Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 16 of 17
Found at i:2318721 original size:28 final size:28
Alignment explanation
Indices: 2318689--2318755 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
2318679 CAAAGCCTAC
2318689 ATTAGTTGGCACATGAATC-AATACCCAT
1 ATTAGTTGGCACATGAATCGAA-ACCCAT
* *
2318717 ATTAGTTGGCTCATGAATCGAAGCCCAT
1 ATTAGTTGGCACATGAATCGAAACCCAT
2318745 ATTAGTTGGCA
1 ATTAGTTGGCA
2318756 TCTAAGTCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
28 33 0.94
29 2 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (28 bp):
ATTAGTTGGCACATGAATCGAAACCCAT
Found at i:2318768 original size:28 final size:28
Alignment explanation
Indices: 2318712--2318797 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
2318702 TGAATCAATA
*
2318712 CCCATATTAGTTGGC-TCATGAA-TCGAAG
1 CCCATATTAGTTGGCATC-T-AAGTCTAAG
2318740 CCCATATTAGTTGGCATCTAAGTCTAAG
1 CCCATATTAGTTGGCATCTAAGTCTAAG
** * *
2318768 CCCATGCTAGTTGGTACCTAAG--TAAG
1 CCCATATTAGTTGGCATCTAAGTCTAAG
2318794 CCCA
1 CCCA
2318798 CGCTAGCTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.16
27 2 0.04
28 39 0.76
29 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (28 bp):
CCCATATTAGTTGGCATCTAAGTCTAAG
Found at i:2318928 original size:28 final size:28
Alignment explanation
Indices: 2318888--2318988 Score: 148
Period size: 28 Copynumber: 3.6 Consensus size: 28
2318878 ACACCTAAGT
*
2318888 AAGCCCACATTAGTTGGCACATGAATCA
1 AAGCCCACATTAGTTGGCACATGAATTA
*
2318916 AAGCCCACATTAGTTGGCACATGAATTG
1 AAGCCCACATTAGTTGGCACATGAATTA
* * *
2318944 AAGCCCATATTAGTTAGCTCATGAATTA
1 AAGCCCACATTAGTTGGCACATGAATTA
*
2318972 AAGCCCACATTAATTGG
1 AAGCCCACATTAGTTGG
2318989 TATCTAAGTC
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 64 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (28 bp):
AAGCCCACATTAGTTGGCACATGAATTA
Found at i:2322496 original size:19 final size:19
Alignment explanation
Indices: 2322472--2322530 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
2322462 CGATACATTA
2322472 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
2322491 TATCGAT---ACA--T-TG
1 TATCGATACAACACTTATG
2322504 TATCGATACAACACTTATG
1 TATCGATACAACACTTATG
2322523 TATCGATA
1 TATCGATA
2322531 TATTTACTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
16 6 0.18
18 1 0.03
19 17 0.50
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (19 bp):
TATCGATACAACACTTATG
Found at i:2322498 original size:32 final size:32
Alignment explanation
Indices: 2322453--2322530 Score: 140
Period size: 32 Copynumber: 2.5 Consensus size: 32
2322443 ATGCAGGGTA
2322453 ACTT-TGTATCGATACATTATATCGATACAAC
1 ACTTATGTATCGATACATTATATCGATACAAC
*
2322484 ACTTATGTATCGATACATTGTATCGATACAAC
1 ACTTATGTATCGATACATTATATCGATACAAC
2322516 ACTTATGTATCGATA
1 ACTTATGTATCGATA
2322531 TATTTACTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 4 0.09
32 41 0.91
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (32 bp):
ACTTATGTATCGATACATTATATCGATACAAC
Found at i:2323224 original size:70 final size:70
Alignment explanation
Indices: 2323140--2323285 Score: 231
Period size: 70 Copynumber: 2.1 Consensus size: 70
2323130 CAACACTGGA
* * *
2323140 CTTAAAGATGATGAAGAT-GAGAAGAGTGATAAAGGTGCCAATATGTTGATTTAAGACCAGTAAT
1 CTTAAAAATGATGAAGATAG-GAAGAGTGATAAAGGTGCCAATATGCTGATTCAAGACCAGTAAT
*
2323204 ATTGGG
65 ATTAGG
*
2323210 CTTAAAAATGATGAAGATAGGAAGAGTGATAAAGGTGCCAATATGCTGATTCAAGACCAGTGATA
1 CTTAAAAATGATGAAGATAGGAAGAGTGATAAAGGTGCCAATATGCTGATTCAAGACCAGTAATA
2323275 TTAGG
66 TTAGG
2323280 CTTAAA
1 CTTAAA
2323286 GATGTAAAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
70 69 0.99
71 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.26
Consensus pattern (70 bp):
CTTAAAAATGATGAAGATAGGAAGAGTGATAAAGGTGCCAATATGCTGATTCAAGACCAGTAATA
TTAGG
Found at i:2323474 original size:49 final size:49
Alignment explanation
Indices: 2323353--2323588 Score: 205
Period size: 52 Copynumber: 4.8 Consensus size: 49
2323343 GAAGAATACT
*
2323353 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGCGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGCGCC
* * *
2323405 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGCGCC
* * * ***
2323454 AATGTGCTAATTCAAAGCCAGCAACATTGGACTTAAAGATGAAAAGAATACC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG--AAG-GCGCC
* * ** *
2323506 AATGTGCTGATTCAACGCCAACGACATTGGGTTTCAAGAT------GCC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGCGCC
* * *
2323549 AATATGTTGATTCAAGGCCAGCGATATTGGACTTAGAAGA
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTA-AAGA
2323589 AGATGCCACC
Statistics
Matches: 153, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
43 29 0.19
44 4 0.03
49 43 0.28
51 3 0.02
52 74 0.48
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.24
Consensus pattern (49 bp):
AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGCGCC
Found at i:2323531 original size:153 final size:155
Alignment explanation
Indices: 2323240--2323535 Score: 393
Period size: 153 Copynumber: 1.9 Consensus size: 155
2323230 GAAGAGTGAT
* * *
2323240 AAAGGTGCCAATATGCTGATTCAAGACCAGTGATATTAGGCTTAAAGATGTAAAGAATGTCAATG
1 AAAGGCGCCAATATGCTGATTCAAGACCAGCGATATTAGGCTTAAAGATG-AAAGAATGCCAATG
* * * * * * * * *
2323305 TGCTGATTCACGATCGGCGACATTAGACTTGAAGATGAGAAGAATACTAATGTGCTGATTCAAGG
65 TGCTAATTCAAGACCAGCAACATTAGACTTAAAGATGAAAAGAATACCAATGTGCTGATTCAACG
*
2323370 CCAGCGACATTGGACTTAAATATGAC
130 CCAACGACATTGGACTTAAATATGAC
* *
2323396 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGATG-AAG-GTGCCAATG
1 AAAGGCGCCAATATGCTGATTCAAGACCAGCGATATTAGG-CTTAAAGATGAAAGAATGCCAATG
*
2323458 TGCTAATTCAA-AGCCAGCAACATTGGACTTAAAGATGAAAAGAATACCAATGTGCTGATTCAAC
65 TGCTAATTCAAGA-CCAGCAACATTAGACTTAAAGATGAAAAGAATACCAATGTGCTGATTCAAC
2323522 GCCAACGACATTGG
129 GCCAACGACATTGG
2323536 GTTTCAAGAT
Statistics
Matches: 122, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
152 1 0.01
153 72 0.59
154 3 0.02
155 2 0.02
156 44 0.36
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (155 bp):
AAAGGCGCCAATATGCTGATTCAAGACCAGCGATATTAGGCTTAAAGATGAAAGAATGCCAATGT
GCTAATTCAAGACCAGCAACATTAGACTTAAAGATGAAAAGAATACCAATGTGCTGATTCAACGC
CAACGACATTGGACTTAAATATGAC
Found at i:2323546 original size:52 final size:51
Alignment explanation
Indices: 2323247--2323535 Score: 260
Period size: 52 Copynumber: 5.6 Consensus size: 51
2323237 GATAAAGGTG
* * * * * *
2323247 CCAATATGCTGATTCAAGACCAGTGATATTAGG-CTTAAAGATGTAAAGAATG
1 CCAATGTGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAAAG-ATA
* * ** * * * *
2323299 TCAATGTGCTGATTCACGATCGGCGACATTAGACTTGAAGATGAGAAGAATA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAG-ATA
* * ***
2323351 CTAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGCG
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGA-AAAGATA
* * * *
2323403 CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAGGTG
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGATA
* * *
2323452 CCAATGTGCTAATTCAAAGCCAGCAACATTGGACTTAAAGATGAAAAGAATA
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAG-ATA
* *
2323504 CCAATGTGCTGATTCAACGCCAACGACATTGG
1 CCAATGTGCTGATTCAAGGCCAGCGACATTGG
2323536 GTTTCAAGAT
Statistics
Matches: 191, Mismatches: 41, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
49 43 0.23
51 4 0.02
52 141 0.74
53 3 0.02
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.24
Consensus pattern (51 bp):
CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAGATA
Found at i:2323546 original size:101 final size:101
Alignment explanation
Indices: 2323353--2323535 Score: 251
Period size: 101 Copynumber: 1.8 Consensus size: 101
2323343 GAAGAATACT
* * * * * *
2323353 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATATGACAAAGGCGCCAATATGCTGATTC
1 AATGTGCTAATTCAAAGCCAGCAACATTGGACTTAAAGATGACAAAGACACCAATATGCTGATTC
* * *
2323418 AAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCC
66 AACGCCAACGACATTGGACTTAAAGATGAAGGTGCC
* *
2323454 AATGTGCTAATTCAAAGCCAGCAACATTGGACTTAAAGATGA-AAAGAATACCAATGTGCTGATT
1 AATGTGCTAATTCAAAGCCAGCAACATTGGACTTAAAGATGACAAAG-ACACCAATATGCTGATT
2323518 CAACGCCAACGACATTGG
65 CAACGCCAACGACATTGG
2323536 GTTTCAAGAT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
100 4 0.06
101 66 0.94
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (101 bp):
AATGTGCTAATTCAAAGCCAGCAACATTGGACTTAAAGATGACAAAGACACCAATATGCTGATTC
AACGCCAACGACATTGGACTTAAAGATGAAGGTGCC
Found at i:2323670 original size:28 final size:28
Alignment explanation
Indices: 2323605--2324247 Score: 606
Period size: 28 Copynumber: 22.6 Consensus size: 28
2323595 CACCAACTTG
**
2323605 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTGACT
* * *
2323634 TATGTGCTTTTGAAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
2323662 TGTGGGC-TTTGAAAAGG-TGCCACTCACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
* *
2323690 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* * *
2323719 TGTAGCCTTTTGAAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
2323747 TGTGGGC-TTTGAAAAGGGTGCCACCGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
2323776 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
**
2323804 TGTGGGCTTTAAAAGGGTTGCCACTGACT
1 TGTGGGCTTTTGAA-GGTTGCCACTGACT
* *
2323833 TGTGGGCTTTCGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
2323861 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
2323890 TGTGGGC-TTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
* * *
2323918 TGTGGGCTTTTGAAAAGATGCCACTAAC-
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* *
2323946 TATGGGCTTTTGAAGGTTTCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
2323974 TGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTGACT
* **
2324003 TGTGGGCTTTTAAAGGTTATCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
** *
2324031 TGTGGGCTTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTT-TGAAGGTTGCCACTGACT
** *
2324060 TGTGGGCTTCCGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
2324088 TGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTTG-AAGGTTGCCACTGACT
* *
2324117 TATGGGC-TTTGAAAGGGGTGCCA-TCGACT
1 TGTGGGCTTTTG-AA-GGTTGCCACT-GACT
2324146 TGTGGGCTTTTGAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* **
2324174 TGTGGGC-TTTGAAAGGGGTGCCACCAACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTGACT
* *
2324203 TGTGGGCTTCTGAAGGTTGCCACTAACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
2324231 TATGGGCTTTGGAAGGT
1 TGTGGGCTTTTGAAGGT
2324248 GAGGAATGTC
Statistics
Matches: 511, Mismatches: 77, Indels: 53
0.80 0.12 0.08
Matches are distributed among these distances:
27 32 0.06
28 243 0.48
29 222 0.43
30 14 0.03
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:2323678 original size:57 final size:57
Alignment explanation
Indices: 2323605--2324247 Score: 652
Period size: 57 Copynumber: 11.3 Consensus size: 57
2323595 CACCAACTTG
** * * * *
2323605 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTATGTGCTTTTG-AAGGTTGCCATTGACT
1 TGTGGGC-TTTGAAA-GGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* *
2323662 TGTGGGCTTTGAAAAGG-TGCCACTCACTTGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* * * * *
2323719 TGTAGCCTTTTG-AAGGTTGCCATTGACTTGTGGGC-TTTGAAAAGGGTGCCACCGACT
1 TGTGGGC-TTTGAAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAGGATGCCACTGACT
* *
2323776 TGTGGGCTTTTG-AAGGTTGCCACTGACTTGTGGGC-TTTAAAAGGGTTGCCACTGACT
1 TGTGGGC-TTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAA-GGATGCCACTGACT
* *
2323833 TGTGGGCTTTCG-AAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTT-GAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* *
2323890 TGTGGGCTTTGAAAAGG-TGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTAAC-
1 TGTGGGCTTTG-AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* * * *
2323946 TATGGGCTTTTG-AAGGTTTCCACTGACTTGTGGGC-TTTGAAAGGGGTGCCACCGACT
1 TGTGGGC-TTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAA-GGATGCCACTGACT
* ** ** *
2324003 TGTGGGCTTTTAAAGGTTATCACTGACTTGTGGGCTTTAAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* * *
2324060 TGTGGGCTTCCG-AAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACT
1 TGTGGGCTT-TGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* * *
2324117 TATGGGCTTTGAAAGGGGTGCCA-TCGACTTGTGGGCTTTTG-AAGGTTGCCACTGACT
1 TGTGGGCTTTGAAA-GGTTGCCACT-GACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* ** * * *
2324174 TGTGGGCTTTGAAAGGGGTGCCACCAACTTGTGGGCTTCTG-AAGGTTGCCACTAACT
1 TGTGGGCTTTGAAA-GGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
* *
2324231 TATGGGCTTTGGAAGGT
1 TGTGGGCTTTGAAAGGT
2324248 GAGGAATGTC
Statistics
Matches: 502, Mismatches: 62, Indels: 45
0.82 0.10 0.07
Matches are distributed among these distances:
55 13 0.03
56 75 0.15
57 373 0.74
58 41 0.08
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (57 bp):
TGTGGGCTTTGAAAGGTTGCCACTGACTTGTGGGCTTTTGAAAGGATGCCACTGACT
Found at i:2324029 original size:227 final size:227
Alignment explanation
Indices: 2323605--2324159 Score: 841
Period size: 227 Copynumber: 2.4 Consensus size: 227
2323595 CACCAACTTG
* * * * * * *
2323605 TGTGGGCTTTTGAAAGGGTTG-CACCAACTTATGTGCTTTTG-AAGGTTGCCATTGACTTGTGGG
1 TGTGGGCTTTCG-AA-GGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGG
* *
2323668 CTTTGAAAAGGTGCCACTCACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTAGCCTTTTGAA
64 CTTTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTAACTTG-AGCCTTTTGAA
* * *
2323733 GGTTGCCATTGACTTGTGGGCTTTGAAAAGGGTGCCACCGACTTGTGGGCTTTTGAAGGTTGCCA
128 GGTTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACCGACTTGTGGGCTTTTAAAGGTTACCA
2323798 CTGACTTGTGGGCTTT-AAAAGGGTTGCCACTGACT
193 CTGACTTGTGGGCTTTAAAAAGGG-TGCCACTGACT
2323833 TGTGGGCTTTCGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCT
1 TGTGGGCTTTCGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCT
*
2323898 TTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTAACTATG-GGCTTTTGAAGG
66 TTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTAACT-TGAGCCTTTTGAAGG
* * *
2323962 TTTCCACTGACTTGTGGGCTTTGAAAGGGGTGCCACCGACTTGTGGGCTTTTAAAGGTTATCACT
130 TTGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACCGACTTGTGGGCTTTTAAAGGTTACCACT
2324027 GACTTGTGGGCTTTAAAAAGGGTGCCACTGACT
195 GACTTGTGGGCTTTAAAAAGGGTGCCACTGACT
* *
2324060 TGTGGGCTTCCGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTATGGGCT
1 TGTGGGCTTTCGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCT
*
2324125 TTGAAAGGGGTGCCA-TCGACTTGTGGGCTTTTGAA
66 TTGAAA-AGGTGCCACT-GACTTGTGGGCTTTTGAA
2324160 GGTTGCCACT
Statistics
Matches: 302, Mismatches: 19, Indels: 12
0.91 0.06 0.04
Matches are distributed among these distances:
226 5 0.02
227 184 0.61
228 111 0.37
229 2 0.01
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.32
Consensus pattern (227 bp):
TGTGGGCTTTCGAAGGTTGCCACTAACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCT
TTGAAAAGGTGCCACTGACTTGTGGGCTTTTGAAAAGATGCCACTAACTTGAGCCTTTTGAAGGT
TGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACCGACTTGTGGGCTTTTAAAGGTTACCACTG
ACTTGTGGGCTTTAAAAAGGGTGCCACTGACT
Found at i:2324655 original size:37 final size:37
Alignment explanation
Indices: 2324605--2324689 Score: 161
Period size: 37 Copynumber: 2.3 Consensus size: 37
2324595 AAAGATGAAG
2324605 CACAAATGCATCATGCAAAATGAAATGTTATAAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATAAATGT
*
2324642 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATGCAAAATGAAATGTTATAAATGT
2324679 CACAAATGCAT
1 CACAAATGCAT
2324690 GATTGTGGCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (37 bp):
CACAAATGCATCATGCAAAATGAAATGTTATAAATGT
Found at i:2325715 original size:15 final size:15
Alignment explanation
Indices: 2325695--2325743 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
2325685 ACCCTTTTTG
2325695 TTGTTTTTTTTCTTT
1 TTGTTTTTTTTCTTT
*
2325710 TTGTTTTTTTGCTTTT
1 TTGTTTTTTTTC-TTT
*
2325726 TTGTTTTTTTTTTTT
1 TTGTTTTTTTTCTTT
2325741 TTG
1 TTG
2325744 CGGAGGACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (15 bp):
TTGTTTTTTTTCTTT
Found at i:2325725 original size:23 final size:23
Alignment explanation
Indices: 2325689--2325744 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
2325679 ATCCGAACCC
*
2325689 TTTTTGTTG-TTTTTTTTCTTTTTG
1 TTTTT-TTGCTTTTTTGT-TTTTTG
*
2325713 TTTTTTTGCTTTTTTGTTTTTTT
1 TTTTTTTGCTTTTTTGTTTTTTG
2325736 TTTTTTTGC
1 TTTTTTTGC
2325745 GGAGGACTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (23 bp):
TTTTTTTGCTTTTTTGTTTTTTG
Found at i:2325732 original size:22 final size:22
Alignment explanation
Indices: 2325700--2325741 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2325690 TTTTGTTGTT
2325700 TTTTTTCTTTTTGTTTTTTTGC
1 TTTTTTCTTTTTGTTTTTTTGC
* *
2325722 TTTTTTGTTTTTTTTTTTTT
1 TTTTTTCTTTTTGTTTTTTT
2325742 TGCGGAGGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.05, G:0.07, T:0.88
Consensus pattern (22 bp):
TTTTTTCTTTTTGTTTTTTTGC
Found at i:2329498 original size:47 final size:47
Alignment explanation
Indices: 2329429--2329523 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
2329419 CCCTTACGTA
2329429 GGATACCTACCTACCTTTGGGCAAAGGTAAATAGGTTTTTGTTGCTC
1 GGATACCTACCTACCTTTGGGCAAAGGTAAATAGGTTTTTGTTGCTC
*
2329476 GGATACCTACCTACCTTTGGGCAAAGGTAGATAGGTTTTTGTTGCTC
1 GGATACCTACCTACCTTTGGGCAAAGGTAAATAGGTTTTTGTTGCTC
2329523 G
1 G
2329524 ACATTACATG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (47 bp):
GGATACCTACCTACCTTTGGGCAAAGGTAAATAGGTTTTTGTTGCTC
Found at i:2347381 original size:22 final size:22
Alignment explanation
Indices: 2347350--2347422 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
2347340 TGTTGAAAAT
2347350 AAAT-TTTTATATAGGGGGAGA
1 AAATCTTTTATATAGGGGGAGA
*
2347371 AAATC-TTT-TATAGGGGTAGA
1 AAATCTTTTATATAGGGGGAGA
*
2347391 AAATCTTTTATATAAGGGGAGA
1 AAATCTTTTATATAGGGGGAGA
* *
2347413 TAATCGTTTA
1 AAATCTTTTA
2347423 AAAGGGAGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 16 0.36
21 10 0.23
22 18 0.41
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (22 bp):
AAATCTTTTATATAGGGGGAGA
Found at i:2347384 original size:20 final size:20
Alignment explanation
Indices: 2347359--2347402 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
2347349 TAAATTTTTA
2347359 TATAGGGGGAGAAAATCTTT
1 TATAGGGGGAGAAAATCTTT
*
2347379 TATAGGGGTAGAAAATCTTT
1 TATAGGGGGAGAAAATCTTT
2347399 TATA
1 TATA
2347403 TAAGGGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (20 bp):
TATAGGGGGAGAAAATCTTT
Found at i:2347802 original size:22 final size:21
Alignment explanation
Indices: 2347771--2347831 Score: 88
Period size: 20 Copynumber: 2.9 Consensus size: 21
2347761 TGTTGAAAAT
2347771 AAATTTTTATATAGGGGGAGA
1 AAATTTTTATATAGGGGGAGA
*
2347792 AAATGTTT-TATAGGGGGAGA
1 AAATTTTTATATAGGGGGAGA
*
2347812 AAATCTTTTATATAAGGGGA
1 AAAT-TTTTATATAGGGGGA
2347832 AATAATCGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 10 0.29
22 9 0.26
ACGTcount: A:0.38, C:0.02, G:0.28, T:0.33
Consensus pattern (21 bp):
AAATTTTTATATAGGGGGAGA
Found at i:2347838 original size:22 final size:21
Alignment explanation
Indices: 2347767--2347855 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 21
2347757 GTATTGTTGA
* *
2347767 AAATAAATTTTTATATAGGGGG
1 AAAT-AATGTTTATATAAGGGG
*
2347789 AGAA-AATGTTT-TATAGGGGG
1 A-AATAATGTTTATATAAGGGG
*
2347809 AGAA-AATCTTTTATATAAGGGG
1 A-AATAAT-GTTTATATAAGGGG
2347831 AAATAATCGTTTA-A-AAGGGAG
1 AAATAAT-GTTTATATAAGGG-G
2347852 AAAT
1 AAAT
2347856 TTTTAGATTT
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
20 21 0.36
21 17 0.29
22 18 0.31
23 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.25, T:0.30
Consensus pattern (21 bp):
AAATAATGTTTATATAAGGGG
Found at i:2348003 original size:421 final size:421
Alignment explanation
Indices: 2347219--2348057 Score: 1642
Period size: 421 Copynumber: 2.0 Consensus size: 421
2347209 GACTTTGTGA
2347219 TTATAAAATACGATGTTTGCTTTATGGTTGTTTTATCCATTTTACTTGCATTTTATGATTGTTTA
1 TTATAAAATACGATGTTTGCTTTATGGTTGTTTTATCCATTTTACTTGCATTTTATGATTGTTTA
2347284 TTTTTCCGCCCTTATCTTGATCTTATTTTTGCTATAACAAAAAGGGGGAGAAGTATTGTTGAAAA
66 TTTTTCCGCCCTTATCTTGATCTTATTTTTGCTATAACAAAAAGGGGGAGAAGTATTGTTGAAAA
* *
2347349 TAAATTTTTATATAGGGGGAGAAAATCTTTTATAGGGGTAGAAAATCTTTTATATAAGGGGAGAT
131 TAAATTTTTATATAGGGGGAGAAAATCTTTTATAGGGGGAGAAAATCTTTTATATAAGGGGAAAT
2347414 AATCGTTTAAAAGGGAGAAATTTTTAGATTTGATAAAGGGAGATTTTTTAAATCTTTTATCAAGG
196 AATCGTTTAAAAGGGAGAAATTTTTAGATTTGATAAAGGGAGATTTTTTAAATCTTTTATCAAGG
2347479 GGGAGAATTTTTAAGAGCCTTAATTATTGTATTAAGGGGTAGAAAAACGAAAACTCGAAAACTTT
261 GGGAGAATTTTTAAGAGCCTTAATTATTGTATTAAGGGGTAGAAAAACGAAAACTCGAAAACTTT
2347544 GATACCAAAACTTTTCTAATGCGTTTCTTGAAGTTGTGTATCAGATTACAGGTTTTGACTCATGT
326 GATACCAAAACTTTTCTAATGCGTTTCTTGAAGTTGTGTATCAGATTACAGGTTTTGACTCATGT
2347609 TGATACAAGAAAATGATTGTATACAAGCATT
391 TGATACAAGAAAATGATTGTATACAAGCATT
2347640 TTATAAAATACGATGTTTGCTTTATGGTTGTTTTATCCATTTTACTTGCATTTTATGATTGTTTA
1 TTATAAAATACGATGTTTGCTTTATGGTTGTTTTATCCATTTTACTTGCATTTTATGATTGTTTA
2347705 TTTTTCCGCCCTTATCTTGATCTTATTTTTGCTATAACAAAAAGGGGGAGAAGTATTGTTGAAAA
66 TTTTTCCGCCCTTATCTTGATCTTATTTTTGCTATAACAAAAAGGGGGAGAAGTATTGTTGAAAA
*
2347770 TAAATTTTTATATAGGGGGAGAAAATGTTTTATAGGGGGAGAAAATCTTTTATATAAGGGGAAAT
131 TAAATTTTTATATAGGGGGAGAAAATCTTTTATAGGGGGAGAAAATCTTTTATATAAGGGGAAAT
2347835 AATCGTTTAAAAGGGAGAAATTTTTAGATTTGATAAAGGGAGATTTTTTAAATCTTTTATCAAGG
196 AATCGTTTAAAAGGGAGAAATTTTTAGATTTGATAAAGGGAGATTTTTTAAATCTTTTATCAAGG
*
2347900 GGGAGAATTTTTAAGAGCCTTAATTATTGTATTAAGGGGTAGAAAAATGAAAACTCGAAAACTTT
261 GGGAGAATTTTTAAGAGCCTTAATTATTGTATTAAGGGGTAGAAAAACGAAAACTCGAAAACTTT
2347965 GATACCAAAACTTTTCTAATGCGTTTCTTGAAGTTGTGTATCAGATTACAGGTTTTGACTCATGT
326 GATACCAAAACTTTTCTAATGCGTTTCTTGAAGTTGTGTATCAGATTACAGGTTTTGACTCATGT
2348030 TGATACAAGAAAATGATTGTATACAAGC
391 TGATACAAGAAAATGATTGTATACAAGC
2348058 CTATACGAAT
Statistics
Matches: 414, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
421 414 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.38
Consensus pattern (421 bp):
TTATAAAATACGATGTTTGCTTTATGGTTGTTTTATCCATTTTACTTGCATTTTATGATTGTTTA
TTTTTCCGCCCTTATCTTGATCTTATTTTTGCTATAACAAAAAGGGGGAGAAGTATTGTTGAAAA
TAAATTTTTATATAGGGGGAGAAAATCTTTTATAGGGGGAGAAAATCTTTTATATAAGGGGAAAT
AATCGTTTAAAAGGGAGAAATTTTTAGATTTGATAAAGGGAGATTTTTTAAATCTTTTATCAAGG
GGGAGAATTTTTAAGAGCCTTAATTATTGTATTAAGGGGTAGAAAAACGAAAACTCGAAAACTTT
GATACCAAAACTTTTCTAATGCGTTTCTTGAAGTTGTGTATCAGATTACAGGTTTTGACTCATGT
TGATACAAGAAAATGATTGTATACAAGCATT
Found at i:2348518 original size:19 final size:20
Alignment explanation
Indices: 2348494--2348546 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
2348484 ATCGATATGT
**
2348494 TGTATCGATACATGTTC-AC
1 TGTATCGATACATGGACAAC
* *
2348513 TGTATCAATACATGGACAAT
1 TGTATCGATACATGGACAAC
2348533 TGTATCGATACATG
1 TGTATCGATACATG
2348547 AAACTAGTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGGACAAC
Found at i:2357302 original size:983 final size:983
Alignment explanation
Indices: 2355764--2358717 Score: 5845
Period size: 983 Copynumber: 3.0 Consensus size: 983
2355754 ACAAGTATTT
2355764 CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
1 CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
*
2355829 AGTCAACTCCCTTGAATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
66 AGTCAACTCCCTTGGATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
2355894 CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
131 CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
2355959 ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
196 ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
2356024 ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
261 ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
2356089 AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
326 AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
2356154 TTTAATACAAAATTTTTACATCCGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
391 TTTAATACAAAATTTTTACATCCGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
2356219 AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
456 AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
*
2356284 TATTAATGGCTTTCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAGTCCTAGCCATT
521 TATTAATGGCTTCCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAGTCCTAGCCATT
2356349 TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
586 TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
2356414 ATTATGTCTAATACCATTTTTATTACAAAAATGATCAAAACCAAGATTCTCAAATTCTCTACCAT
651 ATTATGTCTAATACCATTTTTATTACAAAAATGATCAAAACCAAGATTCTCAAATTCTCTACCAT
*
2356479 GGTCACTTTTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
716 GGTCACTTCTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
2356544 AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
781 AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
2356609 CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
846 CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
2356674 TGTGAACCAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
911 TGTGAACCAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
2356739 TGCTTACC
976 TGCTTACC
2356747 CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
1 CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
2356812 AGTCAACTCCCTTGGATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
66 AGTCAACTCCCTTGGATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
2356877 CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
131 CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
2356942 ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
196 ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
2357007 ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
261 ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
2357072 AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
326 AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
*
2357137 TTTAATACAAAATTTTTACATCTGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
391 TTTAATACAAAATTTTTACATCCGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
2357202 AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
456 AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
*
2357267 TATTAATGGCTTCCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAATCCTAGCCATT
521 TATTAATGGCTTCCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAGTCCTAGCCATT
2357332 TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
586 TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
2357397 ATTATGTCTAATACCATTTTTATTACAAAAATGATCAAAACCAAGATTCTCAAATTCTCTACCAT
651 ATTATGTCTAATACCATTTTTATTACAAAAATGATCAAAACCAAGATTCTCAAATTCTCTACCAT
2357462 GGTCACTTCTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
716 GGTCACTTCTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
2357527 AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
781 AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
2357592 CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
846 CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
2357657 TGTGAACCAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
911 TGTGAACCAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
2357722 TGCTTACC
976 TGCTTACC
2357730 CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
1 CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
2357795 AGTCAACTCCCTTGGATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
66 AGTCAACTCCCTTGGATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
2357860 CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
131 CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
2357925 ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
196 ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
2357990 ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
261 ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
2358055 AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
326 AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
2358120 TTTAATACAAAATTTTTACATCCGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
391 TTTAATACAAAATTTTTACATCCGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
2358185 AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
456 AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
2358250 TATTAATGGCTTCCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAGTCCTAGCCATT
521 TATTAATGGCTTCCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAGTCCTAGCCATT
2358315 TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
586 TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
*
2358380 ATTATGTCTAATACCATTTTTATTACAAAAATGATGAAAACCAAGATTCTCAAATTCTCTACCAT
651 ATTATGTCTAATACCATTTTTATTACAAAAATGATCAAAACCAAGATTCTCAAATTCTCTACCAT
2358445 GGTCACTTCTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
716 GGTCACTTCTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
2358510 AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
781 AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
2358575 CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
846 CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
*
2358640 TGTGAACCAGTTGTAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
911 TGTGAACCAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
2358705 TGCTTACC
976 TGCTTACC
2358713 CTTAA
1 CTTAA
2358718 TGCATGCATC
Statistics
Matches: 1962, Mismatches: 9, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
983 1962 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (983 bp):
CTTAAAGATGATCTAGTTCTTACCCCATGGCTTGGATTACCGATTATCTCACCTTCTTAGACATA
AGTCAACTCCCTTGGATGTCTTCTTTCGATTTAAGTTGGCTCATATTCATCAATTTCTTTTGGAG
CTTCTTCAATTTGGATGTTATCCTCTTGCTCCTTGTGTGATGTTTGCTTTAAATTTTCTTTATAA
ATTTCTGCATCATTGTCAATAAAAGATATCTTCTTCACGGAAGAGTCAGATTCATCAAAAACAAC
ATGGATTGATTCTTTAACAACCAAGGTTCTTTTATTAAACACTCGATAAGCTTTAGAGTTTGTTG
AATAACCAAGAAAAATTCCTTCATCACTTTTAACATCAAATTTACCAAGGTTTTCTTTTCCATTA
TTTAATACAAAATTTTTACATCCGCATGGATGAAAATAACTTATGTTAGGCTTTTTTTCTTTAAA
AAGTTCATATGGAGTTTTCTTTAAAATTGGCCTAATCATAGCTCGGTTTATAATATGGCATGCGA
TATTAATGGCTTCCGCCCAAAAATATCTTGGTAAATTATTTTCACAAAGCATAGTCCTAGCCATT
TCTTCTAAAGTCTAATTTTCCCTTTCAATAATTCCATTTTGTTGAGGAGTTTTAGGAGCTGAGAA
ATTATGTCTAATACCATTTTTATTACAAAAATGATCAAAACCAAGATTCTCAAATTCTCTACCAT
GGTCACTTCTTATACTAGATAAGGAGTAACTTTTTTCATTTTGAACAATTTTACAAAAGGTGATG
AATTTTTCTAAAGCTTCATCTTTAGTGCTTAAGAATATAACCCAAGTATATCTAAAATAATCATC
CACAATAACAAATCCGTACCTTTTACCACCTAGACTTTGCATTCTAGTTGGATCAAATAAGTCGA
TGTGAACCAGTTGCAAAACTTTAGAGGTCATGACAATGTTTATGGGTTTAAAAGAATTTCTTCTA
TGCTTACC
Found at i:2360334 original size:12 final size:12
Alignment explanation
Indices: 2360317--2360342 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2360307 CGAGTCAACT
2360317 TCATCATCATTA
1 TCATCATCATTA
2360329 TCATCATCATTA
1 TCATCATCATTA
2360341 TC
1 TC
2360343 TATGATGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (12 bp):
TCATCATCATTA
Found at i:2362070 original size:19 final size:20
Alignment explanation
Indices: 2362022--2362072 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
2362012 CTGTCAATTT
*
2362022 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAA
** *
2362042 TGTATATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
2362061 CATGTATCGATA
1 CATGTATCGATA
2362073 TAGTGTATCG
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2362081 original size:13 final size:13
Alignment explanation
Indices: 2362063--2362087 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2362053 ACAATGAACA
2362063 TGTATCGATATAG
1 TGTATCGATATAG
2362076 TGTATCGATATA
1 TGTATCGATATA
2362088 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TGTATCGATATAG
Found at i:2362950 original size:31 final size:31
Alignment explanation
Indices: 2362911--2362986 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
2362901 TAATGTGATT
*
2362911 TTTCATTTTTCTTTTTTTCTTTTTTTTAAATC
1 TTTCATTTTTCTTTTTTTC-TTTATTTAAATC
*
2362943 -TTCATTTTTC-ATTTTTCTTTATTTAAATC
1 TTTCATTTTTCTTTTTTTCTTTATTTAAATC
2362972 TTTTCA-TTTTCTTTT
1 -TTTCATTTTTCTTTT
2362987 CCTTTTTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 11 0.29
30 11 0.29
31 16 0.42
ACGTcount: A:0.14, C:0.13, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTCATTTTTCTTTTTTTCTTTATTTAAATC
Found at i:2366555 original size:5 final size:5
Alignment explanation
Indices: 2366547--2366607 Score: 54
Period size: 5 Copynumber: 12.4 Consensus size: 5
2366537 TAATTTAATA
* * * *
2366547 ATTAT ATTAT ATT-T A-TAT ATTTT ATTAT ATTAT AATAT ATAAAA ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT-TAT ATTAT
*
2366596 TTTAT ATTAT AT
1 ATTAT ATTAT AT
2366608 AATTTTTTTT
Statistics
Matches: 43, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
3 1 0.02
4 4 0.09
5 35 0.81
6 3 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
ATTAT
Found at i:2366560 original size:18 final size:19
Alignment explanation
Indices: 2366539--2366586 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
2366529 AAATTTAATA
2366539 ATTTAATA-ATTATATTAT
1 ATTTAATATATTATATTAT
*
2366557 ATTT-ATATATTTTATTAT
1 ATTTAATATATTATATTAT
2366575 ATTATAATATAT
1 ATT-TAATATAT
2366587 AAAAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 16 0.62
19 1 0.04
20 6 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTAATATATTATATTAT
Found at i:2366600 original size:21 final size:21
Alignment explanation
Indices: 2366570--2366609 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2366560 TATATATTTT
2366570 ATTATATTATAATATATAAAA
1 ATTATATTATAATATATAAAA
* *
2366591 ATTATTTTATATTATATAA
1 ATTATATTATAATATATAA
2366610 TTTTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATATTATAATATATAAAA
Found at i:2367079 original size:5 final size:5
Alignment explanation
Indices: 2367069--2367103 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
2367059 AATCTCTTCA
2367069 CTTTT CTTTT CTTTT C-TTT CTTTT CTTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT C-TTTT CTTTT
2367104 TCAATTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:2367090 original size:14 final size:15
Alignment explanation
Indices: 2367071--2367102 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2367061 TCTCTTCACT
2367071 TTTCTTTTC-TTTTC
1 TTTCTTTTCTTTTTC
2367085 TTTCTTTTCTTTTTC
1 TTTCTTTTCTTTTTC
2367100 TTT
1 TTT
2367103 TTCAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTTTTCTTTTTC
Found at i:2367472 original size:12 final size:12
Alignment explanation
Indices: 2367438--2367481 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
2367428 AGTCAGAGGA
2367438 TTCC-TCCATCC
1 TTCCATCCATCC
* *
2367449 TTCTATCGATCC
1 TTCCATCCATCC
2367461 TTCCATCCATCC
1 TTCCATCCATCC
*
2367473 ATCCATCCA
1 TTCCATCCA
2367482 CCAGTCATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 3 0.11
12 24 0.89
ACGTcount: A:0.18, C:0.45, G:0.02, T:0.34
Consensus pattern (12 bp):
TTCCATCCATCC
Found at i:2367524 original size:4 final size:4
Alignment explanation
Indices: 2367515--2367545 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2367505 CACATCAATC
2367515 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
2367546 ATCTCTATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:2367650 original size:4 final size:4
Alignment explanation
Indices: 2367617--2367666 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
2367607 TCAAAGGATT
* * * * *
2367617 CATC CATC CTTC TATC GATC CTTA CATC CATC CATC CATC CATC CATC
1 CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC CATC
2367665 CA
1 CA
2367667 GTCATTGATC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.44, G:0.02, T:0.30
Consensus pattern (4 bp):
CATC
Found at i:2370009 original size:22 final size:23
Alignment explanation
Indices: 2369984--2370038 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
2369974 ATATATGATG
2369984 AAATAATAAT-TTATCAAAAA-GT
1 AAATAAT-ATCTTATCAAAAACGT
*
2370006 AAATTATATCTTATCAAAAACGT
1 AAATAATATCTTATCAAAAACGT
*
2370029 AAATTATATC
1 AAATAATATC
2370039 ATGAGCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 16 0.53
23 12 0.40
ACGTcount: A:0.53, C:0.09, G:0.04, T:0.35
Consensus pattern (23 bp):
AAATAATATCTTATCAAAAACGT
Found at i:2370030 original size:23 final size:22
Alignment explanation
Indices: 2369994--2370038 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
2369984 AAATAATAAT
2369994 TTATCAAAAAGTAAATTATATC
1 TTATCAAAAAGTAAATTATATC
2370016 TTATCAAAAACGTAAATTATATC
1 TTATCAAAAA-GTAAATTATATC
2370039 ATGAGCTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.49, C:0.11, G:0.04, T:0.36
Consensus pattern (22 bp):
TTATCAAAAAGTAAATTATATC
Found at i:2370940 original size:14 final size:15
Alignment explanation
Indices: 2370912--2370942 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2370902 TATGATTGAT
2370912 TTGTAATATATAATA
1 TTGTAATATATAATA
2370927 TTGTAATA-ATAATA
1 TTGTAATATATAATA
2370941 TT
1 TT
2370943 TAAAAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
TTGTAATATATAATA
Found at i:2371004 original size:20 final size:19
Alignment explanation
Indices: 2370970--2371007 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2370960 TAACAAATTC
*
2370970 ATTTTATATATAAATATAG
1 ATTTTATAAATAAATATAG
2370989 ATTTTGATAAATAAATATA
1 ATTTT-ATAAATAAATATA
2371008 TTAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTATAAATAAATATAG
Found at i:2371221 original size:17 final size:16
Alignment explanation
Indices: 2371169--2371275 Score: 90
Period size: 16 Copynumber: 6.6 Consensus size: 16
2371159 AATCGGATCC
*
2371169 GAACTCGAAAAGGCCT
1 GAACTCGAAAAGGCTT
*
2371185 GAACTTGAAAAGGCTT
1 GAACTCGAAAAGGCTT
*
2371201 GAACTCCAAAAGGCTTT
1 GAACTCGAAAAGGC-TT
* * *
2371218 GAACCCGAAAAAGCTC
1 GAACTCGAAAAGGCTT
* *
2371234 GAACCCAAAAAGGCTT
1 GAACTCGAAAAGGCTT
* *
2371250 GAA-TCCGAATAGGCTC
1 GAACT-CGAAAAGGCTT
*
2371266 GAACTTGAAA
1 GAACTCGAAA
2371276 GAACTCGAAT
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
16 57 0.80
17 14 0.20
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (16 bp):
GAACTCGAAAAGGCTT
Found at i:2371239 original size:16 final size:16
Alignment explanation
Indices: 2371218--2371291 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
2371208 AAAAGGCTTT
2371218 GAACCCGAAAAAGCTC
1 GAACCCGAAAAAGCTC
*
2371234 GAACCC-AAAAAGGCTT
1 GAACCCGAAAAA-GCTC
* * *
2371250 GAATCCGAATAGGCTC
1 GAACCCGAAAAAGCTC
**
2371266 GAACTTGAAAGAA-CTC
1 GAACCCGAAA-AAGCTC
*
2371282 GAATCCGAAA
1 GAACCCGAAA
2371292 TAATCCGAAC
Statistics
Matches: 42, Mismatches: 13, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
15 5 0.12
16 33 0.79
17 4 0.10
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (16 bp):
GAACCCGAAAAAGCTC
Found at i:2371242 original size:32 final size:33
Alignment explanation
Indices: 2371168--2371270 Score: 104
Period size: 32 Copynumber: 3.2 Consensus size: 33
2371158 AAATCGGATC
* * **
2371168 CGAACT-CGAAAAGGCCTGAACTTGAAAAGGCT
1 CGAACTCCAAAAAGGCTTGAACCCGAAAAGGCT
* *
2371200 TGAACTCC-AAAAGGCTTTGAACCCGAAAAAGCT
1 CGAACTCCAAAAAGGC-TTGAACCCGAAAAGGCT
* *
2371233 CGAAC-CCAAAAAGGCTTGAATCCGAATAGGCT
1 CGAACTCCAAAAAGGCTTGAACCCGAAAAGGCT
2371265 CGAACT
1 CGAACT
2371271 TGAAAGAACT
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
32 33 0.57
33 25 0.43
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (33 bp):
CGAACTCCAAAAAGGCTTGAACCCGAAAAGGCT
Found at i:2372198 original size:2 final size:2
Alignment explanation
Indices: 2372191--2372218 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2372181 ACAATATCCG
2372191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2372219 TTGACGTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2379752 original size:17 final size:17
Alignment explanation
Indices: 2379730--2379765 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2379720 GTAATATATG
* *
2379730 TAATATATATTTTATAA
1 TAATATAGATATTATAA
2379747 TAATATAGATATTATAA
1 TAATATAGATATTATAA
2379764 TA
1 TA
2379766 TATTCTGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TAATATAGATATTATAA
Found at i:2387499 original size:36 final size:32
Alignment explanation
Indices: 2387421--2387513 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 32
2387411 GAACACTATC
*
2387421 TTTCAAGGCTAAGATAGAAAC-CTCCCAATCT
1 TTTCAAGGCTAAGATAGAACCTCTCCCAATCT
*
2387452 TTTCACGGGCTAAGATAGAACCTCTCTCCATATCTT
1 TTTCA-AGGCTAAGATAGAACCTCTC-CCA-ATC-T
2387488 TTTCGAAGGCTAAGATAGAACCTCTC
1 TTTC-AAGGCTAAGATAGAACCTCTC
2387514 AGCCACTTAG
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
31 5 0.09
32 14 0.26
33 3 0.06
34 3 0.06
35 3 0.06
36 24 0.45
37 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (32 bp):
TTTCAAGGCTAAGATAGAACCTCTCCCAATCT
Found at i:2389869 original size:20 final size:20
Alignment explanation
Indices: 2389844--2389883 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2389834 GAAAAATCCA
*
2389844 GAAGTATTGATACTTTGAGC
1 GAAGTATCGATACTTTGAGC
2389864 GAAGTATCGATACTTTGAGC
1 GAAGTATCGATACTTTGAGC
2389884 AAAATATCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (20 bp):
GAAGTATCGATACTTTGAGC
Found at i:2389891 original size:20 final size:20
Alignment explanation
Indices: 2389852--2389891 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2389842 CAGAAGTATT
* *
2389852 GATACTTTGAGCGAAGTATC
1 GATACTTTGAGCAAAATATC
2389872 GATACTTTGAGCAAAATATC
1 GATACTTTGAGCAAAATATC
2389892 TATTGGCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
GATACTTTGAGCAAAATATC
Found at i:2391291 original size:21 final size:21
Alignment explanation
Indices: 2391267--2391315 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
2391257 ATGCAAATTT
2391267 TTATTTTTATTAGT-TAACTCA
1 TTATTTTTATT-GTGTAACTCA
* *
2391288 TTATTTTCATTTTGTAACTCA
1 TTATTTTTATTGTGTAACTCA
2391309 TT-TTTTT
1 TTATTTTT
2391316 CTTTTCCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.22, C:0.10, G:0.04, T:0.63
Consensus pattern (21 bp):
TTATTTTTATTGTGTAACTCA
Found at i:2391320 original size:20 final size:20
Alignment explanation
Indices: 2391281--2391342 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
2391271 TTTTATTAGT
* *
2391281 TAACTCATTATTTTCATTTTG
1 TAACTCATTTTTTTC-TTTTC
2391302 TAACTCATTTTTTTCTTTTC
1 TAACTCATTTTTTTCTTTTC
* *
2391322 CAACTCATTTACTTTCTTTTC
1 TAACTCATTT-TTTTCTTTTC
2391343 AAGAGTATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.36
21 23 0.64
ACGTcount: A:0.19, C:0.21, G:0.02, T:0.58
Consensus pattern (20 bp):
TAACTCATTTTTTTCTTTTC
Found at i:2392958 original size:36 final size:35
Alignment explanation
Indices: 2392900--2392968 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
2392890 AGATAGAAAC
* *
2392900 CTCCCTATCTTTTCACTAGCTAAAATAGAACCTTT
1 CTCCCTATCTTTTCACAAGCTAAAATAAAACCTTT
*
2392935 CTCCCTATCTTTTTCA-AAGGCTAAGATAAAACCT
1 CTCCCTATC-TTTTCACAA-GCTAAAATAAAACCT
2392969 CTCAATCACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (35 bp):
CTCCCTATCTTTTCACAAGCTAAAATAAAACCTTT
Found at i:2393486 original size:32 final size:32
Alignment explanation
Indices: 2393418--2393486 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
2393408 ATTTACATGT
* **
2393418 ATCGATACATGAACAGTGATGCACATTGATGT
1 ATCGATACATGAACAGTGATGAACATTGATAC
*
2393450 ATCGATACATGAATAGTGATGAACAGTT-ATAC
1 ATCGATACATGAACAGTGATGAACA-TTGATAC
2393482 ATCGA
1 ATCGA
2393487 ATTAAAAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 30 0.94
33 2 0.06
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (32 bp):
ATCGATACATGAACAGTGATGAACATTGATAC
Found at i:2395022 original size:13 final size:13
Alignment explanation
Indices: 2395004--2395030 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2394994 ACATTATGCT
2395004 TTGTATCGATACA
1 TTGTATCGATACA
2395017 TTGTATCGATACA
1 TTGTATCGATACA
2395030 T
1 T
2395031 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2395060 original size:20 final size:19
Alignment explanation
Indices: 2395014--2395070 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
2395004 TTGTATCGAT
*
2395014 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
2395033 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
2395052 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2395071 AAACAGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:2397375 original size:21 final size:20
Alignment explanation
Indices: 2397341--2397383 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2397331 TATTAAAAAG
*
2397341 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
2397362 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
2397382 TT
1 TT
2397384 TGCATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:2397382 original size:20 final size:21
Alignment explanation
Indices: 2397341--2397383 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
2397331 TATTAAAAAG
*
2397341 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
2397362 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
2397382 TT
1 TT
2397384 TGCATGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:2401000 original size:32 final size:32
Alignment explanation
Indices: 2400945--2401042 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 32
2400935 TTCAACGATT
* *
2400945 TGTATCGATACATAAAGTGTTGTATCGATATAA
1 TGTATCGATACAT-AAGTGTTGTATCAATACAA
*
2400978 TGTATCGATACATAAGTGTTGTATAAATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
*
2401010 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCAATACAA
2401042 T
1 T
2401043 ATAAGCTACT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 47 0.78
33 13 0.22
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCAATACAA
Found at i:2401034 original size:19 final size:18
Alignment explanation
Indices: 2400943--2401040 Score: 63
Period size: 19 Copynumber: 5.8 Consensus size: 18
2400933 ATTTCAACGA
2400943 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
2400962 TGTTGTATCGAT--ATAA-
1 T-TTGTATCGATACATAAG
2400978 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
**
2400994 TGTTGTATAAATAC--AA-
1 T-TTGTATCGATACATAAG
2401010 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
2401026 TTTTGTATCAATACA
1 -TTTGTATCGATACA
2401041 ATATAAGCTA
Statistics
Matches: 61, Mismatches: 5, Indels: 26
0.66 0.05 0.28
Matches are distributed among these distances:
13 18 0.30
15 6 0.10
17 4 0.07
18 2 0.03
19 21 0.34
20 10 0.16
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:2401101 original size:13 final size:13
Alignment explanation
Indices: 2401083--2401107 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2401073 ATTACTCAAA
2401083 TGTATCGATACAT
1 TGTATCGATACAT
2401096 TGTATCGATACA
1 TGTATCGATACA
2401108 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2401160 original size:52 final size:53
Alignment explanation
Indices: 2401096--2401244 Score: 223
Period size: 52 Copynumber: 2.9 Consensus size: 53
2401086 ATCGATACAT
***
2401096 TGTATCGATACACTAAT-CTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
2401148 TGTATCGATACACT-ATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* * *
2401200 TGTATCGATACACT-ATGAAATGTATCGAAACATGCAAGCAAATTT
1 TGTATCGATACACTAATAAAATGTATCGATACATGCAGGCAAATTT
2401245 TCATATTTCG
Statistics
Matches: 90, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
51 2 0.02
52 88 0.98
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (53 bp):
TGTATCGATACACTAATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:2406855 original size:22 final size:22
Alignment explanation
Indices: 2406830--2406871 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2406820 TTTTTTAAGA
*
2406830 TTTGACAAAGGGGGAGAAATGC
1 TTTGACAAAAGGGGAGAAATGC
* *
2406852 TTTGATAAAATGGGAGAAAT
1 TTTGACAAAAGGGGAGAAAT
2406872 ATGTTTATCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.05, G:0.31, T:0.24
Consensus pattern (22 bp):
TTTGACAAAAGGGGAGAAATGC
Found at i:2406927 original size:28 final size:28
Alignment explanation
Indices: 2406887--2406949 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
2406877 TATCTAGGAT
2406887 GAGAAAATCTTGTTAACCAATTAAAGAG
1 GAGAAAATCTTGTTAACCAATTAAAGAG
* * *
2406915 GAGAAAATCTTGTTAACCGATTAAGGGG
1 GAGAAAATCTTGTTAACCAATTAAAGAG
2406943 GAGAAAA
1 GAGAAAA
2406950 ACGAAAACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (28 bp):
GAGAAAATCTTGTTAACCAATTAAAGAG
Found at i:2407602 original size:20 final size:20
Alignment explanation
Indices: 2407577--2407629 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2407567 CCTACCCTGT
2407577 TTGTATCGATACAT-AGGACA
1 TTGTATCGATACATAAGGA-A
*
2407597 TTGTATCGATACATAATGAA
1 TTGTATCGATACATAAGGAA
*
2407617 ATGTATCGATACA
1 TTGTATCGATACA
2407630 ATACTTGTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 27 0.90
21 3 0.10
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
TTGTATCGATACATAAGGAA
Found at i:2417481 original size:52 final size:52
Alignment explanation
Indices: 2417419--2417538 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
2417409 AAAAGTTACT
* *
2417419 TGCATGTATCGATACATTTAATAGTGTATCGATACATATGGGCAGATTGGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATATGGGCAAATTGGCC
* * *
2417471 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATATGGGCAAATTGGCC
2417523 TGCATGTATCGATACA
1 TGCATGTATCGATACA
2417539 AAGATCGGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATATGGGCAAATTGGCC
Found at i:2417551 original size:52 final size:52
Alignment explanation
Indices: 2417419--2417558 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 52
2417409 AAAAGTTACT
* *
2417419 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATATGGGCAGATTGGCC
1 TGCATGTATCGATACA-TAAGATAGTGTATCGATACATATGGGCAAATTGGCC
*** * * *
2417471 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATAAGATAGTGTATCGATACATATGGGCAAATTGGCC
*
2417523 TGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TGCATGTATCGATACATAAGAT-AGTGTATCGATACA
2417559 ATGTATCTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
51 4 0.05
52 72 0.95
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (52 bp):
TGCATGTATCGATACATAAGATAGTGTATCGATACATATGGGCAAATTGGCC
Found at i:2417590 original size:34 final size:34
Alignment explanation
Indices: 2417547--2417626 Score: 160
Period size: 34 Copynumber: 2.4 Consensus size: 34
2417537 CAAAGATCGG
2417547 TGTATCGATACAATGTATCTATACATTTGAGTAA
1 TGTATCGATACAATGTATCTATACATTTGAGTAA
2417581 TGTATCGATACAATGTATCTATACATTTGAGTAA
1 TGTATCGATACAATGTATCTATACATTTGAGTAA
2417615 TGTATCGATACA
1 TGTATCGATACA
2417627 TTTTTTGGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (34 bp):
TGTATCGATACAATGTATCTATACATTTGAGTAA
Found at i:2417683 original size:33 final size:33
Alignment explanation
Indices: 2417646--2417712 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2417636 AGTAGCTTAA
2417646 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2417679 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2417712 A
1 A
2417713 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2417686 original size:13 final size:13
Alignment explanation
Indices: 2417668--2417692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2417658 CAAAAAAATA
2417668 TGTATCGATACAT
1 TGTATCGATACAT
2417681 TGTATCGATACA
1 TGTATCGATACA
2417693 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2426722 original size:29 final size:29
Alignment explanation
Indices: 2426598--2427121 Score: 657
Period size: 28 Copynumber: 18.4 Consensus size: 29
2426588 ACGTTCATCT
2426598 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
2426626 TTTCAAAG--C-C-AGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
2426650 TTTCAAAGCCCATAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
2426678 TTTTAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
2426707 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
2426735 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
2426763 TTTCAAAGCCCACAAGCCAGTGGCAC-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
2426791 TTTCAAAGCCCACAAGTCAGTGGTA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
2426819 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
2426847 TTTCAAAGCCCACAAGTAAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
2426876 TTTCAAAGCCCACAAGTCAGTGGCA-TTC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
2426904 TTTCAAAGCCCACAAGTAAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* *
2426933 TTTCAAAGCCCACAAGTCAATGGCAC-CAT
1 TTTCAAAGCCCACAAGTCAGTGGCACTC-C
*
2426962 TTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
*
2426990 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
* ** *
2427019 TTTTAAAGCCCACAAG-CTAGTGATAACTCT
1 TTTCAAAGCCCACAAGTC-AGTG-GCACTCC
* * *
2427049 TTTTAAAGCCCACACGAGTCGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCC
* * *
2427081 TTTCAAAGCCCACAAGTTAGTGGTACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCC
2427110 TTTCAAAGCCCA
1 TTTCAAAGCCCA
2427122 AAAGCCCACA
Statistics
Matches: 441, Mismatches: 37, Indels: 35
0.86 0.07 0.07
Matches are distributed among these distances:
24 20 0.05
25 1 0.00
26 2 0.00
28 226 0.51
29 142 0.32
30 26 0.06
32 23 0.05
33 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCC
Found at i:2426731 original size:57 final size:57
Alignment explanation
Indices: 2426598--2427121 Score: 647
Period size: 57 Copynumber: 9.2 Consensus size: 57
2426588 ACGTTCATCT
* *
2426598 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAG--C-C-AGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCC
* * *
2426650 TTTCAAAGCCCATAAGTTAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCC
* *
2426707 TTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCC
* *
2426763 TTTCAAAGCCCACAAGCCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGTA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTT-AAAGCCCACAAGTCAGTGGCACTCC
* *
2426819 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTAAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCC
* * *
2426876 TTTCAAAGCCCACAAGTCAGTGGCATTCTTTCAAAGCCCACAAGTAAGTGGCACTCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCC
* *
2426933 TTTCAAAGCCCACAAGTCAATGGCA-CCATTTTCAAAGCCCACAAGTTAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTT-AAAGCCCACAAGTCAGTGGCACTCC
* ** *
2426990 TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCACAAG-CTAGTGATAACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTTAAAGCCCACAAGTC-AGTG-GCACTCC
* * * * * *
2427049 TTTTAAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGTACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGCATC-CTTTT-AAAGCCCACAAGTCAGTGGCACTCC
2427110 TTTCAAAGCCCA
1 TTTCAAAGCCCA
2427122 AAAGCCCACA
Statistics
Matches: 415, Mismatches: 36, Indels: 33
0.86 0.07 0.07
Matches are distributed among these distances:
52 33 0.08
54 1 0.00
55 6 0.01
56 102 0.25
57 184 0.44
58 27 0.07
59 15 0.04
60 1 0.00
61 30 0.07
62 16 0.04
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.23
Consensus pattern (57 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCC
Found at i:2427211 original size:35 final size:32
Alignment explanation
Indices: 2427121--2427211 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 32
2427111 TTCAAAGCCC
* *
2427121 AAAAGCCCACACGAGTCGGTGGCAGCTCTTTT
1 AAAAGCCCACACAAGTCGGTGGCACCTCTTTT
* *** *
2427153 CAAAGCCCACACAAGTTAATGGCACCTTTTTT
1 AAAAGCCCACACAAGTCGGTGGCACCTCTTTT
*
2427185 AAAAAAAGCCCACATAAGTCGGTGGCA
1 ---AAAAGCCCACACAAGTCGGTGGCA
2427212 ACACTTTTCA
Statistics
Matches: 44, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
32 25 0.57
35 19 0.43
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (32 bp):
AAAAGCCCACACAAGTCGGTGGCACCTCTTTT
Found at i:2427219 original size:67 final size:66
Alignment explanation
Indices: 2426823--2427223 Score: 216
Period size: 57 Copynumber: 6.5 Consensus size: 66
2426813 GTATCCTTTC
* * *
2426823 AAAGCCCACA--AGTCAGTGGC-A-TCCTTTCAAAGCCCACAAG-TAAGTGGCACTCCTTT----
1 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAA-TGGCACTCTTTTCAAA
2426879 C-
65 CA
* * *
2426880 AAAGCCCACA--AGTCAGTGGC-ATTC-TTTCAAAGCCCACAAG-TAAGTGGCACTCCTTT----
1 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAA-TGGCACTCTTTTCAAA
2426936 C-
65 CA
** * *
2426937 AAAGCCCACA--AGTCAATGGC-AC-CATTTTCAAAGCCCACAAGTTAGTGGCAC-CCTTT----
1 AAAGCCCACACGAGTCGGTGGCAACTC-TTTTCAAAGCCCACAAGTTAATGGCACTCTTTTCAAA
2426993 C-
65 CA
* * * * **
2426994 AAAGCCCACA--AGTCAGTGGC-ACTCTTTTTAAAGCCCACAAGCTAGTGATAACTCTTTT----
1 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAATG-GCACTCTTTTCAAA
*
2427052 -T
65 CA
* *
2427053 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAGTGGTACTCTTTTCAAAG
1 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAATGGCACTCTTTTCAAA-
2427118 CCCA
65 --CA
* *
2427122 AAAGCCCACACGAGTCGGTGGCAGCTCTTTTCAAAGCCCACACAAGTTAATGGCAC-CTTTTTTA
1 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAG-CC-CACAAGTTAATGGCACTC-TTTTCA
2427186 AA-A
63 AACA
** *
2427189 AAAGCCCACATAAGTCGGTGGCAACACTTTTCAAA
1 AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAA
2427224 TCACCACTGT
Statistics
Matches: 299, Mismatches: 23, Indels: 34
0.84 0.06 0.10
Matches are distributed among these distances:
56 1 0.00
57 122 0.41
58 27 0.09
59 16 0.05
61 17 0.06
62 25 0.08
67 32 0.11
69 35 0.12
70 3 0.01
71 21 0.07
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (66 bp):
AAAGCCCACACGAGTCGGTGGCAACTCTTTTCAAAGCCCACAAGTTAATGGCACTCTTTTCAAAC
A
Found at i:2428057 original size:20 final size:20
Alignment explanation
Indices: 2428032--2428079 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
2428022 TACCCAGATT
2428032 TATCGATACAT-TGAAGAATG
1 TATCGATACATGT-AAGAATG
*
2428052 TATCGATACATGTATGAATG
1 TATCGATACATGTAAGAATG
2428072 TATCGATA
1 TATCGATA
2428080 TATTTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
TATCGATACATGTAAGAATG
Found at i:2433654 original size:153 final size:152
Alignment explanation
Indices: 2433494--2433906 Score: 448
Period size: 152 Copynumber: 2.7 Consensus size: 152
2433484 TTATTCGATG
2433494 GGATTTTTCTAAGTTTATAA-TTTTAAAATTCTTCAAATATTATTTTGTAATTCATATTAAATCA
1 GGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTTT-TAATTCATATTAAATCA
* *
2433558 GTTTTAAAAAATTTAATTTATTTTATGAGTTTTAGCATTTTTC-CTACTATCAAGATACATAGCT
65 GTTTTAAAAAATTTAATTTATTTTATGAGTTTTAGCATTTTTCTCT--TACCAAGATACAGAG-T
*
2433622 TTT-TTCTCCATAAATTTC-TCCAAT
127 TTTCTACTCCATAAATTTCTTCCAAT
* **
2433646 AGGATTTTTCTAAGTTTATAATTTTTAAAATTATTCAAATATTATTGTTTAACCCATATTAAATC
1 -GGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATT-TTTAATTCATATTAAATC
* * * **
2433711 AGTTTTTTTTAAAAA---AA-TTATTTTATGAGTGTTAGAATTTTTCTCTTACCAAGATATGGAG
64 AG---TTTTAAAAAATTTAATTTATTTTATGAGTTTTAGCATTTTTCTCTTACCAAGATACAGAG
***
2433772 TTTTCTACTCCATAAATTTCTTTGGAT
126 TTTTCTACTCCATAAATTTCTTCCAAT
* * * * * **
2433799 GGATTTTTCTGAGCTTAAAATTTTTAAAATTCATCAAATATTTTTTATTAATTTCATGCTAAATC
1 GGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTT-TTAA-TTCATATTAAATC
* *
2433864 AGGTTTCAAAAAATTTAATTTATTTTATGAG-TTTCGCATTTTT
64 A-GTTTTAAAAAATTTAATTTATTTTATGAGTTTTAGCATTTTT
2433907 ATATAACAAA
Statistics
Matches: 216, Mismatches: 29, Indels: 29
0.79 0.11 0.11
Matches are distributed among these distances:
151 13 0.06
152 68 0.31
153 57 0.26
154 55 0.25
155 14 0.06
157 9 0.04
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.48
Consensus pattern (152 bp):
GGATTTTTCTAAGTTTATAATTTTTAAAATTCTTCAAATATTATTTTTAATTCATATTAAATCAG
TTTTAAAAAATTTAATTTATTTTATGAGTTTTAGCATTTTTCTCTTACCAAGATACAGAGTTTTC
TACTCCATAAATTTCTTCCAAT
Found at i:2434220 original size:3 final size:3
Alignment explanation
Indices: 2434212--2434257 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
2434202 TCAAATTAAA
2434212 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2434258 AGAAAAGAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:2434268 original size:23 final size:23
Alignment explanation
Indices: 2434221--2434268 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
2434211 AAATAATAAT
* *
2434221 AATAATAATAATAATAATAATAA
1 AATAATAATAATAATAAAAAGAA
2434244 AATAATAATAATAA-AGAAAAGAA
1 AATAATAATAATAATA-AAAAGAA
2434267 AA
1 AA
2434269 GTTTGGAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (23 bp):
AATAATAATAATAATAAAAAGAA
Found at i:2435704 original size:157 final size:156
Alignment explanation
Indices: 2435223--2435813 Score: 591
Period size: 157 Copynumber: 3.8 Consensus size: 156
2435213 AATTTGTAAA
* * * * * *
2435223 TATT-GAAAATTTTGTTCTAATGCCAAAAATATTTGGTTGAATCTTTCTTATAATTTTTGGATCT
1 TATTCGAAAATTTTGTTCTAAGGCCAAAAATACTTGGTCGAATCTTCCTTATAACTTTTGGATGT
* * * * * ** *
2435287 GATTTT-TGTGTTGATTTTGATATGTTTGATATTTAATCTTGTGTTTTAATTATATAGGGACTAA
66 G-TTTTGTATGCTGATTTTGATTTCTTTGATGTTTAATCTTGTGTTTTAATTAGGTAAGGACTAA
* *
2435351 TTTGTAAATTTACAAAGTGTAAGGGGTT
130 TTTGTAAATTTAAAAAGT-TTAGGGGTT
* * * * *
2435379 TATTTGAAAATTTTGTTCTAAGGCCCAAAGTACTTGGCCGAATCTTCCTTGTAACTTTTGGATGT
1 TATTCGAAAATTTTGTTCTAAGGCCAAAAATACTTGGTCGAATCTTCCTTATAACTTTTGGATGT
* * * *
2435444 GTTTTAG-ATGCTGATTTTCCATTTCTTTGATGCTTAATCTTGTGATTTAATTATGTAAGGACTA
66 GTTTT-GTATGCTGATTTT-GATTTCTTTGATGTTTAATCTTGTGTTTTAATTAGGTAAGGACTA
2435508 ATTTGTAAATTTAAAAAGTTTAGGGGGTT
129 ATTTGTAAATTTAAAAAGTTTA-GGGGTT
* * *
2435537 TATTCAAAAATTTTGTTCTAAGGCCAAAAATACTTGGTCGAACCTCCCTTATAACTTTTGGATGT
1 TATTCGAAAATTTTGTTCTAAGGCCAAAAATACTTGGTCGAATCTTCCTTATAACTTTTGGATGT
* * * * *
2435602 GTTTTGTTTGCTAATTTTGATTTCTTGGATGTTTAATTTTGTGTTTTAATTAGGTAAGGATTAA-
66 GTTTTGTATGCTGATTTTGATTTCTTTGATGTTTAATCTTGTGTTTTAATTAGGTAAGGACTAAT
* * * * *
2435666 TTGACAAAATTAGAAAGTTTTGCGGGTC
131 TTG-TAAATTTAAAAAGTTTAG-GGGTT
* * * * * * * *
2435694 TATTCGAAAATTTTGTTCAAAAGCTAAAAGTACTTAG-CTAAATCTTCCTTGTAACTTTCGAGAT
1 TATTCGAAAATTTTGTTCTAAGGCCAAAAATACTTGGTC-GAATCTTCCTTATAACTTTTG-GAT
* * * * * *
2435758 -TGCTTTATCTGTTGATTTTGATTCCTTTGATGTTTAATATTGTGTTTTAATTAGGT
64 GTGTTTTGTATGCTGATTTTGATTTCTTTGATGTTTAATCTTGTGTTTTAATTAGGT
2435814 TAGGGACCTT
Statistics
Matches: 362, Mismatches: 63, Indels: 19
0.82 0.14 0.04
Matches are distributed among these distances:
156 13 0.04
157 214 0.59
158 135 0.37
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.46
Consensus pattern (156 bp):
TATTCGAAAATTTTGTTCTAAGGCCAAAAATACTTGGTCGAATCTTCCTTATAACTTTTGGATGT
GTTTTGTATGCTGATTTTGATTTCTTTGATGTTTAATCTTGTGTTTTAATTAGGTAAGGACTAAT
TTGTAAATTTAAAAAGTTTAGGGGTT
Found at i:2438903 original size:155 final size:155
Alignment explanation
Indices: 2438648--2438970 Score: 348
Period size: 155 Copynumber: 2.1 Consensus size: 155
2438638 TACGGAATAA
* * * * *
2438648 CTTCGACGTAAAAGTACCTGATATCCTTAAAGGACTTAAAAATGAATATAGATGAGACGAACCTA
1 CTTCGACGTAAAAGTACCGGATACCCCTAAAAGACTTAAAAAGGAATATAGATGAGACGAACCTA
** * * *
2438713 TCCTAAATACCCACTTTTAGTATAAAAGCAGACCTAGTGACAACTTAGGACTCGA-TTTTAAAAA
66 TCCTAAATACCCACTTCGAGCATAAAAGCAGACCTAGTGACAACCTAAGACT-GAGTTTTAAAAA
* ** ** *
2438777 ATTACCAAAATGTTCTTAGGGGATGC
130 ATTACAAAAATGCCCTTAAAGGATAC
* * * *
2438803 CTTCGACGTAAAAGTACCGGGTACCCCTAAAAGACTTAAAGAGGACA-ATAGATGAGATGAGCCT
1 CTTCGACGTAAAAGTACCGGATACCCCTAAAAGACTTAAAAAGGA-ATATAGATGAGACGAACCT
* * * * *
2438867 ATCCTTAATATCTATCTTCGA-CATAAAAGCCA-ACCTAGTGACAACCTAAGACTTAGTTTTGAA
65 ATCCTAAATACCCA-CTTCGAGCATAAAAG-CAGACCTAGTGACAACCTAAGACTGAGTTTTAAA
*
2438930 AAATTATAAAAATGCCCTTAAAGGATAC
128 AAATTACAAAAATGCCCTTAAAGGATAC
2438958 CTTCGACGTAAAA
1 CTTCGACGTAAAA
2438971 AAACTCGATA
Statistics
Matches: 138, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
154 1 0.01
155 130 0.94
156 7 0.05
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (155 bp):
CTTCGACGTAAAAGTACCGGATACCCCTAAAAGACTTAAAAAGGAATATAGATGAGACGAACCTA
TCCTAAATACCCACTTCGAGCATAAAAGCAGACCTAGTGACAACCTAAGACTGAGTTTTAAAAAA
TTACAAAAATGCCCTTAAAGGATAC
Found at i:2441305 original size:167 final size:165
Alignment explanation
Indices: 2441112--2441769 Score: 717
Period size: 167 Copynumber: 4.0 Consensus size: 165
2441102 TTTTAGACTA
* * * * *
2441112 AAGAAAAA-CCCCTCGAAAATATTTATGAAACAAAAAACTCAGTTTTTC-AAAGAAAGGGAAAAT
1 AAGAAAAATCCCC-CAAAAAAATTTATGAAATAAAAAACTCA-TATTTCGAAA-AAAAGGAAAAT
* *
2441175 TTCAAGGAAAAAATTTAAAATTCATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAAT
63 TTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAAT
* *
2441240 AAATAATAATATTTGATGAATTTTAAAAATTAAAAACC
128 AAATAATAATATTTGATGAATTTTAAAAATCAAAAAAC
* * * *
2441278 AAGAAAAATCCCCCTAAAAAAATTTATGAAATAGAAAACTCTGTATTTTGAAAAAAAGGAGAATT
1 AAGAAAAATCCCCC-AAAAAAATTTATGAAATAAAAAACTC-ATATTTCGAAAAAAAGGA-AAAT
* * * *
2441343 TTCAA-GAAAAAAATCCAAATTTGTGGAAATGAAGGAATTTTTGAAAACTAAATTAATATGAAAT
63 TTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAAT
* *
2441407 AAATAATAATATTTTATAAATTTTAAAAATCAAAAAAC
128 AAATAATAATATTTGATGAATTTTAAAAATCAAAAAAC
*** * *
2441445 AAGAAAAATCCTCCCAAAAAAATTTAT-AGAATAGAAATTTTCATATTTCAAAAAAAAAGAAAAA
1 AAGAAAAATCC-CCCAAAAAAATTTATGA-AATA-AAAAACTCATATTTC-GAAAAAAAGGAAAA
* * **
2441509 TTTCAAGG-AAAAATTCAAAATTTACGGAAATGAATGAATTTTTGAAAA-TGGAATTAACGTGAA
62 TTTCAAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACT-AAATTAATATGAA
2441572 ATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAAC
126 ATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAAC
* * * * * * *
2441612 AAGAAAAAT-CTCAAAAACAAATTTACGGAGTAGAAAACTCCACATTTCGGAAAAAAA-G-AAAT
1 AAGAAAAATCCCCCAAAA-AAATTTATGAAATAAAAAACT-CATATTTC-GAAAAAAAGGAAAAT
* * * *
2441674 TTCAAGGAAAAAGATTCAAAATTTAT--AAAGGTGAATGAATTTTTGAGAACTGATTTAATCTGA
63 TTCAAGGAAAAA-ATTCAAAATTTATGGAAA--TGAATGAATTTTTGAAAACTAAATTAATATGA
* *
2441737 AATAAATAATTATATTTGATGAATTTTTAAAAT
125 AATAAATAATAATATTTGATGAATTTTAAAAAT
2441770 TTTAAACCCA
Statistics
Matches: 415, Mismatches: 58, Indels: 38
0.81 0.11 0.07
Matches are distributed among these distances:
164 14 0.03
165 12 0.03
166 105 0.25
167 256 0.62
168 28 0.07
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.29
Consensus pattern (165 bp):
AAGAAAAATCCCCCAAAAAAATTTATGAAATAAAAAACTCATATTTCGAAAAAAAGGAAAATTTC
AAGGAAAAAATTCAAAATTTATGGAAATGAATGAATTTTTGAAAACTAAATTAATATGAAATAAA
TAATAATATTTGATGAATTTTAAAAATCAAAAAAC
Found at i:2441620 original size:17 final size:18
Alignment explanation
Indices: 2441598--2441631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2441588 GATGAATTTT
2441598 AAAAATC-AAAAAACAAG
1 AAAAATCTAAAAAACAAG
*
2441615 AAAAATCTCAAAAACAA
1 AAAAATCTAAAAAACAA
2441632 ATTTACGGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.15, G:0.03, T:0.09
Consensus pattern (18 bp):
AAAAATCTAAAAAACAAG
Found at i:2441877 original size:21 final size:21
Alignment explanation
Indices: 2441848--2441887 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2441838 ATTCTAAAAG
*
2441848 AAAATCAATAATTCAAAACAT
1 AAAAACAATAATTCAAAACAT
**
2441869 AAAAACAATTTTTCAAAAC
1 AAAAACAATAATTCAAAAC
2441888 TGATTTGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (21 bp):
AAAAACAATAATTCAAAACAT
Found at i:2455320 original size:15 final size:15
Alignment explanation
Indices: 2455300--2455335 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2455290 AACATAATGA
*
2455300 TAAAAATTAAAAAAT
1 TAAAAATCAAAAAAT
*
2455315 TAAAAATCAAGAAAT
1 TAAAAATCAAAAAAT
2455330 TAAAAA
1 TAAAAA
2455336 AATCAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (15 bp):
TAAAAATCAAAAAAT
Found at i:2455352 original size:11 final size:9
Alignment explanation
Indices: 2455316--2455375 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
2455306 TTAAAAAATT
2455316 AAAAATC-A
1 AAAAATCAA
* *
2455324 AGAAATTAA
1 AAAAATCAA
2455333 AAAAATCAA
1 AAAAATCAA
2455342 AAATCAATCAA
1 AAA--AATCAA
2455353 AAAAATCAA
1 AAAAATCAA
**
2455362 AATTATCAA
1 AAAAATCAA
2455371 AAAAA
1 AAAAA
2455376 AATGATGAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
8 5 0.12
9 27 0.66
11 9 0.22
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.17
Consensus pattern (9 bp):
AAAAATCAA
Found at i:2455356 original size:20 final size:18
Alignment explanation
Indices: 2455316--2455375 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
2455306 TTAAAAAATT
* *
2455316 AAAAATCAAGA-AATTAA
1 AAAAATCAAAATAATCAA
2455333 AAAAATCAAAAATCAATCAA
1 AAAAATC-AAAAT-AATCAA
*
2455353 AAAAATCAAAATTATCAA
1 AAAAATCAAAATAATCAA
2455371 AAAAA
1 AAAAA
2455376 AATGATGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.19
18 13 0.35
19 5 0.14
20 12 0.32
ACGTcount: A:0.72, C:0.10, G:0.02, T:0.17
Consensus pattern (18 bp):
AAAAATCAAAATAATCAA
Found at i:2455376 original size:20 final size:19
Alignment explanation
Indices: 2455331--2455378 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
2455321 TCAAGAAATT
2455331 AAAAAAATCAAAAATCAATC
1 AAAAAAATCAAAAATCAA-C
2455351 AAAAAAATCAAAATTATCAA-
1 AAAAAAATCAAAA--ATCAAC
2455371 AAAAAAAT
1 AAAAAAAT
2455379 GATGAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 21 0.81
22 5 0.19
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAAATCAAAAATCAAC
Found at i:2455543 original size:76 final size:78
Alignment explanation
Indices: 2455405--2455569 Score: 244
Period size: 76 Copynumber: 2.1 Consensus size: 78
2455395 TTGTGAAAGC
** * *
2455405 ATGAAATGATGATGCAAAGCATGTAACATGGATGCCAGTATGAAATGATGATGCAAAGCATGTAA
1 ATGAAATGATGATGCAAAGCATGTAACATGGATGAAAGCATGAAATAATGATGCAAAGCATGTAA
2455470 CGTGGATGCAAGT
66 CGTGGATGCAAGT
** *
2455483 ATGAAATGATGATGCAAAGCATG-AAGGTTG-TGAAAGCATGAAATAATGATGCAAAGCATGTAA
1 ATGAAATGATGATGCAAAGCATGTAACATGGATGAAAGCATGAAATAATGATGCAAAGCATGTAA
*
2455546 TGTGGATGCAAGT
66 CGTGGATGCAAGT
2455559 ATGAAATGATG
1 ATGAAATGATG
2455570 CAGCAAACAA
Statistics
Matches: 79, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
76 52 0.66
77 4 0.05
78 23 0.29
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (78 bp):
ATGAAATGATGATGCAAAGCATGTAACATGGATGAAAGCATGAAATAATGATGCAAAGCATGTAA
CGTGGATGCAAGT
Found at i:2455576 original size:39 final size:39
Alignment explanation
Indices: 2455405--2455569 Score: 244
Period size: 39 Copynumber: 4.3 Consensus size: 39
2455395 TTGTGAAAGC
* *
2455405 ATGAAATGATGATGCAAAGCATGTAACATGGATGCCAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
2455444 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
* * * *
2455483 ATGAAATGATGATGCAAAGCATG-AAGGTTG-TGAAAGC
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
* *
2455520 ATGAAATAATGATGCAAAGCATGTAATGTGGATGCAAGT
1 ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
2455559 ATGAAATGATG
1 ATGAAATGATG
2455570 CAGCAAACAA
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
37 27 0.24
38 10 0.09
39 75 0.67
ACGTcount: A:0.40, C:0.09, G:0.27, T:0.24
Consensus pattern (39 bp):
ATGAAATGATGATGCAAAGCATGTAACGTGGATGCAAGT
Found at i:2459005 original size:28 final size:28
Alignment explanation
Indices: 2458958--2459024 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 28
2458948 TTATGCCATA
*
2458958 TAGAATTTT-AATTAAACCTTTTACATT
1 TAGAATTTTCAATTAAACCTTTTACATG
**
2458985 TAGAATTTTCAATTAGGCCTTTTACATG
1 TAGAATTTTCAATTAAACCTTTTACATG
2459013 TA-AATGTTTCAA
1 TAGAAT-TTTCAA
2459025 GTAAGGTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
27 12 0.34
28 23 0.66
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (28 bp):
TAGAATTTTCAATTAAACCTTTTACATG
Found at i:2459103 original size:42 final size:40
Alignment explanation
Indices: 2459031--2459120 Score: 96
Period size: 42 Copynumber: 2.2 Consensus size: 40
2459021 TCAAGTAAGG
*
2459031 TTTCAC-CACAGAATTTTTCATTAAGCATTTTATTTATTGAAA
1 TTTCACACACAGAATTTTTCATTAAGAATTTTA---ATTGAAA
* *
2459073 TTTCACACATAGAA-TTTTCA-TATAGAATTTTAATTTAAA
1 TTTCACACACAGAATTTTTCATTA-AGAATTTTAATTGAAA
2459112 TTTCACACA
1 TTTCACACA
2459121 ATGGATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 15 0.35
41 2 0.05
42 20 0.47
43 6 0.14
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (40 bp):
TTTCACACACAGAATTTTTCATTAAGAATTTTAATTGAAA
Found at i:2459212 original size:28 final size:27
Alignment explanation
Indices: 2459152--2459219 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
2459142 TTTATGCATA
* **
2459152 ATTTTTTAATTAAACTTTTCTACTTTG
1 ATTTTTTAATTAAACTTTTCTACGTAC
* *
2459179 AATTTTTAATTAAACTTTTGTACGTAC
1 ATTTTTTAATTAAACTTTTCTACGTAC
2459206 ATTTTTTTAATTAA
1 A-TTTTTTAATTAA
2459220 CTCTCAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 23 0.68
28 11 0.32
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (27 bp):
ATTTTTTAATTAAACTTTTCTACGTAC
Found at i:2459327 original size:27 final size:27
Alignment explanation
Indices: 2459268--2459319 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2459258 CGCAATATAA
*
2459268 AATTTTCAATTAAGCTTTTTACATATG
1 AATTTTCAATTAAGCTTTCTACATATG
2459295 AATTTTCAATTAAGCTTTCT-CATAT
1 AATTTTCAATTAAGCTTTCTACATAT
2459320 TAGTTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.48
Consensus pattern (27 bp):
AATTTTCAATTAAGCTTTCTACATATG
Found at i:2460024 original size:11 final size:11
Alignment explanation
Indices: 2460003--2460049 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
2459993 TCATTTAAGC
2460003 AAGAGGAAAAAA
1 AAGA-GAAAAAA
2460015 AAGAGAAAAAA
1 AAGAGAAAAAA
*
2460026 AAAAGAAAGAAA
1 AAGAGAAA-AAA
2460038 AA-AGAAGAAAA
1 AAGAGAA-AAAA
2460049 A
1 A
2460050 TAAAAATCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 22 0.69
12 10 0.31
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAGAAAAAA
Found at i:2460038 original size:22 final size:22
Alignment explanation
Indices: 2460008--2460049 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2459998 TAAGCAAGAG
*
2460008 GAAAAAAAAGAGAAAAAAAAAA
1 GAAAAAAAAAAGAAAAAAAAAA
* *
2460030 GAAAGAAAAAAGAAGAAAAA
1 GAAAAAAAAAAGAAAAAAAA
2460050 TAAAAATCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAAGAAAAAAAAAA
Found at i:2460045 original size:14 final size:13
Alignment explanation
Indices: 2460008--2460047 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2459998 TAAGCAAGAG
2460008 GAAAAAAAAGAGAA
1 GAAAAAAAAGA-AA
2460022 -AAAAAAAAGAAA
1 GAAAAAAAAGAAA
2460034 GAAAAAAGAAGAAA
1 GAAAAAA-AAGAAA
2460048 AATAAAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.08
13 16 0.67
14 6 0.25
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAGAAA
Found at i:2460054 original size:15 final size:13
Alignment explanation
Indices: 2460009--2460055 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
2459999 AAGCAAGAGG
*
2460009 AAAAAAAAGAGAA
1 AAAAAAAAGAAAA
2460022 AAAAAAAAGAAAGA
1 AAAAAAAAGAAA-A
*
2460036 AAAAAGAAGAAAA
1 AAAAAAAAGAAAA
2460049 ATAAAAA
1 A-AAAAA
2460056 TCTAAAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 13 0.45
14 16 0.55
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.02
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:2460403 original size:45 final size:45
Alignment explanation
Indices: 2460354--2460444 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 45
2460344 ACCTTTTTTA
* * * * * *
2460354 AATTTGTGCAATTTATTTTTGTTGCAATTTAAATTTATACACTTT
1 AATTTATGCAATTTACTTTTATTACAACTTAAACTTATACACTTT
* *
2460399 AATTTATGCATTTTACTTTTATTACAACTTAAACTTATGCACTTT
1 AATTTATGCAATTTACTTTTATTACAACTTAAACTTATACACTTT
2460444 A
1 A
2460445 TTACTATTGC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (45 bp):
AATTTATGCAATTTACTTTTATTACAACTTAAACTTATACACTTT
Found at i:2460468 original size:31 final size:31
Alignment explanation
Indices: 2460394--2460470 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
2460384 AAATTTATAC
* *
2460394 ACTTTAATTTATGCATTTTACTTTTATTACA
1 ACTTTAATTTATGCACTTTACTTCTATTACA
* * *
2460425 ACTTAAACTTATGCACTTTA-TTACTATTGCA
1 ACTTTAATTTATGCACTTTACTT-CTATTACA
*
2460456 ATTTTAATTTATGCA
1 ACTTTAATTTATGCA
2460471 ATCTAATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 2 0.05
31 35 0.95
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.49
Consensus pattern (31 bp):
ACTTTAATTTATGCACTTTACTTCTATTACA
Found at i:2461420 original size:40 final size:40
Alignment explanation
Indices: 2461375--2461506 Score: 121
Period size: 39 Copynumber: 3.4 Consensus size: 40
2461365 CACTTAGCAC
*
2461375 TTTTCATACCAAAACATGTCCATTAAGGTCAATTTAGTAA
1 TTTTCATATCAAAACATGTCCATTAAGGTCAATTTAGTAA
* * *
2461415 TTTTCATATAAAAACTAAGT-CTTTATA-GTC-ATATTAGT-A
1 TTTTCATATCAAAAC-ATGTCCATTA-AGGTCAAT-TTAGTAA
* * * *
2461454 TTTTTATATCAAAACATATCCATTAAGTTCATTTTAGTAA
1 TTTTCATATCAAAACATGTCCATTAAGGTCAATTTAGTAA
*
2461494 TTTTC-TATTAAAA
1 TTTTCATATCAAAA
2461507 TTAAGTATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
38 3 0.04
39 34 0.47
40 31 0.43
41 4 0.06
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (40 bp):
TTTTCATATCAAAACATGTCCATTAAGGTCAATTTAGTAA
Found at i:2463826 original size:26 final size:25
Alignment explanation
Indices: 2463774--2463822 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2463764 TTTTAAATAC
* *
2463774 ATAATATTTTAAAAATGATTATGAT
1 ATAAAATTTTAAAAATGATTATAAT
2463799 ATAAAATTTATAAAAATGA-TATAA
1 ATAAAATTT-TAAAAATGATTATAA
2463823 ATATGTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (25 bp):
ATAAAATTTTAAAAATGATTATAAT
Found at i:2464146 original size:11 final size:11
Alignment explanation
Indices: 2464130--2464163 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2464120 ACATTAATGC
2464130 TTGGATATTTT
1 TTGGATATTTT
*
2464141 TTGGATAATTT
1 TTGGATATTTT
*
2464152 TCGGATATTTT
1 TTGGATATTTT
2464163 T
1 T
2464164 CAGCTCTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (11 bp):
TTGGATATTTT
Found at i:2466190 original size:110 final size:111
Alignment explanation
Indices: 2466022--2466225 Score: 311
Period size: 110 Copynumber: 1.8 Consensus size: 111
2466012 ATATATATAC
* * * *
2466022 ATATGCATATTTGAATTGATCGGAGACATGTACGATTCAAACATAATCACATGAAATTTAAATAA
1 ATATGCATATTTAAATTGATCGAAAACATGTACGATTCAAACATAATCACATAAAATTTAAATAA
*
2466087 TTTAATTAATATAAATATAAAAATATAATTATATTTGATTGATGTT
66 TTTAATCAATATAAATATAAAAATATAATTATATTTGATTGATGTT
* * * *
2466133 ATATGCATATTTAAATTGATTGAAAAC-TGTATGATTCAAATATAATCACATAAAATTTAGATAA
1 ATATGCATATTTAAATTGATCGAAAACATGTACGATTCAAACATAATCACATAAAATTTAAATAA
*
2466197 TTTAATCAATATGAATATAAAAATATAAT
66 TTTAATCAATATAAATATAAAAATATAAT
2466226 CACCTTGATT
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
110 60 0.72
111 23 0.28
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (111 bp):
ATATGCATATTTAAATTGATCGAAAACATGTACGATTCAAACATAATCACATAAAATTTAAATAA
TTTAATCAATATAAATATAAAAATATAATTATATTTGATTGATGTT
Found at i:2467963 original size:2 final size:2
Alignment explanation
Indices: 2467952--2467995 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2467942 CTCTGCAATT
*
2467952 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2467994 TA
1 TA
2467996 AACCATCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2468966 original size:79 final size:80
Alignment explanation
Indices: 2468834--2468992 Score: 248
Period size: 79 Copynumber: 2.0 Consensus size: 80
2468824 TAACCTAAGG
* * * * *
2468834 GCTCAAACAAACCCATTAATTTATACATACTTTAAAATAAACCAAGATCCCAAAATTAAAAAATC
1 GCTCAAACAAACACATTAATTTAAAAAAACTTTAAAATAAACCAAGATCCCAAAATTAAAAAAAC
2468899 CCAAGACATGATTCT
66 CCAAGACATGATTCT
* *
2468914 GCTCAAACAAATACATTAA-TTAAAAAAACTTTAAAATAAATCAAGATCCCAAAATTAAAAAAAC
1 GCTCAAACAAACACATTAATTTAAAAAAACTTTAAAATAAACCAAGATCCCAAAATTAAAAAAAC
2468978 CCAAGACATGATTCT
66 CCAAGACATGATTCT
2468993 TTTACTTTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 55 0.76
80 17 0.24
ACGTcount: A:0.51, C:0.20, G:0.05, T:0.24
Consensus pattern (80 bp):
GCTCAAACAAACACATTAATTTAAAAAAACTTTAAAATAAACCAAGATCCCAAAATTAAAAAAAC
CCAAGACATGATTCT
Found at i:2477507 original size:53 final size:51
Alignment explanation
Indices: 2477427--2477577 Score: 200
Period size: 53 Copynumber: 2.9 Consensus size: 51
2477417 AACCAAACTA
** *
2477427 TATCAAACCATCTTGACCATTTAACTATAAAAAAGTCAAATTAGTCTCGACC
1 TATCAAACCATCTTGACCATCCAACTATAAAAAAGTCAAATTAATCTC-ACC
*
2477479 GTATCAAACCATCTTGACCATCCAACTATAAAAAAGTCAAAGTTAATCTCTCC
1 -TATCAAACCATCTTGACCATCCAACTATAAAAAAGTCAAA-TTAATCTCACC
*
2477532 -AT--AACCTTCTTGACCATCCAACTATAAAAAAGTCAAAATTAATCTC
1 TATCAAACCATCTTGACCATCCAACTATAAAAAAGTC-AAATTAATCTC
2477578 TTCATAACCT
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
49 39 0.43
50 3 0.03
51 2 0.02
53 40 0.44
54 7 0.08
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.28
Consensus pattern (51 bp):
TATCAAACCATCTTGACCATCCAACTATAAAAAAGTCAAATTAATCTCACC
Found at i:2477556 original size:49 final size:48
Alignment explanation
Indices: 2477432--2477586 Score: 193
Period size: 49 Copynumber: 3.1 Consensus size: 48
2477422 AACTATATCA
** * *
2477432 AACCATCTTGACCATTTAACTATAAAAAAGTCAAATTAGTCTCGACCGTAT
1 AACCATCTTGACCATCCAACTATAAAAAAGTCAAATTAATCTC-TCC--AT
2477483 CAAACCATCTTGACCATCCAACTATAAAAAAGTCAAAGTTAATCTCTCCAT
1 --AACCATCTTGACCATCCAACTATAAAAAAGTCAAA-TTAATCTCTCCAT
* *
2477534 AACCTTCTTGACCATCCAACTATAAAAAAGTCAAAATTAATCTCTTCAT
1 AACCATCTTGACCATCCAACTATAAAAAAGTC-AAATTAATCTCTCCAT
2477583 AACC
1 AACC
2477587 TTTTTAGTAT
Statistics
Matches: 94, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
49 47 0.50
50 3 0.03
51 2 0.02
53 35 0.37
54 7 0.07
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.28
Consensus pattern (48 bp):
AACCATCTTGACCATCCAACTATAAAAAAGTCAAATTAATCTCTCCAT
Found at i:2477926 original size:15 final size:16
Alignment explanation
Indices: 2477902--2477934 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2477892 TACCCTAAAC
*
2477902 TCAAATCCG-AAATAA
1 TCAAAACCGAAAATAA
2477917 TCAAAACCGAAAATAA
1 TCAAAACCGAAAATAA
2477933 TC
1 TC
2477935 CAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.55, C:0.21, G:0.06, T:0.18
Consensus pattern (16 bp):
TCAAAACCGAAAATAA
Found at i:2482401 original size:13 final size:13
Alignment explanation
Indices: 2482383--2482409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2482373 TAATATTTCA
2482383 AATTTCTTTTTAT
1 AATTTCTTTTTAT
2482396 AATTTCTTTTTAT
1 AATTTCTTTTTAT
2482409 A
1 A
2482410 TTAAAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (13 bp):
AATTTCTTTTTAT
Found at i:2482480 original size:21 final size:22
Alignment explanation
Indices: 2482443--2482496 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
2482433 TATTAAAAAA
*
2482443 TTAAA-ATTTTTATTTTTAAAT
1 TTAAATATATTTATTTTTAAAT
*
2482464 TTAAATATATTTATTTTT-ATT
1 TTAAATATATTTATTTTTAAAT
*
2482485 TTATATATATTT
1 TTAAATATATTT
2482497 TAAAAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAAATATATTTATTTTTAAAT
Found at i:2483022 original size:18 final size:18
Alignment explanation
Indices: 2482968--2483102 Score: 82
Period size: 16 Copynumber: 8.1 Consensus size: 18
2482958 AAATAAATAA
*
2482968 AATATAATAT--ATTATG
1 AATATAATATAAATTATT
*
2482984 AATA-AATTTAAAATT-TT
1 AATATAATAT-AAATTATT
2483001 -ATATAATATAAATTATT
1 AATATAATATAAATTATT
* *
2483018 AATATATTAAAAATT-TT
1 AATATAATATAAATTATT
*
2483035 -ATATAAATATAAAATATT
1 AATAT-AATATAAATTATT
*
2483053 -TTA-AATAT-AATTA-T
1 AATATAATATAAATTATT
*
2483067 AATATAATA-AAATATATA
1 AATATAATATAAAT-TATT
2483085 AATATAAT-TAAA-TATT
1 AATATAATATAAATTATT
2483101 AA
1 AA
2483103 ATTAAATTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
14 1 0.01
15 10 0.11
16 33 0.36
17 18 0.20
18 30 0.33
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (18 bp):
AATATAATATAAATTATT
Found at i:2483031 original size:34 final size:34
Alignment explanation
Indices: 2482969--2483052 Score: 109
Period size: 34 Copynumber: 2.5 Consensus size: 34
2482959 AATAAATAAA
* *
2482969 ATATAATAT--ATTATGAATAAATTTAAAATTTT
1 ATATAATATAAATTATTAATAAATTAAAAATTTT
*
2483001 ATATAATATAAATTATTAATATATTAAAAATTTT
1 ATATAATATAAATTATTAATAAATTAAAAATTTT
*
2483035 ATATAAATATAAAATATT
1 ATAT-AATATAAATTATT
2483053 TTAAATATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
32 9 0.20
34 24 0.53
35 12 0.27
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
ATATAATATAAATTATTAATAAATTAAAAATTTT
Found at i:2483036 original size:20 final size:20
Alignment explanation
Indices: 2482967--2483055 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 20
2482957 GAAATAAATA
* *
2482967 AAATATAATATATTATGA-AT
1 AAATATAAAATATT-TTATAT
*
2482987 AAAT-TTAAA-ATTTTATAT
1 AAATATAAAATATTTTATAT
*
2483005 -AATAT-AAAT-TATTA-AT
1 AAATATAAAATATTTTATAT
*
2483021 ATAT-TAAAA-ATTTTATAT
1 AAATATAAAATATTTTATAT
2483039 AAATATAAAATATTTTA
1 AAATATAAAATATTTTA
2483056 AATATAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 18
0.68 0.09 0.23
Matches are distributed among these distances:
16 3 0.06
17 21 0.40
18 11 0.21
19 8 0.15
20 10 0.19
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (20 bp):
AAATATAAAATATTTTATAT
Found at i:2483038 original size:16 final size:16
Alignment explanation
Indices: 2482993--2483078 Score: 61
Period size: 18 Copynumber: 5.2 Consensus size: 16
2482983 GAATAAATTT
2482993 AAAATTTTATATAATA
1 AAAATTTTATATAATA
* *
2483009 TAAATTATTAATATATTA
1 AAAATT-TT-ATATAATA
2483027 AAAATTTTATATAAATA
1 AAAATTTTATAT-AATA
2483044 TAAAATATTT-TA-AAT-
1 -AAAAT-TTTATATAATA
* *
2483059 ATAATTATAATATAATA
1 AAAATT-TTATATAATA
2483076 AAA
1 AAA
2483079 TATATAAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.09
15 2 0.04
16 15 0.28
17 9 0.17
18 19 0.35
19 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTTTATATAATA
Found at i:2483070 original size:20 final size:20
Alignment explanation
Indices: 2483001--2483071 Score: 55
Period size: 20 Copynumber: 3.8 Consensus size: 20
2482991 TTAAAATTTT
2483001 ATATAA-TATAA-ATTATT-A
1 ATATAATTATAATATT-TTAA
* *
2483019 ATAT-ATTA-AAAATTTTAT
1 ATATAATTATAATATTTTAA
*
2483037 ATA-AATATAAAATATTTTAA
1 ATATAAT-TATAATATTTTAA
2483057 ATATAATTATAATAT
1 ATATAATTATAATAT
2483072 AATAAAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.12
18 14 0.33
19 2 0.05
20 18 0.43
21 3 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAATTATAATATTTTAA
Found at i:2483110 original size:17 final size:18
Alignment explanation
Indices: 2483038--2483104 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
2483028 AAATTTTATA
*
2483038 TAAATATA-AAATAT-TT
1 TAAATATATAAATATAAT
2483054 TAAATATAATTATAATATAAT
1 TAAATAT-A-TA-AATATAAT
*
2483075 AAAATATATAAATATAAT
1 TAAATATATAAATATAAT
2483093 TAAATAT-TAAAT
1 TAAATATATAAAT
2483105 TAAATTTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
16 7 0.16
17 6 0.14
18 14 0.33
19 3 0.07
20 6 0.14
21 7 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATATATAAATATAAT
Found at i:2483485 original size:18 final size:17
Alignment explanation
Indices: 2483458--2483494 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
2483448 TGAAATTTTT
*
2483458 AATTATTAATTTAATTA
1 AATTATTAATATAATTA
2483475 AATTAATTAATATAATTA
1 AATT-ATTAATATAATTA
2483493 AA
1 AA
2483495 ATAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTATTAATATAATTA
Found at i:2483552 original size:20 final size:20
Alignment explanation
Indices: 2483483--2483554 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
2483473 TAAATTAATT
2483483 AATATAATTAAAATAAA-ATTA
1 AATATAA-T-AAATAAATATTA
* *
2483504 AATAT--TAAATATATAATTT
1 AATATAATAAATAAAT-ATTA
* *
2483523 TA-ATAGTAAATAAATATTA
1 AATATAATAAATAAATATTA
2483542 AATATAATAAATA
1 AATATAATAAATA
2483555 TTTAATAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
17 6 0.15
18 3 0.08
19 8 0.21
20 17 0.44
21 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (20 bp):
AATATAATAAATAAATATTA
Found at i:2484003 original size:15 final size:15
Alignment explanation
Indices: 2483980--2484025 Score: 56
Period size: 16 Copynumber: 3.0 Consensus size: 15
2483970 ATAGCTCATA
*
2483980 TTTATAATAATTTTT
1 TTTAAAATAATTTTT
**
2483995 TTTAAAATAACTCATT
1 TTTAAAATAA-TTTTT
2484011 TTTAAAATAATTTTT
1 TTTAAAATAATTTTT
2484026 ATTCAAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTAAAATAATTTTT
Found at i:2484003 original size:31 final size:31
Alignment explanation
Indices: 2483967--2484025 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2483957 GTTTATATTC
* *
2483967 AAAATAGCTCATATTTATAATAATTTTTTTT
1 AAAATAACTCATATTTAAAATAATTTTTTTT
*
2483998 AAAATAACTCATTTTTAAAATAATTTTT
1 AAAATAACTCATATTTAAAATAATTTTT
2484026 ATTCAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (31 bp):
AAAATAACTCATATTTAAAATAATTTTTTTT
Found at i:2486666 original size:16 final size:16
Alignment explanation
Indices: 2486645--2486678 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2486635 TATATGCATA
*
2486645 TATAAATTTTTAAAAT
1 TATAAATATTTAAAAT
2486661 TATAAATATTTAAAAT
1 TATAAATATTTAAAAT
2486677 TA
1 TA
2486679 AAAAATTTGA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATAAATATTTAAAAT
Done.