66 GAA
136150 GAGATGAACG
Statistics
Matches: 547, Mismatches: 73, Indels: 46
0.82 0.11 0.07
Matches are distributed among these distances:
112 28 0.05
113 82 0.15
114 246 0.45
115 62 0.11
116 32 0.06
117 48 0.09
118 48 0.09
119 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (113 bp):
TGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTT
GAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG
Found at i:135757 original size:142 final size:142
Alignment explanation
Indices: 135376--136149 Score: 904
Period size: 142 Copynumber: 5.4 Consensus size: 142
135366 TTTAAAAAAA
* * *
135376 GTGCCACTAATTTGTTTGGGCTTTGAAAAGAGTTGCCACCGACTCGTGTGGGCTTTGAAAAGAGT
1 GTGCCACTAACTTG--TGGGCTTTGAAAAGAGTTGCCACTGACT--TGTGGGCTTTG-AAAGGGT
* *
135441 TCCACTAGCTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
61 GCCACT-GATTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA
* * *
135506 CTTGTAGGCTTCGAAAAG
125 CTTGTGGGCTTTGAAAGG
* * * *
135524 ATACCACTAACTTGTGGGCTTTGAAAAAAG-TGTCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
1 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
* * *
135588 TGACTTATAGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGC
66 TGA-TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT--
135653 GTGGGCTTTGAAAGG
128 GTGGGCTTTGAAAGG
* *
135668 GTGCCACTAACTTGTGGGCTTTG-AAAGAG-TGCCACTGACTTGTGGGTTTTGAAAGGGTGCCAT
1 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
* * *
135731 TGATTCGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGAGCTTTGAAAAGAGTTGCCAAC-GACT
66 TGATT-GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCC-ACTGACT
*
135794 CGTGGGCTTTGAAAGG
127 TGTGGGCTTTGAAAGG
* * * ** * * *
135810 ATGCCCCTGACTTGTGGGCTTTGAAAAGAGTTATCA-TCGACTCGTATGGGCTTTGAAAAGATGC
1 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACT-GACT--TGTGGGCTTTGAAAGGGTGC
*
135874 CACTGACTTATGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
63 CACTGA-TTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
135939 TGTGGGCTTTGAAAGG
127 TGTGGGCTTTGAAAGG
* * * * * *
135955 GTGCTACTAACTTGTGGGCTTT-CAAAG-GATGCCACTGACTTGTGGGCTTTGAAAAAAGTTACC
1 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTG--AAAGGGTGCC
* * * * *
136018 ACCGATTCGTGGGCTTTGAAATGA-TGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGACTT
64 ACTGATT-GTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT
136082 GTGGGCTTTGAAAGG
128 GTGGGCTTTGAAAGG
* *
136097 GTGCCACTGACTTGTGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGAA
1 GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAA
136150 GAGATGAACG
Statistics
Matches: 543, Mismatches: 63, Indels: 48
0.83 0.10 0.07
Matches are distributed among these distances:
140 2 0.00
141 11 0.02
142 226 0.42
143 108 0.20
144 55 0.10
145 53 0.10
146 54 0.10
147 23 0.04
148 11 0.02
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (142 bp):
GTGCCACTAACTTGTGGGCTTTGAAAAGAGTTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCAC
TGATTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
GGCTTTGAAAGG
Found at i:137377 original size:8 final size:8
Alignment explanation
Indices: 137360--137428 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
137350 TCTGGACCCC
137360 TTTTTG-T
1 TTTTTGTT
137367 TTTTTG--
1 TTTTTGTT
137373 TTTTT-TT
1 TTTTTGTT
* *
137380 TTCTTGGT
1 TTTTTGTT
137388 TTTTTGTT
1 TTTTTGTT
*
137396 ATTTTGTT
1 TTTTTGTT
137404 TTTTTGGGTTT
1 TTTTT--G-TT
137415 TTTTTGTT
1 TTTTTGTT
137423 TTTTTG
1 TTTTTG
137429 GGTATGAAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 5 0.10
7 10 0.20
8 26 0.52
9 1 0.02
10 1 0.02
11 7 0.14
ACGTcount: A:0.01, C:0.01, G:0.16, T:0.81
Consensus pattern (8 bp):
TTTTTGTT
Found at i:137389 original size:14 final size:12
Alignment explanation
Indices: 137360--137427 Score: 50
Period size: 11 Copynumber: 5.6 Consensus size: 12
137350 TCTGGACCCC
137360 TTTTTGTTTTTTG
1 TTTTT-TTTTTTG
137373 TTTTTTTTTCTTGG
1 TTTTTTTTT-TT-G
* *
137387 TTTTTTGTTAT-
1 TTTTTTTTTTTG
*
137398 TTTGTTTTTTTG
1 TTTTTTTTTTTG
**
137410 -GGTTTTTTTTG
1 TTTTTTTTTTTG
137421 TTTTTTT
1 TTTTTTT
137428 GGGTATGAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 9
0.68 0.17 0.15
Matches are distributed among these distances:
11 16 0.39
12 8 0.20
13 8 0.20
14 9 0.22
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:137417 original size:27 final size:27
Alignment explanation
Indices: 137360--137426 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
137350 TCTGGACCCC
**
137360 TTTTTGTTTTTTGTTTTTTTTTCTTGGT
1 TTTTTGTTTTTTGTTTTTTTGGCTT-GT
*
137388 TTTTTGTTATTTTGTTTTTTTGGGTT-T
1 TTTTTGTT-TTTTGTTTTTTTGGCTTGT
137415 TTTTTGTTTTTT
1 TTTTTGTTTTTT
137427 TGGGTATGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.11
27 9 0.26
28 8 0.23
29 14 0.40
ACGTcount: A:0.01, C:0.01, G:0.15, T:0.82
Consensus pattern (27 bp):
TTTTTGTTTTTTGTTTTTTTGGCTTGT
Found at i:137424 original size:24 final size:23
Alignment explanation
Indices: 137366--137427 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 23
137356 CCCCTTTTTG
137366 TTTTTTGTTTTTTTTTCTTGGTT
1 TTTTTTGTTTTTTTTTCTTGGTT
*
137389 TTTTGTTATTTTGTTTTT-TTGGGTT
1 TTTT-TTGTTTT-TTTTTCTT-GGTT
137414 TTTTTTGTTTTTTT
1 TTTTTTGTTTTTTT
137428 GGGTATGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 7 0.21
24 14 0.41
25 13 0.38
ACGTcount: A:0.02, C:0.02, G:0.15, T:0.82
Consensus pattern (23 bp):
TTTTTTGTTTTTTTTTCTTGGTT
Found at i:137426 original size:7 final size:7
Alignment explanation
Indices: 137360--137407 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
137350 TCTGGACCCC
137360 TTTTTGT
1 TTTTTGT
137367 TTTTTGT
1 TTTTTGT
137374 TTTTT-T
1 TTTTTGT
*
137380 TTCTTGGT
1 TT-TTTGT
137388 TTTTTGT
1 TTTTTGT
137395 TATTTTGT
1 T-TTTTGT
137403 TTTTT
1 TTTTT
137408 TGGGTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
6 3 0.08
7 23 0.64
8 10 0.28
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.83
Consensus pattern (7 bp):
TTTTTGT
Found at i:139612 original size:28 final size:28
Alignment explanation
Indices: 139578--139659 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
139568 TTTTGGAGAT
*
139578 AATAACGAGGTTGGAGTGTTCCCTC-A-GA
1 AATAACGAGGTTGGAGT-ATCCC-CGATGA
* *
139606 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCCCGATGA
*
139634 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCCCGAT
139660 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 1 0.02
27 5 0.11
28 40 0.87
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCCCGATGA
Found at i:139802 original size:51 final size:50
Alignment explanation
Indices: 139642--139812 Score: 171
Period size: 51 Copynumber: 3.3 Consensus size: 50
139632 GAAATAACGA
* * * *
139642 GGTTGGAGTATCCTCGATTGTGAAAAATTAGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATGA-TA-TTTTGAAAATAAAATCGG
** * * * * * *
139694 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGA-AAAATGATATTTTGAAAATAAAATCGG
*
139747 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAAT-GATATTTTGAAAATAAAATCGG
139798 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
139813 TCAGAAATAA
Statistics
Matches: 94, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
50 4 0.04
51 35 0.37
52 16 0.17
53 32 0.34
54 3 0.03
55 4 0.04
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTTGGAGTATCCCCGATTATGAAAAATGATATTTTGAAAATAAAATCGG
Found at i:139858 original size:27 final size:28
Alignment explanation
Indices: 139795--139866 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
139785 AAAATAAAGT
139795 CGGGGTTGGAGTATCCCCTCAGAAATAA
1 CGGGGTTGGAGTATCCCCTCAGAAATAA
* *
139823 CGGGGTTGGAGTATCCCC-GATG-ATTAA
1 CGGGGTTGGAGTATCCCCTCA-GAAATAA
*
139850 CGGGGTTGGAGTGTCCC
1 CGGGGTTGGAGTATCCC
139867 AGATTGTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCAGAAATAA
Found at i:142366 original size:13 final size:13
Alignment explanation
Indices: 142348--142373 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
142338 ACAAAGATCC
142348 ATGTATCGATACA
1 ATGTATCGATACA
142361 ATGTATCGATACA
1 ATGTATCGATACA
142374 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142369 original size:33 final size:33
Alignment explanation
Indices: 142327--142393 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
142317 AAAATTTCCA
***
142327 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
142360 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
142393 A
1 A
142394 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:142437 original size:19 final size:18
Alignment explanation
Indices: 142413--142480 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
142403 CAGTAGCTAA
142413 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
142432 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
142447 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
142464 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
142481 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:142453 original size:13 final size:13
Alignment explanation
Indices: 142435--142459 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
142425 ACAATACTTA
142435 TGTATCGATACAT
1 TGTATCGATACAT
142448 TGTATCGATACA
1 TGTATCGATACA
142460 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:142457 original size:32 final size:32
Alignment explanation
Indices: 142416--142478 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
142406 TAGCTAATTA
*
142416 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
142448 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
142479 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:142560 original size:21 final size:21
Alignment explanation
Indices: 142536--142592 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
142526 CATTTGTAGG
142536 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
142557 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
142578 ATGTATCGATACATT
1 ATGTATCGATACATT
142593 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:142603 original size:1 final size:1
Alignment explanation
Indices: 142597--142643 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
142587 TACATTTAAA
***
142597 TTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
142644 CAAACACTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:142625 original size:23 final size:23
Alignment explanation
Indices: 142595--142639 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
142585 GATACATTTA
142595 AATTTTTTTTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTTTTTTTC
142618 AATTTTTTTTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTTTTTTTT
142640 TTTTCAAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.09, C:0.02, G:0.00, T:0.89
Consensus pattern (23 bp):
AATTTTTTTTTTTTTTTTTTTTC
Found at i:143323 original size:55 final size:54
Alignment explanation
Indices: 143239--143861 Score: 930
Period size: 55 Copynumber: 11.3 Consensus size: 54
143229 ATAAATTGTA
* * * * * *
143239 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
143294 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
143349 TCCTGCTCTTTGAGGATTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
143404 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
143459 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
143514 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
143569 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
143624 TCCTGCTCGTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
143679 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
143734 TCCTGCTCTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
143789 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
143844 TCCTGCTCTTTGGGGACT
1 TCCTGCTCTTTGAGGACT
143862 AAAAAGCGGA
Statistics
Matches: 538, Mismatches: 23, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
54 12 0.02
55 516 0.96
56 10 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:143701 original size:27 final size:27
Alignment explanation
Indices: 143671--143814 Score: 64
Period size: 27 Copynumber: 5.3 Consensus size: 27
143661 TGTGGGCTTT
143671 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
143698 GAAA-ATG-CCACCAACTTGTGTGGGCTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGACTG
*
143725 TAAAAGGTGTCCTGCTCTTTGAGGACTG
1 GA-AAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
143753 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
143781 GAAAGGTGTCCTGCTCTTTGAGGACT-
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
143807 GAAAGGTG
1 GAAAGGTG
143815 CCACCAACTT
Statistics
Matches: 78, Mismatches: 29, Indels: 21
0.61 0.23 0.16
Matches are distributed among these distances:
25 6 0.08
26 18 0.23
27 19 0.24
28 19 0.24
29 10 0.13
30 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:144847 original size:1 final size:1
Alignment explanation
Indices: 144843--144893 Score: 57
Period size: 1 Copynumber: 51.0 Consensus size: 1
144833 CTTTTCTCTC
* * * * *
144843 TTTTTCTTTGTTTTGTTTTTTTGTTTTTTTTTTTTTCTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
144894 GAAGAGAAGG
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.00, C:0.04, G:0.06, T:0.90
Consensus pattern (1 bp):
T
Found at i:144861 original size:31 final size:30
Alignment explanation
Indices: 144826--144894 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
144816 GCTTAAGTAG
144826 GTTTTTTCT-TTTCTCTCTTTTTCTTTGTTTT
1 GTTTTTT-TGTTTCTCTCTTTTTCTTT-TTTT
* * *
144857 GTTTTTTTGTTTTTTTTTTTTTCTTTTTTT
1 GTTTTTTTGTTTCTCTCTTTTTCTTTTTTT
144887 -TTTTTTTG
1 GTTTTTTTG
144895 AAGAGAAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.24
30 5 0.15
31 21 0.62
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (30 bp):
GTTTTTTTGTTTCTCTCTTTTTCTTTTTTT
Found at i:144892 original size:15 final size:15
Alignment explanation
Indices: 144827--144893 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
144817 CTTAAGTAGG
* *
144827 TTTTTTCTTTTCTCT
1 TTTTTTCTTTTTTTT
*
144842 CTTTTTCTTTGTTTTGT
1 TTTTTTCTTT-TTTT-T
*
144859 TTTTTT-GTTTTTTT
1 TTTTTTCTTTTTTTT
144873 TTTTTTCTTTTTTTT
1 TTTTTTCTTTTTTTT
144888 TTTTTT
1 TTTTTT
144894 GAAGAGAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
14 7 0.16
15 26 0.60
16 4 0.09
17 6 0.14
ACGTcount: A:0.00, C:0.09, G:0.04, T:0.87
Consensus pattern (15 bp):
TTTTTTCTTTTTTTT
Found at i:157372 original size:28 final size:28
Alignment explanation
Indices: 157291--157372 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
157281 TTTTGGAGAT
*
157291 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
157319 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
157347 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
157373 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:157478 original size:105 final size:104
Alignment explanation
Indices: 157350--157694 Score: 272
Period size: 105 Copynumber: 3.3 Consensus size: 104
157340 CCGATGAAAT
* * *
157350 AACGAGGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAATTGGAG
1 AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
*
157415 TATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAA
66 TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * * * * *
157454 AACCGGGGTTGGAGTATCCCCGATTATGAAAAATCGATA-TTTTGAAAATAAAGTCGGGGTTGGA
1 AA-CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
* * * * * ** *
157518 GTATCCCCTCAGAAATAACGG-G--GTTGGAGTATCCCCGATGAT-T
65 GTAT-CCC-C-G-ATTAAAGGAGAAATTGGTGT-T--CTGAAAATAA
* *
157561 AACGGGGTTGGAGTGTCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTT
1 AACGGGGTTGGAGTATCCCCGATTGTGAA-AAATT-G-G-TATTTTTGGAAATAAAATCGGAGTT
* ** * *
157626 GGAGTATCCCCGATTATA-GA-AAATTAATGTTTTGAAAGTAA
62 GGAGTATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
* * *
157667 AATCGGAGTTGGAATATCCTCGATTGTG
1 AA-CGGGGTTGGAGTATCCCCGATTGTG
157695 GAGAATTGAG
Statistics
Matches: 180, Mismatches: 43, Indels: 33
0.70 0.17 0.13
Matches are distributed among these distances:
104 27 0.15
105 43 0.24
106 30 0.17
107 33 0.18
108 16 0.09
109 1 0.01
110 4 0.02
111 26 0.14
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.30
Consensus pattern (104 bp):
AACGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAG
TATCCCCGATTAAAGGAGAAATTGGTGTTCTGAAAATAA
Found at i:157515 original size:51 final size:51
Alignment explanation
Indices: 157355--157525 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
157345 GAAATAACGA
* * *
157355 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
157407 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
157460 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
157511 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
157526 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:157571 original size:27 final size:28
Alignment explanation
Indices: 157508--157583 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
157498 AAAATAAAGT
*
157508 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
157536 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
157563 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
157584 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:160069 original size:13 final size:13
Alignment explanation
Indices: 160051--160076 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
160041 ACAAAGATCC
160051 ATGTATCGATACA
1 ATGTATCGATACA
160064 ATGTATCGATACA
1 ATGTATCGATACA
160077 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:160072 original size:33 final size:33
Alignment explanation
Indices: 160030--160096 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
160020 AAAATTTCCA
***
160030 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
160063 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
160096 A
1 A
160097 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:160140 original size:19 final size:18
Alignment explanation
Indices: 160116--160183 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
160106 CAGTAGCTAA
160116 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
160135 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
160150 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
160167 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
160184 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:160156 original size:13 final size:13
Alignment explanation
Indices: 160138--160162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
160128 ACAATACTTA
160138 TGTATCGATACAT
1 TGTATCGATACAT
160151 TGTATCGATACA
1 TGTATCGATACA
160163 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:160160 original size:32 final size:32
Alignment explanation
Indices: 160119--160181 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
160109 TAGCTAATTA
*
160119 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
160151 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
160182 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:160263 original size:21 final size:21
Alignment explanation
Indices: 160239--160295 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
160229 CATTTGTAGG
160239 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
160260 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
160281 ATGTATCGATACATT
1 ATGTATCGATACATT
160296 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:160326 original size:19 final size:19
Alignment explanation
Indices: 160302--160339 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
160292 CATTTAAATT
160302 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
160321 TTTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTTCAA
160340 ACACTTTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTTTTTTTTCAA
Found at i:172801 original size:20 final size:20
Alignment explanation
Indices: 172776--172897 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
172766 TAACTAGATA
172776 TATCGATACATTGAAAAATG
1 TATCGATACATTGAAAAATG
172796 TATCGATACATCTGGGTAAAAAGATAGAATG
1 TATCGATACAT-T--G--AAAA-AT-----G
172827 TATCGATACATT-AAAGAATG
1 TATCGATACATTGAAA-AATG
** * * *
172847 TAAAGATACATTCATACATG
1 TATCGATACATTGAAAAATG
*
172867 TATCGATACATTGAAAGATG
1 TATCGATACATTGAAAAATG
172887 TATCGATACAT
1 TATCGATACAT
172898 CTAGGTACTT
Statistics
Matches: 80, Mismatches: 9, Indels: 26
0.70 0.08 0.23
Matches are distributed among these distances:
20 51 0.64
21 3 0.04
23 1 0.01
25 9 0.11
26 3 0.04
30 1 0.01
31 12 0.15
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (20 bp):
TATCGATACATTGAAAAATG
Found at i:178844 original size:28 final size:28
Alignment explanation
Indices: 178804--179229 Score: 243
Period size: 28 Copynumber: 14.6 Consensus size: 28
178794 ATCAGGGACG
* *
178804 TCTTTTCAAAGCCCAAAAGTTAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
178832 TCTTTTCAAAGCCCACATAAGTCGGTGGCAA
1 TCTTTTCAAAGCCCAC--AAGTCAGTGGC-A
* *
178863 CCTCTCTTAAAAGCCCACAAGTCAGTGGCA
1 --TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
178893 TCCTTTCAAAGCCCACACAAGTCGGTGGCAA
1 TCTTTTCAAAG-CC-CACAAGTCAGTGGC-A
*
178924 CCTCTTTCAAAGCCCACAAGTCAGTGGCA
1 TCT-TTTCAAAGCCCACAAGTCAGTGGCA
* ** *
178953 CCCCTT-AAAACTCACACAAGTC-GATGGCAA
1 TCTTTTCAAAGC-C-CACAAGTCAG-TGGC-A
* * **
178983 CCTCTCTTAAAAGCTTACAAGTCAGTGGCA
1 --TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * * * *
179013 TCATTCTCCAAGTCCACAAGTTAGTGACA
1 TC-TTTTCAAAGCCCACAAGTCAGTGGCA
* * * * * *
179042 CCCTTTCAAAACCTACAAGTTAGTGGTA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* *
179070 -CTTTTTCCAAG-TCAGCAAGTCAGTGGCA
1 TC-TTTTCAAAGCCCA-CAAGTCAGTGGCA
* *
179098 TCTTTT-AAAGCCCACGAGTCAGTGGCT
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
* * *
179125 TCCTTTCAAAAGCCCACAAGTTAATGGCA
1 TCTTTTC-AAAGCCCACAAGTCAGTGGCA
* * * *
179154 TATTTTCAAAGCCTACAAATTAGTGGCA
1 TCTTTTCAAAGCCCACAAGTCAGTGGCA
*
179182 TCCTTTT-AAAGCCCACAAGTCAATGGCAA
1 T-CTTTTCAAAGCCCACAAGTCAGTGGC-A
*
179211 TCCTTCTCTAAAGCCCACA
1 T-CTTTTC-AAAGCCCACA
179230 CAAGTTGGTG
Statistics
Matches: 304, Mismatches: 66, Indels: 53
0.72 0.16 0.13
Matches are distributed among these distances:
27 25 0.08
28 105 0.35
29 69 0.23
30 38 0.12
31 36 0.12
32 13 0.04
33 18 0.06
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (28 bp):
TCTTTTCAAAGCCCACAAGTCAGTGGCA
Found at i:178892 original size:61 final size:61
Alignment explanation
Indices: 178811--179014 Score: 286
Period size: 61 Copynumber: 3.4 Consensus size: 61
178801 ACGTCTTTTC
* * * *
178811 AAAGCCCAAAAGTTAGTGGCATCTTTTCAAAGCCCACATAAGTCGGTGGCAACCTCTCTTA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCTCTTA
*
178872 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCT-TTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCTCTTA
* * * * *
178932 AAAGCCCACAAGTCAGTGGCACCCCTT-AAAACTCACACAAGTCGATGGCAACCTCTCTTA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCTCTTA
**
178992 AAAGCTTACAAGTCAGTGGCATC
1 AAAGCCCACAAGTCAGTGGCATC
179015 ATTCTCCAAG
Statistics
Matches: 128, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 26 0.20
60 49 0.38
61 53 0.41
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.21
Consensus pattern (61 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCTCTTA
Found at i:179031 original size:60 final size:60
Alignment explanation
Indices: 178811--179033 Score: 261
Period size: 60 Copynumber: 3.7 Consensus size: 60
178801 ACGTCTTTTC
* * * * *
178811 AAAGCCCAAAAGTTAGTGGCATCTTTTCAAAGCCCACATAAGTCGGTGGCAACCTCTCTTA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-TCACACAAGTCGGTGGCAACCTCTCTTA
* *
178872 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACACAAGTCGGTGGCAACCTCT-TTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAG-TCACACAAGTCGGTGGCAACCTCTCTTA
* * * * *
178932 AAAGCCCACAAGTCAGTGGCACCCCTTAAAACTCACACAAGTCGATGGCAACCTCTCTTA
1 AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCACACAAGTCGGTGGCAACCTCTCTTA
** * *
178992 AAAGCTTACAAGTCAGTGGCATCATTCTCCAAGTC-CACAAGT
1 AAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGTCACACAAGT
179034 TAGTGACACC
Statistics
Matches: 140, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
59 22 0.16
60 60 0.43
61 58 0.41
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (60 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTCAAAGTCACACAAGTCGGTGGCAACCTCTCTTA
Found at i:180066 original size:41 final size:41
Alignment explanation
Indices: 180010--180092 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
180000 AGTCACATTT
* *
180010 TTACCCAGATGTATCGATACATCTTTCAATGTATCGATACA
1 TTACCCAAATATATCGATACATCTTTCAATGTATCGATACA
*
180051 TTACCCAAATATATCGATACATTTTTCAATGTATCGATACA
1 TTACCCAAATATATCGATACATCTTTCAATGTATCGATACA
180092 T
1 T
180093 GAATGAATGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (41 bp):
TTACCCAAATATATCGATACATCTTTCAATGTATCGATACA
Found at i:180134 original size:20 final size:20
Alignment explanation
Indices: 180018--180135 Score: 114
Period size: 20 Copynumber: 5.8 Consensus size: 20
180008 TTTTACCCAG
180018 ATGTATCGATACA-TCTTTCA
1 ATGTATCGATACATTC-TTCA
*
180038 ATGTATCGATACATTAC-CCAA
1 ATGTATCGATACATT-CTTC-A
* *
180059 ATATATCGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
*** *
180079 ATGTATCGATACATGAATGA
1 ATGTATCGATACATTCTTCA
*
180099 ATGTATTGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
180119 AAGTATCGATACATTCT
1 ATGTATCGATACATTCT
180136 GTCTTTTTAG
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 60 0.77
21 17 0.22
22 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:184624 original size:132 final size:131
Alignment explanation
Indices: 184386--184630 Score: 368
Period size: 132 Copynumber: 1.9 Consensus size: 131
184376 GACGATAAGC
** *
184386 CCTTTTGTATATATTTTTTTGTATTACTTTTCTTTGACATTACATTAATTTCATCTTTGCACCTA
1 CCTTTTGTATATATTACTTTGTATAACTTTTCTTTGACATTACATTAATTTCATCTTTGCACCTA
* *
184451 TTTGCATCTATGAATATATACATGCATTCATTCATGGCATACATTTTTTAAGCCTTTATCTTCGG
66 TTTGCATCTATGAATACATACATGCATTCATTCATGACATACATTTTTTAAGCCTTTATCTTCGG
184516 A
131 A
* * *
184517 CCTTTTTTATATATTACTTTGTTATAACTTTTCTTTGACATTACATTATTTTCATTTTTGCA-CT
1 CCTTTTGTATATATTACTTTG-TATAACTTTTCTTTGACATTACATTAATTTCATCTTTGCACCT
*
184581 CATTTGCATAC-ATGAATACATGCATGCATTCATTCATGACATACATTTTT
65 -ATTTGCAT-CTATGAATACATACATGCATTCATTCATGACATACATTTTT
184631 CTTTGAAAGC
Statistics
Matches: 102, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
131 20 0.20
132 81 0.79
133 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.49
Consensus pattern (131 bp):
CCTTTTGTATATATTACTTTGTATAACTTTTCTTTGACATTACATTAATTTCATCTTTGCACCTA
TTTGCATCTATGAATACATACATGCATTCATTCATGACATACATTTTTTAAGCCTTTATCTTCGG
A
Found at i:185657 original size:34 final size:35
Alignment explanation
Indices: 185621--185685 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
185611 CTAAATAAGA
185621 AAAAAATGAAAAATG-AAG-AA-GAAAAAAAAGAAG
1 AAAAAAT-AAAAATGCAAGAAATGAAAAAAAAGAAG
*
185654 AAAAAATAAAAATGCATGAAATGAAAAAAAAG
1 AAAAAATAAAAATGCAAGAAATGAAAAAAAAG
185686 TGCAGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 7 0.25
33 9 0.32
34 2 0.07
35 10 0.36
ACGTcount: A:0.74, C:0.02, G:0.15, T:0.09
Consensus pattern (35 bp):
AAAAAATAAAAATGCAAGAAATGAAAAAAAAGAAG
Found at i:187161 original size:88 final size:88
Alignment explanation
Indices: 186914--187206 Score: 327
Period size: 88 Copynumber: 3.3 Consensus size: 88
186904 ATTTACACCA
* * * **
186914 TTAGATCACATTGGCATTTGCATCATTTCATGTACATTTTCCTTTTTATTAATGTTTGCAGCTGC
1 TTAGATGACATTGGCATTTGCATCATTTCAAGTACATTTTCCTTTTTATTAATGCTTGCATTTGC
* * * *
186979 ATTATTTCATGTACATCTACACT
66 ATTATTTCATGCACATTTGCATT
* * * * * * * *
187002 TTAGATGATATTGGTATTTGCATTATTTC-AGTGCCTTTTCCTCTTTATTGACGCTTGCATTTGC
1 TTAGATGACATTGGCATTTGCATCATTTCAAGTACATTTTCCTTTTTATTAATGCTTGCATTTGC
**
187066 ATTATTTCACACACATTTGCATT
66 ATTATTTCATGCACATTTGCATT
* * * *
187089 TTAGATGACATTAGTATTTGCATCATTTCAAGTATATTTTCCTTTTTATTAATGCTTGCATTTGT
1 TTAGATGACATTGGCATTTGCATCATTTCAAGTACATTTTCCTTTTTATTAATGCTTGCATTTGC
* *
187154 ATCATTTCGTGCACATTTGCATT
66 ATTATTTCATGCACATTTGCATT
* * *
187177 TTAGATAACATTGGCATTTGCCTTATTTCA
1 TTAGATGACATTGGCATTTGCATCATTTCA
187207 CATACACTGC
Statistics
Matches: 166, Mismatches: 38, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
87 69 0.42
88 97 0.58
ACGTcount: A:0.23, C:0.17, G:0.13, T:0.47
Consensus pattern (88 bp):
TTAGATGACATTGGCATTTGCATCATTTCAAGTACATTTTCCTTTTTATTAATGCTTGCATTTGC
ATTATTTCATGCACATTTGCATT
Found at i:187818 original size:62 final size:60
Alignment explanation
Indices: 187667--187867 Score: 183
Period size: 60 Copynumber: 3.3 Consensus size: 60
187657 GTAAACTATT
* * *
187667 TTAGTTTCACTTAAGTCATTATTTAGGTTTCTGGTTTTATCTAGGCCATTTCATTAAGTC
1 TTAGTTTCACTTAAGTCATTGTTTAGGTTTCTAGTTCTATCTAGGCCATTTCATTAAGTC
* * * * *
187727 TTGGTTTCATTTAAGCCACTGTTTAGGTTTCTAGTTCTATCTAGGCCATTT-ATTTTTTAGTC
1 TTAGTTTCACTTAAGTCATTGTTTAGGTTTCTAGTTCTATCTAGGCCATTTCA---TTAAGTC
** * * * * *
187789 TTAGTTTCACACAAGTCATTGTTTAGGTTTAT-GATTTTATCCAGGCCATTTCGTTGAGT-
1 TTAGTTTCACTTAAGTCATTGTTTAGGTTTCTAG-TTCTATCTAGGCCATTTCATTAAGTC
** *
187848 TCGGTTTCACCTAAGTCATT
1 TTAGTTTCACTTAAGTCATT
187868 TCGTAGACTT
Statistics
Matches: 113, Mismatches: 23, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
59 17 0.15
60 49 0.43
61 1 0.01
62 46 0.41
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.47
Consensus pattern (60 bp):
TTAGTTTCACTTAAGTCATTGTTTAGGTTTCTAGTTCTATCTAGGCCATTTCATTAAGTC
Done.