Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold2409.1
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: 247890
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Warning! 106 characters in sequence are not A, C, G, or T
Found at i:2825 original size:66 final size:69
Alignment explanation
Indices: 2695--2825 Score: 160
Period size: 66 Copynumber: 1.9 Consensus size: 69
2685 GGGATGTATC
* * *
2695 CCATGTAGACAAGAGAGCTACGAGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTG
1 CCATGTAGACAAGAGAGCTAC---AGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
2760 AAGGACA
63 AAGGACA
* * *
2767 CCATGTAGACAAGAGAGCTAC-GAGG-TAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACAGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
2826 TTCACCATGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
66 23 0.43
67 5 0.09
68 4 0.08
72 21 0.40
ACGTcount: A:0.33, C:0.15, G:0.31, T:0.21
Consensus pattern (69 bp):
CCATGTAGACAAGAGAGCTACAGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTGAAG
GACA
Found at i:12915 original size:26 final size:26
Alignment explanation
Indices: 12886--12945 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
12876 TTTACTAAAC
** * *
12886 TACCCCTAAGTATGAAATTACCATTA
1 TACCCCTAAGTACAAAATGACCATGA
12912 TACCCCTAAGTACAAAATGACCATGA
1 TACCCCTAAGTACAAAATGACCATGA
12938 TACCCCTA
1 TACCCCTA
12946 GGGTTAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.25
Consensus pattern (26 bp):
TACCCCTAAGTACAAAATGACCATGA
Found at i:13124 original size:27 final size:27
Alignment explanation
Indices: 13053--13179 Score: 116
Period size: 27 Copynumber: 4.7 Consensus size: 27
13043 GGAAGCGTTT
13053 TGGTAGCTATGCCACAAATATCTGTTTC
1 TGGTAGCTATGCCACAAATATCTG-TTC
* * *
13081 TGGTAGCTATGCAACAAACATCTATTC
1 TGGTAGCTATGCCACAAATATCTGTTC
* *
13108 TGGTGGCTCTGCCAC-AATATCTGTATC
1 TGGTAGCTATGCCACAAATATCTGT-TC
* *
13135 TGGT-GACTCTGTCA-AAATATCTGTTC
1 TGGTAG-CTATGCCACAAATATCTGTTC
* * *
13161 TGGCAGCCATGCTACAAAT
1 TGGTAGCTATGCCACAAAT
13180 TCTATGGCGT
Statistics
Matches: 80, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
26 17 0.21
27 42 0.52
28 21 0.26
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (27 bp):
TGGTAGCTATGCCACAAATATCTGTTC
Found at i:16402 original size:12 final size:12
Alignment explanation
Indices: 16387--16418 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
16377 GATTTTGCTT
*
16387 TTTTTTTTTCAA
1 TTTTTTTTACAA
16399 TTTTTTTTACAA
1 TTTTTTTTACAA
16411 TTTTTTTT
1 TTTTTTTT
16419 GAAACTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTTTTACAA
Found at i:17607 original size:14 final size:14
Alignment explanation
Indices: 17588--17630 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
17578 TTAAAGAAGC
17588 AATTCATTAAATTA
1 AATTCATTAAATTA
17602 AATTCATTAAA-TA
1 AATTCATTAAATTA
* *
17615 AACTCATTTAATTA
1 AATTCATTAAATTA
17629 AA
1 AA
17631 CTAAGATGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (14 bp):
AATTCATTAAATTA
Found at i:20193 original size:100 final size:100
Alignment explanation
Indices: 20020--20220 Score: 366
Period size: 100 Copynumber: 2.0 Consensus size: 100
20010 ACTCATCGAA
20020 CTTCGATTAAATAATTTATTCATCAATTAATTCCACTCCCACTATTTTTAGTGATTTTTCAATCT
1 CTTCGATTAAATAATTTATTCATCAATTAATTCCACTCCCACTATTTTTAGTGATTTTTCAATCT
*
20085 CATGTCACTGCTGCTGCCAGCATCTGTTACGAAAG
66 CATATCACTGCTGCTGCCAGCATCTGTTACGAAAG
* *
20120 CTTCGATTACATAATTTATTCATCAATTAATTCCACTCCTACTATTTTTAGTGATTTTTCAATCT
1 CTTCGATTAAATAATTTATTCATCAATTAATTCCACTCCCACTATTTTTAGTGATTTTTCAATCT
*
20185 CATATCACTGCTGCTTCCAGCATCTGTTACGAAAG
66 CATATCACTGCTGCTGCCAGCATCTGTTACGAAAG
20220 C
1 C
20221 AACTATGCCC
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (100 bp):
CTTCGATTAAATAATTTATTCATCAATTAATTCCACTCCCACTATTTTTAGTGATTTTTCAATCT
CATATCACTGCTGCTGCCAGCATCTGTTACGAAAG
Found at i:21142 original size:27 final size:27
Alignment explanation
Indices: 21112--21263 Score: 232
Period size: 27 Copynumber: 5.6 Consensus size: 27
21102 ATATTAAGCC
* * *
21112 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
*
21139 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
21167 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
21194 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
*
21222 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
*
21249 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
21264 GCACAATTTA
Statistics
Matches: 118, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
27 65 0.55
28 53 0.45
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:21196 original size:55 final size:55
Alignment explanation
Indices: 21112--21288 Score: 255
Period size: 55 Copynumber: 3.2 Consensus size: 55
21102 ATATTAAGCC
* * *
21112 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
*
21167 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
* * * * * *
21222 CGCACACTTAGTGCTACATAGTCAATTCACACACTTAGTGCTGCACAATTTAAACC
1 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAACT
21278 CGCACACTTAG
1 CGCACACTTAG
21289 CGCCAATCTC
Statistics
Matches: 110, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 94 0.85
56 16 0.15
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.25
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAACT
Found at i:21758 original size:12 final size:12
Alignment explanation
Indices: 21741--21766 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
21731 ATGGCATACT
21741 TATGTATATATA
1 TATGTATATATA
21753 TATGTATATATA
1 TATGTATATATA
21765 TA
1 TA
21767 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:29434 original size:28 final size:28
Alignment explanation
Indices: 29368--29520 Score: 229
Period size: 28 Copynumber: 5.5 Consensus size: 28
29358 ATATTAAGTC
* * *
29368 CGCACACTCAGTGCTATATAATC-AGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29395 CGCACACCTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
29423 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
29451 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
29479 CGCACACTTAGTGCTACATAGTC-AATT
1 CGCACACTTAGTGCTACATAATCAAACT
29506 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29521 GCACAATTTA
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 38 0.33
28 78 0.67
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:29509 original size:83 final size:83
Alignment explanation
Indices: 29368--29520 Score: 236
Period size: 83 Copynumber: 1.8 Consensus size: 83
29358 ATATTAAGTC
* *
29368 CGCACACTCAGTGCTATATAATCAGCTCGCACACCTAGTGCTACATAATCAAACTCGCACACTTA
1 CGCACACTCAGTGCTACATAATCAACTCGCACACCTAGTGCTACATAATCAAACTCGCACACTTA
29433 GTGCTACATAGTCAAACT
66 GTGCTACATAGTCAAACT
* * * *
29451 CGCACACTTAGTGCTACATAATCAAACTCGCACACTTAGTGCTACATAGTC-AATTCGCACACTT
1 CGCACACTCAGTGCTACATAATC-AACTCGCACACCTAGTGCTACATAATCAAACTCGCACACTT
29515 AGTGCT
65 AGTGCT
29521 GCACAATTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 39 0.62
84 24 0.38
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.25
Consensus pattern (83 bp):
CGCACACTCAGTGCTACATAATCAACTCGCACACCTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAAACT
Found at i:29539 original size:56 final size:55
Alignment explanation
Indices: 29367--29541 Score: 233
Period size: 56 Copynumber: 3.1 Consensus size: 55
29357 CATATTAAGT
* * * * *
29367 CCGCACACTCAGTGCTATATAATCAGCTCGCACACCTAGTGCTACATAATCAAAC
1 CCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAAC
*
29422 TCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAATCAAAC
1 CCGCACACTTAGTGCTACATAGTC-AACTCGCACACTTAGTGCTACATAATCAAAC
* * * * *
29478 TCGCACACTTAGTGCTACATAGTCAATTCGCACACTTAGTGCTGCACAATTTAAAC
1 CCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAA-TCAAAC
29534 CCGCACAC
1 CCGCACAC
29542 GTAGCGCCAA
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
55 42 0.39
56 65 0.61
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (55 bp):
CCGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCTACATAATCAAAC
Found at i:37608 original size:28 final size:27
Alignment explanation
Indices: 37542--37638 Score: 131
Period size: 27 Copynumber: 3.6 Consensus size: 27
37532 ATATTAAGTC
* * *
37542 CGCACACTCAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTACATAATCAACT
*
37569 CGCACACCTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
* *
37597 CGCACACTTAGTGCTACATAGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
37624 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
37639 GCACAATTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
27 38 0.61
28 24 0.39
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:42313 original size:26 final size:28
Alignment explanation
Indices: 42284--42340 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
42274 CACTCCCTCA
42284 CTTTTTCCTT-TCTTTTT-ATCGTTTTT
1 CTTTTTCCTTCTCTTTTTAATCGTTTTT
* *
42310 C-TTTTCTTTCTCTTTTTCAATCTTTTTT
1 CTTTTTCCTTCTCTTTTT-AATCGTTTTT
42338 CTT
1 CTT
42341 GTACTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
25 7 0.28
26 8 0.32
28 9 0.36
29 1 0.04
ACGTcount: A:0.05, C:0.21, G:0.02, T:0.72
Consensus pattern (28 bp):
CTTTTTCCTTCTCTTTTTAATCGTTTTT
Found at i:45568 original size:12 final size:10
Alignment explanation
Indices: 45541--45572 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
45531 ATTTATTAAC
45541 AAACACATTA
1 AAACACATTA
45551 AAACACATTA
1 AAACACATTA
*
45561 AAACACACTA
1 AAACACATTA
45571 AA
1 AA
45573 TAAGCGTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (10 bp):
AAACACATTA
Found at i:56110 original size:20 final size:20
Alignment explanation
Indices: 56085--56127 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
56075 ACATTTGATC
56085 GATGAATGACAAAGGGAAAT
1 GATGAATGACAAAGGGAAAT
56105 GATGAATGACAAAGGGAAAT
1 GATGAATGACAAAGGGAAAT
56125 GAT
1 GAT
56128 CCTTCCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.49, C:0.05, G:0.30, T:0.16
Consensus pattern (20 bp):
GATGAATGACAAAGGGAAAT
Found at i:60480 original size:27 final size:27
Alignment explanation
Indices: 60450--60627 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
60440 ATATTGAGCC
* *
60450 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
60477 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
60504 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
60532 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
60559 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
60586 CGCACACTTAGTGCAACATAGTCAAAC-
1 CGCACACTTAGTGCTACATAATC-AACT
60613 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
60628 GTACAATTTA
Statistics
Matches: 128, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 103 0.80
28 25 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:60589 original size:82 final size:81
Alignment explanation
Indices: 60471--60626 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
60461 TGCTATATAA
* *
60471 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAAC-CGCA
60536 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
60553 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAACCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCA
60617 CACTTAGTGC
65 CACTTAGTGC
60627 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.78
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAACCGCAC
ACTTAGTGCCGCATGG
Found at i:63185 original size:20 final size:22
Alignment explanation
Indices: 63147--63186 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
63137 ATGCAATATT
63147 TAAAATGCTAACTAAAATGTCC
1 TAAAATGCTAACTAAAATGTCC
63169 TAAAATGC-AAC-AAAATGT
1 TAAAATGCTAACTAAAATGT
63187 ACTTGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (22 bp):
TAAAATGCTAACTAAAATGTCC
Found at i:67812 original size:80 final size:80
Alignment explanation
Indices: 66889--67799 Score: 1732
Period size: 80 Copynumber: 11.4 Consensus size: 80
66879 CGGAATTTAG
* * * * * * * *
66889 CCGGATATAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
*
66954 CCTTCGGGTCTTAGC
66 CCTTCGGGTCTTGGC
66969 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67034 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67049 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67114 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67129 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67194 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67209 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67274 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67289 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67354 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67369 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67434 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67449 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67514 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67529 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67594 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67609 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
67674 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67689 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
*
67754 CCTTTGGGTCTTGGC
66 CCTTCGGGTCTTGGC
67769 CCGGATAAAATCACTAGCACAATTGCCTTCG
1 CCGGATAAAATCACTAGCACAATTGCCTTCG
67800 AGACTTAGCC
Statistics
Matches: 821, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 821 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (80 bp):
CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
CCTTCGGGTCTTGGC
Found at i:75571 original size:15 final size:15
Alignment explanation
Indices: 75551--75580 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
75541 TAGTCGATTG
75551 AACGAATACTATTAA
1 AACGAATACTATTAA
75566 AACGAATACTATTAA
1 AACGAATACTATTAA
75581 TTGAATGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
AACGAATACTATTAA
Found at i:75762 original size:80 final size:80
Alignment explanation
Indices: 75639--76562 Score: 1749
Period size: 80 Copynumber: 11.6 Consensus size: 80
75629 CGGAATTTAG
* * * * * * * *
75639 CCGGATATAACCACAAGCACAAATGCCCTCGGGTCTTAGCCCGGATATATCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
*
75704 CCTTCGGGTCTTAGC
66 CCTTCGGGTCTTGGC
75719 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
75784 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
75799 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
75864 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
75879 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
75944 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
75959 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76024 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
76039 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76104 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
76119 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76184 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
76199 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76264 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
76279 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76344 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
76359 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76424 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
76439 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
76504 CCTTCGGGTCTTGGC
66 CCTTCGGGTCTTGGC
* *
76519 CCGGATAAAATCACTAGCACAATTGCCTTCGGGACTTAGCCCGG
1 CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGG
76563 ATATCATTCA
Statistics
Matches: 833, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 833 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (80 bp):
CCGGATAAAATCACTAGCACAATTGCCTTCGGGTCTTATCCCGGGTATAGCAACTCGCACAAATG
CCTTCGGGTCTTGGC
Found at i:84703 original size:30 final size:30
Alignment explanation
Indices: 84667--84738 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
84657 CAAAAATAAT
84667 AAAATTAAATATAAAAATAAACAAAAACTG
1 AAAATTAAATATAAAAATAAACAAAAACTG
84697 AAAATTAAATATAAAAATAAACAAAAACTG
1 AAAATTAAATATAAAAATAAACAAAAACTG
84727 AAAATTAAATAT
1 AAAATTAAATAT
84739 CTTCACAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (30 bp):
AAAATTAAATATAAAAATAAACAAAAACTG
Found at i:92364 original size:20 final size:22
Alignment explanation
Indices: 92293--92387 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 22
92283 AAAGATTTTG
**
92293 GTAGTTTATCTGTA-ATTT-TA
1 GTAGTTTATCTACATATTTCTA
* * *
92313 GTGGTTTATCCACATATTTCTT
1 GTAGTTTATCTACATATTTCTA
* *
92335 GCACTTTATCTACA-ATTT-TA
1 GTAGTTTATCTACATATTTCTA
* * *
92355 GTGGTTTATCAACATATTTCTG
1 GTAGTTTATCTACATATTTCTA
92377 GTAGTTTATCT
1 GTAGTTTATCT
92388 GCAAATACTG
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
20 21 0.39
21 12 0.22
22 21 0.39
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (22 bp):
GTAGTTTATCTACATATTTCTA
Found at i:92384 original size:22 final size:22
Alignment explanation
Indices: 92307--92386 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 22
92297 TTTATCTGTA
* *
92307 ATTT-TAGTGGTTTATCCACAT
1 ATTTCTAGTAGTTTATCAACAT
* * * *
92328 ATTTCTTGCACTTTATCTACA-
1 ATTTCTAGTAGTTTATCAACAT
*
92349 ATTT-TAGTGGTTTATCAACAT
1 ATTTCTAGTAGTTTATCAACAT
*
92370 ATTTCTGGTAGTTTATC
1 ATTTCTAGTAGTTTATC
92387 TGCAAATACT
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
20 11 0.25
21 12 0.27
22 21 0.48
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.49
Consensus pattern (22 bp):
ATTTCTAGTAGTTTATCAACAT
Found at i:92385 original size:42 final size:42
Alignment explanation
Indices: 92287--92387 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
92277 AAGGAGAAAG
** *
92287 ATTT-TGGTAGTTTATCTGTAATTTTAGTGGTTTATCCACAT
1 ATTTCTGGTAGTTTATCTACAATTTTAGTGGTTTATCAACAT
* * *
92328 ATTTCTTGCACTTTATCTACAATTTTAGTGGTTTATCAACAT
1 ATTTCTGGTAGTTTATCTACAATTTTAGTGGTTTATCAACAT
92370 ATTTCTGGTAGTTTATCT
1 ATTTCTGGTAGTTTATCT
92388 GCAAATACTG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 4 0.08
42 46 0.92
ACGTcount: A:0.23, C:0.13, G:0.14, T:0.50
Consensus pattern (42 bp):
ATTTCTGGTAGTTTATCTACAATTTTAGTGGTTTATCAACAT
Found at i:97092 original size:38 final size:38
Alignment explanation
Indices: 97038--97110 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
97028 CTCCTCGTCA
**
97038 ATCAACTAGTTGCCATCCCAACAGGATCTTCCGATTCC
1 ATCAACTAGTCACCATCCCAACAGGATCTTCCGATTCC
*
97076 ATCAACTAGTCACCATCCCAACAGGATCTTGCGAT
1 ATCAACTAGTCACCATCCCAACAGGATCTTCCGAT
97111 CTTCCACTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.25
Consensus pattern (38 bp):
ATCAACTAGTCACCATCCCAACAGGATCTTCCGATTCC
Found at i:105798 original size:46 final size:46
Alignment explanation
Indices: 105746--105840 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
105736 ACAAAGATAG
105746 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
*
105792 AAACCAAAATATTATCTCCTAAACTTTAGGATCTAATCTCCTAATT
1 AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
105838 AAA
1 AAA
105841 AGAAAAGAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (46 bp):
AAACCAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:113728 original size:17 final size:17
Alignment explanation
Indices: 113708--113741 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
113698 GATGACAAAT
113708 TGTTGTCATTGACATAG
1 TGTTGTCATTGACATAG
113725 TGTTGTCATTGACATAG
1 TGTTGTCATTGACATAG
113742 AGATGTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.41
Consensus pattern (17 bp):
TGTTGTCATTGACATAG
Found at i:113748 original size:17 final size:17
Alignment explanation
Indices: 113711--113749 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
113701 GACAAATTGT
* *
113711 TGTCATTGACATAGTGT
1 TGTCATTGACATAGAGA
113728 TGTCATTGACATAGAGA
1 TGTCATTGACATAGAGA
113745 TGTCA
1 TGTCA
113750 AAATCAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (17 bp):
TGTCATTGACATAGAGA
Found at i:121977 original size:20 final size:20
Alignment explanation
Indices: 121954--121994 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
121944 TCCAATAAGA
*
121954 TCATTTGAGCTCAATTTAGC
1 TCATTCGAGCTCAATTTAGC
121974 TCATTCGAGCTCAATTTAGC
1 TCATTCGAGCTCAATTTAGC
121994 T
1 T
121995 TTCTATCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (20 bp):
TCATTCGAGCTCAATTTAGC
Found at i:131153 original size:30 final size:30
Alignment explanation
Indices: 131097--131153 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
131087 CTAAGCAAAT
**
131097 TTAGCTGATGATAGCGAATCGGTTAAGTGA
1 TTAGCTGATGATAGCGAATCAATTAAGTGA
*
131127 TTAGTTGATGATAGCGAATCAATTAAG
1 TTAGCTGATGATAGCGAATCAATTAAG
131154 CATATATGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (30 bp):
TTAGCTGATGATAGCGAATCAATTAAGTGA
Found at i:133486 original size:17 final size:17
Alignment explanation
Indices: 133464--133515 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
133454 AGCTGATTGA
*
133464 TGACAAATTGTTGTCAT
1 TGACAAAGTGTTGTCAT
133481 TGACAAAGTGTTGTCAT
1 TGACAAAGTGTTGTCAT
*
133498 TGACATAGTGTTGTCAT
1 TGACAAAGTGTTGTCAT
133515 T
1 T
133516 AACATAGGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (17 bp):
TGACAAAGTGTTGTCAT
Found at i:133520 original size:17 final size:17
Alignment explanation
Indices: 133472--133522 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
133462 GATGACAAAT
*
133472 TGTTGTCATTGACAAAG
1 TGTTGTCATTGACATAG
133489 TGTTGTCATTGACATAG
1 TGTTGTCATTGACATAG
*
133506 TGTTGTCATTAACATAG
1 TGTTGTCATTGACATAG
133523 GGATGTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (17 bp):
TGTTGTCATTGACATAG
Found at i:133529 original size:17 final size:17
Alignment explanation
Indices: 133492--133530 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
133482 GACAAAGTGT
* * *
133492 TGTCATTGACATAGTGT
1 TGTCATTAACATAGGGA
133509 TGTCATTAACATAGGGA
1 TGTCATTAACATAGGGA
133526 TGTCA
1 TGTCA
133531 AAATCAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (17 bp):
TGTCATTAACATAGGGA
Found at i:137750 original size:25 final size:26
Alignment explanation
Indices: 137720--137768 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
137710 AGCCCAATGA
* *
137720 TCCCATT-GAATTCCTTTGGCCAAAT
1 TCCCATTAAAATTCCTTTGCCCAAAT
137745 TCCCATTAAAATTCCTTTGCCCAA
1 TCCCATTAAAATTCCTTTGCCCAA
137769 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.35
Consensus pattern (26 bp):
TCCCATTAAAATTCCTTTGCCCAAAT
Found at i:137770 original size:25 final size:25
Alignment explanation
Indices: 137711--137770 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 25
137701 TAAGAATTCA
*
137711 GCCCAATGATCCCATTGAATTCCTTTG
1 GCCCAAT--TCCCATTAAATTCCTTTG
*
137738 GCCAAATTCCCATTAAAATTCCTTT-
1 GCCCAATTCCCATT-AAATTCCTTTG
137763 GCCCAATT
1 GCCCAATT
137771 TTTTATTTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 14 0.48
26 9 0.31
27 6 0.21
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (25 bp):
GCCCAATTCCCATTAAATTCCTTTG
Found at i:146375 original size:27 final size:27
Alignment explanation
Indices: 146341--146406 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
146331 CGTAAAGGTT
* *
146341 GTAAAATTATTGGAATACCATCGAAGG
1 GTAAAATTATCGAAATACCATCGAAGG
*
146368 GTAAAATTATCGAAATACCCTCGAAGG
1 GTAAAATTATCGAAATACCATCGAAGG
*
146395 GTAAAATGATCG
1 GTAAAATTATCG
146407 TGATGCCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (27 bp):
GTAAAATTATCGAAATACCATCGAAGG
Found at i:146422 original size:27 final size:27
Alignment explanation
Indices: 146392--146616 Score: 251
Period size: 27 Copynumber: 8.5 Consensus size: 27
146382 ATACCCTCGA
* * *
146392 AGGGTAAAATGATCGTGATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTGT
* *
146419 AGGGTAAAATGACCGTGATGCCCTTGT
1 AGGGTAAAATGACCGTAATGCCCCTGT
* * * *
146446 AAGGTAAAATGATCGTAATTCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCCTGT
*
146473 AGGGTAAAATGACCGTAATG-CCCTTT
1 AGGGTAAAATGACCGTAATGCCCCTGT
*
146499 ATGGTAAAAT-ACCGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTGT
* * *
146525 AGGATACAATGACCGTAATG--CCTCT
1 AGGGTAAAATGACCGTAATGCCCCTGT
* *
146550 AGGGTAAAATAACCGTAGTGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCCTGT
* * *
146577 AGGGTAAAATGAACGTAATTCCCTTGT
1 AGGGTAAAATGACCGTAATGCCCCTGT
146604 AGGGTAAAATGAC
1 AGGGTAAAATGAC
146617 TATTTTGTCT
Statistics
Matches: 164, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
25 29 0.18
26 26 0.16
27 109 0.66
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (27 bp):
AGGGTAAAATGACCGTAATGCCCCTGT
Found at i:146537 original size:52 final size:54
Alignment explanation
Indices: 146365--146616 Score: 278
Period size: 54 Copynumber: 4.7 Consensus size: 54
146355 ATACCATCGA
* * * * * * * *
146365 AGGGTAAAATTATCGAAATACCCTCGAAGGGTAAAATGATCGTGATGCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTAT
* * * *
146419 AGGGTAAAATGACCGTGATGCCCTTGTAAGGTAAAATGATCGTAATTCCCCTAT
1 AGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTAT
* *
146473 AGGGTAAAATGACCGTAATGCCCTT-TATGGTAAAAT-ACCGTAATGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTAT
* * * * * *
146525 AGGATACAATGACCGTAATG-CC-TCTAGGGTAAAATAACCGTAGTGCCCCTGT
1 AGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTAT
* *
146577 AGGGTAAAATGAACGTAATTCCCTTGTAGGGTAAAATGAC
1 AGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGAC
146617 TATTTTGTCT
Statistics
Matches: 169, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.01
51 12 0.07
52 62 0.37
53 12 0.07
54 82 0.49
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (54 bp):
AGGGTAAAATGACCGTAATGCCCTTGTAGGGTAAAATGACCGTAATGCCCCTAT
Found at i:146698 original size:24 final size:24
Alignment explanation
Indices: 146634--146791 Score: 190
Period size: 24 Copynumber: 6.6 Consensus size: 24
146624 TCTCTCGTGG
* *
146634 TTAAATGATTGATTTGCCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
* * * * * *
146658 GTAAATAAATGACTTGTCCGAGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
146682 GTAAATGACTGATTTGTCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
* *
146706 TTAAATGACTAATTTGTTTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
146730 TTAAATGACTGATTTATCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
146754 TTAAATGACTGATTTATCTGTGAT
1 TTAAATGACTGATTTGTCTGTGAT
*
146778 TTATATGACTGATT
1 TTAAATGACTGATT
146792 CTGTGCATGG
Statistics
Matches: 115, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 115 1.00
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (24 bp):
TTAAATGACTGATTTGTCTGTGAT
Found at i:146744 original size:13 final size:13
Alignment explanation
Indices: 146726--146791 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
146716 AATTTGTTTG
*
146726 TGATTTAAATGAC
1 TGATTTATATGAC
*
146739 TGATTTATCTG--
1 TGATTTATATGAC
*
146750 TGATTTAAATGAC
1 TGATTTATATGAC
*
146763 TGATTTATCTG--
1 TGATTTATATGAC
146774 TGATTTATATGAC
1 TGATTTATATGAC
146787 TGATT
1 TGATT
146792 CTGTGCATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 19 0.45
13 23 0.55
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.47
Consensus pattern (13 bp):
TGATTTATATGAC
Found at i:146755 original size:11 final size:11
Alignment explanation
Indices: 146739--146781 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
146729 TTTAAATGAC
146739 TGATTTATCTG
1 TGATTTATCTG
**
146750 TGATTTAAATG
1 TGATTTATCTG
146761 ACTGATTTATCTG
1 --TGATTTATCTG
146774 TGATTTAT
1 TGATTTAT
146782 ATGACTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 17 0.65
13 9 0.35
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (11 bp):
TGATTTATCTG
Found at i:146903 original size:27 final size:27
Alignment explanation
Indices: 146860--146919 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
146850 GGAAGTACTG
146860 TACTGGTGGCTCTGCCACA-ATCACTAT
1 TACTGGTGGCTCTGCCACATAT-ACTAT
*
146887 TACTGGTGGCT-TGGCCACATATACTGT
1 TACTGGTGGCTCT-GCCACATATACTAT
146914 TACTGG
1 TACTGG
146920 CAGCTTTGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 1 0.03
27 27 0.90
28 2 0.07
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACATATACTAT
Found at i:146925 original size:27 final size:27
Alignment explanation
Indices: 146873--146925 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
146863 TGGTGGCTCT
**
146873 GCCACAATCACTATTACTGGTGGCTTG
1 GCCACAATCACTATTACTGGCAGCTTG
*
146900 GCCACATAT-ACTGTTACTGGCAGCTT
1 GCCACA-ATCACTATTACTGGCAGCTT
146926 TGCTGCGATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (27 bp):
GCCACAATCACTATTACTGGCAGCTTG
Found at i:146985 original size:32 final size:32
Alignment explanation
Indices: 146940--147060 Score: 172
Period size: 32 Copynumber: 3.8 Consensus size: 32
146930 GCGATGCTAT
* *
146940 TGATGGCTTTGTGCCGATCATATTACCATTAT
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
*
146972 TGATGG-TTGTGTGCCGATCATATTACTACTAC
1 TGATGGCTT-TGTGCCGATCATATTACTATTAC
*
147004 TGATGGCTTTGTGCCGATCATACTACTATTAC
1 TGATGGCTTTGTGCCGATCATATTACTATTAC
* *
147036 TGATGGCTTTATGCCAATCATATTA
1 TGATGGCTTTGTGCCGATCATATTA
147061 TTGTACTTAT
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
31 2 0.03
32 75 0.95
33 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACTATTAC
Found at i:153214 original size:9 final size:9
Alignment explanation
Indices: 153195--153252 Score: 80
Period size: 9 Copynumber: 6.4 Consensus size: 9
153185 AAATTAATCA
*
153195 AATTAATCG
1 AATTAACCG
*
153204 AATTACCCG
1 AATTAACCG
153213 AATTAACCG
1 AATTAACCG
*
153222 AATTAACTG
1 AATTAACCG
*
153231 AATTACCCG
1 AATTAACCG
153240 AATTAACCG
1 AATTAACCG
153249 AATT
1 AATT
153253 GAATCACTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:153218 original size:27 final size:27
Alignment explanation
Indices: 153186--153252 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
153176 TTTGATTAAA
*
153186 AATTAATCAAATTAA-TCGAATTACCCG
1 AATTAACCAAATTAACT-GAATTACCCG
*
153213 AATTAACCGAATTAACTGAATTACCCG
1 AATTAACCAAATTAACTGAATTACCCG
*
153240 AATTAACCGAATT
1 AATTAACCAAATT
153253 GAATCACTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 36 0.97
28 1 0.03
ACGTcount: A:0.43, C:0.19, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTAACCAAATTAACTGAATTACCCG
Found at i:166343 original size:50 final size:49
Alignment explanation
Indices: 166284--166421 Score: 136
Period size: 47 Copynumber: 2.8 Consensus size: 49
166274 CGAAACACCT
* * * * *
166284 TTTGTGGACAAGCCACCATTGATTTTTAGATAAATTGCCACTAATAACAC
1 TTTGGGGACAAGCCACCA-TAATTTATAGATAAACTGCCACTAACAACAC
* * * * * *
166334 TTTGGGGACAAGCCGCCA-CATATGTAGATATACTGCCA-TTACAACAC
1 TTTGGGGACAAGCCACCATAATTTATAGATAAACTGCCACTAACAACAC
*
166381 TTTGGGGACAAGCCACCACTAATTTACAGATAAACTGCCAC
1 TTTGGGGACAAGCCACCA-TAATTTATAGATAAACTGCCAC
166422 ATACTTCCAC
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
47 24 0.34
48 15 0.21
49 15 0.21
50 16 0.23
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (49 bp):
TTTGGGGACAAGCCACCATAATTTATAGATAAACTGCCACTAACAACAC
Found at i:168925 original size:20 final size:19
Alignment explanation
Indices: 168869--168925 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
168859 TTTACTTTTC
*
168869 AAAAATTTATAAAAAAACTA
1 AAAAATATA-AAAAAAACTA
* * *
168889 AAGAATATATAATAAACTTA
1 AAAAATATAAAAAAAAC-TA
168909 AAAAATATAAAAAAAAC
1 AAAAATATAAAAAAAAC
168926 CTCAAAACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATATAAAAAAAACTA
Found at i:168932 original size:20 final size:20
Alignment explanation
Indices: 168867--168932 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
168857 TCTTTACTTT
*
168867 TCAAAAATTTATAAAAAAA-C
1 TCAAAAATATA-AAAAAAACC
* * *
168887 T-AAAGAATATATAATAAACT
1 TCAAA-AATATAAAAAAAACC
*
168907 TAAAAAATATAAAAAAAACC
1 TCAAAAATATAAAAAAAACC
168927 TCAAAA
1 TCAAAA
168933 CCCTACAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 8 0.23
20 24 0.69
21 3 0.09
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.23
Consensus pattern (20 bp):
TCAAAAATATAAAAAAAACC
Found at i:171254 original size:26 final size:26
Alignment explanation
Indices: 171225--171277 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
171215 TGTTGTTATA
171225 GGCCTCAGTAAGATGTTTGATTAAGT
1 GGCCTCAGTAAGATGTTTGATTAAGT
171251 GGCCTCAGTAAGATGTTTGATTAAGT
1 GGCCTCAGTAAGATGTTTGATTAAGT
171277 G
1 G
171278 AAACCATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.11, G:0.28, T:0.34
Consensus pattern (26 bp):
GGCCTCAGTAAGATGTTTGATTAAGT
Found at i:175785 original size:10 final size:9
Alignment explanation
Indices: 175741--175791 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
175731 TAAAAAGACC
175741 AAAAAATAT
1 AAAAAATAT
* *
175750 AAAAATTTT
1 AAAAAATAT
*
175759 GAAAAAT-T
1 AAAAAATAT
175767 CAAAAAATAT
1 -AAAAAATAT
175777 AAAAGAATAT
1 AAAA-AATAT
175787 AAAAA
1 AAAAA
175792 TTTATAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
8 1 0.03
9 23 0.68
10 10 0.29
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (9 bp):
AAAAAATAT
Found at i:175790 original size:27 final size:27
Alignment explanation
Indices: 175740--175793 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
175730 TTAAAAAGAC
* *
175740 CAAAAAATATAAAAATTTTGAAAAATT
1 CAAAAAATATAAAAAATATGAAAAATT
175767 CAAAAAATATAAAAGAATAT-AAAAATT
1 CAAAAAATATAAAA-AATATGAAAAATT
175794 TATAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (27 bp):
CAAAAAATATAAAAAATATGAAAAATT
Found at i:176648 original size:16 final size:15
Alignment explanation
Indices: 176627--176678 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
176617 TTTTTTGAGA
*
176627 ATTTTAAAATTTTTG
1 ATTTTAAAATTTATG
*
176642 TATTTTACAATTTATG
1 -ATTTTAAAATTTATG
* *
176658 AATTTAAAATGTTAGG
1 ATTTTAAAAT-TTATG
176674 ATTTT
1 ATTTT
176679 TAATTGCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 8 0.28
16 21 0.72
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.54
Consensus pattern (15 bp):
ATTTTAAAATTTATG
Found at i:178170 original size:32 final size:31
Alignment explanation
Indices: 178125--178220 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
178115 CTTAGATAAT
178125 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
178156 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
178188 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
178219 TT
1 TT
178221 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:178801 original size:43 final size:44
Alignment explanation
Indices: 178733--178854 Score: 180
Period size: 47 Copynumber: 2.8 Consensus size: 44
178723 AATTAGTTAA
178733 TAAAAAAAAAGC-AACAAGCGC-AAAAAAAAGTTGAGAAAAATC-
1 TAAAAAAAAAGCAAAC-AGCGCAAAAAAAAAGTTGAGAAAAATCT
178775 T-AAAAAAAAGCAAACAGCGCAAAAAAAAGAGTTGAGAAAAATCTT
1 TAAAAAAAAAGCAAACAGCGCAAAAAAAA-AGTTGAGAAAAATC-T
178820 TAAAAAAAAAAGCAAACAGCGCAAAAAAAAAGTTG
1 T-AAAAAAAAAGCAAACAGCGCAAAAAAAAAGTTG
178855 CCTACCTCTC
Statistics
Matches: 73, Mismatches: 0, Indels: 10
0.88 0.00 0.12
Matches are distributed among these distances:
41 15 0.21
42 11 0.15
43 14 0.19
45 1 0.01
46 5 0.07
47 27 0.37
ACGTcount: A:0.63, C:0.11, G:0.15, T:0.11
Consensus pattern (44 bp):
TAAAAAAAAAGCAAACAGCGCAAAAAAAAAGTTGAGAAAAATCT
Found at i:184428 original size:32 final size:31
Alignment explanation
Indices: 184383--184478 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
184373 CTTAGATAAT
184383 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
184414 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
* *
184446 TTGAAAGAGTTTTAATAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
184477 TT
1 TT
184479 GTAATTTGCC
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 32 0.52
32 30 0.48
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:184828 original size:4 final size:4
Alignment explanation
Indices: 184782--184812 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
184772 ATCTATCCTT
184782 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
184813 ACTAATTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:192521 original size:91 final size:91
Alignment explanation
Indices: 192366--192549 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
192356 ACAACATGAA
192366 AAGATTGTTAAAACCCTTTTAAAAGACAACTCAAGAACAATTCTTGAAACAAAAACTCAAAGAGA
1 AAGATTGTTAAAACCCTTTTAAAAGACAACTCAAGAACAATTCTTGAAACAAAAACTCAAAGAGA
192431 ATTTATTAACTCAAAAGAGAATTGTT
66 ATTTATTAACTCAAAAGAGAATTGTT
192457 AAGATTGTTAAAACCCTTTTAAAAGACAACTCAAGAACAATTCTTGAAACAAAAACTCAAAGAGA
1 AAGATTGTTAAAACCCTTTTAAAAGACAACTCAAGAACAATTCTTGAAACAAAAACTCAAAGAGA
192522 ATTTATTAACTCAAAAGAGAATTGTT
66 ATTTATTAACTCAAAAGAGAATTGTT
192548 AA
1 AA
192550 ATAATAATGA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (91 bp):
AAGATTGTTAAAACCCTTTTAAAAGACAACTCAAGAACAATTCTTGAAACAAAAACTCAAAGAGA
ATTTATTAACTCAAAAGAGAATTGTT
Found at i:194345 original size:28 final size:29
Alignment explanation
Indices: 194312--194391 Score: 99
Period size: 28 Copynumber: 2.8 Consensus size: 29
194302 TCAAAGATTG
* *
194312 CCACAAAGGCTTCCATTTAATAGAGG-CA
1 CCACAAAGGCTTCCATTTAACAAAGGTCA
*
194340 CCACAAAGGCTTCCATTTAACAAAGGTCG
1 CCACAAAGGCTTCCATTTAACAAAGGTCA
* *
194369 CCATAAAGACTTCCATTTTAACA
1 CCACAAAGGCTTCCA-TTTAACA
194392 GAGATCGCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 24 0.53
29 14 0.31
30 7 0.16
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (29 bp):
CCACAAAGGCTTCCATTTAACAAAGGTCA
Found at i:194487 original size:29 final size:30
Alignment explanation
Indices: 194454--194524 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
194444 TACGAAAATT
*
194454 GCCACAAAGGCATTTA-TTTAA-TAGAGATA
1 GCCACAAAGGCATTCACTTTAACTA-AGATA
*
194483 GCCACTAAGGC--TCACTTTTAACTAAGATA
1 GCCACAAAGGCATTCAC-TTTAACTAAGATA
194512 GCCACAAAGGCAT
1 GCCACAAAGGCAT
194525 CCTTTTACGA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
27 2 0.06
29 30 0.88
30 2 0.06
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (30 bp):
GCCACAAAGGCATTCACTTTAACTAAGATA
Found at i:194529 original size:29 final size:29
Alignment explanation
Indices: 194258--194531 Score: 96
Period size: 30 Copynumber: 9.5 Consensus size: 29
194248 AGTGTTACCA
* * * *
194258 AAAGGCATCCTTCT-ATAGAGAGAACCAT
1 AAAGGCATCCTTTTAATAGAGATAGCCAC
* * * *
194286 AAAGGCATTCTTTTTATCAAAGATTGCCAC
1 AAAGGCATCCTTTTAAT-AGAGATAGCCAC
* * **
194316 AAAGGCTTCCATTTAATAGAGGCA-CCAC
1 AAAGGCATCCTTTTAATAGAGATAGCCAC
* * * * * * *
194344 AAAGGCTTCCATTTAACAAAGGTCGCCAT
1 AAAGGCATCCTTTTAATAGAGATAGCCAC
* * * * **
194373 AAAGACTTCCATTTTAACAGAGATCGCTGC
1 AAAGGCATCC-TTTTAATAGAGATAGCCAC
** * * *
194403 AAAGGCTATTATTTTAATAGAGTTTGCCAT
1 AAAGGC-ATCCTTTTAATAGAGATAGCCAC
* * ** * *
194433 AACGGC-T-TTTTTACGA-AAATTGCCAC
1 AAAGGCATCCTTTTAATAGAGATAGCCAC
*
194459 AAAGGCAT-TTATTTAATAGAGATAGCCAC
1 AAAGGCATCCT-TTTAATAGAGATAGCCAC
*
194488 TAAGGC-TCACTTTTAACTA-AGATAGCCAC
1 AAAGGCATC-CTTTTAA-TAGAGATAGCCAC
194517 AAAGGCATCCTTTTA
1 AAAGGCATCCTTTTA
194532 CGAAAATTGT
Statistics
Matches: 182, Mismatches: 52, Indels: 23
0.71 0.20 0.09
Matches are distributed among these distances:
26 12 0.07
27 9 0.05
28 43 0.24
29 56 0.31
30 61 0.34
31 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (29 bp):
AAAGGCATCCTTTTAATAGAGATAGCCAC
Found at i:202579 original size:23 final size:23
Alignment explanation
Indices: 202543--202589 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
202533 CAACAAAAGC
202543 ATATTTTTATAAAAAAAGTAAAA
1 ATATTTTTATAAAAAAAGTAAAA
*
202566 ATATTTCTTA-AAAAAGAGTAAAA
1 ATATTT-TTATAAAAAAAGTAAAA
202589 A
1 A
202590 CATATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (23 bp):
ATATTTTTATAAAAAAAGTAAAA
Found at i:210150 original size:15 final size:15
Alignment explanation
Indices: 210097--210153 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
210087 TTAATAAGAT
*
210097 TTAATATTAAATTTAA
1 TTAATATTATA-TTAA
* *
210113 TCTAATATTTATCTTGA
1 T-TAATA-TTATATTAA
*
210130 TAAATATTATATTAA
1 TTAATATTATATTAA
210145 TTAATATTA
1 TTAATATTA
210154 AAGTTGTAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
15 15 0.47
16 5 0.16
17 9 0.28
18 3 0.09
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (15 bp):
TTAATATTATATTAA
Found at i:213632 original size:25 final size:26
Alignment explanation
Indices: 213582--213633 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
213572 AGTTTTAGAG
213582 AGAAAATTTTCTAAAGAGATTATTCT
1 AGAAAATTTTCTAAAGAGATTATTCT
* * *
213608 AGAAAA-TTTCTAGAGATATTTTTCT
1 AGAAAATTTTCTAAAGAGATTATTCT
213633 A
1 A
213634 ATTTACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (26 bp):
AGAAAATTTTCTAAAGAGATTATTCT
Found at i:215652 original size:58 final size:58
Alignment explanation
Indices: 215585--215699 Score: 185
Period size: 58 Copynumber: 2.0 Consensus size: 58
215575 GAATATTAAA
* * *
215585 TAAGATAAATTTTCTATTATAGATCAAGAAGAATGAAATTCGGAGTTAGACTAGGGAG
1 TAAGATAAATTTGCTATTATAGATCAAGAAGAATGAAATTCAGAGTTAGACCAGGGAG
* *
215643 TAAGCTAAATTTGCTATTATAGATTAAGAAGAATGAAATTCAGAGTTAGACCAGGGA
1 TAAGATAAATTTGCTATTATAGATCAAGAAGAATGAAATTCAGAGTTAGACCAGGGA
215700 AAGAAAAAGA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.29
Consensus pattern (58 bp):
TAAGATAAATTTGCTATTATAGATCAAGAAGAATGAAATTCAGAGTTAGACCAGGGAG
Found at i:216020 original size:50 final size:50
Alignment explanation
Indices: 215961--216104 Score: 155
Period size: 50 Copynumber: 2.9 Consensus size: 50
215951 CATTGAGATT
* * *
215961 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGAG
*** * *
216011 ATGAGAGGTCCCCCATAAGACCATGTCTTGGACATGACATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGAG
* * * * * *
216061 ATGAGA-CTCCTATGTAAGACCATATCTAGGATATGACATTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCA
216105 GTATAGAAAA
Statistics
Matches: 77, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
49 29 0.38
50 48 0.62
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGACATGGGCACCGAG
Found at i:220723 original size:12 final size:12
Alignment explanation
Indices: 220706--220730 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
220696 AGTTTACGAA
220706 AACTCAGTGTGT
1 AACTCAGTGTGT
220718 AACTCAGTGTGT
1 AACTCAGTGTGT
220730 A
1 A
220731 CTGGCCCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (12 bp):
AACTCAGTGTGT
Found at i:221126 original size:27 final size:27
Alignment explanation
Indices: 221092--221157 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
221082 TAGAGCATAT
221092 AGTCATTTTATAACATAGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
** **
221119 AGTCATTTTACCATGTAGGGGCATAAC
1 AGTCATTTTATAACATAGGGGCATAAC
221146 AGTCATTTTATA
1 AGTCATTTTATA
221158 TTAGTTTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (27 bp):
AGTCATTTTATAACATAGGGGCATAAC
Found at i:225781 original size:50 final size:50
Alignment explanation
Indices: 225713--225830 Score: 139
Period size: 50 Copynumber: 2.4 Consensus size: 50
225703 AAGACACCAG
* * * * *
225713 TCTTATCGCCTTGACGTTGCAATGGAATAGATTGAAGCCACAACGGCGAA
1 TCTTATCTCCCTGGCGTTGCAACGGAATAGATTGAAGCCACAACGGCAAA
* * * *
225763 TCTTA-CTTCCCTGGCGTTGCAGCGGAGTAGATTGAAGCCACAATGGTAAA
1 TCTTATC-TCCCTGGCGTTGCAACGGAATAGATTGAAGCCACAACGGCAAA
225813 TCTTATCTCCCTGGCGTT
1 TCTTATCTCCCTGGCGTT
225831 AAGACTTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.02
50 55 0.96
51 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (50 bp):
TCTTATCTCCCTGGCGTTGCAACGGAATAGATTGAAGCCACAACGGCAAA
Found at i:226031 original size:100 final size:99
Alignment explanation
Indices: 225909--226215 Score: 400
Period size: 100 Copynumber: 3.1 Consensus size: 99
225899 CAGTGGAACG
* * *
225909 GATTGAAGCCACAACGGCGAATCTTGCTTCCCTGGCAGTGTAGTGGAACAGATTAAAGCTACGAC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGC-GTGTAGTGGAACAGATTGAAGCTACGAC
225974 GGCGAATCTGATTTCCCCGACATTGCAATTAAAAA
65 GGCGAATCTGATTTCCCCGACATTGCAATTAAAAA
* * * * ** *
226009 TATTGAAGCCACAACGGTGAATCTTACTTCTCTGATCGTGTAGTGGAATAGATTGAAGCTGTGGC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTG-GCGTGTAGTGGAACAGATTGAAGCTACGAC
*
226074 GGCGGATCTGATTTCCCCGACATTGCAATTAAAAA
65 GGCGAATCTGATTTCCCCGACATTGCAATTAAAAA
* *
226109 GATTGAAGCCACAACTGTGAATCTTACTTTCCTGGCGGTGTAGTGGAACAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGC-GTGTAGTGGAACAGATTGAAGCTACGAC
* * * * * *
226174 GGTGAATATTG-TTTCCTCAACATTGCAGTTAAACA
65 GGCGAAT-CTGATTTCCCCGACATTGCAATTAAAAA
226209 GATTGAA
1 GATTGAA
226216 AATGACGAAT
Statistics
Matches: 177, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
99 1 0.01
100 173 0.98
101 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (99 bp):
GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGTGTAGTGGAACAGATTGAAGCTACGACG
GCGAATCTGATTTCCCCGACATTGCAATTAAAAA
Found at i:226180 original size:50 final size:50
Alignment explanation
Indices: 225900--226167 Score: 148
Period size: 50 Copynumber: 5.4 Consensus size: 50
225890 TTGGCATTAC
* * * *
225900 AGTGGAACGGATTGAAGCCACAACGGCGAATCTTGCTTCCCTGGCAGTGT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTTCCTGACAGTGT
* * * * * * *
225950 AGTGGAACAGATTAAAGCTACGACGGCGAATCTGA-TTTCCCCGACATTGC
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTT-CCTGACAGTGT
* ** * * *
226000 AATTAAAAATATTGAAGCCACAACGGTGAATCTTAC-TTCTCTGATC-GTGT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTTC-CTGA-CAGTGT
* ***** * * * * *
226050 AGTGGAATAGATTGAAGCTGTGGCGGCGGATCTGA-TTTCCCCGACATTGC
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTT-CCTGACAGTGT
* ** * * * * *
226100 AATTAAAAAGATTGAAGCCACAACTGTGAATCTTACTTTCCTGGCGGTGT
1 AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTTCCTGACAGTGT
226150 AGTGGAACAGATTGAAGC
1 AGTGGAACAGATTGAAGC
226168 TACGACGGTG
Statistics
Matches: 148, Mismatches: 62, Indels: 16
0.65 0.27 0.07
Matches are distributed among these distances:
49 4 0.03
50 139 0.94
51 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (50 bp):
AGTGGAACAGATTGAAGCCACAACGGCGAATCTTACTTTCCTGACAGTGT
Found at i:226334 original size:45 final size:45
Alignment explanation
Indices: 226267--226389 Score: 165
Period size: 45 Copynumber: 2.7 Consensus size: 45
226257 TGAGGCCAAT
* *
226267 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGATAGCA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
* * * * * *
226312 AGTCTTATCTCCTTGAGGTTGCAGCGGAGTAGACTGAAGATAGCA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
*
226357 AATCCTATCTCCCTGAAGTTGCAGTAGAGCAGA
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
226390 TCAAAATGAT
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (45 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCA
Found at i:228262 original size:45 final size:45
Alignment explanation
Indices: 228204--228356 Score: 225
Period size: 45 Copynumber: 3.4 Consensus size: 45
228194 CACCAGTATA
* *
228204 CAGTAATCAGTAACAGTAACAGTATTCAACACACAAAGTGTTGAAC
1 CAGTAA-CAGTAACAGTAACAGTATTCGACACACAAAGTGTTGAAT
* * * * *
228250 CTGTAACAGTAACGGTAACTGTATTCGACACACAAAGTATTGAGT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTTGAAT
*
228295 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAAT
1 CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTTGAAT
228340 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
228357 GTCGGCACAT
Statistics
Matches: 94, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
45 89 0.95
46 5 0.05
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGTTGAAT
Found at i:228644 original size:39 final size:40
Alignment explanation
Indices: 228560--228644 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
228550 TTCTTTACTT
* * * *
228560 CAGTAATTTCACAATTCAATGCATTATACATAACAATATT
1 CAGTATTTTCACAATTCAATGCATAATACAAAACAATATC
*
228600 CAGTATTTTCACAATTCACT-CAGTAAT-CAAAACAATATC
1 CAGTATTTTCACAATTCAATGCA-TAATACAAAACAATATC
228639 CAGTAT
1 CAGTAT
228645 CCCATAATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 18 0.46
40 21 0.54
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (40 bp):
CAGTATTTTCACAATTCAATGCATAATACAAAACAATATC
Found at i:229751 original size:3 final size:3
Alignment explanation
Indices: 229743--229790 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
229733 GATTGTATCC
* *
229743 TTA TTA TTA -TA TTA TTTA TTA TTT TTA TCA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
229787 TTA T
1 TTA T
229791 ACATATACAC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:229833 original size:25 final size:24
Alignment explanation
Indices: 229807--229947 Score: 87
Period size: 24 Copynumber: 6.0 Consensus size: 24
229797 ACACACGCAT
229807 TTTTTTATAATATATATGCATATA
1 TTTTTTATAATATATATGCATATA
* *
229831 TTTTTTATAAATACATGTGC--ATA
1 TTTTTTAT-AATATATATGCATATA
* * **
229854 TTATATAT-ATATAT-TTTAT-TA
1 TTTTTTATAATATATATGCATATA
* ** **
229875 TTATTTTATACATATACACACGCAT-
1 TT-TTTTATA-ATATATATGCATATA
229900 TTTTTTATAATATATATGCATATA
1 TTTTTTATAATATATATGCATATA
* *
229924 TTTTTTATAAATACATGTGCATAT
1 TTTTTTAT-AATATATATGCATAT
229948 TATATATATA
Statistics
Matches: 85, Mismatches: 22, Indels: 19
0.67 0.17 0.15
Matches are distributed among these distances:
20 1 0.01
21 9 0.11
22 4 0.05
23 18 0.21
24 28 0.33
25 24 0.28
26 1 0.01
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (24 bp):
TTTTTTATAATATATATGCATATA
Found at i:229873 original size:93 final size:93
Alignment explanation
Indices: 229776--229976 Score: 402
Period size: 93 Copynumber: 2.2 Consensus size: 93
229766 TTTATCATTA
229776 TTATTATTATTTTATACATATACACACGCATTTTTTTATAATATATATGCATATATTTTTTATAA
1 TTATTATTATTTTATACATATACACACGCATTTTTTTATAATATATATGCATATATTTTTTATAA
229841 ATACATGTGCATATTATATATATATATT
66 ATACATGTGCATATTATATATATATATT
229869 TTATTATTATTTTATACATATACACACGCATTTTTTTATAATATATATGCATATATTTTTTATAA
1 TTATTATTATTTTATACATATACACACGCATTTTTTTATAATATATATGCATATATTTTTTATAA
229934 ATACATGTGCATATTATATATATATATT
66 ATACATGTGCATATTATATATATATATT
229962 TTATTATTATTTTAT
1 TTATTATTATTTTAT
229977 TCTCATAGTT
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 108 1.00
ACGTcount: A:0.36, C:0.08, G:0.04, T:0.52
Consensus pattern (93 bp):
TTATTATTATTTTATACATATACACACGCATTTTTTTATAATATATATGCATATATTTTTTATAA
ATACATGTGCATATTATATATATATATT
Found at i:230023 original size:18 final size:17
Alignment explanation
Indices: 229986--230024 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
229976 TTCTCATAGT
* *
229986 TTTTATATACATTTATA
1 TTTTATATACATATACA
230003 TTTTATAATACATATACA
1 TTTTAT-ATACATATACA
230021 TTTT
1 TTTT
230025 CCTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATATACATATACA
Found at i:231898 original size:7 final size:7
Alignment explanation
Indices: 231886--231912 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
231876 GAATTATCAT
231886 TTTAAAC
1 TTTAAAC
231893 TTTAAAC
1 TTTAAAC
231900 TTTAAAC
1 TTTAAAC
231907 TTTAAA
1 TTTAAA
231913 TTTCCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAC
Found at i:241622 original size:30 final size:30
Alignment explanation
Indices: 241588--241648 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
241578 CTTTAAAGGG
* *
241588 TTAATA-TATATTTGGTATCTAAATTTAACT
1 TTAATATTA-ATTTGGTACCTAAATTAAACT
241618 TTAATATTCAATTTGGTACCTAAATTAAACT
1 TTAATATT-AATTTGGTACCTAAATTAAACT
241649 GCATCATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 6 0.22
31 20 0.74
32 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.46
Consensus pattern (30 bp):
TTAATATTAATTTGGTACCTAAATTAAACT
Done.