Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 134 of 202
Found at i:41568922 original size:15 final size:16
Alignment explanation
Indices: 41568888--41568933 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
41568878 GTTTAATGGA
41568888 AAAATTATAAATAAATC
1 AAAATTA-AAATAAATC
*
41568905 AAAATTAAACTAAA-C
1 AAAATTAAAATAAATC
*
41568920 -AAATTAAAACAAAT
1 AAAATTAAAATAAAT
41568934 TAGACTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 11 0.44
15 1 0.04
16 6 0.24
17 7 0.28
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATTAAAATAAATC
Found at i:41569921 original size:37 final size:37
Alignment explanation
Indices: 41569879--41569950 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
41569869 GATGTATAGC
* *
41569879 TCTTCGGAGCATTTGGCATGTTATCAATTGGATTAGG
1 TCTTCGGAGCATTTGACATGCTATCAATTGGATTAGG
* * *
41569916 TCTTCGGGGCATTTGACGTGCTATCGATTGGATTA
1 TCTTCGGAGCATTTGACATGCTATCAATTGGATTA
41569951 ACTATTATGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (37 bp):
TCTTCGGAGCATTTGACATGCTATCAATTGGATTAGG
Found at i:41571784 original size:21 final size:22
Alignment explanation
Indices: 41571738--41571786 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
41571728 ACAATACCGG
41571738 TATCGCGATACCAAGGAAGAGGA
1 TATCGCGATACCAA-GAAGAGGA
* *
41571761 TATCGCGATACCCA-AAGTGGA
1 TATCGCGATACCAAGAAGAGGA
41571782 TATCG
1 TATCG
41571787 TGATGCAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.46
23 13 0.54
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (22 bp):
TATCGCGATACCAAGAAGAGGA
Found at i:41591365 original size:49 final size:49
Alignment explanation
Indices: 41591304--41591529 Score: 170
Period size: 50 Copynumber: 4.6 Consensus size: 49
41591294 TATGTCCTAA
* * *
41591304 ACATAGTCTTACATGGGATGTTTTC-TATACTG-CCAATGCCATATCCCAG
1 ACATGGTCTTACATGGGA-GTTCTCATAT-CGGCCCAATGCCATATCCCAG
* * *
41591353 ATATGGTCTTACATGGGAGTTCTCATATCGGCTCCCATGCCATGTCCCAG
1 ACATGGTCTTACATGGGAGTTCTCATATCGGC-CCAATGCCATATCCCAG
** ** * * *
41591403 ACATGGTCTTACGGGGGACCTCTCATCTCGATG-CCAACGCCATGTCCCAG
1 ACATGGTCTTACATGGGAGTTCTCATATCG--GCCCAATGCCATATCCCAG
* ** * * ** *
41591453 ACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACACCATGTCCCAG
1 ACATGGTCTTACATGGGAGTTCTCATATCGG-CCCAATGCCATATCCCAG
**
41591503 ACATGGTCTTACATGGGACCTCTCATA
1 ACATGGTCTTACATGGGAGTTCTCATA
41591530 ATATCAATGA
Statistics
Matches: 150, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
48 8 0.05
49 19 0.13
50 122 0.81
52 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.27
Consensus pattern (49 bp):
ACATGGTCTTACATGGGAGTTCTCATATCGGCCCAATGCCATATCCCAG
Found at i:41591402 original size:50 final size:50
Alignment explanation
Indices: 41591334--41591576 Score: 254
Period size: 50 Copynumber: 4.7 Consensus size: 50
41591324 TTTTCTATAC
* * * **
41591334 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** * *
41591384 CT-CCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGA
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
41591434 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
41591484 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATATCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATATC---GG
* * *
41591540 TGCCAATGTCATGTCCCAAACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
41591577 TCTCATTCCC
Statistics
Matches: 162, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 122 0.75
51 1 0.01
53 4 0.02
56 34 0.21
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:41603621 original size:28 final size:28
Alignment explanation
Indices: 41603565--41603621 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
41603555 GTTAAGGGTG
* * *
41603565 TTACATCGTGTTTACTGTCCCGACGGAC
1 TTACATCGTCTTTACTGTCCCAACAGAC
* *
41603593 TTACCTCGTCTTTATTGTCCCAACAGAC
1 TTACATCGTCTTTACTGTCCCAACAGAC
41603621 T
1 T
41603622 ATTTATGTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (28 bp):
TTACATCGTCTTTACTGTCCCAACAGAC
Found at i:41603645 original size:33 final size:33
Alignment explanation
Indices: 41603603--41603691 Score: 119
Period size: 33 Copynumber: 2.7 Consensus size: 33
41603593 TTACCTCGTC
41603603 TTTATTGTCCCAACAGACTAT-T-TATGTTCTGTG
1 TTTATTGTCCCAACAGACTATCTCTAT-TT-TGTG
*
41603636 TTTATTGTCCCAACGGACTATCTCTATTTTGTG
1 TTTATTGTCCCAACAGACTATCTCTATTTTGTG
* *
41603669 TTTATTGCCCCAACAAACTATCT
1 TTTATTGTCCCAACAGACTATCT
41603692 TTGTTATGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 44 0.88
34 3 0.06
35 3 0.06
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.43
Consensus pattern (33 bp):
TTTATTGTCCCAACAGACTATCTCTATTTTGTG
Found at i:41605230 original size:16 final size:16
Alignment explanation
Indices: 41605206--41605239 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
41605196 TGCAATTTGG
41605206 TTTAAATTTATTTTAT
1 TTTAAATTTATTTTAT
*
41605222 TTTATATTTATTTTAT
1 TTTAAATTTATTTTAT
41605238 TT
1 TT
41605240 CTTTTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAAATTTATTTTAT
Found at i:41613181 original size:33 final size:33
Alignment explanation
Indices: 41613139--41613511 Score: 352
Period size: 33 Copynumber: 11.3 Consensus size: 33
41613129 TAACATCAAT
* *
41613139 AGAGAAAGTCTGTTGGGACAGTAAACACAGAAC
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* ***
41613172 AAAGAAAGTCCATTGAGACAGTAAACACAGAAC
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* * *
41613205 AGAGAAAGTCTACTGGGACAATAAACACAGAAC
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* * ** * * *
41613238 AAAAAAAGTCCACTGAGCCAATAAACACAGAAT
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
*
41613271 AGAGAAAGT-TCGCTGAGATAGTAAACACAGAAC
1 AGAGAAAGTCT-GCTGAGACAGTAAACACAGAAC
* *
41613304 AGAGAAAGTCTGCTGGGATAGTAAACACAGAAC
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* ** * * **
41613337 AGAAAAAGTCCACTGAGCCAGTAAATACAGAGT
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* * * *
41613370 AGAAAAAGTCTGCTGAGATAGTAAGCACAGAAT
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* * * * *
41613403 AAAGAAAGTCCGCTAAGATAGTAAACATAGAAC
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* * * *
41613436 AGAGAAAGTCCGCTGAGATAGTAAACACATAAT
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
* **
41613469 AGAGATAGTCTGCTGAGACAAAAAACACAGAAC
1 AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
41613502 AGAGAAAGTC
1 AGAGAAAGTC
41613512 CACCAGGACA
Statistics
Matches: 278, Mismatches: 60, Indels: 4
0.81 0.18 0.01
Matches are distributed among these distances:
33 277 1.00
34 1 0.00
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14
Consensus pattern (33 bp):
AGAGAAAGTCTGCTGAGACAGTAAACACAGAAC
Found at i:41613314 original size:99 final size:99
Alignment explanation
Indices: 41613157--41613526 Score: 400
Period size: 99 Copynumber: 3.7 Consensus size: 99
41613147 TCTGTTGGGA
* * *** * *
41613157 CAGTAAACACAGAACAAAGAAAGTCCATTGAGACAGTAAACACAGAACAGAGAAAGTCTACTGGG
1 CAGTAAACACAGAATAGAGAAAGTCTGCTGAGACAGTAAACACAGAACAGAGAAAGTCCACTAGG
*
41613222 ACAATAAACACAGAACAAAAAAAGTCCACTGAGC
66 ACAATAAACACAGAACAGAAAAAGTCCACTGAGC
* * ** *
41613256 CAATAAACACAGAATAGAGAAAGT-TCGCTGAGATAGTAAACACAGAACAGAGAAAGTCTGCTGG
1 CAGTAAACACAGAATAGAGAAAGTCT-GCTGAGACAGTAAACACAGAACAGAGAAAGTCCACTAG
* *
41613320 GATAGTAAACACAGAACAGAAAAAGTCCACTGAGC
65 GACAATAAACACAGAACAGAAAAAGTCCACTGAGC
* * * * * * * * *
41613355 CAGTAAATACAGAGTAGAAAAAGTCTGCTGAGATAGTAAGCACAGAATAAAGAAAGTCCGCTAAG
1 CAGTAAACACAGAATAGAGAAAGTCTGCTGAGACAGTAAACACAGAACAGAGAAAGTCCACTAGG
* * * * * *
41613420 ATAGTAAACATAGAACAGAGAAAGTCCGCTGAGA
66 ACAATAAACACAGAACAGAAAAAGTCCACTGAGC
* * * ** *
41613454 TAGTAAACACATAATAGAGATAGTCTGCTGAGACAAAAAACACAGAACAGAGAAAGTCCACCAGG
1 CAGTAAACACAGAATAGAGAAAGTCTGCTGAGACAGTAAACACAGAACAGAGAAAGTCCACTAGG
41613519 ACAATAAA
66 ACAATAAA
41613527 AACGAGGTAA
Statistics
Matches: 227, Mismatches: 42, Indels: 4
0.83 0.15 0.01
Matches are distributed among these distances:
99 226 1.00
100 1 0.00
ACGTcount: A:0.48, C:0.17, G:0.21, T:0.14
Consensus pattern (99 bp):
CAGTAAACACAGAATAGAGAAAGTCTGCTGAGACAGTAAACACAGAACAGAGAAAGTCCACTAGG
ACAATAAACACAGAACAGAAAAAGTCCACTGAGC
Found at i:41617419 original size:24 final size:24
Alignment explanation
Indices: 41617379--41617424 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
41617369 GTCAAGATTA
*
41617379 TTATTTAATTAATATAATATATTC
1 TTATTTAATTAATATAAAATATTC
*
41617403 TTATTTAAGTTTA-ATAAAATAT
1 TTATTTAA-TTAATATAAAATAT
41617425 GTAAATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTTAATTAATATAAAATATTC
Found at i:41626418 original size:18 final size:18
Alignment explanation
Indices: 41626391--41626425 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41626381 TTAAAATTAG
* *
41626391 AAAAATTAAAAATATTTT
1 AAAAAATAAAAAAATTTT
41626409 AAAAAATAAAAAAATTT
1 AAAAAATAAAAAAATTT
41626426 AATTTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATAAAAAAATTTT
Found at i:41628614 original size:21 final size:21
Alignment explanation
Indices: 41628588--41628643 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
41628578 AATAGCGGTG
* *
41628588 GCGGTGAGATTAGATATTGTA
1 GCGGTGAGATTAGATACTATA
*
41628609 GCGGTGAAATTAGATACTATA
1 GCGGTGAGATTAGATACTATA
*
41628630 GCAGTGAGATTAGA
1 GCGGTGAGATTAGA
41628644 AACAATAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.30, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTATA
Found at i:41628651 original size:21 final size:21
Alignment explanation
Indices: 41628607--41628651 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
41628597 TTAGATATTG
* * *
41628607 TAGCGGTGAAATTAGATACTA
1 TAGCAGTGAAATTAGAAACAA
*
41628628 TAGCAGTGAGATTAGAAACAA
1 TAGCAGTGAAATTAGAAACAA
41628649 TAG
1 TAG
41628652 TGGAGTGTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.09, G:0.24, T:0.24
Consensus pattern (21 bp):
TAGCAGTGAAATTAGAAACAA
Found at i:41630453 original size:107 final size:107
Alignment explanation
Indices: 41630279--41630477 Score: 353
Period size: 107 Copynumber: 1.9 Consensus size: 107
41630269 GTTTTAAGAG
41630279 GATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGATT
1 GATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGATT
*
41630344 TTCCAAACGCGAAGTATTGCCTTATTTTAAAAGTTTAAAAAT
66 TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAT
* * * *
41630386 GATATTTGGCTATTTGGTCGAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTTCTTGATT
1 GATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGATT
41630451 TTCCAAACGCGAAATATTGCCTTATTT
66 TTCCAAACGCGAAATATTGCCTTATTT
41630478 AGAAAAAACT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 87 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (107 bp):
GATATTTGGCTATTTAGTCAAACGAGAAATCGAAACCCAGCACGTTAGGGCACGTTTCCTCGATT
TTCCAAACGCGAAATATTGCCTTATTTTAAAAGTTTAAAAAT
Found at i:41631150 original size:22 final size:22
Alignment explanation
Indices: 41631125--41631166 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
41631115 AAAATATGAA
41631125 ATATAA-AATATAAAAAGTATAT
1 ATATAATAA-ATAAAAAGTATAT
*
41631147 ATATAATAAATGAAAAGTAT
1 ATATAATAAATAAAAAGTAT
41631167 GTACGTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
ATATAATAAATAAAAAGTATAT
Found at i:41631394 original size:22 final size:23
Alignment explanation
Indices: 41631338--41631394 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
41631328 AGTTTAAAAT
41631338 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
41631361 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
41631382 AAAATATATAAAA
1 AAAATATATAAAA
41631395 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:41632124 original size:13 final size:13
Alignment explanation
Indices: 41632106--41632130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41632096 AAATGCGTAG
41632106 ATAAATAAATGAA
1 ATAAATAAATGAA
41632119 ATAAATAAATGA
1 ATAAATAAATGA
41632131 TAGATGATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
ATAAATAAATGAA
Found at i:41649618 original size:30 final size:30
Alignment explanation
Indices: 41649582--41649647 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
41649572 ATTTTATACA
*
41649582 TCATCATTATCTCATTTTGCCACTACATTT
1 TCATCATTATCTCATTTTGCCACTACATTC
41649612 TCATCATTATCTCATTTTGCCACTACATTC
1 TCATCATTATCTCATTTTGCCACTACATTC
41649642 TCATCA
1 TCATCA
41649648 CGATATTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.24, C:0.29, G:0.03, T:0.44
Consensus pattern (30 bp):
TCATCATTATCTCATTTTGCCACTACATTC
Found at i:41651048 original size:23 final size:22
Alignment explanation
Indices: 41651014--41651057 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
41651004 TTATGAAACA
*
41651014 TATAAGGGACTCTATCACCACC
1 TATAAGGGACTCTATAACCACC
41651036 TATAAGTGGACTCTATAACCAC
1 TATAAG-GGACTCTATAACCAC
41651058 ATATTAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (22 bp):
TATAAGGGACTCTATAACCACC
Found at i:41652676 original size:85 final size:84
Alignment explanation
Indices: 41652527--41652685 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 84
41652517 AAAAAATGCC
* * *
41652527 GCTATAGAACATGACCTTTAGCGGCATTTTACCCATAAACGCCGCTAAAGAACATGACCATTAGC
1 GCTAAAGAACATGACATTTAGCGGCATTTTACCCACAAACGCCGCTAAAGAACATGACCATTAGC
41652592 GGCGCTTTATCACAAACGCT
66 GGCG-TTTATCACAAACGCT
* * * * * *
41652612 GCTAAAGAACATGACATTTAGCGGCGCTTTTA-TCACAAACGTCGCTAAATAACATGATCTTTAG
1 GCTAAAGAACATGACATTTAGCGGC-ATTTTACCCACAAACGCCGCTAAAGAACATGACCATTAG
41652676 CGGCGTTTAT
65 CGGCGTTTAT
41652686 GAAAATATGC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
84 5 0.08
85 54 0.84
86 5 0.08
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (84 bp):
GCTAAAGAACATGACATTTAGCGGCATTTTACCCACAAACGCCGCTAAAGAACATGACCATTAGC
GGCGTTTATCACAAACGCT
Found at i:41652680 original size:43 final size:42
Alignment explanation
Indices: 41652526--41652680 Score: 188
Period size: 43 Copynumber: 3.6 Consensus size: 42
41652516 GAAAAAATGC
* * * *
41652526 CGCTATAGAACATGACCTTTAGCGGC-ATTTTACCCATAAACG
1 CGCTAAAGAACATGACCTTTAGCGGCGCTTTTA-TCACAAACG
*
41652568 CCGCTAAAGAACATGACCATTAGCGGCGC-TTTATCACAAACG
1 -CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
*
41652610 CTGCTAAAGAACATGACATTTAGCGGCGCTTTTATCACAAACG
1 C-GCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
* *
41652653 TCGCTAAATAACATGATCTTTAGCGGCG
1 -CGCTAAAGAACATGACCTTTAGCGGCG
41652681 TTTATGAAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 32 0.33
43 64 0.65
44 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
CGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAACG
Found at i:41658679 original size:41 final size:40
Alignment explanation
Indices: 41658618--41658799 Score: 128
Period size: 41 Copynumber: 4.5 Consensus size: 40
41658608 GAGGGAATTA
41658618 TATATTTTTATTAA-ATTATATTTAATAATAATTATTTTAAAT
1 TATA-TTTTA-TAATATTATATTTAATAATAATT-TTTTAAAT
* * **
41658660 TATATTTTATAGTATTATATATT-ATGAT--TTTAGTAAAT
1 TATATTTTATAATATTATAT-TTAATAATAATTTTTTAAAT
* * * *
41658698 TCATA--TAAGAATATT-TA-ATATTAATAATTTTATTAAAT
1 T-ATATTTTATAATATTATATTTAATAATAATTTT-TTAAAT
*
41658736 TATATATTTTTAATCAATTATATTTAATAATAATTATTTTAAAT
1 TATAT-TTTATAAT--ATTATATTTAATAATAATT-TTTTAAAT
*
41658780 TATATTTTATAGTATTATAT
1 TATATTTTATAATATTATAT
41658800 ATTATGATTT
Statistics
Matches: 106, Mismatches: 19, Indels: 31
0.68 0.12 0.20
Matches are distributed among these distances:
34 1 0.01
35 3 0.03
36 2 0.02
37 13 0.12
38 13 0.12
39 5 0.05
40 6 0.06
41 23 0.22
42 9 0.08
43 8 0.08
44 21 0.20
45 2 0.02
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (40 bp):
TATATTTTATAATATTATATTTAATAATAATTTTTTAAAT
Found at i:41658738 original size:61 final size:61
Alignment explanation
Indices: 41658673--41658863 Score: 221
Period size: 61 Copynumber: 3.2 Consensus size: 61
41658663 ATTTTATAGT
41658673 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAATAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAATAATTTTATTAA
* * * ** * * * * *
41658734 ATTATATATTTTTAATCAATTATATTTA-ATAATAATTATTTTAA-ATT-AT-ATTTTA-TAGT
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAA-TA-TTTAATATTAATAATTTTATTA-A
*
41658793 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAATAATTTTATTAA
41658854 ATTATATATT
1 ATTATATATT
41658864 TTAATTGAAA
Statistics
Matches: 101, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
58 7 0.07
59 31 0.31
60 15 0.15
61 41 0.41
62 7 0.07
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (61 bp):
ATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAATAATTTTATTAA
Found at i:41658746 original size:18 final size:18
Alignment explanation
Indices: 41658712--41658758 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
41658702 ATAAGAATAT
41658712 TTAATATTA-ATAATTTTA
1 TTAA-ATTATATAATTTTA
*
41658730 TTAAATTATATATTTTTA
1 TTAAATTATATAATTTTA
* *
41658748 ATCAATTATAT
1 TTAAATTATAT
41658759 TTAATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TTAAATTATATAATTTTA
Found at i:41658747 original size:120 final size:120
Alignment explanation
Indices: 41658613--41658898 Score: 511
Period size: 120 Copynumber: 2.4 Consensus size: 120
41658603 AAGTGGAGGG
41658613 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
*
41658678 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAATAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
* *
41658733 AATTATATATTTTTAATCAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
1 AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
41658798 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
* *
41658853 AATTATATATTTTAATTGAAA-TATATTTAATAATAATTATGTTAAA
1 AATTATATATTTTTATT-AAATTATATTTAATAATAATTATTTTAAA
41658899 ATATGATTAA
Statistics
Matches: 158, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
120 156 0.99
121 2 0.01
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
AATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTAT
ATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
Found at i:41659098 original size:44 final size:45
Alignment explanation
Indices: 41659035--41659131 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 45
41659025 CTATTACACC
*
41659035 TCCATTCCATTCAACCAAACACA-AGAA-TACTATTACGCCTCTAT
1 TCCATTACATTCAACCAAACA-ATAGAATTACTATTACGCCTCTAT
* ** *
41659079 TCCATTACATTCAACCAAACAATTGAATTGTTATTACGTCTCTAT
1 TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
41659124 TCCATTAC
1 TCCATTAC
41659132 GCCTCTATTC
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.50
45 22 0.48
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (45 bp):
TCCATTACATTCAACCAAACAATAGAATTACTATTACGCCTCTAT
Found at i:41659132 original size:16 final size:16
Alignment explanation
Indices: 41659111--41659207 Score: 158
Period size: 16 Copynumber: 6.1 Consensus size: 16
41659101 TTGAATTGTT
*
41659111 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
41659127 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
41659143 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
41659159 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
41659175 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
*
41659191 ATTACGCCTTTATTCC
1 ATTACGCCTCTATTCC
41659207 A
1 A
41659208 ATACAGCGAA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 75 1.00
ACGTcount: A:0.22, C:0.35, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:41661051 original size:8 final size:7
Alignment explanation
Indices: 41660976--41661209 Score: 84
Period size: 7 Copynumber: 32.9 Consensus size: 7
41660966 ACTAATTAAT
*
41660976 CTAAATC
1 CTAAACC
41660983 CTAAACCC
1 CTAAA-CC
*
41660991 CTAACCC
1 CTAAACC
*
41660998 CT-ATCTC
1 CTAAAC-C
41661005 CTAAACC
1 CTAAACC
*
41661012 CTAAATC
1 CTAAACC
* *
41661019 ATAAAAC
1 CTAAACC
*
41661026 TTAAACC
1 CTAAACC
*
41661033 ATAAACC
1 CTAAACC
41661040 CTAAATCC
1 CTAAA-CC
*
41661048 CT-AACA
1 CTAAACC
*
41661054 CTTAACC
1 CTAAACC
*
41661061 CTTAACCC
1 C-TAAACC
41661069 CTAAACC
1 CTAAACC
*
41661076 TTAAACC
1 CTAAACC
*
41661083 C-CAACTC
1 CTAAAC-C
*
41661090 TTAAACC
1 CTAAACC
*
41661097 ATAAACC
1 CTAAACC
*
41661104 ATAAACC
1 CTAAACC
*
41661111 AC-AATCC
1 -CTAAACC
41661118 CTAAACC
1 CTAAACC
*
41661125 CATAATCC
1 C-TAAACC
*
41661133 ATAAACC
1 CTAAACC
*
41661140 TTAAA--
1 CTAAACC
*
41661145 ATAGTAACTC
1 CTA--AAC-C
*
41661155 TTAAACC
1 CTAAACC
*
41661162 TTAAACC
1 CTAAACC
*
41661169 TTAAACC
1 CTAAACC
*
41661176 CTAAACT
1 CTAAACC
* *
41661183 ATATACC
1 CTAAACC
41661190 CTAAACC
1 CTAAACC
*
41661197 ATAAACC
1 CTAAACC
41661204 CTAAAC
1 CTAAAC
41661210 TATAATGATA
Statistics
Matches: 171, Mismatches: 40, Indels: 32
0.70 0.16 0.13
Matches are distributed among these distances:
5 2 0.01
6 9 0.05
7 131 0.77
8 27 0.16
10 2 0.01
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACC
Found at i:41661563 original size:40 final size:40
Alignment explanation
Indices: 41661519--41661621 Score: 125
Period size: 40 Copynumber: 2.6 Consensus size: 40
41661509 TTTTTTTGTT
* * *
41661519 GCGTTTTTGATAAAGCGCCGCTAAAGCTCGATCTATAGCG
1 GCGTTTTTCAAAAAGCGCCGCTAAAGCTCAATCTATAGCG
* * *
41661559 GCGTTTTTCAAAAAGTGTCGCTAATGCTCAATCTATAGCG
1 GCGTTTTTCAAAAAGCGCCGCTAAAGCTCAATCTATAGCG
* * *
41661599 GTGTTTTTCAAAAAACACCGCTA
1 GCGTTTTTCAAAAAGCGCCGCTA
41661622 GTGCCACTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCGCCGCTAAAGCTCAATCTATAGCG
Found at i:41661738 original size:40 final size:40
Alignment explanation
Indices: 41661701--41661780 Score: 115
Period size: 40 Copynumber: 2.0 Consensus size: 40
41661691 CCACTAATAG
41661701 TCGACCTATAGCGGCGTTGTTCAAAAAGCACCGCTAATGC
1 TCGACCTATAGCGGCGTTGTTCAAAAAGCACCGCTAATGC
* * * **
41661741 TCGATCTATAGCGGTGTTTTTCAAAAAGTGCCGCTAATGC
1 TCGACCTATAGCGGCGTTGTTCAAAAAGCACCGCTAATGC
41661781 CACTAATGCT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (40 bp):
TCGACCTATAGCGGCGTTGTTCAAAAAGCACCGCTAATGC
Found at i:41661890 original size:154 final size:155
Alignment explanation
Indices: 41661509--41661934 Score: 557
Period size: 155 Copynumber: 2.8 Consensus size: 155
41661499 ACAAATAAAT
** * * * * * *
41661509 TTTTTTTGTTGCGTTTTTGATAAAGCGCCGCTAAAGCTCGATCTATAGCGGCGTTTTTCAAAAAG
1 TTTTTTTGCCGCGTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAG
* * *
41661574 TGTCGCTAATGCTCAATCTATAGCGGTGTTTTTCAAAAAACACCGCTAGTGCCACTAAAGCTCAA
66 TGCCGCTAATGCTCAATCTATAGCGGTGTTTTTCAAAAAGCACCGCTAATGCCACTAAAGCTCAA
* * * *
41661639 CATAAAATGATGGCGTTGTGCTTAA
131 CATAAAACGACGGCCTTATGCTTAA
* * * *
41661664 TTTTTTTGCCGCGTTTTCCAAAAAGTGCCACTAATAGTCGACCTATAGCGGCGTTGTTCAAAAAG
1 TTTTTTTGCCGCGTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAG
** * ** *
41661729 CACCGCTAATGCTCGATCTATAGCGGTGTTTTTCAAAAAGTGCCGCTAATGCCACTAATGCTCAA
66 TGCCGCTAATGCTCAATCTATAGCGGTGTTTTTCAAAAAGCACCGCTAATGCCACTAAAGCTCAA
41661794 CATAAAACGACGGCCTTATGCTTAA
131 CATAAAACGACGGCCTTATGCTTAA
* *
41661819 TTTTTTT-CGGGGTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAG
1 TTTTTTTGCCGCGTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAG
* * * * *
41661883 TGCCGCTAATGCTCTACCTATAGTGGCGTTTTTCAAAAAGCACCACTAATGC
66 TGCCGCTAATGCTCAATCTATAGCGGTGTTTTTCAAAAAGCACCGCTAATGC
41661935 TCGATCTATA
Statistics
Matches: 231, Mismatches: 40, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
154 94 0.41
155 137 0.59
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (155 bp):
TTTTTTTGCCGCGTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAG
TGCCGCTAATGCTCAATCTATAGCGGTGTTTTTCAAAAAGCACCGCTAATGCCACTAAAGCTCAA
CATAAAACGACGGCCTTATGCTTAA
Found at i:41661892 original size:40 final size:40
Alignment explanation
Indices: 41661830--41662014 Score: 262
Period size: 40 Copynumber: 4.6 Consensus size: 40
41661820 TTTTTTCGGG
* *
41661830 GTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGC
* * *
41661870 GTTTTTCAAAAAGTGCCGCTAATGCTCTACCTATAGTGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGC
* * * *
41661910 GTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCGGA
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGC
* * *
41661950 GTTTTTCAAAAAGTGCCGCTAATGCTCGATCTATAGCGGT
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGC
41661990 GTTTTTCAAAAAGCGCCGCTAATGC
1 GTTTTTCAAAAAGCGCCGCTAATGC
41662015 CACTACAGCT
Statistics
Matches: 128, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 128 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGC
Found at i:41661944 original size:80 final size:80
Alignment explanation
Indices: 41661830--41662014 Score: 289
Period size: 80 Copynumber: 2.3 Consensus size: 80
41661820 TTTTTTCGGG
* *
41661830 GTTTTTCAAAAAGCGCCACTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGTGCCGCTAATGC
1 GTTTTTCAAAAAGCGCCACTAATGCTCGACCTATAGCGGAGTTTTTCAAAAAGTGCCGCTAATGC
* *
41661895 TCTACCTATAGTGGC
66 TCGACCTATAGCGGC
* *
41661910 GTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCGGAGTTTTTCAAAAAGTGCCGCTAATGC
1 GTTTTTCAAAAAGCGCCACTAATGCTCGACCTATAGCGGAGTTTTTCAAAAAGTGCCGCTAATGC
* *
41661975 TCGATCTATAGCGGT
66 TCGACCTATAGCGGC
*
41661990 GTTTTTCAAAAAGCGCCGCTAATGC
1 GTTTTTCAAAAAGCGCCACTAATGC
41662015 CACTACAGCT
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 95 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (80 bp):
GTTTTTCAAAAAGCGCCACTAATGCTCGACCTATAGCGGAGTTTTTCAAAAAGTGCCGCTAATGC
TCGACCTATAGCGGC
Found at i:41664879 original size:7 final size:7
Alignment explanation
Indices: 41664867--41664907 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
41664857 TATAAGTGCA
41664867 TATATAT
1 TATATAT
41664874 TATATAT
1 TATATAT
41664881 TATATAT
1 TATATAT
* *
41664888 AATACAT
1 TATATAT
41664895 T-TATAT
1 TATATAT
41664901 TATATAT
1 TATATAT
41664908 AACCCCAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 24 0.83
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:41666455 original size:14 final size:14
Alignment explanation
Indices: 41666421--41666455 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41666411 TTCACTAACC
* *
41666421 CCCAATCCTACTTA
1 CCCAATTCTACTAA
41666435 CCCAATTCTACTAA
1 CCCAATTCTACTAA
41666449 CCCAATT
1 CCCAATT
41666456 TTTAGGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.31, C:0.40, G:0.00, T:0.29
Consensus pattern (14 bp):
CCCAATTCTACTAA
Found at i:41668700 original size:21 final size:21
Alignment explanation
Indices: 41668650--41668700 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
41668640 AATTTAAATC
*
41668650 TATTTAAAGATCCATTAAAAA
1 TATTTAAAAATCCATTAAAAA
** *
41668671 TATAGAAAAATACC-TTTAAAA
1 TATTTAAAAAT-CCATTAAAAA
41668692 TATTTAAAA
1 TATTTAAAA
41668701 TTCCCCTAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (21 bp):
TATTTAAAAATCCATTAAAAA
Found at i:41669741 original size:365 final size:368
Alignment explanation
Indices: 41669065--41669789 Score: 1087
Period size: 365 Copynumber: 2.0 Consensus size: 368
41669055 CAAATTCTAG
*
41669065 TTATTTTGTGTAAAATTAACATTTATACCTAGGGTTACAAGGGTATGGATGGCACACACATTAAA
1 TTATTTTGTGTAAAATTAACATCTATACCTAGGGTTACAAGGGTATGGATGGCACACACATTAAA
* *
41669130 AATAATGGATTTTGTAAAAAAAAAAATAGTTATTTTGCATGAGAAAGGATTTGAACTTAGAACCT
66 AACAATGGATTTTGT---AAAAAAAATAGTTATTTTGCATGAGAAAGGATTCGAACTTAGAACCT
* * * ** *
41669195 CAATTTAATTTTCGTGCTTTTTCATTTATCAATTAACCACTAGGCTATTTCTTTATATTTGAAAT
128 CAATTTAATTTGCATGCTTTTGCATTTATCAATTAACCACTAGAATATTTCCTTATATTTGAAAT
* * *
41669260 AATTTTACAATATTTATTTTAAAAATAAGGTGTGTCACATACTAGGGTTTGAGGCAAAATTAATA
193 AATTTTACAATATTTATTTTAAAAACAAGGCGTGTCACATACTAGGGTTTGAGGCAAAATTAACA
*
41669325 AAATAATAAAAATAGTGAGGGAGAAGGGATTTGAACTTGGATTTCAAGGAACGTTTCACTAACAC
258 AAATAATAAAAATAGTGAGGGAGAAGGGATTTGAACTTGGATTTCAAGGAACGTTTCACAAACAC
* * * * *
41669390 TTATCCAATAAAATAATATATTATTTATTCCTAAACCCTAAACTAA
323 ATATCCAACAAAACAATACATCATTTATTCCTAAACCCTAAACTAA
* * *
41669436 TTATTTTGTGTAAAATTATCATCTATACCTAGGGTTACAAGGTTATGGATGGCATACACATTAAA
1 TTATTTTGTGTAAAATTAACATCTATACCTAGGGTTACAAGGGTATGGATGGCACACACATTAAA
* * * * * *
41669501 AACAATGGATTTTGT-ATAAAAA-AGTTGTTTTGCATGGGAAATGATTCGAACTTGGGACCTCAA
66 AACAATGGATTTTGTAAAAAAAATAGTTATTTTGCATGAGAAAGGATTCGAACTTAGAACCTCAA
* *
41669564 TTTAATTTGCATGCTTTTGCATTTATCAATTAACCACTAGAATATTTCCTTCTTTTTGAAATAAT
131 TTTAATTTGCATGCTTTTGCATTTATCAATTAACCACTAGAATATTTCCTTATATTTGAAATAAT
* *
41669629 TTTGCAATA-TTATTTTAAAAACAAGGCGTGTTACATACTAGGGTTTGAGGCAAAATTAACAAAA
196 TTTACAATATTTATTTTAAAAACAAGGCGTGTCACATACTAGGGTTTGAGGCAAAATTAACAAAA
* *
41669693 TATTAAAAATGGTGAGGGAGAAGGGATTTGAACTTGGATTTCAAGGAACGTTTCACAAACACATA
261 TAATAAAAATAGTGAGGGAGAAGGGATTTGAACTTGGATTTCAAGGAACGTTTCACAAACACATA
* *
41669758 TTCAACAAACCAATACATCATTTATTCCTAAA
326 TCCAACAAAACAATACATCATTTATTCCTAAA
41669790 AACTCATTGA
Statistics
Matches: 319, Mismatches: 35, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
365 138 0.43
366 100 0.31
367 6 0.02
371 75 0.24
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (368 bp):
TTATTTTGTGTAAAATTAACATCTATACCTAGGGTTACAAGGGTATGGATGGCACACACATTAAA
AACAATGGATTTTGTAAAAAAAATAGTTATTTTGCATGAGAAAGGATTCGAACTTAGAACCTCAA
TTTAATTTGCATGCTTTTGCATTTATCAATTAACCACTAGAATATTTCCTTATATTTGAAATAAT
TTTACAATATTTATTTTAAAAACAAGGCGTGTCACATACTAGGGTTTGAGGCAAAATTAACAAAA
TAATAAAAATAGTGAGGGAGAAGGGATTTGAACTTGGATTTCAAGGAACGTTTCACAAACACATA
TCCAACAAAACAATACATCATTTATTCCTAAACCCTAAACTAA
Found at i:41674230 original size:16 final size:16
Alignment explanation
Indices: 41674192--41674230 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
41674182 TTTGAGTTCC
41674192 AAAATTGTGTTTCAAA
1 AAAATTGTGTTTCAAA
41674208 AAGAATTGAT-TTTCAAA
1 AA-AATTG-TGTTTCAAA
41674225 AAAATT
1 AAAATT
41674231 AGATAATTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 6 0.29
17 14 0.67
18 1 0.05
ACGTcount: A:0.49, C:0.05, G:0.10, T:0.36
Consensus pattern (16 bp):
AAAATTGTGTTTCAAA
Found at i:41695587 original size:59 final size:62
Alignment explanation
Indices: 41695472--41695588 Score: 177
Period size: 62 Copynumber: 1.9 Consensus size: 62
41695462 AGCGATTATC
* * *
41695472 TTAATATTAAATTTAATTTAATTTTTATCTTGTAGATAAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAAGAT
*
41695534 TTAATATTAAATTTAATCTCATATTTAT-TT-T-GATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATA
41695589 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 23 0.45
60 1 0.02
61 2 0.04
62 25 0.49
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (62 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGTAGATAAATATTATATTAATTTAATAAGAT
Found at i:41697795 original size:43 final size:43
Alignment explanation
Indices: 41697747--41697862 Score: 144
Period size: 43 Copynumber: 2.7 Consensus size: 43
41697737 CCAATCAACA
* * * *
41697747 CAAATATACTTGCACACACAGTGCATCATCT-GACGAATCGAAG
1 CAAATATACTAGCACACATAGTGCATCAT-TAGACGAACCAAAG
**
41697790 CAAATATACTAAAACACATAGTGCATCATTAGACGAACCAAAG
1 CAAATATACTAGCACACATAGTGCATCATTAGACGAACCAAAG
* *
41697833 TAAATATACTGGCACACATAGTGCATCATT
1 CAAATATACTAGCACACATAGTGCATCATT
41697863 GATCTACAAC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
42 1 0.02
43 61 0.98
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (43 bp):
CAAATATACTAGCACACATAGTGCATCATTAGACGAACCAAAG
Found at i:41704919 original size:88 final size:88
Alignment explanation
Indices: 41704801--41704983 Score: 332
Period size: 88 Copynumber: 2.1 Consensus size: 88
41704791 CCTATTGAAT
*
41704801 TTGG-TATCATATGATGGATATCTGGTCCTATTCATCCTCAGATTTGTTTTTAGAGCTTTTGTGA
1 TTGGTTATCATATGATGGATATCTGGTCCTATTCAACCTCAGATTTGTTTTTAGAGCTTTTGTGA
41704865 GCTCGTATAAATCCTGTAAATGG
66 GCTCGTATAAATCCTGTAAATGG
*
41704888 TTGGTTATCATATGATGGATATCTGGTCCTATTCAACCTTAGATTTGTTTTTAGAGCTTTTGTGA
1 TTGGTTATCATATGATGGATATCTGGTCCTATTCAACCTCAGATTTGTTTTTAGAGCTTTTGTGA
*
41704953 GCTCGTATAAATCCTGTAAATTG
66 GCTCGTATAAATCCTGTAAATGG
41704976 TTGGTTAT
1 TTGGTTAT
41704984 TCTAATTAAT
Statistics
Matches: 92, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 4 0.04
88 88 0.96
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (88 bp):
TTGGTTATCATATGATGGATATCTGGTCCTATTCAACCTCAGATTTGTTTTTAGAGCTTTTGTGA
GCTCGTATAAATCCTGTAAATGG
Found at i:41714959 original size:12 final size:13
Alignment explanation
Indices: 41714936--41714964 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41714926 TTTTGTTTTG
41714936 TTTCCTTTTTCTT
1 TTTCCTTTTTCTT
41714949 TTTCC-TTTTCTT
1 TTTCCTTTTTCTT
41714961 TTTC
1 TTTC
41714965 ACTCTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCCTTTTTCTT
Found at i:41715969 original size:23 final size:23
Alignment explanation
Indices: 41715929--41715978 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
41715919 ATTTCCAAAC
*
41715929 AAAAATTAAAACATCCAAAATTT
1 AAAAATTAAAACATCCAAAAATT
*
41715952 AAAAATTAAAA-GTCCCAAAAATT
1 AAAAATTAAAACAT-CCAAAAATT
41715975 AAAA
1 AAAA
41715979 TAAAATTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.64, C:0.12, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAAATTAAAACATCCAAAAATT
Found at i:41717976 original size:25 final size:25
Alignment explanation
Indices: 41717940--41717992 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
41717930 TATTATACAT
41717940 TTGTTTTAAAATTTATTATGTATTA
1 TTGTTTTAAAATTTATTATGTATTA
*
41717965 TTGTTTTGAAATTTATTATGTATTA
1 TTGTTTTAAAATTTATTATGTATTA
41717990 TTG
1 TTG
41717993 ACTGTTGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.60
Consensus pattern (25 bp):
TTGTTTTAAAATTTATTATGTATTA
Found at i:41727531 original size:20 final size:20
Alignment explanation
Indices: 41727478--41727531 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
41727468 TATTTAAGCT
*
41727478 AAAGTAAGTAAATAAAATGG
1 AAAGTAAGTAAATGAAATGG
*
41727498 AAAGTAAGTAAATGCAATGG
1 AAAGTAAGTAAATGAAATGG
41727518 AAAGTAAGTAAATG
1 AAAGTAAGTAAATG
41727532 GAAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.56, C:0.02, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAGTAAGTAAATGAAATGG
Found at i:41736062 original size:30 final size:30
Alignment explanation
Indices: 41736005--41736066 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
41735995 GATTTTTGAA
* *
41736005 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
41736035 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
41736065 AA
1 AA
41736067 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:41738970 original size:21 final size:20
Alignment explanation
Indices: 41738946--41738987 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
41738936 TGAAATGCAA
41738946 TCAACATAACA-TGAATTAAAT
1 TCAACATAA-ATTG-ATTAAAT
*
41738967 TCAAGATAAATTGATTAAAT
1 TCAACATAAATTGATTAAAT
41738987 T
1 T
41738988 AACCATTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (20 bp):
TCAACATAAATTGATTAAAT
Found at i:41739578 original size:14 final size:14
Alignment explanation
Indices: 41739559--41739585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41739549 CATTTCTTGG
41739559 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
41739573 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
41739586 ACTAGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:41742767 original size:27 final size:27
Alignment explanation
Indices: 41742737--41743222 Score: 587
Period size: 27 Copynumber: 18.0 Consensus size: 27
41742727 GTATAACAGC
** *
41742737 CATTTTATGCTATGGGGGTATTTTGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* *
41742764 CATTTTAACCTATGGGGGTATTTCAGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * * *
41742791 CATTCTACACTATGGGGTTATTTCGAT
1 CATTTTACCCTATGGGGGTATTTCGGT
* *
41742818 CATTCTACCCTATGGGGTTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * * *
41742845 CATTTTAACCTATGAGGGTATTTTGAT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * **
41742872 CATTCTACCCTATGTGGGTATTTTAGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* *
41742899 TATTTTACCCTATGGGGGTATTTCAGT
1 CATTTTACCCTATGGGGGTATTTCGGT
41742926 -ATTTTACCCTATGGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * *
41742952 CATTTTATCCTATGAGGGTATTTCAGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * *
41742979 CATTTTACTCAATAGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
*
41743006 CATTTTACCCTATGGGGGTATTTCGAT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * * *
41743033 TATTCTACCCTCTGGGGGTACTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* *
41743060 CATTCTACTCTATGGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* * *
41743087 CATTTTACCCTATGAGGATATTTCAGT
1 CATTTTACCCTATGGGGGTATTTCGGT
**
41743114 CATTTTACCCTATAAGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
*
41743141 CATTTTACCCTATAGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
* *
41743168 CATTTTACCCTATGGGGTTATTTCAGT
1 CATTTTACCCTATGGGGGTATTTCGGT
41743195 CATTTTACCCTATGGGGGTATTTCGGT
1 CATTTTACCCTATGGGGGTATTTCGGT
41743222 C
1 C
41743223 CAACATGGCC
Statistics
Matches: 394, Mismatches: 64, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 0.06
27 369 0.94
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.42
Consensus pattern (27 bp):
CATTTTACCCTATGGGGGTATTTCGGT
Found at i:41754456 original size:40 final size:40
Alignment explanation
Indices: 41754412--41754507 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 40
41754402 CTTCGTGCCA
41754412 GTGTATCTATCGGGCTAAATGCCTAG-AAGGCTTT-GTATCG
1 GTGTATCTATCGGGCTAAATGCCTAGCAA-G-TTTCGTATCG
* * *
41754452 GTGTATCTATAGAGCTAAATGCCTAGCAAGTTTCGTGTCG
1 GTGTATCTATCGGGCTAAATGCCTAGCAAGTTTCGTATCG
41754492 GTGTA-CTTATCGGGCT
1 GTGTATC-TATCGGGCT
41754508 TAGTACCTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
39 4 0.08
40 42 0.88
41 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (40 bp):
GTGTATCTATCGGGCTAAATGCCTAGCAAGTTTCGTATCG
Found at i:41757264 original size:19 final size:19
Alignment explanation
Indices: 41757240--41757289 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
41757230 TGTATGGAGC
41757240 CACACAGCTTGGGCTCTGT
1 CACACAGCTTGGGCTCTGT
*
41757259 CACACAGCCTGGGCTCTGT
1 CACACAGCTTGGGCTCTGT
*
41757278 CACACGGCTTGG
1 CACACAGCTTGG
41757290 ACATGCAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.16, C:0.34, G:0.28, T:0.22
Consensus pattern (19 bp):
CACACAGCTTGGGCTCTGT
Found at i:41759025 original size:22 final size:23
Alignment explanation
Indices: 41759000--41759043 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
41758990 TTCTTAGGGT
*
41759000 TTAGGTATTAATTTA-GTTTTAA
1 TTAGGTATTAAATTAGGTTTTAA
*
41759022 TTAGGTTTTAAATTAGGTTTTA
1 TTAGGTATTAAATTAGGTTTTA
41759044 TTTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (23 bp):
TTAGGTATTAAATTAGGTTTTAA
Found at i:41759037 original size:12 final size:12
Alignment explanation
Indices: 41759000--41759043 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
41758990 TTCTTAGGGT
* *
41759000 TTAGGTATTAAT
1 TTAGGTTTTAAA
41759012 TTA-GTTTT-AA
1 TTAGGTTTTAAA
41759022 TTAGGTTTTAAA
1 TTAGGTTTTAAA
41759034 TTAGGTTTTA
1 TTAGGTTTTA
41759044 TTTTATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 4 0.14
11 9 0.32
12 15 0.54
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (12 bp):
TTAGGTTTTAAA
Found at i:41760431 original size:14 final size:15
Alignment explanation
Indices: 41760409--41760444 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
41760399 TACAATGATG
*
41760409 AAATAAAAAAT-TGA
1 AAATTAAAAATGTGA
41760423 AAATTAAAAATGTGA
1 AAATTAAAAATGTGA
41760438 AAATTAA
1 AAATTAA
41760445 TTCTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (15 bp):
AAATTAAAAATGTGA
Found at i:41760432 original size:15 final size:16
Alignment explanation
Indices: 41760412--41760444 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
41760402 AATGATGAAA
41760412 TAAAAAAT-TGAAAAT
1 TAAAAAATGTGAAAAT
41760427 T-AAAAATGTGAAAAT
1 TAAAAAATGTGAAAAT
41760442 TAA
1 TAA
41760445 TTCTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.38
15 9 0.56
16 1 0.06
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (16 bp):
TAAAAAATGTGAAAAT
Found at i:41761023 original size:6 final size:6
Alignment explanation
Indices: 41761012--41761047 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
41761002 AAAAAACTCC
41761012 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
41761048 AAACTAATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:41763217 original size:12 final size:12
Alignment explanation
Indices: 41763200--41763237 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
41763190 TCAGAGAGTT
41763200 ACACGGCCTA-GC
1 ACACGGCC-AGGC
41763212 ACACGGCCAGGC
1 ACACGGCCAGGC
41763224 ACACGGCCAGGC
1 ACACGGCCAGGC
41763236 AC
1 AC
41763238 GCGGATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 1 0.04
12 24 0.96
ACGTcount: A:0.26, C:0.42, G:0.29, T:0.03
Consensus pattern (12 bp):
ACACGGCCAGGC
Found at i:41770748 original size:33 final size:33
Alignment explanation
Indices: 41770700--41770795 Score: 138
Period size: 33 Copynumber: 2.9 Consensus size: 33
41770690 TTTCTAGTAT
* * **
41770700 CAGTGTGGGCCTTAGCCCAATACAATATTAGAA
1 CAGTGCGGGCCTTAGCCCAATATAATAACAGAA
*
41770733 TAGTGCGGGCCTTAGCCCAATATAATAACAGAA
1 CAGTGCGGGCCTTAGCCCAATATAATAACAGAA
*
41770766 CAGTGCGAGCCTTAGCCCAATATAATAACA
1 CAGTGCGGGCCTTAGCCCAATATAATAACA
41770796 TTGTGGGTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (33 bp):
CAGTGCGGGCCTTAGCCCAATATAATAACAGAA
Found at i:41771017 original size:27 final size:28
Alignment explanation
Indices: 41770979--41771038 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
41770969 AGCTATCAGT
*
41770979 ACAGT-ATATGTGGCATAGCCACCA-ATA
1 ACAGTAATATGTGGCAGAGCCACCAGA-A
41771006 ACAGTAAT-TGTGGCAGAGCCACCAGAA
1 ACAGTAATATGTGGCAGAGCCACCAGAA
41771033 ACAGTA
1 ACAGTA
41771039 CTTCCTCCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 27 0.90
28 3 0.10
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (28 bp):
ACAGTAATATGTGGCAGAGCCACCAGAA
Found at i:41771257 original size:26 final size:26
Alignment explanation
Indices: 41771223--41771467 Score: 312
Period size: 26 Copynumber: 9.4 Consensus size: 26
41771213 TCCCTACGGT
*
41771223 GGTATTTCGGTAATTTGCCCATCG-G
1 GGTATTTCGGTAATTTACCCATCGAG
* * *
41771248 GGATATTTCGATAATTTACCTATCGGG
1 GG-TATTTCGGTAATTTACCCATCGAG
*
41771275 GGTATTTCAGTAATTTACCCATCGAG
1 GGTATTTCGGTAATTTACCCATCGAG
* *
41771301 GGTATTTCGGTAATTTAACCATTGAG
1 GGTATTTCGGTAATTTACCCATCGAG
*
41771327 GGTATTTCGATAATTTACCCATCGAG
1 GGTATTTCGGTAATTTACCCATCGAG
*
41771353 GGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGGTAATTTACCCATCGAG
***
41771379 GGTATTTTTATAATTTACCCATCGAG
1 GGTATTTCGGTAATTTACCCATCGAG
* * * * *
41771405 TGTATTTTGATCATTTTCCCATCGAG
1 GGTATTTCGGTAATTTACCCATCGAG
*
41771431 GGTATTTTGGTAATTTACCCATCGAG
1 GGTATTTCGGTAATTTACCCATCGAG
41771457 GGTATTTCGGT
1 GGTATTTCGGT
41771468 CAACACAATG
Statistics
Matches: 192, Mismatches: 26, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
25 2 0.01
26 187 0.97
27 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (26 bp):
GGTATTTCGGTAATTTACCCATCGAG
Found at i:41782887 original size:18 final size:18
Alignment explanation
Indices: 41782866--41782907 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
41782856 CCTTAGCTTT
41782866 GTCTTCGTCATAGTGTTC
1 GTCTTCGTCATAGTGTTC
*
41782884 GTCTTCGTTATAGTGTTC
1 GTCTTCGTCATAGTGTTC
41782902 GTCTTC
1 GTCTTC
41782908 ATCTTCGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (18 bp):
GTCTTCGTCATAGTGTTC
Found at i:41784904 original size:50 final size:50
Alignment explanation
Indices: 41784778--41785020 Score: 181
Period size: 50 Copynumber: 4.8 Consensus size: 50
41784768 CTAATAATAC
* * * * *
41784778 ATGCCAAAGCTATGTCCCAAACATAGTCTTACATGGGA-TGT-T-TTCT-G
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACT-TCTAATCTCG
* * * * *
41784825 TACTGCCAAT-CTCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATCG
1 -A-TGCCAATGC-CATGTCCCAGACATGGTCTTACATGGGACTTCTAATCTCG
* ** * * *
41784877 ATGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATCTCG
* * *
41784927 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CT-TC-TAATCTC---G
*
41784983 ATGCCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
41785021 TCTCATCCCC
Statistics
Matches: 151, Mismatches: 31, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
48 2 0.01
49 30 0.20
50 71 0.47
51 5 0.03
52 3 0.02
53 5 0.03
56 35 0.23
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACTTCTAATCTCG
Found at i:41784989 original size:56 final size:50
Alignment explanation
Indices: 41784828--41785027 Score: 190
Period size: 50 Copynumber: 3.9 Consensus size: 50
41784818 TTTTCTGTAC
* * ** * * *
41784828 TGCCAAT-CTCATATCCCAGATATGGTCTTACATGGGAGTTCTTATATCGA
1 TGCCAATGC-CATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGA
* ** *
41784878 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGA
* *
41784928 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCT---TGA
*
41784984 TGCCAATTCCATGTCCCAGACATGGTCTTACATGGGA--TCTCATC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATC
41785028 CCCTTAATGT
Statistics
Matches: 123, Mismatches: 20, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
50 75 0.61
51 4 0.03
53 4 0.03
54 4 0.03
56 36 0.29
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGA
Found at i:41788859 original size:18 final size:19
Alignment explanation
Indices: 41788824--41788860 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
41788814 CATGACATTG
41788824 AATGAAATGTATGTATACA
1 AATGAAATGTATGTATACA
41788843 AATG-AATGT-TGTGATACA
1 AATGAAATGTATGT-ATACA
41788861 TATGCTAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 10 0.59
19 4 0.24
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
AATGAAATGTATGTATACA
Found at i:41789735 original size:39 final size:39
Alignment explanation
Indices: 41789681--41789760 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
41789671 ATATATGATG
41789681 TATATTTATATTCAGCTAATGATAGGTAAAATAAATTCA
1 TATATTTATATTCAGCTAATGATAGGTAAAATAAATTCA
41789720 TATATTTATATTCAGCTAATGATAGGTAAAATAAATTCA
1 TATATTTATATTCAGCTAATGATAGGTAAAATAAATTCA
41789759 TA
1 TA
41789761 CGCCTATAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (39 bp):
TATATTTATATTCAGCTAATGATAGGTAAAATAAATTCA
Found at i:41790741 original size:16 final size:17
Alignment explanation
Indices: 41790720--41790752 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41790710 TTGTTTTGTT
41790720 ATATGTTCTG-TATATG
1 ATATGTTCTGATATATG
*
41790736 ATATGTTTTGATATATG
1 ATATGTTCTGATATATG
41790753 CTAAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (17 bp):
ATATGTTCTGATATATG
Found at i:41791542 original size:31 final size:31
Alignment explanation
Indices: 41791506--41791570 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
41791496 ATAAAAATAT
41791506 AAATGAAATTACATTTAAATTTTTACAGAAA
1 AAATGAAATTACATTTAAATTTTTACAGAAA
41791537 AAATGAAATTACATTTAAATTTTTACAGAAA
1 AAATGAAATTACATTTAAATTTTTACAGAAA
41791568 AAA
1 AAA
41791571 AAAACTGGTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (31 bp):
AAATGAAATTACATTTAAATTTTTACAGAAA
Found at i:41800307 original size:20 final size:20
Alignment explanation
Indices: 41800279--41800316 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41800269 TATAGACTAA
41800279 AACAAAC-AACACATTTCATC
1 AACAAACAAACA-ATTTCATC
*
41800299 AACACACAAACAATTTCA
1 AACAAACAAACAATTTCA
41800317 CATTCAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (20 bp):
AACAAACAAACAATTTCATC
Found at i:41801478 original size:3 final size:3
Alignment explanation
Indices: 41801463--41801528 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
41801453 TCTAGATGAT
*
41801463 AAC AAC AAT AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
41801511 AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC
41801529 TATATACATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.67, C:0.32, G:0.00, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:41808045 original size:359 final size:358
Alignment explanation
Indices: 41807369--41808092 Score: 1189
Period size: 359 Copynumber: 2.0 Consensus size: 358
41807359 ATATCAATAA
* * *
41807369 TCATATTAATATCAATTAAAACATAAATATTGTCCCTTATACGAGCTCTTGAGGCCCTAAATATG
1 TCAT-TTAATATCAATTAAAACATAAATATTCTCCCTTATACGAGCCCTTGAGGCCCTAAATATA
*
41807434 CGTTAGAAATAAGTCGAGACTAAATCAAAAACTCAGAGAATTTTTTAGAAAACAATAAAAATTGT
65 CGTTAGAAACAAGTCGAGACTAAATCAAAAACTCAGAGAATTTTTTAGAAAACAATAAAAATTGT
* * *
41807499 AAACACTGCAGTGGTCACACACCGCGTGGGCATTCGAAGTAGGAACACATGGCCATGTCCGTGCC
130 AAACACTGCAGGGGTCACACACCGCGTGGGCATTCAAAGTAGGAACACAAGGCCATGTCCGTGCC
* *
41807564 CGTATAACTCACTGACTTGGGCCACACGGCCAAGCTACATGCCCGTGTGTCAGGCCGTGTACCCT
195 CATATAACTCACTGACTTGGGCCACACGGCCAAGCCACATGCCCGTGTGTCAGGCCGTGTACCCT
*
41807629 TCAAAATAACATCACACGCCCATGTACCAGGCTATGTGCTAGGCCATGTAATAGACTAACTTGCA
260 TCAAAATAACATCACACGCCCATGTACCAGGCCATGTGCTAGGCCATGTAATAGACTAACTTGCA
*
41807694 ACCCTTTGAAAGCTACAGGGGACACACGACCGTG
325 ACCCTTTGAAAGCTACAGGGGACACACGACCATG
41807728 TCATTTAATATCAATTAAAAACATAAATATTCTCCCTTATACGAGCCCTTGAGGCCCTAAATATA
1 TCATTTAATATCAATT-AAAACATAAATATTCTCCCTTATACGAGCCCTTGAGGCCCTAAATATA
* *
41807793 CGTTAGAAACAAGTCGAGACTAAATCGAAAACTCAGAGAATTTTTTAGAAAACAATAAAAATTTT
65 CGTTAGAAACAAGTCGAGACTAAATCAAAAACTCAGAGAATTTTTTAGAAAACAATAAAAATTGT
* * * * * *
41807858 CAACACTGTAGGGGTCACACGCCGTGTGGGCATTCAAAGTAGGGACACAAGGCCATGTCTGTGCC
130 AAACACTGCAGGGGTCACACACCGCGTGGGCATTCAAAGTAGGAACACAAGGCCATGTCCGTGCC
* * *
41807923 CATGTAACTTACTGACTTGGGCCACACGGCCAAGCCACATGCCCGTGTGTTAGGCCGTGTACCCT
195 CATATAACTCACTGACTTGGGCCACACGGCCAAGCCACATGCCCGTGTGTCAGGCCGTGTACCCT
* *
41807988 TCAAAA-AAGCCTCACACGCCCATGTACCAGGCCATGTGCTAGGCCATGTAATAGACTAACTTGT
260 TCAAAATAA-CATCACACGCCCATGTACCAGGCCATGTGCTAGGCCATGTAATAGACTAACTTGC
*
41808052 AACCCTTTGAAAGCTACATGGGACACACGACCATG
324 AACCCTTTGAAAGCTACAGGGGACACACGACCATG
41808087 TCATTT
1 TCATTT
41808093 GGCCGTGTGT
Statistics
Matches: 338, Mismatches: 25, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
358 14 0.04
359 324 0.96
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (358 bp):
TCATTTAATATCAATTAAAACATAAATATTCTCCCTTATACGAGCCCTTGAGGCCCTAAATATAC
GTTAGAAACAAGTCGAGACTAAATCAAAAACTCAGAGAATTTTTTAGAAAACAATAAAAATTGTA
AACACTGCAGGGGTCACACACCGCGTGGGCATTCAAAGTAGGAACACAAGGCCATGTCCGTGCCC
ATATAACTCACTGACTTGGGCCACACGGCCAAGCCACATGCCCGTGTGTCAGGCCGTGTACCCTT
CAAAATAACATCACACGCCCATGTACCAGGCCATGTGCTAGGCCATGTAATAGACTAACTTGCAA
CCCTTTGAAAGCTACAGGGGACACACGACCATG
Found at i:41809271 original size:25 final size:25
Alignment explanation
Indices: 41809232--41809316 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 25
41809222 TCCTGTACCT
*
41809232 GTATGCTCA-TACGAGCTATAAATCG
1 GTATGCTCACT-CGAGCTGTAAATCG
* *
41809257 GTATGCTCACTCGAGTTGTAGATCG
1 GTATGCTCACTCGAGCTGTAAATCG
** * *
41809282 GTATGCTTTCACGAGCTGTAAATTG
1 GTATGCTCACTCGAGCTGTAAATCG
41809307 GTATGCTCAC
1 GTATGCTCAC
41809317 ATGAGTTGTG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
25 47 0.98
26 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.32
Consensus pattern (25 bp):
GTATGCTCACTCGAGCTGTAAATCG
Found at i:41809763 original size:16 final size:17
Alignment explanation
Indices: 41809742--41809773 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
41809732 CACTGTAGCC
41809742 CAAAATTAT-ATTTTGT
1 CAAAATTATCATTTTGT
41809758 CAAAATTATCATTTTG
1 CAAAATTATCATTTTG
41809774 CCCTATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (17 bp):
CAAAATTATCATTTTGT
Found at i:41818796 original size:8 final size:8
Alignment explanation
Indices: 41818783--41818812 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
41818773 AAAATTGAAC
41818783 ATAAATTT
1 ATAAATTT
41818791 ATAAATTT
1 ATAAATTT
41818799 ATAAATTT
1 ATAAATTT
41818807 ATAAAT
1 ATAAAT
41818813 AGTTCAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
ATAAATTT
Found at i:41826565 original size:22 final size:21
Alignment explanation
Indices: 41826539--41826611 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 21
41826529 GTACCTTTGC
*
41826539 AGAAGTACAATTACTTCATGGG
1 AGAAGTACAAATACTTC-TGGG
** *
41826561 AGAAGTACAGGTACCTCT-GG
1 AGAAGTACAAATACTTCTGGG
* *
41826581 TGAAGTATAAATACTTCTTGGG
1 AGAAGTACAAATACTTC-TGGG
41826603 AGAAGTACA
1 AGAAGTACA
41826612 GGTACCTCTT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
20 14 0.36
21 2 0.05
22 23 0.59
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.26
Consensus pattern (21 bp):
AGAAGTACAAATACTTCTGGG
Found at i:41826586 original size:42 final size:42
Alignment explanation
Indices: 41826523--41826630 Score: 153
Period size: 42 Copynumber: 2.6 Consensus size: 42
41826513 TGGAACAATG
* * *
41826523 GTACAGGTACCTTTGCAGAAGTACAATTACTTCATGGGAGAA
1 GTACAGGTACCTCTGGAGAAGTACAAATACTTCATGGGAGAA
* * *
41826565 GTACAGGTACCTCTGGTGAAGTATAAATACTTCTTGGGAGAA
1 GTACAGGTACCTCTGGAGAAGTACAAATACTTCATGGGAGAA
*
41826607 GTACAGGTACCTCTTGAGAAGTAC
1 GTACAGGTACCTCTGGAGAAGTAC
41826631 CGGTGCAAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (42 bp):
GTACAGGTACCTCTGGAGAAGTACAAATACTTCATGGGAGAA
Found at i:41826621 original size:22 final size:21
Alignment explanation
Indices: 41826523--41826630 Score: 87
Period size: 20 Copynumber: 5.2 Consensus size: 21
41826513 TGGAACAATG
*
41826523 GTACAGGTACCT-TTGCAGAA
1 GTACAGGTACCTCTTGGAGAA
** * *
41826543 GTACAATTACTTCATGGGAGAA
1 GTACAGGTACCTC-TTGGAGAA
*
41826565 GTACAGGTACCTC-TGGTGAA
1 GTACAGGTACCTCTTGGAGAA
* ** *
41826585 GTATAAATACTTCTTGGGAGAA
1 GTACAGGTACCTCTT-GGAGAA
41826607 GTACAGGTACCTCTT-GAGAA
1 GTACAGGTACCTCTTGGAGAA
41826627 GTAC
1 GTAC
41826631 CGGTGCAAGT
Statistics
Matches: 65, Mismatches: 19, Indels: 8
0.71 0.21 0.09
Matches are distributed among these distances:
20 32 0.49
21 1 0.02
22 32 0.49
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (21 bp):
GTACAGGTACCTCTTGGAGAA
Found at i:41829889 original size:29 final size:29
Alignment explanation
Indices: 41829807--41829928 Score: 109
Period size: 29 Copynumber: 4.2 Consensus size: 29
41829797 GTATCGATAC
** *
41829807 CCATCGAATATGAAAAGGGATGGTGACGA
1 CCATCGAATATGAAAAGGGATGGTTTCAA
* *
41829836 CCATCGAACATGAAAGGGGATGGTTTCAA
1 CCATCGAATATGAAAAGGGATGGTTTCAA
* * * *
41829865 CCCTTGAATATGAAAAGAGATGGTTTCGA
1 CCATCGAATATGAAAAGGGATGGTTTCAA
* * * * *
41829894 TCATCGATTAAAGAAAATGGATGGTTTCGA
1 CCATCGAAT-ATGAAAAGGGATGGTTTCAA
41829924 CCATC
1 CCATC
41829929 ATTTAGCACA
Statistics
Matches: 73, Mismatches: 19, Indels: 1
0.78 0.20 0.01
Matches are distributed among these distances:
29 52 0.71
30 21 0.29
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (29 bp):
CCATCGAATATGAAAAGGGATGGTTTCAA
Found at i:41838297 original size:20 final size:19
Alignment explanation
Indices: 41838266--41838318 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
41838256 GTTGGCGCGG
* *
41838266 AAATATCAATACCTTAGGA
1 AAATATCGATACCTTAAGA
41838285 AATATATCGATACCTTAAGA
1 AA-ATATCGATACCTTAAGA
41838305 AAAGTATCGATACC
1 AAA-TATCGATACC
41838319 GGATCGATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (19 bp):
AAATATCGATACCTTAAGA
Found at i:41840167 original size:20 final size:21
Alignment explanation
Indices: 41840142--41840181 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
41840132 TGGAGCAAGA
41840142 ATATCGATACCTT-AGAAAAT
1 ATATCGATACCTTAAGAAAAT
41840162 ATATCGATACCTTAAGAAAA
1 ATATCGATACCTTAAGAAAA
41840182 GTATCAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (21 bp):
ATATCGATACCTTAAGAAAAT
Found at i:41846985 original size:23 final size:23
Alignment explanation
Indices: 41846959--41847010 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
41846949 TTTGATAGAT
41846959 TAAAAAAT-TAAGTGTTGAAAAAA
1 TAAAAAATATAAGTGTTG-AAAAA
41846982 TAAAAAATAAATAAGTGTTGAAAAA
1 TAAAAAAT--ATAAGTGTTGAAAAA
41847007 TAAA
1 TAAA
41847011 TATTAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.31
25 9 0.35
26 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25
Consensus pattern (23 bp):
TAAAAAATATAAGTGTTGAAAAA
Found at i:41847009 original size:14 final size:14
Alignment explanation
Indices: 41846990--41847032 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
41846980 AATAAAAAAT
41846990 AAATAAGTGTTGAA
1 AAATAAGTGTTGAA
* * *
41847004 AAATAAATATTAAA
1 AAATAAGTGTTGAA
41847018 AAATTAAGTGTTGAA
1 AAA-TAAGTGTTGAA
41847033 TATAAGTTAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.56, C:0.00, G:0.14, T:0.30
Consensus pattern (14 bp):
AAATAAGTGTTGAA
Found at i:41847025 original size:29 final size:28
Alignment explanation
Indices: 41846957--41847032 Score: 104
Period size: 29 Copynumber: 2.8 Consensus size: 28
41846947 TCTTTGATAG
41846957 ATTAAAAAATTAAGTGTTGAAAAAATAAA
1 ATTAAAAAATTAAGTGTTG-AAAAATAAA
*
41846986 A--AATAAA-TAAGTGTTGAAAAATAAA
1 ATTAAAAAATTAAGTGTTGAAAAATAAA
41847011 TATTAAAAAATTAAGTGTTGAA
1 -ATTAAAAAATTAAGTGTTGAA
41847033 TATAAGTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 9 0.22
26 10 0.24
27 5 0.12
28 5 0.12
29 12 0.29
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (28 bp):
ATTAAAAAATTAAGTGTTGAAAAATAAA
Found at i:41850844 original size:27 final size:27
Alignment explanation
Indices: 41850800--41850871 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
41850790 TTGTACATGT
41850800 ATGCTCACACAAGGTGTGAAAATGGGC
1 ATGCTCACACAAGGTGTGAAAATGGGC
* *
41850827 ATGCTCACACGAGTTGTGAAAATGGGTC
1 ATGCTCACACAAGGTGTGAAAATGGG-C
* *
41850855 -TGCTTACACAAGCTGTG
1 ATGCTCACACAAGGTGTG
41850872 GGTCGAAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (27 bp):
ATGCTCACACAAGGTGTGAAAATGGGC
Found at i:41854816 original size:27 final size:27
Alignment explanation
Indices: 41854752--41854824 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
41854742 CGATTATTGT
* *
41854752 TCGCCAAGCCTGCTGGCGAACACCAAC
1 TCGCCAAACCTACTGGCGAACACCAAC
* * *
41854779 TTGTCAGACCTACTGGC-ACACACCAAC
1 TCGCCAAACCTACTGGCGA-ACACCAAC
*
41854806 TCGCCAAACCTATTGGCGA
1 TCGCCAAACCTACTGGCGA
41854825 TCACATTTCT
Statistics
Matches: 35, Mismatches: 9, Indels: 3
0.74 0.19 0.06
Matches are distributed among these distances:
26 1 0.03
27 33 0.94
28 1 0.03
ACGTcount: A:0.27, C:0.37, G:0.19, T:0.16
Consensus pattern (27 bp):
TCGCCAAACCTACTGGCGAACACCAAC
Found at i:41855840 original size:17 final size:16
Alignment explanation
Indices: 41855802--41855844 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
41855792 TGTTATAAGT
*
41855802 TAATAATTAAAATAAA
1 TAATAAATAAAATAAA
*
41855818 TGAATAAATAAAACTTAA
1 T-AATAAATAAAA-TAAA
41855836 TAATAAATA
1 TAATAAATA
41855845 TGATAAAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 18 0.78
18 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (16 bp):
TAATAAATAAAATAAA
Found at i:41859945 original size:22 final size:22
Alignment explanation
Indices: 41859871--41859937 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
41859861 AATAATTCCT
* **
41859871 GAGCTTAGTACGTGAAACATGA
1 GAGCTTAGTACGTTAGCCATGA
41859893 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAGCCATGA
41859915 GAGCTTAGTACGTTAGCCATGA
1 GAGCTTAGTACGTTAGCCATGA
41859937 G
1 G
41859938 GGTTTAGTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.25
Consensus pattern (22 bp):
GAGCTTAGTACGTTAGCCATGA
Found at i:41861781 original size:9 final size:9
Alignment explanation
Indices: 41861767--41861793 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
41861757 TTTGCACAAA
41861767 ACACAAAAT
1 ACACAAAAT
41861776 ACACAAAAT
1 ACACAAAAT
41861785 ACACAAAAT
1 ACACAAAAT
41861794 TTAAACACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (9 bp):
ACACAAAAT
Found at i:41873767 original size:28 final size:28
Alignment explanation
Indices: 41873701--41873759 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
41873691 TGATGTGTAG
**
41873701 GGTTGGTTGGGCATTGATTGCCCTTAAC
1 GGTTGGTTGGGCATTGAACGCCCTTAAC
*
41873729 GGTTGGTTGGGCATTGAACGCCTTTAAC
1 GGTTGGTTGGGCATTGAACGCCCTTAAC
41873757 GGT
1 GGT
41873760 GTTTTGGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.15, C:0.17, G:0.34, T:0.34
Consensus pattern (28 bp):
GGTTGGTTGGGCATTGAACGCCCTTAAC
Found at i:41873918 original size:103 final size:103
Alignment explanation
Indices: 41873739--41873940 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
41873729 GGTTGGTTGG
* * * *
41873739 GCATTGAACGCCTTTAACGGTGTTTTGGGATGGCCGAAGACGGTGTGTAGCGAATAGGGGTGGGA
1 GCATTGAACGCCCTTAACGGTGTGTTGGGATGGCCGAAGACGGTGTGCAGCGAATAGGGGTAGGA
41873804 ATATCTGCATCTGAATCTGACATGTTCTGTATATAAAA
66 ATATCTGCATCTGAATCTGACATGTTCTGTATATAAAA
*
41873842 GCATTGAACGCCCTTAACGGTGTGTTGGGATGGCTGAAGACGGTGTGCAGCGAATAGGGGTAGGA
1 GCATTGAACGCCCTTAACGGTGTGTTGGGATGGCCGAAGACGGTGTGCAGCGAATAGGGGTAGGA
41873907 ATATCTGCATCTGAATCTGACATGTTCTGTATAT
66 ATATCTGCATCTGAATCTGACATGTTCTGTATAT
41873941 GAAACTGAAA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.29
Consensus pattern (103 bp):
GCATTGAACGCCCTTAACGGTGTGTTGGGATGGCCGAAGACGGTGTGCAGCGAATAGGGGTAGGA
ATATCTGCATCTGAATCTGACATGTTCTGTATATAAAA
Found at i:41875492 original size:20 final size:19
Alignment explanation
Indices: 41875446--41875485 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
41875436 TAGCGTGGCT
41875446 TTTAATAATTTTTATCAAC
1 TTTAATAATTTTTATCAAC
41875465 TTTAATAAGTTTTTAT-AAC
1 TTTAATAA-TTTTTATCAAC
41875484 TT
1 TT
41875486 ATTATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (19 bp):
TTTAATAATTTTTATCAAC
Found at i:41875590 original size:16 final size:16
Alignment explanation
Indices: 41875569--41875610 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
41875559 TAGATGTGAT
41875569 TTTTTTAAAATAATTA
1 TTTTTTAAAATAATTA
* **
41875585 TTTTTTATAATTTTTA
1 TTTTTTAAAATAATTA
41875601 TTTTTTAAAA
1 TTTTTTAAAA
41875611 AAGTTTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTTTTAAAATAATTA
Found at i:41875618 original size:78 final size:76
Alignment explanation
Indices: 41875536--41875688 Score: 261
Period size: 78 Copynumber: 2.0 Consensus size: 76
41875526 TTTCCATACT
41875536 TTTTATTTTGTTCAAGTTCATTCTAGATGTGATTTTTTTAAAATAATTATTTTTTATAATTTTTA
1 TTTTATTTTGTTCAAGTTCATTCTAGATGTGA-TTTTTTAAAATAATTA-TTTTTATAATTTTTA
*
41875601 TTTTTTAAAAAAG
64 TTTTTAAAAAAAG
* *
41875614 TTTTATTTTGTTTAAGTTCATTCTAGATGTGATTTTTTAAAATAATTATTTTTATGATTTTTATT
1 TTTTATTTTGTTCAAGTTCATTCTAGATGTGATTTTTTAAAATAATTATTTTTATAATTTTTATT
41875679 TTTAAAAAAA
66 TTTAAAAAAA
41875689 AATATTTATT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
76 25 0.35
77 16 0.22
78 31 0.43
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (76 bp):
TTTTATTTTGTTCAAGTTCATTCTAGATGTGATTTTTTAAAATAATTATTTTTATAATTTTTATT
TTTAAAAAAAG
Found at i:41882388 original size:16 final size:16
Alignment explanation
Indices: 41882367--41882411 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
41882357 TAATGTTATT
41882367 CGGGCTATGTGCCTAG
1 CGGGCTATGTGCCTAG
41882383 CGGGCTATGTGCCTAG
1 CGGGCTATGTGCCTAG
*
41882399 CGGGCTTTGTGCC
1 CGGGCTATGTGCC
41882412 AGTGATATTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.09, C:0.27, G:0.38, T:0.27
Consensus pattern (16 bp):
CGGGCTATGTGCCTAG
Found at i:41882434 original size:38 final size:38
Alignment explanation
Indices: 41882390--41882595 Score: 241
Period size: 38 Copynumber: 5.4 Consensus size: 38
41882380 TAGCGGGCTA
* * *
41882390 TGTGCCTAGCGGGCTTTGTGCCAGTGATATTCGGGCTC
1 TGTGCCTAGCAGGCTTTGTGCCGGTGATATTCGAGCTC
* *
41882428 TGTGCCTAGTAGGCTTTGTGCTGGTGATATTCGAGCTC
1 TGTGCCTAGCAGGCTTTGTGCCGGTGATATTCGAGCTC
* * * * *
41882466 TGTGCCTAGCAAGCTATGTGCTGGTGATATTTGAGCTA
1 TGTGCCTAGCAGGCTTTGTGCCGGTGATATTCGAGCTC
* * * * *
41882504 TATGCCTAGCAGGCTTTGTACCAGTGTTATTCGAGCTT
1 TGTGCCTAGCAGGCTTTGTGCCGGTGATATTCGAGCTC
*
41882542 TGTGCCTAGCAGGCTTTGTGCCGGTGTTATTCGAGCTC
1 TGTGCCTAGCAGGCTTTGTGCCGGTGATATTCGAGCTC
** *
41882580 CATGCCTAGTAGGCTT
1 TGTGCCTAGCAGGCTT
41882596 CATGCCGATG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 142 1.00
ACGTcount: A:0.15, C:0.21, G:0.30, T:0.34
Consensus pattern (38 bp):
TGTGCCTAGCAGGCTTTGTGCCGGTGATATTCGAGCTC
Found at i:41882977 original size:31 final size:31
Alignment explanation
Indices: 41882940--41883002 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
41882930 GAGCTAAAGT
41882940 AAGTAAATGGAAGGGTTCAAAGTCTTATAAA
1 AAGTAAATGGAAGGGTTCAAAGTCTTATAAA
41882971 AAGTAAATGGAAGGGTTCAAAGTCTTATAAA
1 AAGTAAATGGAAGGGTTCAAAGTCTTATAAA
41883002 A
1 A
41883003 TCCTATTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.25
Consensus pattern (31 bp):
AAGTAAATGGAAGGGTTCAAAGTCTTATAAA
Found at i:41889417 original size:27 final size:27
Alignment explanation
Indices: 41889387--41889440 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
41889377 GTACATATAT
41889387 AAACATCCATATCAAAGCAAACTTTGA
1 AAACATCCATATCAAAGCAAACTTTGA
41889414 AAACATCCATATCAAAGCAAACTTTGA
1 AAACATCCATATCAAAGCAAACTTTGA
41889441 GAGATGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.22
Consensus pattern (27 bp):
AAACATCCATATCAAAGCAAACTTTGA
Found at i:41889810 original size:17 final size:17
Alignment explanation
Indices: 41889788--41889825 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
41889778 CATAAAATTA
41889788 ATTTAAAAATATTTTTT
1 ATTTAAAAATATTTTTT
*
41889805 ATTT--AAGTATTTTTT
1 ATTTAAAAATATTTTTT
41889820 ATTTAA
1 ATTTAA
41889826 GTTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
15 14 0.78
17 4 0.22
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
ATTTAAAAATATTTTTT
Found at i:41889817 original size:15 final size:15
Alignment explanation
Indices: 41889797--41889827 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41889787 AATTTAAAAA
41889797 TATTTTTTATTTAAG
1 TATTTTTTATTTAAG
41889812 TATTTTTTATTTAAG
1 TATTTTTTATTTAAG
41889827 T
1 T
41889828 TAAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTTTATTTAAG
Found at i:41891605 original size:24 final size:24
Alignment explanation
Indices: 41891578--41891624 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41891568 AATAATAAAG
* *
41891578 AAAAATTTTTAAAAATGACACTGC
1 AAAAATGTTTAAAAAAGACACTGC
41891602 AAAAATGTTTAAAAAAGACACTG
1 AAAAATGTTTAAAAAAGACACTG
41891625 ACGCAACATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.11, G:0.11, T:0.26
Consensus pattern (24 bp):
AAAAATGTTTAAAAAAGACACTGC
Found at i:41893466 original size:36 final size:36
Alignment explanation
Indices: 41893426--41893501 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
41893416 AGGATGATGA
41893426 TTTCTCTTCATCTTTCCTCCTTTCTTATACTAATAT
1 TTTCTCTTCATCTTTCCTCCTTTCTTATACTAATAT
*
41893462 TTTCTCTTCATCTTTCCTCCTTTCTTGTACTAATAT
1 TTTCTCTTCATCTTTCCTCCTTTCTTATACTAATAT
41893498 TTTC
1 TTTC
41893502 GTAATAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.14, C:0.28, G:0.01, T:0.57
Consensus pattern (36 bp):
TTTCTCTTCATCTTTCCTCCTTTCTTATACTAATAT
Found at i:41893517 original size:11 final size:11
Alignment explanation
Indices: 41893503--41893541 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
41893493 AATATTTTCG
41893503 TAATAAAATAT
1 TAATAAAATAT
41893514 TAATAAAA-AT
1 TAATAAAATAT
41893524 CTAATTAAAATAT
1 -TAA-TAAAATAT
41893537 TAATA
1 TAATA
41893542 TTATAACATT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 8 0.32
13 2 0.08
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:41894026 original size:21 final size:21
Alignment explanation
Indices: 41894001--41894043 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
41893991 ATCTATCTCA
41894001 TATTATTTTCAACCAAGGGGT
1 TATTATTTTCAACCAAGGGGT
41894022 TATTATTTTCAACCAAGGGGT
1 TATTATTTTCAACCAAGGGGT
41894043 T
1 T
41894044 TTGGGGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (21 bp):
TATTATTTTCAACCAAGGGGT
Found at i:41900490 original size:11 final size:11
Alignment explanation
Indices: 41900453--41900492 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
41900443 ATAATGCGAG
*
41900453 ATTTTTCTGTA
1 ATTTTTCTGTT
*
41900464 ATTTTTCTTTT
1 ATTTTTCTGTT
41900475 ATTTTTCTGTT
1 ATTTTTCTGTT
*
41900486 GTTTTTC
1 ATTTTTC
41900493 GGCCATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.10, C:0.10, G:0.07, T:0.72
Consensus pattern (11 bp):
ATTTTTCTGTT
Found at i:41902888 original size:13 final size:13
Alignment explanation
Indices: 41902870--41902895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41902860 TTGTATAAAG
41902870 GTTTGATTAATTT
1 GTTTGATTAATTT
41902883 GTTTGATTAATTT
1 GTTTGATTAATTT
41902896 TTTTTTGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.15, T:0.62
Consensus pattern (13 bp):
GTTTGATTAATTT
Found at i:41905807 original size:41 final size:42
Alignment explanation
Indices: 41905761--41905846 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
41905751 CCTGATCAGT
41905761 ATACGACACAT-AAGTGCCTGAAAT-G-ACATACGAAGTGTCTG
1 ATACGACACATGAAGTGCCTGAAATGGCACATA--AAGTGTCTG
* *
41905802 ATACGACACATGAGGTGCCTGATATGGCACATAAAGTGTCTG
1 ATACGACACATGAAGTGCCTGAAATGGCACATAAAGTGTCTG
41905844 ATA
1 ATA
41905847 TATGACACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 11 0.28
42 23 0.57
43 1 0.03
44 5 0.12
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (42 bp):
ATACGACACATGAAGTGCCTGAAATGGCACATAAAGTGTCTG
Found at i:41905847 original size:21 final size:21
Alignment explanation
Indices: 41905765--41905861 Score: 79
Period size: 21 Copynumber: 4.6 Consensus size: 21
41905755 ATCAGTATAC
* *
41905765 GACACAT-AAGTGCCTGAAAT
1 GACACATAAAGTGTCTGATAT
* ** *
41905785 GACATACGAAGTGTCTGATAC
1 GACACATAAAGTGTCTGATAT
* * *
41905806 GACACATGAGGTGCCTGATAT
1 GACACATAAAGTGTCTGATAT
*
41905827 GGCACATAAAGTGTCTGATATAT
1 GACACATAAAGTGTCTG--ATAT
41905850 GACACATAAAGT
1 GACACATAAAGT
41905862 TCCTGAACGG
Statistics
Matches: 59, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 5 0.08
21 39 0.66
23 15 0.25
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (21 bp):
GACACATAAAGTGTCTGATAT
Found at i:41907273 original size:30 final size:28
Alignment explanation
Indices: 41907237--41907293 Score: 87
Period size: 30 Copynumber: 2.0 Consensus size: 28
41907227 TTTATTTTAC
*
41907237 ATAATAATATAATATAATATAATATATTTT
1 ATAATAAAATAATAT-AT-TAATATATTTT
41907267 ATAATAAAATAATATATTAATATATTT
1 ATAATAAAATAATATATTAATATATTT
41907294 AAAACATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 10 0.38
29 2 0.08
30 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
ATAATAAAATAATATATTAATATATTTT
Found at i:41907278 original size:20 final size:22
Alignment explanation
Indices: 41907244--41907284 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
41907234 TACATAATAA
41907244 TATAATATAATATAATATATTT
1 TATAATATAATATAATATATTT
41907266 TATAATA-AA-ATAATATATT
1 TATAATATAATATAATATATT
41907285 AATATATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAATATAATATAATATATTT
Found at i:41907296 original size:22 final size:22
Alignment explanation
Indices: 41907241--41907297 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
41907231 TTTTACATAA
*
41907241 TAATATAATATAATATAATATAT
1 TAATAT-ATATAAAATAATATAT
*
41907264 T-TTATA-ATAAAATAATATAT
1 TAATATATATAAAATAATATAT
*
41907284 TAATATATTTAAAA
1 TAATATATATAAAA
41907298 CATAAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
20 14 0.50
21 5 0.18
22 8 0.29
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
TAATATATATAAAATAATATAT
Found at i:41907306 original size:30 final size:32
Alignment explanation
Indices: 41907235--41907306 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 32
41907225 TGTTTATTTT
* *
41907235 ACATAATAATATAATATAATATAATATATTTTAT
1 ACATAA-AA-ATAATATAATATAATATATTTAAA
41907269 A-AT-AAAATAATAT-AT-TAATATATTTAAA
1 ACATAAAAATAATATAATATAATATATTTAAA
41907297 ACATAAAAAT
1 ACATAAAAAT
41907307 CTAAGATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
28 12 0.35
29 4 0.12
30 12 0.35
31 2 0.06
32 1 0.03
33 2 0.06
34 1 0.03
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (32 bp):
ACATAAAAATAATATAATATAATATATTTAAA
Found at i:41914746 original size:32 final size:32
Alignment explanation
Indices: 41914651--41914759 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
41914641 CCACAGAGAA
* * *
41914651 AGGCAGCACACCACTGGTCATGCCCATTTCAC
1 AGGCGGCACACCGCTGGTCATGCCCATTCCAC
* *
41914683 AGGCGGCAC-CAGTTGAGATCATGCCCATTCCAC
1 AGGCGGCACACCGCTG-G-TCATGCCCATTCCAC
*
41914716 AGGCGGCACACCGCTGGTCAAGCCCATTCCAC
1 AGGCGGCACACCGCTGGTCATGCCCATTCCAC
*
41914748 AGGTGGCACACC
1 AGGCGGCACACC
41914760 TCTGACTTGT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
31 3 0.05
32 34 0.52
33 24 0.37
34 4 0.06
ACGTcount: A:0.24, C:0.37, G:0.24, T:0.16
Consensus pattern (32 bp):
AGGCGGCACACCGCTGGTCATGCCCATTCCAC
Found at i:41914880 original size:3 final size:3
Alignment explanation
Indices: 41914872--41914930 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
41914862 AAATAAAATT
41914872 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
41914920 GAA GAA GAA GA
1 GAA GAA GAA GA
41914931 GAGCGGGAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41915345 original size:16 final size:16
Alignment explanation
Indices: 41915324--41915437 Score: 60
Period size: 16 Copynumber: 7.0 Consensus size: 16
41915314 TTTTATTTTT
41915324 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
* *
41915340 TTATGT-GTGTT-TTAGG
1 TTATGTAAT-TTATT-TG
*
41915356 TTGAT-TAGATTTATTTT
1 TT-ATGTA-ATTTATTTG
41915373 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
* *
41915389 TTATGT-GTGTT-TTAGG
1 TTATGTAAT-TTATT-TG
*
41915405 TTGAT-TAGATTTATTTT
1 TT-ATGTA-ATTTATTTG
41915422 TTATGTAATTTATTTG
1 TTATGTAATTTATTTG
41915438 GCATGTTAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
15 6 0.08
16 44 0.61
17 16 0.22
18 6 0.08
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (16 bp):
TTATGTAATTTATTTG
Found at i:41915451 original size:49 final size:49
Alignment explanation
Indices: 41915315--41915437 Score: 237
Period size: 49 Copynumber: 2.5 Consensus size: 49
41915305 TAAAGAATGT
41915315 TTTATTTTTTTATGTAATTTATTTGTTATGTGTGTTTTAGGTTGATTAGA
1 TTTA-TTTTTTATGTAATTTATTTGTTATGTGTGTTTTAGGTTGATTAGA
41915365 TTTATTTTTTATGTAATTTATTTGTTATGTGTGTTTTAGGTTGATTAGA
1 TTTATTTTTTATGTAATTTATTTGTTATGTGTGTTTTAGGTTGATTAGA
41915414 TTTATTTTTTATGTAATTTATTTG
1 TTTATTTTTTATGTAATTTATTTG
41915438 GCATGTTAAT
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
49 69 0.95
50 4 0.05
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.63
Consensus pattern (49 bp):
TTTATTTTTTATGTAATTTATTTGTTATGTGTGTTTTAGGTTGATTAGA
Found at i:41917087 original size:14 final size:14
Alignment explanation
Indices: 41917068--41917102 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
41917058 TGACATTTTT
*
41917068 TTCTAATGATACTA
1 TTCTAACGATACTA
41917082 TTCTAACGATACTA
1 TTCTAACGATACTA
41917096 TTCTAAC
1 TTCTAAC
41917103 ATGTAATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:41917777 original size:6 final size:6
Alignment explanation
Indices: 41917766--41917816 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
41917756 CCAGAGCTCA
* * * *
41917766 AGCCAG AGCCAG AGCTTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCCG
1 AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG AGCCTG
41917814 AGC
1 AGC
41917817 AGTCGCATAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.33, T:0.12
Consensus pattern (6 bp):
AGCCTG
Found at i:41917787 original size:18 final size:18
Alignment explanation
Indices: 41917746--41917816 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
41917736 GGATAGAGTC
* *
41917746 TGAGCCCGAACCAGAGCT
1 TGAGCCTGAGCCAGAGCT
** *
41917764 CAAGCCAGAGCCAGAGCT
1 TGAGCCTGAGCCAGAGCT
* *
41917782 TGAGCCTGAGCCTGAGCC
1 TGAGCCTGAGCCAGAGCT
*
41917800 TGAGCCTGAGCCCGAGC
1 TGAGCCTGAGCCAGAGC
41917817 AGTCGCATAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.24, C:0.34, G:0.31, T:0.11
Consensus pattern (18 bp):
TGAGCCTGAGCCAGAGCT
Found at i:41918386 original size:27 final size:27
Alignment explanation
Indices: 41918302--41918405 Score: 112
Period size: 27 Copynumber: 4.1 Consensus size: 27
41918292 TTGCAACATT
41918302 AAAACTTGGAACAAACTTTGTAATAT-
1 AAAACTTGGAACAAACTTTGTAATATA
* * ** * *
41918328 -AAA-TT-G-A-ATACATTACAACATT
1 AAAACTTGGAACAAACTTTGTAATATA
41918350 AAAACTTGGAACAAACTTTGTAATATA
1 AAAACTTGGAACAAACTTTGTAATATA
41918377 AAAACTTGGAACAAACTTTGTAATATA
1 AAAACTTGGAACAAACTTTGTAATATA
41918404 AA
1 AA
41918406 TTAAATACAT
Statistics
Matches: 61, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
21 9 0.15
22 1 0.02
23 4 0.07
24 4 0.07
25 4 0.07
26 1 0.02
27 38 0.62
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.30
Consensus pattern (27 bp):
AAAACTTGGAACAAACTTTGTAATATA
Found at i:41918392 original size:75 final size:73
Alignment explanation
Indices: 41918302--41918452 Score: 275
Period size: 75 Copynumber: 2.0 Consensus size: 73
41918292 TTGCAACATT
*
41918302 AAAACTTGGAACAAACTTTGTAATATAAATTGAATACATTACAACATTAAAACTTGGAACAAACT
1 AAAACTTGGAACAAACTTTGTAATATAAATTAAATACATTACAACATT-AAACTTGGAACAAACT
41918367 TTGTAATATA
65 TTGTAATA-A
41918377 AAAACTTGGAACAAACTTTGTAATATAAATTAAATACATTACAACATTAAACTTGGAACAAACTT
1 AAAACTTGGAACAAACTTTGTAATATAAATTAAATACATTACAACATTAAACTTGGAACAAACTT
41918442 TGTAATAA
66 TGTAATAA
41918450 AAA
1 AAA
41918453 TTAGGTACAT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
73 4 0.05
74 24 0.32
75 47 0.63
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.30
Consensus pattern (73 bp):
AAAACTTGGAACAAACTTTGTAATATAAATTAAATACATTACAACATTAAACTTGGAACAAACTT
TGTAATAA
Done.