Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D10
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: 67973905
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 188 of 228
Found at i:55895890 original size:17 final size:18
Alignment explanation
Indices: 55895852--55895890 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
55895842 AGAATTTTTT
* *
55895852 TTGAAAACACGAAAATTG
1 TTGAAAACACGAAAAATA
55895870 TTGAAAACAC-AAAAATA
1 TTGAAAACACGAAAAATA
55895887 TTGA
1 TTGA
55895891 TAAATTACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (18 bp):
TTGAAAACACGAAAAATA
Found at i:55896308 original size:8 final size:8
Alignment explanation
Indices: 55896295--55896378 Score: 75
Period size: 9 Copynumber: 10.2 Consensus size: 8
55896285 CAACTCGGGC
55896295 TTCTTTTT
1 TTCTTTTT
55896303 TTCTTTTT
1 TTCTTTTT
*
55896311 TCCTTTCCTT
1 TTCTTT--TT
*
55896321 TT-TTCTT
1 TTCTTTTT
*
55896328 TT-TTTTC
1 TTCTTTTT
55896335 TT-TTTTT
1 TTCTTTTT
55896342 TTCTTTTTT
1 TTC-TTTTT
55896351 TTCTTTTT
1 TTCTTTTT
55896359 TTCTTTTTT
1 TTC-TTTTT
55896368 TTCTCTTTT
1 TTCT-TTTT
55896377 TT
1 TT
55896379 TTTGGACTGG
Statistics
Matches: 64, Mismatches: 6, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
7 15 0.23
8 22 0.34
9 24 0.38
10 3 0.05
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTCTTTTT
Found at i:55896323 original size:1 final size:1
Alignment explanation
Indices: 55896319--55896381 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
55896309 TTTCCTTTCC
* * * * * * *
55896319 TTTTTTCTTTTTTTTCTTTTTTTTTCTTTTTTTTCTTTTTTTCTTTTTTTTCTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
55896382 GGACTGGGCT
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:55896333 original size:9 final size:9
Alignment explanation
Indices: 55896319--55896379 Score: 97
Period size: 9 Copynumber: 6.7 Consensus size: 9
55896309 TTTCCTTTCC
55896319 TTTTTTCTT
1 TTTTTTCTT
55896328 TTTTTTCTTT
1 TTTTTTC-TT
55896338 TTTTTTCTT
1 TTTTTTCTT
55896347 TTTTTTC-T
1 TTTTTTCTT
55896355 TTTTTTCTT
1 TTTTTTCTT
55896364 TTTTTTCTCT
1 TTTTTTCT-T
55896374 TTTTTT
1 TTTTTT
55896380 TTGGACTGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.16
9 25 0.51
10 16 0.33
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:55896379 original size:19 final size:18
Alignment explanation
Indices: 55896295--55896379 Score: 109
Period size: 19 Copynumber: 4.6 Consensus size: 18
55896285 CAACTCGGGC
55896295 TTCTTTTTTTCTTTTTTCCT
1 TTCTTTTTTTCTTTTTT--T
*
55896315 TTCCTTTTTTC-TTTTTT
1 TTCTTTTTTTCTTTTTTT
*
55896332 TTCTTTTTTTTTCTTTTTT
1 TTCTTTTTTTCT-TTTTTT
55896351 TTCTTTTTTTCTTTTTTT
1 TTCTTTTTTTCTTTTTTT
55896369 TCTCTTTTTTT
1 T-TCTTTTTTT
55896380 TTGGACTGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.17
18 7 0.12
19 31 0.53
20 10 0.17
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (18 bp):
TTCTTTTTTTCTTTTTTT
Found at i:55896379 original size:28 final size:27
Alignment explanation
Indices: 55896295--55896380 Score: 120
Period size: 27 Copynumber: 3.1 Consensus size: 27
55896285 CAACTCGGGC
*
55896295 TTCTTTTTTTCTTTTTTCCTTTC-CTTTT
1 TTCTTTTTTTCTTTTTT--TTTCTTTTTT
55896323 TTCTTTTTTTTCTTTTTTTTTCTTTTTT
1 TTC-TTTTTTTCTTTTTTTTTCTTTTTT
55896351 TTCTTTTTTTCTTTTTTTTCTCTTTTTT
1 TTCTTTTTTTCTTTTTTTT-TCTTTTTT
55896379 TT
1 TT
55896381 TGGACTGGGC
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
27 20 0.37
28 20 0.37
29 14 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (27 bp):
TTCTTTTTTTCTTTTTTTTTCTTTTTT
Found at i:55896678 original size:17 final size:18
Alignment explanation
Indices: 55896658--55896696 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
55896648 TTTAAAATAA
55896658 TTTTATTTTTTTCTCTT-
1 TTTTATTTTTTTCTCTTC
* *
55896675 TTTTCTTTTTTTTTCTTC
1 TTTTATTTTTTTCTCTTC
55896693 TTTT
1 TTTT
55896697 TCTTCTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTATTTTTTTCTCTTC
Found at i:55896683 original size:15 final size:14
Alignment explanation
Indices: 55896665--55896715 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
55896655 TAATTTTATT
*
55896665 TTTTTCTCTTTTTTC
1 TTTTTCT-TTTCTTC
55896680 TTTTT-TTTTCTTC
1 TTTTTCTTTTCTTC
55896693 TTTTTCTTCTTCTTC
1 TTTTTCTT-TTCTTC
55896708 TTTTTCTT
1 TTTTTCTT
55896716 CTTCCCTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
13 11 0.33
14 3 0.09
15 19 0.58
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTCTTC
Found at i:55896688 original size:12 final size:12
Alignment explanation
Indices: 55896663--55896718 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
55896653 AATAATTTTA
*
55896663 TTTTT-TTCTCT
1 TTTTTCTTCTTT
55896674 TTTTTC-T-TTT
1 TTTTTCTTCTTT
55896684 TTTTTCTTCTTT
1 TTTTTCTTCTTT
* *
55896696 TTCTTCTTCTTC
1 TTTTTCTTCTTT
55896708 TTTTTCTTCTT
1 TTTTTCTTCTT
55896719 CCCTCTTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
10 8 0.21
11 7 0.18
12 23 0.61
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTTCTTT
Found at i:55896701 original size:9 final size:9
Alignment explanation
Indices: 55896665--55896718 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
55896655 TAATTTTATT
55896665 TTTTTC-TC
1 TTTTTCTTC
55896673 TTTTTTCTT-
1 -TTTTTCTTC
55896682 TTTTT-TTC
1 TTTTTCTTC
55896690 TTCTTT-TTC
1 TT-TTTCTTC
*
55896699 TTCTTCTTC
1 TTTTTCTTC
55896708 TTTTTCTTC
1 TTTTTCTTC
55896717 TT
1 TT
55896719 CCCTCTTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
7 2 0.05
8 9 0.23
9 27 0.69
10 1 0.03
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:55896716 original size:15 final size:15
Alignment explanation
Indices: 55896677--55896719 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
55896667 TTTCTCTTTT
55896677 TTCTTTTT-TT-TTC
1 TTCTTTTTCTTCTTC
55896690 TTCTTTTTCTTCTTC
1 TTCTTTTTCTTCTTC
55896705 TTCTTTTTCTTCTTC
1 TTCTTTTTCTTCTTC
55896720 CCTCTTTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 8 0.29
14 2 0.07
15 18 0.64
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCTTCTTC
Found at i:55897117 original size:29 final size:29
Alignment explanation
Indices: 55897083--55897221 Score: 167
Period size: 29 Copynumber: 4.8 Consensus size: 29
55897073 AAATGTTGGG
55897083 AAAATTTAGGGGTCAAAATGTAATTTCAA
1 AAAATTTAGGGGTCAAAATGTAATTTCAA
*
55897112 AAAATTTATGGG-CTAAAATGTAATTTCAA
1 AAAATTTAGGGGTC-AAAATGTAATTTCAA
* *
55897141 AAAATTTTAGGGGTCAAAATATAAATTT-AGG
1 AAAA-TTTAGGGGTCAAAATGT-AATTTCA-A
* * *
55897172 AAAATTTAGGAGTTAAAATGCAATTTCAA
1 AAAATTTAGGGGTCAAAATGTAATTTCAA
55897201 AAAATTTAGGGGTC-AAATGTA
1 AAAATTTAGGGGTCAAAATGTA
55897222 TTTTTTTTTG
Statistics
Matches: 92, Mismatches: 12, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
28 7 0.08
29 47 0.51
30 28 0.30
31 10 0.11
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (29 bp):
AAAATTTAGGGGTCAAAATGTAATTTCAA
Found at i:55897152 original size:59 final size:58
Alignment explanation
Indices: 55897083--55897221 Score: 185
Period size: 60 Copynumber: 2.4 Consensus size: 58
55897073 AAATGTTGGG
*
55897083 AAAATTTAGGGGTCAAAATGTAATTTCA-AAAAATTTATGG-GCTAAAATGTAATTTCAA
1 AAAATTTAGGGGTCAAAATGTAATTT-AGAAAAATTTA-GGAGCTAAAATGCAATTTCAA
* * *
55897141 AAAATTTTAGGGGTCAAAATATAAATTTAGGAAAATTTAGGAGTTAAAATGCAATTTCAA
1 AAAA-TTTAGGGGTCAAAATGT-AATTTAGAAAAATTTAGGAGCTAAAATGCAATTTCAA
55897201 AAAATTTAGGGGTC-AAATGTA
1 AAAATTTAGGGGTCAAAATGTA
55897222 TTTTTTTTTG
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
57 1 0.01
58 9 0.12
59 29 0.40
60 33 0.46
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (58 bp):
AAAATTTAGGGGTCAAAATGTAATTTAGAAAAATTTAGGAGCTAAAATGCAATTTCAA
Found at i:55900385 original size:46 final size:45
Alignment explanation
Indices: 55900332--55900657 Score: 368
Period size: 46 Copynumber: 7.6 Consensus size: 45
55900322 TTTGAGTACT
* *
55900332 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
55900378 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
55900414 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
55900460 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
55900496 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
55900542 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGTTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
55900588 TCTGATCAAGTGACAAAATGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
55900633 TCTGATC-AGGGGC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
55900658 ATCATACGTA
Statistics
Matches: 242, Mismatches: 18, Indels: 43
0.80 0.06 0.14
Matches are distributed among these distances:
36 58 0.24
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 13 0.05
44 5 0.02
45 21 0.09
46 129 0.53
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:55900409 original size:36 final size:36
Alignment explanation
Indices: 55900368--55900522 Score: 184
Period size: 36 Copynumber: 4.0 Consensus size: 36
55900358 GGTAGCTTTA
55900368 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55900404 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
55900449 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
55900486 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
55900522 G
1 G
55900523 TTAGCCTTAG
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 65 0.63
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 30 0.29
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:55900469 original size:82 final size:82
Alignment explanation
Indices: 55900332--55900640 Score: 440
Period size: 82 Copynumber: 3.7 Consensus size: 82
55900322 TTTGAGTACT
*
55900332 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
55900397 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
55900414 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
55900479 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * * *
55900496 TCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
55900561 GATAAGTGGTAGCCTTAGTTACACTTA
66 GATAA---GT-G-C-----TACACTTA
* * *
55900588 TCTGATCAAGTGACAAAATGATAAGTGGTAGC-CTAGCTACACTTATCTGATCA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCA
55900641 GGGGCAAGTG
Statistics
Matches: 207, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
82 146 0.71
85 2 0.01
86 1 0.00
87 1 0.00
91 20 0.10
92 37 0.18
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:55900650 original size:128 final size:125
Alignment explanation
Indices: 55900332--55900657 Score: 339
Period size: 128 Copynumber: 2.6 Consensus size: 125
55900322 TTTGAGTACT
* * *
55900332 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGA-AAAATGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAG-GGAAAAGT
*
55900397 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
63 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
55900460 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTATCTGATCAAGTGACAAAGTG
1 TCTGATCAAGTGAAAAA-TGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGA-AAAGTG
* * *
55900516 ATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGTT
64 AT-A-----AG---T-GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCT
55900581 ACACTTA
119 ACACTTA
* **
55900588 TCTGATCAAGTGACAAAATGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGGCAAGTGA
1 TCTGATCAAGTGA-AAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGA
55900652 TAAGTG
65 TAAGTG
55900658 ATCATACGTA
Statistics
Matches: 165, Mismatches: 11, Indels: 47
0.74 0.05 0.21
Matches are distributed among these distances:
117 1 0.01
118 23 0.14
119 1 0.01
120 1 0.01
122 2 0.01
124 4 0.02
125 3 0.02
126 1 0.01
127 4 0.02
128 89 0.54
129 6 0.04
131 2 0.01
132 2 0.01
133 2 0.01
134 1 0.01
135 8 0.05
136 3 0.02
137 12 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (125 bp):
TCTGATCAAGTGAAAAATGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGGGAAAAGTGAT
AAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:55902668 original size:59 final size:60
Alignment explanation
Indices: 55902603--55902720 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 60
55902593 ATATAAAAAA
* *
55902603 TATAAATTACATTTTGACCCCCT-AACTTTCTTA-AAATTATATTTTGA-CCCTTAACTTTT
1 TATAAATTACATTTT-ACCCCCTAAACTTT-TTAGAAATTACATTTTGACCCCCTAACTTTT
* * *
55902662 TATAAATTACATTTTAGCCCTTAAACTTTTTAGAAGTTACATTTTGACCCCCTAACTTT
1 TATAAATTACATTTTACCCCCTAAACTTTTTAGAAATTACATTTTGACCCCCTAACTTT
55902721 CCTAAGATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
58 8 0.16
59 33 0.65
60 10 0.20
ACGTcount: A:0.31, C:0.20, G:0.05, T:0.44
Consensus pattern (60 bp):
TATAAATTACATTTTACCCCCTAAACTTTTTAGAAATTACATTTTGACCCCCTAACTTTT
Found at i:55902732 original size:30 final size:29
Alignment explanation
Indices: 55902606--55902735 Score: 138
Period size: 30 Copynumber: 4.4 Consensus size: 29
55902596 TAAAAAATAT
55902606 AAATTACATTTTGACCCCCTAACTTTCTTA
1 AAATTACATTTTGACCCCCTAACTTT-TTA
* *
55902636 AAATTATATTTTGA-CCCTTAACTTTTTA
1 AAATTACATTTTGACCCCCTAACTTTTTA
* *
55902664 TAAATTACATTTT-AGCCCTTAAACTTTTTA
1 -AAATTACATTTTGACCCCCT-AACTTTTTA
* *
55902694 GAAGTTACATTTTGACCCCCTAACTTTCCTA
1 -AAATTACATTTTGACCCCCTAACTTT-TTA
*
55902725 AGATTACATTT
1 AAATTACATTT
55902736 CAATCCCAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
28 4 0.05
29 26 0.31
30 48 0.56
31 7 0.08
ACGTcount: A:0.31, C:0.21, G:0.05, T:0.43
Consensus pattern (29 bp):
AAATTACATTTTGACCCCCTAACTTTTTA
Found at i:55905200 original size:16 final size:16
Alignment explanation
Indices: 55905179--55905262 Score: 132
Period size: 16 Copynumber: 5.2 Consensus size: 16
55905169 TTTGGTTCGC
55905179 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
55905195 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
*
55905211 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
*
55905227 TGTATTAGATTAGAGG
1 TGTATTGGATTAGAGG
*
55905243 TGTATTGGTTTAGAGG
1 TGTATTGGATTAGAGG
55905259 TGTA
1 TGTA
55905263 ATAGCTAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.27, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:55905519 original size:18 final size:17
Alignment explanation
Indices: 55905498--55905532 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55905488 TTATTATTAA
*
55905498 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
55905516 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
55905533 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:55905639 original size:18 final size:17
Alignment explanation
Indices: 55905611--55905652 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
55905601 AACATAAATA
55905611 TTAAT-AAATATAT--T
1 TTAATAAAATATATAAT
55905625 TTAATTAAAATATATAAT
1 TTAA-TAAAATATATAAT
55905643 TTAATAAAAT
1 TTAATAAAAT
55905653 TCTTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.17
15 1 0.04
16 8 0.33
17 6 0.25
18 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAATAAAATATATAAT
Found at i:55905734 original size:120 final size:119
Alignment explanation
Indices: 55905481--55905704 Score: 396
Period size: 120 Copynumber: 1.9 Consensus size: 119
55905471 ATCATATTTA
* *
55905481 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAAATATTAATAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
55905546 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATAC-GTAAAATATAAATT
*
55905601 AACATAAATATTAATAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTCA
1 AACATAAATATTAATAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
55905666 TATTCTTATA-TAATTTATTCAAATCATAATATATGATAC
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATAC
55905705 TATAATTAAT
Statistics
Matches: 100, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
119 28 0.28
120 72 0.72
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (119 bp):
AACATAAATATTAATAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACGTAAAATATAAATT
Found at i:55905781 original size:26 final size:27
Alignment explanation
Indices: 55905706--55905787 Score: 87
Period size: 26 Copynumber: 3.0 Consensus size: 27
55905696 ATATGATACT
* *
55905706 ATAATTAATATTAAATATATTTTAATTA
1 ATAATTATTATTAAATATAATTTAA-TA
* *
55905734 A-AATATATGATTAAATACAATTTAA-A
1 ATAAT-TATTATTAAATATAATTTAATA
*
55905760 ATAATTATTATTAAATATAATTTCATA
1 ATAATTATTATTAAATATAATTTAATA
55905787 A
1 A
55905788 AATGTTCTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 19 0.43
27 8 0.18
28 17 0.39
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (27 bp):
ATAATTATTATTAAATATAATTTAATA
Found at i:55908895 original size:33 final size:33
Alignment explanation
Indices: 55908856--55908965 Score: 136
Period size: 33 Copynumber: 3.3 Consensus size: 33
55908846 ATTATAAAGC
55908856 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
55908889 ATGTATAATTGACCTAAAATTACTTGTTGGTTT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
* *
55908922 AATGT-T-ATTTACCTTAAAA-AACATTGTTGGTGT
1 -ATGTATAATTGACC-TAAAATTA-ATTGTTGGTGT
55908955 ATGTATAATTG
1 ATGTATAATTG
55908966 TTGGTTTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
32 11 0.17
33 47 0.72
34 7 0.11
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.44
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTGT
Found at i:55908991 original size:51 final size:51
Alignment explanation
Indices: 55908912--55909014 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
55908902 CTAAAATTAC
*
55908912 TTGTTGGTTTAATGTTATTTACCTTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
55908963 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
1 TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
55909014 T
1 T
55909015 CTTTTAATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (51 bp):
TTGTTGGTTTAATGTTATTTACCCTAAAAAACATTGTTGGTGTATGTATAA
Found at i:55912345 original size:31 final size:31
Alignment explanation
Indices: 55912286--55912431 Score: 186
Period size: 31 Copynumber: 4.7 Consensus size: 31
55912276 ATCCAATGCT
* *
55912286 CAAATC-AATTTGGCAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
55912316 CGAATCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
** *
55912347 CAAATCAAATTCGGCAATGTATATTTATAAA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* *
55912378 CAATTCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
55912409 CAAATCAAATTCTGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
55912432 AAACATATAC
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
30 5 0.05
31 94 0.95
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:55912450 original size:62 final size:62
Alignment explanation
Indices: 55912286--55912451 Score: 167
Period size: 62 Copynumber: 2.7 Consensus size: 62
55912276 ATCCAATGCT
* * ** *
55912286 CAAATC-AATTTGGCAATATATATCCATATACGAA-TCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATAAACATAAAC-AATTCAAATTCGACAATGTATAACCATATA
*** * * *
55912347 CAAATCAAATTCGGCAATGTATATTTATAAACAATTCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATAAACATAAACAATTCAAATTCGACAATGTATAACCATATA
* * *
55912409 CAAATCAAATTCTGCAATGTATAAAACATATAC-ATTTAAATTC
1 CAAATCAAATTCGGCAATGTAT-AAACATAAACAATTCAAATTC
55912452 AAAAACATTT
Statistics
Matches: 88, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
61 8 0.09
62 74 0.84
63 6 0.07
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (62 bp):
CAAATCAAATTCGGCAATGTATAAACATAAACAATTCAAATTCGACAATGTATAACCATATA
Found at i:55912465 original size:93 final size:93
Alignment explanation
Indices: 55912292--55912466 Score: 201
Period size: 93 Copynumber: 1.9 Consensus size: 93
55912282 TGCTCAAATC
* * *
55912292 AATTTGGCAATATATATCCATATACGAATCAAATTCGACAATGTATAACCATATACAAATCAAAT
1 AATTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATAAACATATACAAATCAAAT
*** **
55912357 TCGGCAATGTATATTTATAAACAATTCA
66 TCAAAAACATATATTTATAAACAATTCA
* * * *
55912385 AATTCGGCAATGTATATCTATATACAAATCAAATTCTG-CAATGTATAAAACATATAC-ATTTAA
1 AATTCGGCAATATATATCCATATACAAATCAAATTC-GACAATGTAT-AAACATATACAAATCAA
*
55912448 ATTCAAAAACATTTATTTA
64 ATTCAAAAACATATATTTA
55912467 CTTATGAACT
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
93 57 0.85
94 10 0.15
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (93 bp):
AATTCGGCAATATATATCCATATACAAATCAAATTCGACAATGTATAAACATATACAAATCAAAT
TCAAAAACATATATTTATAAACAATTCA
Found at i:55922997 original size:16 final size:16
Alignment explanation
Indices: 55922973--55923007 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
55922963 CATTAAACAC
*
55922973 AACATCTACATTCGTT
1 AACACCTACATTCGTT
*
55922989 AACACCTACCTTCGTT
1 AACACCTACATTCGTT
55923005 AAC
1 AAC
55923008 GAAAATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.31
Consensus pattern (16 bp):
AACACCTACATTCGTT
Found at i:55926507 original size:24 final size:24
Alignment explanation
Indices: 55926462--55926507 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
55926452 CTCATTGTGG
**
55926462 TTTATTTTTATTTTATTTAATCCA
1 TTTATTTTTATTTTATAAAATCCA
55926486 TTTATTTTT-TTTTATGAAAATC
1 TTTATTTTTATTTTAT-AAAATC
55926508 AATATTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTATTTTTATTTTATAAAATCCA
Found at i:55927015 original size:9 final size:9
Alignment explanation
Indices: 55927001--55927079 Score: 61
Period size: 10 Copynumber: 8.2 Consensus size: 9
55926991 AATTCATTAT
55927001 AAATTATAA
1 AAATTATAA
55927010 AAATTATAA
1 AAATTATAA
*
55927019 AAATCATTAA
1 AAATTA-TAA
55927029 AAATATATAA
1 AAAT-TATAA
*
55927039 AAATTTGTAAAA
1 AAA--T-TATAA
55927051 AAATT-TAA
1 AAATTATAA
*
55927059 AAATCATAA
1 AAATTATAA
*
55927068 AATTTTATAA
1 AA-ATTATAA
55927078 AA
1 AA
55927080 TTTTATAAAG
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
8 6 0.11
9 20 0.36
10 21 0.38
11 1 0.02
12 8 0.14
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:55927050 original size:29 final size:27
Alignment explanation
Indices: 55926914--55927080 Score: 81
Period size: 28 Copynumber: 6.0 Consensus size: 27
55926904 CCTTGCTTTT
**
55926914 ATTAAAAATTATAAAAAAAATTAAAATC
1 ATTAAAAATTAT-AAAAATTTTAAAATC
* * *
55926942 AAT-AAAATCTATAAATAATATT-ATAT-
1 ATTAAAAAT-TATAAA-AATTTTAAAATC
* * * *
55926968 TTTAATAAA-AATAAAATATTATAAATTC
1 ATTAA-AAATTATAAAA-ATTTTAAAATC
* *
55926996 ATTATAAATTATAAAAATTATAAAAATC
1 ATTAAAAATTATAAAAATT-TTAAAATC
**
55927024 ATTAAAAATATATAAAAATTTGTAAAAAA
1 ATTAAAAAT-TATAAAAATTT-TAAAATC
* *
55927053 ATTTAAAAATCATAAAATTTTATAAAAT
1 A-TTAAAAATTATAAAAATTT-TAAAAT
55927081 TTTATAAAGT
Statistics
Matches: 103, Mismatches: 24, Indels: 23
0.69 0.16 0.15
Matches are distributed among these distances:
25 1 0.01
26 9 0.09
27 20 0.19
28 36 0.35
29 29 0.28
30 8 0.08
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
ATTAAAAATTATAAAAATTTTAAAATC
Found at i:55927077 original size:10 final size:10
Alignment explanation
Indices: 55927064--55927088 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55927054 TTTAAAAATC
55927064 ATAAAATTTT
1 ATAAAATTTT
55927074 ATAAAATTTT
1 ATAAAATTTT
55927084 ATAAA
1 ATAAA
55927089 GTCGTAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAAAATTTT
Found at i:55927326 original size:37 final size:37
Alignment explanation
Indices: 55927282--55927401 Score: 127
Period size: 37 Copynumber: 3.2 Consensus size: 37
55927272 ACTAGGGGTC
55927282 ATTTTTTATGATTTTTATAAAATTTTATAATTTTTTT
1 ATTTTTTATGATTTTTATAAAATTTTATAATTTTTTT
* ** *
55927319 ATTTTTTACGATTTTTATAAAGAAATTATAA-TTTTTA
1 ATTTTTTATGATTTTTATAAA-ATTTTATAATTTTTTT
*** * *
55927356 ATAAATTATAATTTTTAT-AATTTTTATAATTTTTTTT
1 ATTTTTTATGATTTTTATAAAATTTTATAA-TTTTTTT
55927393 ATTTTTTAT
1 ATTTTTTAT
55927402 AATGTTTAAT
Statistics
Matches: 64, Mismatches: 16, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
35 6 0.09
36 2 0.03
37 49 0.77
38 7 0.11
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (37 bp):
ATTTTTTATGATTTTTATAAAATTTTATAATTTTTTT
Found at i:55927388 original size:8 final size:9
Alignment explanation
Indices: 55927284--55927409 Score: 76
Period size: 9 Copynumber: 13.7 Consensus size: 9
55927274 TAGGGGTCAT
*
55927284 TTTTTATGA
1 TTTTTATAA
55927293 TTTTTATAAA
1 TTTTTAT-AA
*
55927303 ATTTTATAA
1 TTTTTATAA
* *
55927312 TTTTTTTAT
1 TTTTTATAA
**
55927321 TTTTTACGA
1 TTTTTATAA
55927330 TTTTTATAAA
1 TTTTTAT-AA
***
55927340 GAAATTATAA
1 -TTTTTATAA
55927350 TTTTTAATAA
1 TTTTT-ATAA
*
55927360 --ATTATAA
1 TTTTTATAA
55927367 TTTTTATAA
1 TTTTTATAA
55927376 TTTTTATAA
1 TTTTTATAA
* *
55927385 TTTTTTTTAT
1 -TTTTTATAA
55927395 TTTTTATAA
1 TTTTTATAA
*
55927404 TGTTTA
1 TTTTTA
55927410 ATAAGAGCAT
Statistics
Matches: 86, Mismatches: 24, Indels: 14
0.69 0.19 0.11
Matches are distributed among these distances:
7 4 0.05
8 2 0.02
9 55 0.64
10 21 0.24
11 4 0.05
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:55928115 original size:22 final size:21
Alignment explanation
Indices: 55928090--55928133 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
55928080 ACTAAAGCAT
*
55928090 ATTGACGATAAAGTTAAAAAAA
1 ATTGA-GAGAAAGTTAAAAAAA
*
55928112 ATTGAGAGAAATTTAAAAAAA
1 ATTGAGAGAAAGTTAAAAAAA
55928133 A
1 A
55928134 AAATTAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.02, G:0.14, T:0.23
Consensus pattern (21 bp):
ATTGAGAGAAAGTTAAAAAAA
Found at i:55928669 original size:23 final size:23
Alignment explanation
Indices: 55928641--55928694 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
55928631 GTTTTGGTGC
*
55928641 TGTTATTTTT-CTGTTGTTTTTGT
1 TGTTATTTTTGCTATTGTTTTT-T
55928664 TGTTATTTTTGCTATTGTTTTTT
1 TGTTATTTTTGCTATTGTTTTTT
55928687 TGTTATTT
1 TGTTATTT
55928695 GTACTGGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 19 0.66
24 10 0.34
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (23 bp):
TGTTATTTTTGCTATTGTTTTTT
Found at i:55930855 original size:17 final size:18
Alignment explanation
Indices: 55930823--55930856 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55930813 CAAGAAGCAA
*
55930823 AAAAAATGGGCCGAATTG
1 AAAAAATGGGCAGAATTG
55930841 AAAAAAT-GGCAGAATT
1 AAAAAATGGGCAGAATT
55930857 AGTGGCTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.18
Consensus pattern (18 bp):
AAAAAATGGGCAGAATTG
Found at i:55932266 original size:9 final size:9
Alignment explanation
Indices: 55932251--55932283 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
55932241 ATGTAGTGAT
55932251 TTAATTCGG
1 TTAATTCGG
*
55932260 GTAATTCGG
1 TTAATTCGG
55932269 TTAATTCGG
1 TTAATTCGG
55932278 TTAATT
1 TTAATT
55932284 TTTAACCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.21, T:0.45
Consensus pattern (9 bp):
TTAATTCGG
Found at i:55940399 original size:14 final size:14
Alignment explanation
Indices: 55940379--55940420 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
55940369 AGAAATTGAA
55940379 AAAAATAAGTGTTG
1 AAAAATAAGTGTTG
* *
55940393 GAAAATAAGTATTG
1 AAAAATAAGTGTTG
55940407 AAAAATTAAGTGTT
1 AAAAA-TAAGTGTT
55940421 AAATTTATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (14 bp):
AAAAATAAGTGTTG
Found at i:55968494 original size:90 final size:89
Alignment explanation
Indices: 55968337--55968519 Score: 215
Period size: 90 Copynumber: 2.0 Consensus size: 89
55968327 GTCATTGCTT
* * * * *
55968337 TTTTTTGCACTTATTTAGATATTTAAACTTTCAAAATGTATCAAAAAGAACCTCAAACATTAAAA
1 TTTTTTGCACTCAATTAGATACTTAAACTTTCAAAATGCATAAAAAAGAACCTCAAACATTAAAA
* *
55968402 AAAAAGAAGCAATTAAGCCCCTAC
66 AAAAAAAAGAAATTAAGCCCCTAC
* * *** **
55968426 ATTTTTTGCACTCAATTAGATACTTAAGCTTTC-AAATGCATAAAAAAGACCCTCAATTTTTTTC
1 -TTTTTTGCACTCAATTAGATACTTAAACTTTCAAAATGCATAAAAAAGAACCTCAA-ACATTAA
55968490 AAAAAAAAAAGAAATTAAGCCCCTAC
64 AAAAAAAAAAGAAATTAAGCCCCTAC
55968516 TTTT
1 TTTT
55968520 ATTAAAAATT
Statistics
Matches: 78, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 24 0.31
90 54 0.69
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.32
Consensus pattern (89 bp):
TTTTTTGCACTCAATTAGATACTTAAACTTTCAAAATGCATAAAAAAGAACCTCAAACATTAAAA
AAAAAAAAGAAATTAAGCCCCTAC
Found at i:55968626 original size:10 final size:10
Alignment explanation
Indices: 55968584--55968694 Score: 60
Period size: 10 Copynumber: 11.7 Consensus size: 10
55968574 TAATAAAAAT
55968584 AAATAT-TAA
1 AAATATATAA
* *
55968593 AAATTTATTAG
1 AAATATA-TAA
*
55968604 AAAT-TAGAA
1 AAATATATAA
55968613 AAATATATAA
1 AAATATATAA
55968623 AAATCAT-TAA
1 AAAT-ATATAA
55968633 AAA-ATAT-A
1 AAATATATAA
*
55968641 AAAT-TGTAA
1 AAATATATAA
* *
55968650 AATTTTATAA
1 AAATATATAA
*
55968660 AAATCGTA-AA
1 AAAT-ATATAA
55968670 AAAT-TAT-A
1 AAATATATAA
*
55968678 AAATATATAG
1 AAATATATAA
55968688 AAATATA
1 AAATATA
55968695 AAATTTTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
8 15 0.19
9 18 0.23
10 36 0.46
11 10 0.13
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (10 bp):
AAATATATAA
Found at i:55968643 original size:29 final size:29
Alignment explanation
Indices: 55968584--55968643 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
55968574 TAATAAAAAT
* * *
55968584 AAATATTAAAAATTTATTAGAAATTAGAA
1 AAATATTAAAAATTCATTAAAAAATAGAA
*
55968613 AAATATATAAAAA-TCATTAAAAAATATAA
1 AAATAT-TAAAAATTCATTAAAAAATAGAA
55968642 AA
1 AA
55968644 TTGTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (29 bp):
AAATATTAAAAATTCATTAAAAAATAGAA
Found at i:55968645 original size:37 final size:37
Alignment explanation
Indices: 55968611--55968770 Score: 102
Period size: 37 Copynumber: 4.4 Consensus size: 37
55968601 TAGAAATTAG
*
55968611 AAAAATATATAAAAATCATTAAAAAA-TATAAAATTGT
1 AAAAATATATAAAAATC-GTAAAAAATTATAAAATTGT
* * *
55968648 AAAATTTTATAAAAATCGTAAAAAATTATAAAA-TAT
1 AAAAATATATAAAAATCGTAAAAAATTATAAAATTGT
* ** * *
55968684 ATAGAA-ATAT-AAAAT--TTTAAAATTTTAAAAGTCGT
1 A-AAAATATATAAAAATCGTAAAAAATTATAAAA-TTGT
* *
55968719 AAGAAAT-TATATAAAAT-GTAAAAAAATATAAATTTCGT
1 AA-AAATATATA-AAAATCGTAAAAAATTATAAAATT-GT
*
55968757 AAAAATTTATAAAA
1 AAAAATATATAAAA
55968771 TTATCTAACA
Statistics
Matches: 93, Mismatches: 19, Indels: 22
0.69 0.14 0.16
Matches are distributed among these distances:
33 12 0.13
34 1 0.01
35 12 0.13
36 13 0.14
37 37 0.40
38 18 0.19
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (37 bp):
AAAAATATATAAAAATCGTAAAAAATTATAAAATTGT
Found at i:55968680 original size:8 final size:8
Alignment explanation
Indices: 55968628--55968713 Score: 50
Period size: 8 Copynumber: 10.1 Consensus size: 8
55968618 TATAAAAATC
55968628 ATTA-AAA
1 ATTATAAA
*
55968635 AATATAAA
1 ATTATAAA
*
55968643 ATTGTAAA
1 ATTATAAA
55968651 ATTTTATAAAA
1 A--TTAT-AAA
*
55968662 ATCGTAAAAA
1 AT--TATAAA
55968672 ATTATAAA
1 ATTATAAA
55968680 ATATATAGAA
1 AT-TATA-AA
55968690 A-TATAAA
1 ATTATAAA
*
55968697 ATTTTAAA
1 ATTATAAA
*
55968705 ATTTTAAA
1 ATTATAAA
55968713 A
1 A
55968714 GTCGTAAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
7 6 0.10
8 35 0.56
9 5 0.08
10 11 0.17
11 6 0.10
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (8 bp):
ATTATAAA
Found at i:55968707 original size:54 final size:53
Alignment explanation
Indices: 55968632--55968770 Score: 156
Period size: 52 Copynumber: 2.5 Consensus size: 53
55968622 AAAATCATTA
*
55968632 AAAAATATAAAATTGTAAAATTTTATAAAAATCGTAAAAAATTATA-AAATATAT
1 AAAAATATAAAATTTTAAAA-TTTATAAAAATCGTAAAAAATTATATAAA-ATAT
* * * *
55968686 AGAAATATAAAATTTTAAAATTT-TAAAAGTCGTAAGAAATTATATAAAATGT
1 AAAAATATAAAATTTTAAAATTTATAAAAATCGTAAAAAATTATATAAAATAT
*
55968738 AAAAAAATATAAATTTCGTAAAAATTTATAAAA
1 AAAAATATA-AAATTT--T-AAAATTTATAAAA
55968771 TTATCTAACA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
52 29 0.40
53 12 0.17
54 18 0.25
55 1 0.01
56 7 0.10
57 5 0.07
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (53 bp):
AAAAATATAAAATTTTAAAATTTATAAAAATCGTAAAAAATTATATAAAATAT
Found at i:55968767 original size:19 final size:18
Alignment explanation
Indices: 55968637--55968771 Score: 84
Period size: 19 Copynumber: 7.4 Consensus size: 18
55968627 CATTAAAAAA
* *
55968637 TATAAAATTGTAAAATTT
1 TATAAAATCGTAAAAATT
*
55968655 TATAAAAATCGTAAAAAAT
1 TAT-AAAATCGTAAAAATT
*
55968674 TATAAAAT-ATATAGAAA--
1 TATAAAATCGTA-A-AAATT
* *
55968691 TATAAAAT-TTTAAAATT
1 TATAAAATCGTAAAAATT
55968708 T-TAAAAGTCGTAAGAAATT
1 TATAAAA-TCGTAA-AAATT
**
55968727 ATATAAAAT-GTAAAAAAA
1 -TATAAAATCGTAAAAATT
*
55968745 TATAAATTTCGTAAAAATT
1 TATAAA-ATCGTAAAAATT
55968764 TATAAAAT
1 TATAAAAT
55968772 TATCTAACAA
Statistics
Matches: 91, Mismatches: 14, Indels: 24
0.71 0.11 0.19
Matches are distributed among these distances:
15 3 0.03
16 6 0.07
17 19 0.21
18 16 0.18
19 40 0.44
20 2 0.02
21 5 0.05
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (18 bp):
TATAAAATCGTAAAAATT
Found at i:55968937 original size:19 final size:18
Alignment explanation
Indices: 55968913--55968955 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
55968903 GATTTTTTAC
55968913 AATTTTTATAAAAAATTCT
1 AATTTTTA-AAAAAATTCT
*
55968932 AA-TTTTAATAAAATTCT
1 AATTTTTAAAAAAATTCT
55968949 AATTTTT
1 AATTTTT
55968956 TATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 9 0.41
19 2 0.09
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTTTTAAAAAAATTCT
Found at i:55968963 original size:26 final size:26
Alignment explanation
Indices: 55968933--55968994 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
55968923 AAAAATTCTA
55968933 ATTTTAATAAAATTCTA-ATTTTT-TAT
1 ATTTTAATAAAATT-TATATTTTTAT-T
**
55968959 ATTTTTCTAAAATTTATATTTTTATT
1 ATTTTAATAAAATTTATATTTTTATT
55968985 ATTTTTAATA
1 A-TTTTAATA
55968995 GAGCAGGGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 2 0.07
26 20 0.69
27 7 0.24
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
ATTTTAATAAAATTTATATTTTTATT
Found at i:55970792 original size:26 final size:26
Alignment explanation
Indices: 55970763--55970818 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
55970753 TTTAATTTTG
*
55970763 TTTATATTATA-TATATCGTATTATTA
1 TTTATATTAAATTATAT-GTATTATTA
* *
55970789 TTTATTTTAAATTATATGTTTTATTA
1 TTTATATTAAATTATATGTATTATTA
55970815 TTTA
1 TTTA
55970819 ATAGATGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (26 bp):
TTTATATTAAATTATATGTATTATTA
Found at i:55973695 original size:15 final size:15
Alignment explanation
Indices: 55973664--55973702 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
55973654 AGAATATTTT
*
55973664 TATAATT-TAAAATA
1 TATAATTATAAAAGA
*
55973678 TATATTTATAAAAGA
1 TATAATTATAAAAGA
55973693 TATAATTATA
1 TATAATTATA
55973703 TTTCATAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (15 bp):
TATAATTATAAAAGA
Found at i:55979971 original size:15 final size:14
Alignment explanation
Indices: 55979936--55979977 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
55979926 TGAATTGAAA
*
55979936 AAAATAAGTGTT-G
1 AAAATAAGTATTAG
55979949 AAAATAAGTATTAG
1 AAAATAAGTATTAG
55979963 AAAATTAAGTATTAG
1 AAAA-TAAGTATTAG
55979978 TTATTTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 11 0.42
14 5 0.19
15 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (14 bp):
AAAATAAGTATTAG
Found at i:55980824 original size:1 final size:1
Alignment explanation
Indices: 55980818--55980845 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
55980808 CAATATCTAG
55980818 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
55980846 GAGACCCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:56005028 original size:12 final size:11
Alignment explanation
Indices: 56005011--56005036 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
56005001 CCAGACACCC
56005011 AAAAAAAAAAG
1 AAAAAAAAAAG
56005022 AAAAAAAAAAG
1 AAAAAAAAAAG
56005033 AAAA
1 AAAA
56005037 CTAATCAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:56010236 original size:15 final size:15
Alignment explanation
Indices: 56010216--56010248 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
56010206 ATAATATGTG
56010216 AATAA-TATTATTTAA
1 AATAATTATT-TTTAA
56010231 AATAATTATTTTTAA
1 AATAATTATTTTTAA
56010246 AAT
1 AAT
56010249 TTACTATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAATTATTTTTAA
Found at i:56010281 original size:18 final size:18
Alignment explanation
Indices: 56010243--56010278 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
56010233 TAATTATTTT
*
56010243 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
56010261 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
56010279 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:56015711 original size:7 final size:7
Alignment explanation
Indices: 56015681--56015714 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
56015671 TATTATTCTA
56015681 TTTATTT
1 TTTATTT
*
56015688 TTCATTT
1 TTTATTT
*
56015695 TTCATTT
1 TTTATTT
56015702 TTTATTT
1 TTTATTT
56015709 TTTATT
1 TTTATT
56015715 CATTAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTATTT
Found at i:56020482 original size:16 final size:16
Alignment explanation
Indices: 56020463--56020507 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
56020453 AAAATATGTA
56020463 TAAAATTATTAAATAT
1 TAAAATTATTAAATAT
*
56020479 TAAAA-TAATATAATAT
1 TAAAATTATTA-AATAT
*
56020495 AAAAATTATTAAA
1 TAAAATTATTAAA
56020508 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 16 0.67
17 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATTATTAAATAT
Found at i:56021188 original size:19 final size:20
Alignment explanation
Indices: 56021158--56021201 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
56021148 CAAACACCAT
56021158 AAAATATAATTT-TATTTTA
1 AAAATATAATTTATATTTTA
56021177 GAAAAT-TAATTTATATTTTA
1 -AAAATATAATTTATATTTTA
56021197 AAAAT
1 AAAAT
56021202 CATTTTCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
AAAATATAATTTATATTTTA
Found at i:56021199 original size:18 final size:18
Alignment explanation
Indices: 56021157--56021199 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
56021147 CCAAACACCA
56021157 TAAAATATAATTTTATTT
1 TAAAATATAATTTTATTT
56021175 TAGAAA-ATTAATTTATATTT
1 TA-AAATA-TAATTT-TATTT
56021195 TAAAA
1 TAAAA
56021200 ATCATTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 12 0.55
20 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAAATATAATTTTATTT
Found at i:56021724 original size:30 final size:32
Alignment explanation
Indices: 56021688--56021747 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 32
56021678 TTTGAGAAAG
56021688 TTATTTTAAATATAAA-GAAA-A-TATTTATAT
1 TTATTTTAAAT-TAAATGAAATATTATTTATAT
56021718 TTATTTTAAATTAAATGAAATATTATTTAT
1 TTATTTTAAATTAAATGAAATATTATTTAT
56021748 TGATTAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 4 0.15
30 15 0.56
31 1 0.04
32 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATTTTAAATTAAATGAAATATTATTTATAT
Found at i:56032289 original size:29 final size:29
Alignment explanation
Indices: 56032243--56032299 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
56032233 ATTTTTGTAT
56032243 TATTTATATATTTGAAATGTAGT-TTTCA
1 TATTTATATATTTGAAATGTAGTCTTTCA
* * *
56032271 TATTTTTATTTTTAGAAATTTAGTCTTTC
1 TATTTATATATTT-GAAATGTAGTCTTTC
56032300 CACTTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 9 0.38
30 4 0.17
ACGTcount: A:0.28, C:0.05, G:0.09, T:0.58
Consensus pattern (29 bp):
TATTTATATATTTGAAATGTAGTCTTTCA
Found at i:56035469 original size:20 final size:20
Alignment explanation
Indices: 56035429--56035469 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
56035419 TTATTAACAC
*
56035429 TTTTTATATTTTTAAACTTA
1 TTTTTATATTTTAAAACTTA
* *
56035449 TTTTTTTATTTTAAAATTTA
1 TTTTTATATTTTAAAACTTA
56035469 T
1 T
56035470 AAATTAGGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTTATATTTTAAAACTTA
Found at i:56036240 original size:14 final size:14
Alignment explanation
Indices: 56036223--56036250 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
56036213 TCTTTTCTTC
56036223 ATTTTTTTCTCTAT
1 ATTTTTTTCTCTAT
56036237 ATTTTTTTCTCTAT
1 ATTTTTTTCTCTAT
56036251 TGCATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTTTCTCTAT
Found at i:56036849 original size:3 final size:3
Alignment explanation
Indices: 56036843--56036896 Score: 56
Period size: 3 Copynumber: 17.3 Consensus size: 3
56036833 ATTGAATTGC
* *
56036843 ATT ATT ATT A-T ATT ATCT ATT ATTT ATT ATAT ATT ATT ATT AGT AGT
1 ATT ATT ATT ATT ATT AT-T ATT A-TT ATT AT-T ATT ATT ATT ATT ATT
56036890 ATT ATT A
1 ATT ATT A
56036897 CTTCCATACG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
2 2 0.04
3 34 0.76
4 9 0.20
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:56037039 original size:27 final size:25
Alignment explanation
Indices: 56036969--56037041 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 25
56036959 ATTGTACATG
* *
56036969 TATATATTTTATATATTTTATTATTA
1 TATATATCTTATA-ATTTTTTTATTA
*
56036995 T-TTTATCTTCATAA-TTTTTTATTA
1 TATATATCTT-ATAATTTTTTTATTA
56037019 TATATATACTTATACATTTTTTT
1 TATATAT-CTTATA-ATTTTTTT
56037042 CTATTTTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
24 10 0.26
25 14 0.37
26 8 0.21
27 6 0.16
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.64
Consensus pattern (25 bp):
TATATATCTTATAATTTTTTTATTA
Found at i:56043000 original size:44 final size:44
Alignment explanation
Indices: 56042949--56043402 Score: 345
Period size: 44 Copynumber: 10.3 Consensus size: 44
56042939 TACTGGTGGC
* *
56042949 GAAGTAGATCCAAGAAAGCAGATTTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * *** * * *
56042993 GAAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGC
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
*
56043038 GAAGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * * * * * *
56043082 GAAGTAGATTC-AAGATACCAGATCTTATCTCCCCATACTAGTGGTG-
1 GAAGTAGA-TCGAAGAAAGCAGATCTTGTCT--TCAT-GTATTGGCGT
*
56043128 GAA-TAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * * *** * *
56043171 GAAGTAGATCGAAGATACCAGATCTTGTCTCCCCATACTGGTGGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
* *
56043216 GGAGTAGATCGAAGAAAACAGATC---T-TT-ATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * * * *
56043255 AAAGTAGATTGAATAAAACAGATATTGTCTTCATGTATTGGCGT
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
* * * ***
56043299 GAAGTAGATTGGAGAAGGCAGATCTTGTCTTCCCATACTGTGGC--
1 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTA-T-TGGCGT
* * * *
56043343 GAAGTACATC-AGAGATAGCAGATCTTGTCTTCCTGTAGTGGCAGT
1 GAAGTAGATCGA-AGAAAGCAGATCTTGTCTTCATGTATTGGC-GT
56043388 GAAGTAGATCGAAGA
1 GAAGTAGATCGAAGA
56043403 TACGAGTCTT
Statistics
Matches: 316, Mismatches: 73, Indels: 41
0.73 0.17 0.10
Matches are distributed among these distances:
39 21 0.07
40 5 0.02
41 1 0.00
42 12 0.04
43 8 0.03
44 159 0.50
45 93 0.29
46 11 0.03
47 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (44 bp):
GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGT
Found at i:56043074 original size:89 final size:89
Alignment explanation
Indices: 56042923--56043286 Score: 499
Period size: 89 Copynumber: 4.1 Consensus size: 89
56042913 TGAATACAAA
* *
56042923 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATTTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAACAGATCTTGTCTTCATGTATT
56042988 GGCGTGAAGTAGATCGAAGATACC
66 GGCGTGAAGTAGATCGAAGATACC
*
56043012 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAGCAGATCTTGTCTTCATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAACAGATCTTGTCTTCATGTATT
56043077 GGCGTGAAGTAGATTC-AAGATACC
66 GGCGTGAAGTAGA-TCGAAGATACC
* * * * *
56043101 AGATCTTATCTCCCCATACTAGTGGTGGAA-TAGATCGAAGAAAACAGATCTTGTCTTCATGTAT
1 AGATCTTGTCTTCCCATACTGGTGG-CGAAGTAGATCCAAGAAAACAGATCTTGTCTTCATGTAT
56043165 TGGCGTGAAGTAGATCGAAGATACC
65 TGGCGTGAAGTAGATCGAAGATACC
* * * *
56043190 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAACAGATC---T-TT-ATGTATT
1 AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAACAGATCTTGTCTTCATGTATT
* * * * *
56043250 GGCGTAAAGTAGATTGAATAAAAC
66 GGCGTGAAGTAGATCGAAGATACC
*
56043274 AGATATTGTCTTC
1 AGATCTTGTCTTC
56043287 ATGTATTGGC
Statistics
Matches: 253, Mismatches: 18, Indels: 13
0.89 0.06 0.05
Matches are distributed among these distances:
84 37 0.15
85 2 0.01
86 1 0.00
88 4 0.02
89 204 0.81
90 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.29
Consensus pattern (89 bp):
AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCCAAGAAAACAGATCTTGTCTTCATGTATT
GGCGTGAAGTAGATCGAAGATACC
Found at i:56045039 original size:3 final size:3
Alignment explanation
Indices: 56045033--56045083 Score: 59
Period size: 3 Copynumber: 16.3 Consensus size: 3
56045023 ATTGAATTGC
*
56045033 ATT ATT ATT A-T ATT ATCT ATT ATTT ATT ATAT ATT ATT ATT AGT ATT
1 ATT ATT ATT ATT ATT AT-T ATT A-TT ATT AT-T ATT ATT ATT ATT ATT
56045080 ATT A
1 ATT A
56045084 CTTCCATACG
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 2 0.05
3 31 0.74
4 9 0.21
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:56051631 original size:12 final size:12
Alignment explanation
Indices: 56051605--56051638 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
56051595 AAGATACATA
56051605 AATAAATAGTAAT
1 AATAAATA-TAAT
56051618 AATAAATATAAT
1 AATAAATATAAT
56051630 AATAAATAT
1 AATAAATAT
56051639 GGTACAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.62
13 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
AATAAATATAAT
Found at i:56053328 original size:44 final size:44
Alignment explanation
Indices: 56053280--56053399 Score: 177
Period size: 44 Copynumber: 2.7 Consensus size: 44
56053270 TCATCGTTTT
* *
56053280 AATCTGCTCTACTGCAACTTCAGGGAAATAAGATTAGTAGCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTC
* * *
56053324 AATCTGCTCCACTGCAACTTCAAGGAGATAAGATTGGTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTC
* *
56053368 AACCTGCTCCACTGCAACTTTAGGGAGATAAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAG
56053400 GTTTGCCATA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTC
Found at i:56053534 original size:143 final size:143
Alignment explanation
Indices: 56053277--56053973 Score: 862
Period size: 143 Copynumber: 4.9 Consensus size: 143
56053267 GATTCATCGT
* * ** * * *
56053277 TTTAATCTGCTCTACTGCAACTTCAGGGAAATAAGATTAG-TAG-CTTCAATCTGCTCCACTGCA
1 TTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCT-GTCTTCAGTCTGCTCCGCTGCA
* ** * * * * *
56053340 ACTTCAAGGAGATAAGATTGGTATCTTCAACCTGCTCCACTGCAACTTTAGGGAGATAAGGTTTG
65 ACTTCAAGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCG
56053405 CCATAATTTGTAGC
130 CCATAATTTGTAGC
* * *
56053419 TTTAATCTGTTCCACTGCAACGCCAGGGAAATAAAATTCGCCGTCTTCAGTTTGCTCCGCTGCAA
1 TTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAA
* * * * *
56053484 CTTCAATGAGATAAGGCTGGTGGCTTCAATATACTCCACTGCAACTTTAGGAAGATAAGATTCGC
66 CTTCAAGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGC
56053549 CATAATTTGTAGC
131 CATAATTTGTAGC
* * * * *
56053562 TTTAATCTGTTCCGA-TACAACGCCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTACA
1 TTTAATCTGTTCC-ACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCA
* * * * * **
56053626 ACTTCAGGGAGATAAGGCTGGTGGCTTTAATCTGCTTCACTGTAACTTCAAAAAGATAAGATTCG
65 ACTTCAAGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCG
56053691 CCATAATTTGTAGC
130 CCATAATTTGTAGC
* * * *
56053705 TTTAATCTGTTCCACTGCAGCACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCTGCTGTAA
1 TTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAA
* * * * * * *
56053770 CTTTAGGGAGATATGGTTGATGGCTTCAATCTGCTTCATTGCAACTTCAGGAAGATAAGATTCCC
66 CTTCAAGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGC
56053835 CATAATTTGTAGC
131 CATAATTTGTAGC
* * * * * *
56053848 TTTAATCTGTTGCACTTCAATGCTAGGGAAATAAGATTCACTGTCTTCAGTCTGCTCCGCTGCTA
1 TTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAA
*
56053913 CTTC-AGAGAGATAAGGTTGGTGGCTTCAATTTGCTCCACTGCAACTTCAGGAAGATAAGAT
66 CTTCAAG-GAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGAT
56053974 CTGCCACAAC
Statistics
Matches: 475, Mismatches: 75, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
142 37 0.08
143 437 0.92
144 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (143 bp):
TTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCAA
CTTCAAGGAGATAAGGTTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGC
CATAATTTGTAGC
Found at i:56058059 original size:19 final size:19
Alignment explanation
Indices: 56058037--56058076 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
56058027 TATGAAATTT
*
56058037 AATGCATATG-ATGAAATGC
1 AATGCAGATGCATG-AATGC
56058056 AATGCAGATGCATGAATGC
1 AATGCAGATGCATGAATGC
56058075 AA
1 AA
56058077 AAAGAGGCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 16 0.84
20 3 0.16
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (19 bp):
AATGCAGATGCATGAATGC
Found at i:56060129 original size:4 final size:4
Alignment explanation
Indices: 56060098--56060142 Score: 51
Period size: 4 Copynumber: 12.0 Consensus size: 4
56060088 AAACAAAAAG
* *
56060098 TAAA AAAA TAAA -AAA TGAA TAAA T--A TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
56060143 AAGAAAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 29 0.85
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:56060136 original size:18 final size:17
Alignment explanation
Indices: 56060092--56060144 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 17
56060082 CAAGAAAAAC
*
56060092 AAAAAGTAAA-AAA-AT
1 AAAAAATAAATAAATAT
*
56060107 AAAAAATGAATAAATAT
1 AAAAAATAAATAAATAT
56060124 AAATAAATAAATAAATA-
1 AAA-AAATAAATAAATAT
56060141 AAAA
1 AAAA
56060145 GAAAAGTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 8 0.25
16 4 0.12
17 8 0.25
18 12 0.38
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAAAATAAATAAATAT
Found at i:56062213 original size:29 final size:30
Alignment explanation
Indices: 56062157--56062231 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
56062147 ATCTCAAAAT
* * *
56062157 TATACATGAACTTTGATTTAATATGCAATTG
1 TATACATGAACTTTAATTT-AGATGCAATTA
*
56062188 TATACATGAACTTTAATTT-GGTGCAATTA
1 TATACATGAACTTTAATTTAGATGCAATTA
*
56062217 TATACAAGAAACTTT
1 TATACATG-AACTTT
56062232 CAAATGTATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 14 0.37
30 6 0.16
31 18 0.47
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.40
Consensus pattern (30 bp):
TATACATGAACTTTAATTTAGATGCAATTA
Found at i:56066462 original size:16 final size:16
Alignment explanation
Indices: 56066429--56066463 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
56066419 TTACTATGTG
*
56066429 TATAAAATATTTGAAA
1 TATAAAATATTAGAAA
*
56066445 TATAAAATATTAGTAA
1 TATAAAATATTAGAAA
56066461 TAT
1 TAT
56066464 TTTCAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (16 bp):
TATAAAATATTAGAAA
Found at i:56071194 original size:22 final size:22
Alignment explanation
Indices: 56071169--56071238 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
56071159 AATTTCTAAT
56071169 TTATATTTATATTTTACAAATA
1 TTATATTTATATTTTACAAATA
* * *
56071191 TTATCTATTGTTTGTATTT-CAATTA
1 TTA--TATT-TATAT-TTTACAAATA
* *
56071216 TTCTATTTATTTTTTACAAATA
1 TTATATTTATATTTTACAAATA
56071238 T
1 T
56071239 ATTTATGGCT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
21 3 0.08
22 12 0.33
23 4 0.11
24 4 0.11
25 10 0.28
26 3 0.08
ACGTcount: A:0.31, C:0.07, G:0.03, T:0.59
Consensus pattern (22 bp):
TTATATTTATATTTTACAAATA
Found at i:56079777 original size:3 final size:3
Alignment explanation
Indices: 56079771--56079806 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
56079761 GATTAAGTAA
*
56079771 AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
56079807 GGTGGAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:56080429 original size:5 final size:5
Alignment explanation
Indices: 56080419--56080454 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
56080409 AAGAGGAAAG
*
56080419 AAAAT AAAAT AAAAT AAAAAT AAGAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT
56080455 TTGAAATCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:56080440 original size:16 final size:16
Alignment explanation
Indices: 56080419--56080453 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
56080409 AAGAGGAAAG
56080419 AAAATAAAATAAAATA
1 AAAATAAAATAAAATA
*
56080435 AAAATAAGATAAAATA
1 AAAATAAAATAAAATA
56080451 AAA
1 AAA
56080454 TTTGAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (16 bp):
AAAATAAAATAAAATA
Found at i:56086740 original size:9 final size:9
Alignment explanation
Indices: 56086728--56086775 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
56086718 TTTAAATATT
56086728 TTTTTATAA
1 TTTTTATAA
*
56086737 TTTTCA-ATA
1 TTTTTATA-A
*
56086746 TTTTT-GAA
1 TTTTTATAA
56086754 TTTTTATAA
1 TTTTTATAA
56086763 TTTTTATAA
1 TTTTTATAA
56086772 TTTT
1 TTTT
56086776 CAATTTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
8 7 0.21
9 26 0.79
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTTATAA
Found at i:56086755 original size:17 final size:19
Alignment explanation
Indices: 56086728--56086779 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 19
56086718 TTTAAATATT
*
56086728 TTTTTATAATTTTCAAT-A
1 TTTTTAGAATTTTCAATAA
*
56086746 TTTTT-GAATTTT-TATAA
1 TTTTTAGAATTTTCAATAA
*
56086763 TTTTTATAATTTTCAAT
1 TTTTTAGAATTTTCAAT
56086780 TTTAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.07
17 12 0.44
18 11 0.41
19 2 0.07
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTTTAGAATTTTCAATAA
Found at i:56086939 original size:19 final size:17
Alignment explanation
Indices: 56086915--56086952 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 17
56086905 TTTTACTAAA
56086915 TATATATTTTCTAAATTTT
1 TATATATTTT-T-AATTTT
56086934 TATATATTTTTAATTTT
1 TATATATTTTTAATTTT
56086951 TA
1 TA
56086953 ATTAATTGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 8 0.42
18 1 0.05
19 10 0.53
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATATATTTTTAATTTT
Found at i:56087873 original size:20 final size:20
Alignment explanation
Indices: 56087848--56087887 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56087838 GATTGAATCC
56087848 CATGATTAATTTACATTTGA
1 CATGATTAATTTACATTTGA
56087868 CATGATTAATTTACATTTGA
1 CATGATTAATTTACATTTGA
56087888 AGCTTTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
CATGATTAATTTACATTTGA
Found at i:56088219 original size:42 final size:42
Alignment explanation
Indices: 56088081--56088220 Score: 210
Period size: 42 Copynumber: 3.3 Consensus size: 42
56088071 TAAACAAAAA
* * *
56088081 CGCCGCTAAAGATCATGTTCTTTAGTGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
* *
56088123 CGCCGCTAAAGAATATGATCTTTAGCGGC-TTTTGTTTCTAAA
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT-TTTCTAAG
*
56088165 CGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
56088207 CGCCGCTAAAGAAC
1 CGCCGCTAAAGAAC
56088221 GTCGTTAAAG
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
41 4 0.05
42 80 0.91
43 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAG
Found at i:56088285 original size:42 final size:41
Alignment explanation
Indices: 56088226--56088430 Score: 173
Period size: 42 Copynumber: 4.8 Consensus size: 41
56088216 AGAACGTCGT
*
56088226 TAAAGAACATGATCTTTAGCGGCGATTTCTACAAAGCGCCGC
1 TAAAGAACATGATCTTTAGCGGCG-TTTGTACAAAGCGCCGC
* * *
56088268 TAAAGGACATGATCTTTAGTGGCGTTTGTGA-ATATGCGCCGC
1 TAAAGAACATGATCTTTAGCGGCGTTTGT-ACA-AAGCGCCGC
* ** * *
56088310 TAAAGAACATGTTCTTTAATGGCGCTTTGTAGAAAACGCCGC
1 TAAAGAACATGATCTTTAGCGGCG-TTTGTACAAAGCGCCGC
* * * * *
56088352 TAAAGACCATGTTCTTTAGCCGCGCTTTTTTTACAAA-TGCCGC
1 TAAAGAACATGATCTTTAG-CG-GC-GTTTGTACAAAGCGCCGC
56088395 TAAAGAACAT-ATTCTTTAGCGGCGTTTTTGTACAAA
1 TAAAGAACATGA-TCTTTAGCGGCG--TTTGTACAAA
56088431 AACGCCACTA
Statistics
Matches: 133, Mismatches: 20, Indels: 20
0.77 0.12 0.12
Matches are distributed among these distances:
41 7 0.05
42 88 0.66
43 28 0.21
44 10 0.08
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (41 bp):
TAAAGAACATGATCTTTAGCGGCGTTTGTACAAAGCGCCGC
Found at i:56088307 original size:97 final size:97
Alignment explanation
Indices: 56088129--56088317 Score: 238
Period size: 97 Copynumber: 1.9 Consensus size: 97
56088119 TAAGCGCCGC
* * * *
56088129 TAAAGAATATGATCTTTAGCGGCTTTTGTTTCTAAACGCCGCTAAAGAACATGATCTTTAGCAGC
1 TAAAGAACATGATCTTTAGCGGCATTTGCTACTAAACGCCGCTAAAGAACATGATCTTTAGCAGC
* ***
56088194 GTTTTTTTCTAAGCGCCGCTAAAGAACGTCGT
66 GTTTGTGAATAAGCGCCGCTAAAGAACGTCGT
* **
56088226 TAAAGAACATGATCTTTAGCGGCGATTT-CTAC-AAAGCGCCGCTAAAGGACATGATCTTTAGTG
1 TAAAGAACATGATCTTTAGCGGC-ATTTGCTACTAAA-CGCCGCTAAAGAACATGATCTTTAGCA
*
56088289 GCGTTTGTGAATATGCGCCGCTAAAGAAC
64 GCGTTTGTGAATAAGCGCCGCTAAAGAAC
56088318 ATGTTCTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
96 3 0.04
97 72 0.92
98 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (97 bp):
TAAAGAACATGATCTTTAGCGGCATTTGCTACTAAACGCCGCTAAAGAACATGATCTTTAGCAGC
GTTTGTGAATAAGCGCCGCTAAAGAACGTCGT
Found at i:56088350 original size:139 final size:139
Alignment explanation
Indices: 56088087--56088357 Score: 308
Period size: 139 Copynumber: 1.9 Consensus size: 139
56088077 AAAACGCCGC
* * * * * * * *
56088087 TAAAGATCATGTTCTTTAGTGGCGTTTTTTTCTAAGCGCCGCTAAAGAATATGATCTTTAGCGGC
1 TAAAGAACATGATCTTTAGCGGCGATTTCTACAAAGCGCCGCTAAAGAACATGATCTTTAGCGGC
* *** * * * * * *
56088152 TTTTGTTTCTAAACGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTTTTCTAAGCGCCGCTAAA
66 GTTTGTGAATAAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTGTACAAAACGCCGCTAAA
56088217 GAACGTCGT
131 GAACGTCGT
* *
56088226 TAAAGAACATGATCTTTAGCGGCGATTTCTACAAAGCGCCGCTAAAGGACATGATCTTTAGTGGC
1 TAAAGAACATGATCTTTAGCGGCGATTTCTACAAAGCGCCGCTAAAGAACATGATCTTTAGCGGC
** * ** *
56088291 GTTTGTGAATATGCGCCGCTAAAGAACATGTTCTTTAATGGCGCTTTGTAGAAAACGCCGCTAAA
66 GTTTGTGAATAAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTGTACAAAACGCCGCTAAA
56088356 GA
131 GA
56088358 CCATGTTCTT
Statistics
Matches: 106, Mismatches: 26, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
139 106 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (139 bp):
TAAAGAACATGATCTTTAGCGGCGATTTCTACAAAGCGCCGCTAAAGAACATGATCTTTAGCGGC
GTTTGTGAATAAACGCCGCTAAAGAACATGATCTTTAACAGCGCTTTGTACAAAACGCCGCTAAA
GAACGTCGT
Found at i:56088829 original size:21 final size:21
Alignment explanation
Indices: 56088805--56088855 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
56088795 TTCTTTTGAA
*
56088805 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
56088826 CCTCCGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
56088847 CCTTTGCTT
1 CCTCTGCTT
56088856 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.47, G:0.18, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:56091425 original size:127 final size:125
Alignment explanation
Indices: 56091036--56091445 Score: 327
Period size: 127 Copynumber: 3.3 Consensus size: 125
56091026 AGTTTGCGGC
* *
56091036 GTTTTAAATAAACACGCCACTAAAGAGTTCAAATCATTTAAGAAAATGACGCCGTTTTCGTACAC
1 GTTTTACATAAAAACGCCACTAAA-A-TTCAAATCATTTAAGAAAATGACGCCGTTTTCGTACAC
* * * * * *
56091101 ACAAACATTTATGGATTTGCGGCGTTTCTATAAAAAACACCACGATTGCATACCTTCTGTGGC
64 ACAAAAAATTATAGATTTGCGGCGTTTCTAT-AAAAACGCCACTATTGCATACCTTCTGTGGT
* * * * * *
56091164 GTTTTCCA-AAAAACGCCACTAAAATTCAAATTCCTGTAATGAAACA-G-CGACATTCT-G-A-A
1 GTTTTACATAAAAACGCCACTAAAATTCAAA-TCATTTAA-GAAA-ATGACGCCGTTTTCGTACA
***** * * * * * ** * * *
56091223 CATTTTGTAA-TACATATTTGTGGCGTTT-TCATACTAAACGCCGCTAAAGCTTACAGTT-TG-C
63 CA-CAAAAAATTATAGATTTGCGGCGTTTCT-ATA-AAAACGCCACTATTGCATAC-CTTCTGTG
56091284 GT
124 GT
* *
56091286 CGTTTTAAATAAAAACGCCACTAAATAGTTCAAATCGTTTAAGAAAATGACGCCGTTTTCGTACA
1 -GTTTTACATAAAAACGCCACTAAA-A-TTCAAATCATTTAAGAAAATGACGCCGTTTTCGTACA
56091351 CACAAAAAATTATAGATTTGCGGCGTTTCTATAAAAACGCCACTATTGCATACCTTCTGTGGT
63 CACAAAAAATTATAGATTTGCGGCGTTTCTATAAAAACGCCACTATTGCATACCTTCTGTGGT
* * *
56091414 GTTTTTCATAAAAAAGTCACTAAAATTCAAAT
1 GTTTTACATAAAAACGCCACTAAAATTCAAAT
56091446 TCCTGTGGCC
Statistics
Matches: 208, Mismatches: 54, Indels: 43
0.68 0.18 0.14
Matches are distributed among these distances:
122 3 0.01
123 41 0.20
124 24 0.12
125 27 0.13
126 23 0.11
127 59 0.28
128 30 0.14
129 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (125 bp):
GTTTTACATAAAAACGCCACTAAAATTCAAATCATTTAAGAAAATGACGCCGTTTTCGTACACAC
AAAAAATTATAGATTTGCGGCGTTTCTATAAAAACGCCACTATTGCATACCTTCTGTGGT
Found at i:56091437 original size:251 final size:251
Alignment explanation
Indices: 56090953--56091451 Score: 829
Period size: 251 Copynumber: 2.0 Consensus size: 251
56090943 TTCCTCAAAC
* *
56090953 GAAACGGCGACGTTCTGAACATTTTGTAATACACATTTGTGGCATTTTCATACTAAACGCCGCTA
1 GAAACAGCGACATTCTGAACATTTTGTAATACACATTTGTGGCATTTTCATACTAAACGCCGCTA
*
56091018 AAGCTTACAGTTTGCGGCGTTTTAAATAAACACGCCACTAAAGAGTTCAAATCATTTAAGAAAAT
66 AAGCTTACAGTTTGCGGCGTTTTAAATAAAAACGCCACTAAAGAGTTCAAATCATTTAAGAAAAT
* * *
56091083 GACGCCGTTTTCGTACACACAAACATTTATGGATTTGCGGCGTTTCTATAAAAAACACCACGATT
131 GACGCCGTTTTCGTACACACAAAAAATTATAGATTTGCGGCGTTTCTATAAAAAACACCACGATT
*
56091148 GCATACCTTCTGTGGCGTTTTCCAAAAAACGCCACTAAAATTCAAATTCCTGTAAT
196 GCATACCTTCTGTGGCGTTTTCCAAAAAAAGCCACTAAAATTCAAATTCCTGTAAT
* *
56091204 GAAACAGCGACATTCTGAACATTTTGTAATACATATTTGTGGCGTTTTCATACTAAACGCCGCTA
1 GAAACAGCGACATTCTGAACATTTTGTAATACACATTTGTGGCATTTTCATACTAAACGCCGCTA
* * *
56091269 AAGCTTACAGTTTGCGTCGTTTTAAATAAAAACGCCACTAAATAGTTCAAATCGTTTAAGAAAAT
66 AAGCTTACAGTTTGCGGCGTTTTAAATAAAAACGCCACTAAAGAGTTCAAATCATTTAAGAAAAT
* *
56091334 GACGCCGTTTTCGTACACACAAAAAATTATAGATTTGCGGCGTTTCTAT-AAAAACGCCACTATT
131 GACGCCGTTTTCGTACACACAAAAAATTATAGATTTGCGGCGTTTCTATAAAAAACACCACGATT
* * *
56091398 GCATACCTTCTGTGGTGTTTTTCATAAAAAAGTCACTAAAATTCAAATTCCTGT
196 GCATACCTTCTGTGGCGTTTTCCA-AAAAAAGCCACTAAAATTCAAATTCCTGT
56091452 GGCCAAACAG
Statistics
Matches: 230, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
250 35 0.15
251 195 0.85
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (251 bp):
GAAACAGCGACATTCTGAACATTTTGTAATACACATTTGTGGCATTTTCATACTAAACGCCGCTA
AAGCTTACAGTTTGCGGCGTTTTAAATAAAAACGCCACTAAAGAGTTCAAATCATTTAAGAAAAT
GACGCCGTTTTCGTACACACAAAAAATTATAGATTTGCGGCGTTTCTATAAAAAACACCACGATT
GCATACCTTCTGTGGCGTTTTCCAAAAAAAGCCACTAAAATTCAAATTCCTGTAAT
Found at i:56091833 original size:7 final size:7
Alignment explanation
Indices: 56091821--56091852 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
56091811 CCTTAGACAT
56091821 TAAACCC
1 TAAACCC
56091828 TAAACCC
1 TAAACCC
56091835 TAAACCC
1 TAAACCC
*
56091842 TTAACCC
1 TAAACCC
56091849 TAAA
1 TAAA
56091853 TTGACCTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.44, C:0.38, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:56092209 original size:39 final size:39
Alignment explanation
Indices: 56092127--56092215 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
56092117 CCATATTCCT
* * *
56092127 TAAACCTTGAATCATAGAACATATATAAACCTTAAATCC
1 TAAACCTTAAATCATAAAACATATATAAACCTTAAATCA
*
56092166 TAAACCCTAAATCATAAAACATATATAAA-CTATAAA-CTA
1 TAAACCTTAAATCATAAAACATATATAAACCT-TAAATC-A
56092205 TAAACCTTAAA
1 TAAACCTTAAA
56092216 CCTCAACCCT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
38 3 0.07
39 40 0.93
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (39 bp):
TAAACCTTAAATCATAAAACATATATAAACCTTAAATCA
Found at i:56094897 original size:16 final size:17
Alignment explanation
Indices: 56094878--56094911 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
56094868 TATATAATGT
56094878 ACTACTATTATA-TATA
1 ACTACTATTATATTATA
*
56094894 ACTAGTATTATATTATA
1 ACTACTATTATATTATA
56094911 A
1 A
56094912 ATTATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (17 bp):
ACTACTATTATATTATA
Found at i:56096049 original size:10 final size:10
Alignment explanation
Indices: 56096029--56096129 Score: 79
Period size: 10 Copynumber: 10.2 Consensus size: 10
56096019 ACCCATTTTT
56096029 ATTTT-AAAA
1 ATTTTAAAAA
56096038 ATTTTAAAAA
1 ATTTTAAAAA
**
56096048 ATTAAAAAAA
1 ATTTTAAAAA
56096058 GTATTTTAAAAA
1 --ATTTTAAAAA
*
56096070 TATTTTAAAAT
1 -ATTTTAAAAA
*
56096081 ATTTTAAAAT
1 ATTTTAAAAA
56096091 ATTTT--AAA
1 ATTTTAAAAA
56096099 A--TT-AAAA
1 ATTTTAAAAA
56096106 ATATTTAAAAA
1 AT-TTTAAAAA
56096117 ATATTTAAAAA
1 AT-TTTAAAAA
56096128 AT
1 AT
56096130 ATTTTAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 14
0.80 0.06 0.14
Matches are distributed among these distances:
6 2 0.03
7 4 0.05
8 3 0.04
9 5 0.06
10 29 0.37
11 27 0.35
12 8 0.10
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:56096068 original size:11 final size:10
Alignment explanation
Indices: 56096054--56096139 Score: 88
Period size: 10 Copynumber: 8.5 Consensus size: 10
56096044 AAAAATTAAA
56096054 AAAAGTATTTT
1 AAAA-TATTTT
56096065 AAAAATATTTT
1 -AAAATATTTT
56096076 AAAATATTTT
1 AAAATATTTT
56096086 AAAATATTTT
1 AAAATATTTT
*
56096096 -AAA-A-TTA
1 AAAATATTTT
*
56096103 AAAATATTTAA
1 AAAATATTT-T
*
56096114 AAAATATTTAA
1 AAAATATTT-T
56096125 AAAATATTTT
1 AAAATATTTT
56096135 AAAAT
1 AAAAT
56096140 TAAAAAAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 4 0.06
10 27 0.40
11 27 0.40
12 4 0.06
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (10 bp):
AAAATATTTT
Found at i:56096138 original size:10 final size:10
Alignment explanation
Indices: 56096028--56096139 Score: 97
Period size: 11 Copynumber: 11.1 Consensus size: 10
56096018 GACCCATTTT
56096028 TATTTTAAAA
1 TATTTTAAAA
56096038 -ATTTTAAAA
1 TATTTTAAAA
* **
56096047 AATTAAAAAAA
1 TATT-TTAAAA
56096058 GTATTTTAAAAA
1 -TATTTT-AAAA
56096070 TATTTTAAAA
1 TATTTTAAAA
56096080 TATTTTAAAA
1 TATTTTAAAA
56096090 TATTTT-AAA
1 TATTTTAAAA
*
56096099 -A-TTAAAAA
1 TATTTTAAAA
*
56096107 TATTTAAAAAA
1 TATTT-TAAAA
*
56096118 TATTTAAAAAA
1 TATTT-TAAAA
56096129 TATTTTAAAA
1 TATTTTAAAA
56096139 T
1 T
56096140 TAAAAAAAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
7 2 0.02
8 4 0.05
9 13 0.15
10 30 0.34
11 31 0.36
12 7 0.08
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:56096168 original size:42 final size:40
Alignment explanation
Indices: 56096086--56096190 Score: 158
Period size: 42 Copynumber: 2.6 Consensus size: 40
56096076 AAAATATTTT
* * *
56096086 AAAATATTTTAAAATT-AAAAATATTTAAAAAATATTTAA
1 AAAATATTTTAAAATTAAAAAAAATTAAAAAAATATGTAA
56096125 AAAATATTTTAAAATTAAAAAAAATTAAAACAAAGTATGTAA
1 AAAATATTTTAAAATTAAAAAAAATTAAAA-AAA-TATGTAA
56096167 AAAATATTTTAAAATTAAAAAAAA
1 AAAATATTTTAAAATTAAAAAAAA
56096191 AATATATTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
39 16 0.27
40 11 0.18
41 3 0.05
42 30 0.50
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (40 bp):
AAAATATTTTAAAATTAAAAAAAATTAAAAAAATATGTAA
Found at i:56099299 original size:14 final size:15
Alignment explanation
Indices: 56099282--56099325 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
56099272 ATGAATTATT
56099282 ATATTTAAATTA-AA
1 ATATTTAAATTATAA
56099296 ATATTTATAACTTATAA
1 ATATTTA-AA-TTATAA
56099313 A-ATTTAAATTATA
1 ATATTTAAATTATA
56099326 GGTTACAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 12 0.44
15 4 0.15
16 8 0.30
17 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATTTAAATTATAA
Found at i:56100625 original size:43 final size:42
Alignment explanation
Indices: 56100493--56100656 Score: 161
Period size: 43 Copynumber: 3.8 Consensus size: 42
56100483 TTTTATAAAT
* * * *
56100493 AAACGCCGCTATAGATCAGGATCTTTAGCGATGCTTTTT-TAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCG-CGCTTTTTCAAC
* * *
56100535 AAACGCTGCTATAGATCAAGACCTTTAGCG-GCTCTTATACCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGCGCT-TT-TTCAAC
* *
56100578 AAACGCCGCTATAGCTCAAGACCTTTAGCAGCGCTTTTTCAAA
1 AAACGCCGCTATAGATCAAGACCTTTAGC-GCGCTTTTTCAAC
* * *
56100621 AAACGCTGCTATAGATTACGACCTTTAGCGACGCTT
1 AAACGCCGCTATAGATCAAGACCTTTAGCG-CGCTT
56100657 CTCGCAAAAA
Statistics
Matches: 102, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
40 3 0.03
41 2 0.02
42 29 0.28
43 62 0.61
44 3 0.03
45 3 0.03
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGCGCTTTTTCAAC
Found at i:56100668 original size:86 final size:85
Alignment explanation
Indices: 56100493--56100670 Score: 207
Period size: 86 Copynumber: 2.1 Consensus size: 85
56100483 TTTTATAAAT
* * * * *
56100493 AAACGCCGCTATAGATCAGGATCTTTAGCGATGCTTTTTTACAAACGCTGCTATAGATCAAGACC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTTAAAAAACGCTGCTATAGATCAAGACC
* * *
56100558 TTTAGCGGCTCTTATACCAC
66 TTTAGCGACGCTTATACCAA
* * *
56100578 AAACGCCGCTATAGCTCAAGACCTTTAGC-AGCGCTTTTTCAAAAAACGCTGCTATAGATTACGA
1 AAACGCCGCTATAGATCAAGACCTTTAGCGA-CGCTTTTT-AAAAAACGCTGCTATAGATCAAGA
*
56100642 CCTTTAGCGACGCTTCT-CGCAA
64 CCTTTAGCGACGCTTATAC-CAA
56100664 AAACGCC
1 AAACGCC
56100671 ACTAAAAACA
Statistics
Matches: 78, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
84 1 0.01
85 34 0.44
86 43 0.55
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.26
Consensus pattern (85 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTTAAAAAACGCTGCTATAGATCAAGACC
TTTAGCGACGCTTATACCAA
Found at i:56104627 original size:89 final size:83
Alignment explanation
Indices: 56104521--56104733 Score: 255
Period size: 83 Copynumber: 2.6 Consensus size: 83
56104511 TATAAATAAC
* *
56104521 TTATTTAATATATAAATTAAAAAGTACTAATTAATTCAAATCTTAAACCCT-AACCCGACCCCAA
1 TTATTTAATATAAAAATTAAAAA--AC--ACTAATT--AATC-TAAACCCTAAACCCGACCCCAA
56104585 ATCCCTAACCCCTAACCACTAAACT
59 ATCCCTAACCCCTAACCACTAAACT
*
56104610 TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCTTAAACCCGACCCCAAATCCCTA
1 TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCGACCCCAAATCCCTA
56104675 ACCCCTAA--A-T----T
66 ACCCCTAACCACTAAACT
* *
56104686 TTATTTAATATATAACTT-AAAAACACTAATTAATCTAAACCCTAAACC
1 TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCCTAAACC
56104734 ATAACCCGAT
Statistics
Matches: 117, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
75 29 0.25
76 17 0.15
80 1 0.01
81 1 0.01
82 7 0.06
83 32 0.27
85 6 0.05
87 2 0.02
89 22 0.19
ACGTcount: A:0.45, C:0.24, G:0.01, T:0.29
Consensus pattern (83 bp):
TTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCCTAAACCCGACCCCAAATCCCTA
ACCCCTAACCACTAAACT
Found at i:56104689 original size:76 final size:75
Alignment explanation
Indices: 56104594--56104733 Score: 226
Period size: 76 Copynumber: 1.9 Consensus size: 75
56104584 AATCCCTAAC
*
56104594 CCCTAACCACTAAACTTTATTTAATATAAAAATTAAAAAACACTAATTAATCTAAACCTTAAACC
1 CCCTAACCACTAAACTTTATTTAATATAAAAATT-AAAAACACTAATTAATCTAAACCCTAAACC
56104659 CGACCCCAAAT
65 CGACCCCAAAT
* * * *
56104670 CCCTAACCCCTAAATTTTATTTAATATATAACTTAAAAACACTAATTAATCTAAACCCTAAACC
1 CCCTAACCACTAAACTTTATTTAATATAAAAATTAAAAACACTAATTAATCTAAACCCTAAACC
56104734 ATAACCCGAT
Statistics
Matches: 59, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
75 29 0.49
76 30 0.51
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.29
Consensus pattern (75 bp):
CCCTAACCACTAAACTTTATTTAATATAAAAATTAAAAACACTAATTAATCTAAACCCTAAACCC
GACCCCAAAT
Found at i:56104732 original size:7 final size:7
Alignment explanation
Indices: 56104720--56104786 Score: 50
Period size: 7 Copynumber: 10.0 Consensus size: 7
56104710 ACTAATTAAT
56104720 CTAAACC
1 CTAAACC
56104727 CTAAACC
1 CTAAACC
*
56104734 AT-AACC
1 CTAAACC
* *
56104740 C-GATCC
1 CTAAACC
56104746 CT-AACC
1 CTAAACC
56104752 CTAAACC
1 CTAAACC
* *
56104759 ATAACCC
1 CTAAACC
*
56104766 CTAACCC
1 CTAAACC
*
56104773 CTAATCC
1 CTAAACC
56104780 CTAAACC
1 CTAAACC
56104787 TTATTTAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
6 13 0.27
7 35 0.73
ACGTcount: A:0.37, C:0.45, G:0.01, T:0.16
Consensus pattern (7 bp):
CTAAACC
Found at i:56104917 original size:14 final size:14
Alignment explanation
Indices: 56104898--56104937 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
56104888 CCCATAACCT
56104898 AATCCCTAACCCTG
1 AATCCCTAACCCTG
*
56104912 AATCCCTAACCCTT
1 AATCCCTAACCCTG
*
56104926 AAACCCTAACCC
1 AATCCCTAACCC
56104938 CTAACACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.45, G:0.03, T:0.20
Consensus pattern (14 bp):
AATCCCTAACCCTG
Found at i:56104939 original size:21 final size:22
Alignment explanation
Indices: 56104905--56104951 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
56104895 CCTAATCCCT
* *
56104905 AACCCTGAATCCCTAACCCTTA
1 AACCCTGAACCCCTAACACTTA
56104927 AACCCT-AACCCCTAACACTTA
1 AACCCTGAACCCCTAACACTTA
56104948 AACC
1 AACC
56104952 TTATTTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.36, C:0.43, G:0.02, T:0.19
Consensus pattern (22 bp):
AACCCTGAACCCCTAACACTTA
Found at i:56105074 original size:164 final size:164
Alignment explanation
Indices: 56104744--56105092 Score: 517
Period size: 164 Copynumber: 2.1 Consensus size: 164
56104734 ATAACCCGAT
* *
56104744 CCCT-AACCCTAAACCATAACCCCTAACCCCTAATCCCTAAACCTTATTTAATATATAATTAAAA
1 CCCTGAACCCTAAACCTTAAACCCTAACCCCTAATCCCTAAACCTTATTTAATATATAATTAAAA
* *
56104808 CACACTAATTAATCTAAATCCCTAAACTCTAACCTAACACCGATTTTATAAACCCTAAATCCCTA
66 CACACTAATTAATCTAAATCCCTAAACTCTAACCTAACACCAAATTTATAAACCCTAAATCCCTA
*
56104873 ACTCTTAATATCTAACCCATAACCTAATCCCTAA
131 ACTCTTAACATCTAACCCATAACCTAATCCCTAA
* *
56104907 CCCTGAATCCCTAACCCTTAAACCCTAACCCCTAA-CACTTAAACCTTATTTAATATATAATTAA
1 CCCTGAA-CCCTAAACCTTAAACCCTAACCCCTAATC-CCTAAACCTTATTTAATATATAATTAA
* * * *
56104971 AATACACTAATTAATCTAAAT-CCTAAACTCTAACTTAACACTAAATTTCTAAACCCTAAATCCC
64 AACACACTAATTAATCTAAATCCCTAAACTCTAACCTAACACCAAATTTATAAACCCTAAATCCC
*
56105035 TAACTCTTAACATCTAACCCCTAACCTAA-CCCTTAA
129 TAACTCTTAACATCTAACCCATAACCTAATCCC-TAA
*
56105071 CCCTTAACCCATAAACCTTAAA
1 CCCTGAACCC-TAAACCTTAAA
56105093 TCACATTAAC
Statistics
Matches: 167, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
163 10 0.06
164 87 0.52
165 70 0.42
ACGTcount: A:0.40, C:0.32, G:0.01, T:0.28
Consensus pattern (164 bp):
CCCTGAACCCTAAACCTTAAACCCTAACCCCTAATCCCTAAACCTTATTTAATATATAATTAAAA
CACACTAATTAATCTAAATCCCTAAACTCTAACCTAACACCAAATTTATAAACCCTAAATCCCTA
ACTCTTAACATCTAACCCATAACCTAATCCCTAA
Found at i:56105133 original size:14 final size:15
Alignment explanation
Indices: 56105114--56105146 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
56105104 CTTAAACCAG
56105114 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
56105128 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
56105143 AATC
1 AATC
56105147 TATAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:56107681 original size:151 final size:151
Alignment explanation
Indices: 56107261--56107845 Score: 742
Period size: 151 Copynumber: 3.9 Consensus size: 151
56107251 TAGTTCAAAA
* **
56107261 AAATTTAGT-AAAAAACCCTTATTTCGGCCCTTTATTCGTATTTTTTTTCGAATTTTATTACTTA
1 AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTA
* * *
56107325 AAAAAATATACTATTTTCTAATTTTATTATTTTCCATTATTTTAGTACATTATATTTGAAATTTA
66 AAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
* *
56107390 AATAAATTTAGTGTGTTTTTT
131 AATAAATTTACTGTTTTTTTT
** * *
56107411 AAATAAATTAAAAAAACCCTTATTTCGGCCCTTTGCTCGTATTTTTTCCCGAATTTTATTACTTT
1 AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTAC-TT
56107476 CAATAAAAATATATTATTTTCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
65 -AA-AAAAATATATTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* *
56107540 TGTATTAAT-TATTT-CTGTTTTTTTT
127 T-T-TAAATAAATTTACTGTTTTTTTT
* * * *
56107565 AAATTTAGT-AAAAAACCCTAACTTCGGCCATTTGTTCGTATTTTTTCCCTAATTTTATTACTTT
1 AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTAC-TT
*
56107629 TAAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
65 AAAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
*
56107694 AAATAAATTTAGCAT-TTTTTTAAAT
130 AAATAAATTTA-C-TGTTTTTT--TT
* ** *
56107719 AAATTT--TAAAAAAACCCTTATTTCGGCCCTTTACTT-GTATTTTCCCCCTAATTTTATTACTT
1 AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTT-GTTCGTATTTTTTCCCGAATTTTATTACTT
* *
56107781 -TAAAAATATCA-TATTTTCTAATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAAATT
65 AAAAAAATAT-ATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
56107844 TA
129 TA
56107846 TTAATTTAGT
Statistics
Matches: 384, Mismatches: 34, Indels: 33
0.85 0.08 0.07
Matches are distributed among these distances:
149 4 0.01
150 12 0.03
151 168 0.44
152 14 0.04
153 96 0.25
154 80 0.21
155 6 0.02
156 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (151 bp):
AAATTTAGTAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTCCCGAATTTTATTACTTA
AAAAAATATATTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
AATAAATTTACTGTTTTTTTT
Found at i:56108085 original size:9 final size:10
Alignment explanation
Indices: 56108071--56108228 Score: 89
Period size: 10 Copynumber: 16.0 Consensus size: 10
56108061 AAAAATTACC
56108071 TTCTTT-TTT
1 TTCTTTCTTT
56108080 TTCTTTCTTT
1 TTCTTTCTTT
* *
56108090 TTCCTTCCTT
1 TTCTTTCTTT
*
56108100 CTCTCTTCTTCT
1 TTCT-TTCTT-T
*
56108112 CCTCCTTTCTTT
1 --TTCTTTCTTT
*
56108124 TTCTTTCTTC
1 TTCTTTCTTT
* *
56108134 TCCTTTCCTT
1 TTCTTTCTTT
56108144 TTCTTTC--T
1 TTCTTTCTTT
56108152 TTCTTTCTTT
1 TTCTTTCTTT
56108162 TTC-TTC---
1 TTCTTTCTTT
* *
56108168 TCCTTTCCTT
1 TTCTTTCTTT
56108178 TTCTTTCTTT
1 TTCTTTCTTT
*
56108188 CTT-TTTTTTT
1 -TTCTTTCTTT
*
56108198 TTCTTCTCATT
1 TTCTT-TCTTT
* *
56108209 TCCTTTCCTT
1 TTCTTTCTTT
56108219 TTCTTTCTTT
1 TTCTTTCTTT
56108229 CTTTCTTCTC
Statistics
Matches: 112, Mismatches: 23, Indels: 27
0.69 0.14 0.17
Matches are distributed among these distances:
6 2 0.02
7 3 0.03
8 8 0.07
9 11 0.10
10 66 0.59
11 13 0.12
12 2 0.02
13 5 0.04
14 2 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:56108117 original size:23 final size:22
Alignment explanation
Indices: 56108091--56108148 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
56108081 TCTTTCTTTT
56108091 TCCTTCCTTCTCTCTTCTTCTCC
1 TCCTTCCTT-TCTCTTCTTCTCC
* *
56108114 TCCTTTCTTTTTCTTTCTTCTCC
1 TCCTTCCTTTCTC-TTCTTCTCC
56108137 T--TTCCTTT-TCTT
1 TCCTTCCTTTCTCTT
56108149 TCTTTCTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.06
20 2 0.06
21 6 0.19
22 3 0.10
23 18 0.58
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (22 bp):
TCCTTCCTTTCTCTTCTTCTCC
Found at i:56108130 original size:4 final size:4
Alignment explanation
Indices: 56108123--56108235 Score: 77
Period size: 4 Copynumber: 25.5 Consensus size: 4
56108113 CTCCTTTCTT
56108123 TTTC TTTC TTCTCC TTTCC TTTTC TTTC TTTC TTTC -TT- TTTC TTCTCC
1 TTTC TTTC TT-T-C TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C
* *
56108171 TTTCC TTTTC TTTC TTTC TTTT TTTT TTTC TTCTC ATTTCC TTTCC TTTTC
1 TTT-C -TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTT-C -TTTC
56108222 TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TT
56108236 CTCATTTCCC
Statistics
Matches: 95, Mismatches: 2, Indels: 24
0.79 0.02 0.20
Matches are distributed among these distances:
3 4 0.04
4 54 0.57
5 19 0.20
6 18 0.19
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:56108154 original size:34 final size:34
Alignment explanation
Indices: 56108073--56108244 Score: 174
Period size: 34 Copynumber: 5.0 Consensus size: 34
56108063 AAATTACCTT
* *
56108073 CTTTTTTTTCTTTCTTTTTCCTTCCTTCT-CTCTT-
1 CTTTTCTTTCTTTCTTTTT-CTTTCTTCTCCT-TTC
* * *
56108107 CTTCTCCTCCTTTCTTTTTCTTTCTTCTCCTTTC
1 CTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTC
56108141 CTTTTCTTTCTTTCTTTCTT-TTTCTTCTCCTTTC
1 CTTTTCTTTCTTTCTTT-TTCTTTCTTCTCCTTTC
* *
56108175 CTTTTCTTTCTTTCTTTTTTTTTTTCTTCTCATTTC
1 CTTTTCTTTCTTTC--TTTTTCTTTCTTCTCCTTTC
* *
56108211 CTTTCCTTTTCTTTC--TTTCTTTCTTCTCATTTC
1 CTTTTC-TTTCTTTCTTTTTCTTTCTTCTCCTTTC
56108244 C
1 C
56108245 CTCTCCTTCT
Statistics
Matches: 120, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
33 28 0.23
34 59 0.49
35 4 0.03
36 21 0.17
37 8 0.07
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (34 bp):
CTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTC
Found at i:56108171 original size:54 final size:53
Alignment explanation
Indices: 56108082--56108244 Score: 149
Period size: 54 Copynumber: 3.1 Consensus size: 53
56108072 TCTTTTTTTT
* * * * * *
56108082 CTTTCTTTTTCCTTCCTTCTCTCTTCTTCTCCTCCTTTCTTTTTCTTTCTTCTC
1 CTTTCCTTTTCTTTCTTTCTTTCTTTTTCTTCTCCTTTC-TTTTCTTTCTTCTC
56108136 CTTTCCTTTTCTTTCTTTCTTTCTTTTTCTTCTCCTTTCCTTTTCTTTCTT-T-
1 CTTTCCTTTTCTTTCTTTCTTTCTTTTTCTTCTCCTTT-CTTTTCTTTCTTCTC
* * * *
56108188 CTTT--TTTTTTTTCTTCTCATTTCCTTTCCTT-TTCTTTC-TTTCTTTCTTCTC
1 CTTTCCTTTTCTTTCTT-TC-TTTCTTTTTCTTCTCCTTTCTTTTCTTTCTTCTC
*
56108239 ATTTCC
1 CTTTCC
56108245 CTCTCCTTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
49 10 0.11
50 12 0.13
51 10 0.11
52 14 0.15
53 1 0.01
54 43 0.47
55 1 0.01
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.67
Consensus pattern (53 bp):
CTTTCCTTTTCTTTCTTTCTTTCTTTTTCTTCTCCTTTCTTTTCTTTCTTCTC
Found at i:56109939 original size:41 final size:41
Alignment explanation
Indices: 56109894--56110013 Score: 204
Period size: 41 Copynumber: 2.9 Consensus size: 41
56109884 ACTGGCACTT
*
56109894 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
*
56109935 AGCCTGCTAGACATAAAGTCTGAAATATTTCACCGGCATCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
* *
56109976 AGCCTGCTAGACTTAAAGTCTAAAATGTTTCACCGGCA
1 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCA
56110014 GTAAACCTGA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (41 bp):
AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
Found at i:56111599 original size:2 final size:2
Alignment explanation
Indices: 56111592--56111616 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56111582 TATTTTACTA
56111592 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
56111617 ACATATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56112110 original size:21 final size:20
Alignment explanation
Indices: 56112084--56112122 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
56112074 GTTATAAAAA
56112084 AATAAA-AATATTTTCATTTTT
1 AATAAATAAT-TTTT-ATTTTT
56112105 AATAAATAATTTTTATTT
1 AATAAATAATTTTTATTT
56112123 CTATTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 10 0.59
22 3 0.18
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (20 bp):
AATAAATAATTTTTATTTTT
Found at i:56114308 original size:15 final size:16
Alignment explanation
Indices: 56114288--56114321 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
56114278 AATCTATTAA
56114288 AAATTATAAAAAT-AT
1 AAATTATAAAAATGAT
*
56114303 AAATTATTAAAATGAT
1 AAATTATAAAAATGAT
56114319 AAA
1 AAA
56114322 ATTACATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATGAT
Done.