Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold74
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: 4633657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 25 characters in sequence are not A, C, G, or T
File 7 of 24
Found at i:1376406 original size:27 final size:27
Alignment explanation
Indices: 1376368--1376506 Score: 112
Period size: 27 Copynumber: 5.3 Consensus size: 27
1376358 TTAGATGTTG
*
1376368 AGATGATTCTTGAAAAGCCTTTTGTCT
1 AGATGATTCTTGAAAAGCCTTTTGGCT
* * *
1376395 AGATGATCCTTGAATA----TTT-GTT
1 AGATGATTCTTGAAAAGCCTTTTGGCT
*
1376417 AAGATGATTCTTGAAAAACCTTTTGGCT
1 -AGATGATTCTTGAAAAGCCTTTTGGCT
* *
1376445 AGATGATGCCTT-AGAAACCCTTTTGGCT
1 AGATGAT-TCTTGA-AAAGCCTTTTGGCT
* *
1376473 AAATGATTCTT-ATAAGCCATTTTGGCT
1 AGATGATTCTTGAAAAGCC-TTTTGGCT
1376500 AGATGAT
1 AGATGAT
1376507 GAAGGAAACA
Statistics
Matches: 89, Mismatches: 14, Indels: 18
0.74 0.12 0.15
Matches are distributed among these distances:
22 1 0.01
23 17 0.19
26 4 0.04
27 43 0.48
28 24 0.27
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (27 bp):
AGATGATTCTTGAAAAGCCTTTTGGCT
Found at i:1376760 original size:61 final size:61
Alignment explanation
Indices: 1376671--1376819 Score: 148
Period size: 61 Copynumber: 2.5 Consensus size: 61
1376661 AAACATATCG
* * *
1376671 TTGAAGAAAAAT-T-TTGCTAAATATCATCTTAACATA-AATTATCTAACC-AAAGAACACC
1 TTGATGAAAAATATCTTGCTAAAAATCATCTTAACATAGAATCATCTAACCGAAA-AACACC
* ** * * *
1376729 TTGATGAAAAAATATCTTGCTAAAAAACATC-TCCCTTAGAATCATCTCACCGAAAAACATC
1 TTGATG-AAAAATATCTTGCTAAAAATCATCTTAACATAGAATCATCTAACCGAAAAACACC
*
1376790 TTGATG-AAAATATCTTGTTAAAAATCATCT
1 TTGATGAAAAATATCTTGCTAAAAATCATCT
1376820 CCTCTATAAA
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
58 5 0.07
59 27 0.36
60 5 0.07
61 34 0.46
62 3 0.04
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (61 bp):
TTGATGAAAAATATCTTGCTAAAAATCATCTTAACATAGAATCATCTAACCGAAAAACACC
Found at i:1376834 original size:59 final size:59
Alignment explanation
Indices: 1376718--1376848 Score: 153
Period size: 59 Copynumber: 2.2 Consensus size: 59
1376708 ATTATCTAAC
*
1376718 CAAAGAACACCTTGATGAAAAAATATCTTGCTAAAAAACATCTCCCTTAGAATCATCTC-A
1 CAAA-AACATCTTGATG-AAAAATATCTTGCTAAAAAACATCTCCCTTAGAATCATCTCGA
* *
1376778 CCGAAAAACATCTTGATG-AAAATATCTTGTTAAAAATCATCTCCTCTATA-AA-CATCTCGA
1 -C-AAAAACATCTTGATGAAAAATATCTTGCTAAAAAACATCTCC-CT-TAGAATCATCTCGA
1376838 CAAAAACATCT
1 CAAAAACATCT
1376849 CGTCAAAAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
58 10 0.16
59 31 0.49
60 5 0.08
61 14 0.22
62 3 0.05
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.27
Consensus pattern (59 bp):
CAAAAACATCTTGATGAAAAATATCTTGCTAAAAAACATCTCCCTTAGAATCATCTCGA
Found at i:1376846 original size:14 final size:15
Alignment explanation
Indices: 1376827--1376867 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
1376817 TCTCCTCTAT
1376827 AAACATCTCGAC-AA
1 AAACATCTCGACAAA
*
1376841 AAACATCTCGTCAAA
1 AAACATCTCGACAAA
1376856 AAATCATCTCGA
1 AAA-CATCTCGA
1376868 AACATCCCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 11 0.48
15 5 0.22
16 7 0.30
ACGTcount: A:0.46, C:0.27, G:0.07, T:0.20
Consensus pattern (15 bp):
AAACATCTCGACAAA
Found at i:1376859 original size:59 final size:58
Alignment explanation
Indices: 1376735--1376864 Score: 133
Period size: 59 Copynumber: 2.2 Consensus size: 58
1376725 CACCTTGATG
*
1376735 AAAAAATATCTTGCTAAAAAACATCTCCCTTAGAATCATCTCACCGAAAAACATCTTG
1 AAAAAATATCTTGCTAAAAAACATCTCCCTTAGAATCATCTCACCGAAAAACATCTTC
* * *
1376793 ATGAAAATATCTTGTTAAAAATCATCTCCTCTATA-AA-CATCTCGA-C-AAAAACATCTCGTC
1 A-AAAAATATCTTGCTAAAAAACATCTCC-CT-TAGAATCATCTC-ACCGAAAAACATCT--TC
1376853 AAAAAATCATCT
1 AAAAAAT-ATCT
1376865 CGAAACATCC
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
58 11 0.18
59 36 0.60
60 11 0.18
61 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.28
Consensus pattern (58 bp):
AAAAAATATCTTGCTAAAAAACATCTCCCTTAGAATCATCTCACCGAAAAACATCTTC
Found at i:1382036 original size:322 final size:322
Alignment explanation
Indices: 1381445--1382084 Score: 1163
Period size: 322 Copynumber: 2.0 Consensus size: 322
1381435 GTAAGGTGCC
* *
1381445 TTTTAATGGAACAAAATCATAAGACTTTTAGATTAAAACGAAAAATACCTAGCAGGTAAATGTAG
1 TTTTAATGGAACAAAATCATAAGACTTTTAGATTAAAACGAAAAATACCTAACAAGTAAATGTAG
*
1381510 GTTTTAACAAATGATATGGGAATAATTACCAGTTAAAATATGGGAGCTAAGTGCTATACCATGAG
66 GTTTTAACAAATGATATGGGAATAATTACCAGTTAAAATATGGGAGCGAAGTGCTATACCATGAG
*
1381575 AGTCGCCTCTAAAAATGCTACACAGTGTGAGCAATCTCTAGAATCTTAACACTTGGTGTAATCAT
131 AGTCACCTCTAAAAATGCTACACAGTGTGAGCAATCTCTAGAATCTTAACACTTGGTGTAATCAT
*
1381640 GGTTCTGTCTATTCTATGTTGGGTTTGACAAGGACATTAAGCTTTAGCAAGGGAGTTTGTACCAC
196 GGTTCTGTCTATTCTATGTTGGGTTTGACAAGGACATTAAGCTTTAGCAAGGGAGTTTGTAACAC
*
1381705 CCTTATCCCATATTGAAAAATTCTGAGAATTCACTATGATATATATGTAAAGACTTAAGCCT
261 CCTTATCCCATATTGAAAAATTCTGAGAATTCACTATCATATATATGTAAAGACTTAAGCCT
* *
1381767 TTTTAGTGGAACAAAATCATAAGACTTTTAGATTAAAACGAAAAATACCTAACAAGTAGATGTAG
1 TTTTAATGGAACAAAATCATAAGACTTTTAGATTAAAACGAAAAATACCTAACAAGTAAATGTAG
* *
1381832 GTTTTAACAAATGATATGGGAATAATTACCAGTTGAAATATGGGAGCGAAGTGCTATACTATGAG
66 GTTTTAACAAATGATATGGGAATAATTACCAGTTAAAATATGGGAGCGAAGTGCTATACCATGAG
1381897 AGTCACCTCTAAAAATGCTACACAGTGTGAGCAATCTCTAGAATCTTAACACTTGGTGTAATCAT
131 AGTCACCTCTAAAAATGCTACACAGTGTGAGCAATCTCTAGAATCTTAACACTTGGTGTAATCAT
* *
1381962 GGTTCTGTCTATTCTATGTTGGGTTTGGCAAGGACATTAAGCTTTAGCGAGGGAGTTTGTAACAC
196 GGTTCTGTCTATTCTATGTTGGGTTTGACAAGGACATTAAGCTTTAGCAAGGGAGTTTGTAACAC
*
1382027 CCTTATCCCATATTGAAAAATTCTGAGGATTCACTATCATATATATGTAAAGACTTAA
261 CCTTATCCCATATTGAAAAATTCTGAGAATTCACTATCATATATATGTAAAGACTTAA
1382085 ACCTATACTT
Statistics
Matches: 305, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
322 305 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (322 bp):
TTTTAATGGAACAAAATCATAAGACTTTTAGATTAAAACGAAAAATACCTAACAAGTAAATGTAG
GTTTTAACAAATGATATGGGAATAATTACCAGTTAAAATATGGGAGCGAAGTGCTATACCATGAG
AGTCACCTCTAAAAATGCTACACAGTGTGAGCAATCTCTAGAATCTTAACACTTGGTGTAATCAT
GGTTCTGTCTATTCTATGTTGGGTTTGACAAGGACATTAAGCTTTAGCAAGGGAGTTTGTAACAC
CCTTATCCCATATTGAAAAATTCTGAGAATTCACTATCATATATATGTAAAGACTTAAGCCT
Found at i:1386173 original size:19 final size:20
Alignment explanation
Indices: 1386139--1386186 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1386129 GATTTTATTT
1386139 AAATTCAAAGTAC-AAAAATTA
1 AAATT-AAA-TACAAAAAATTA
*
1386160 TAATTAAATACAAAAAATTA
1 AAATTAAATACAAAAAATTA
1386180 AAATTAA
1 AAATTAA
1386187 TTTTAATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 17 0.71
21 4 0.17
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (20 bp):
AAATTAAATACAAAAAATTA
Found at i:1386631 original size:30 final size:31
Alignment explanation
Indices: 1386585--1386642 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
1386575 AAGATTACCA
* *
1386585 AAATTATTTCAAATATTATTAAAATTGTTAT
1 AAATTATATCAAATATTATCAAAATTGTTAT
1386616 AAATTATAT-AAATATTATCAAAATTGT
1 AAATTATATCAAATATTATCAAAATTGT
1386643 CTTGAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (31 bp):
AAATTATATCAAATATTATCAAAATTGTTAT
Found at i:1386899 original size:21 final size:21
Alignment explanation
Indices: 1386875--1386965 Score: 80
Period size: 21 Copynumber: 4.3 Consensus size: 21
1386865 TTCAAGATTA
1386875 TATCAAAAGTTAATT-AAATTT
1 TATCAAAAGTT-ATTAAAATTT
1386896 TATCAAAAGTTATTAAAATTT
1 TATCAAAAGTTATTAAAATTT
* * *
1386917 TATTAAAATTTGA-CAAAATTAT
1 TATCAAAAGTT-ATTAAAATT-T
* * *
1386939 TAT-AAATGCTATCAAAATTT
1 TATCAAAAGTTATTAAAATTT
1386959 TATCAAA
1 TATCAAA
1386966 GTTTGCTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
20 8 0.14
21 46 0.78
22 5 0.08
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (21 bp):
TATCAAAAGTTATTAAAATTT
Found at i:1386962 original size:11 final size:11
Alignment explanation
Indices: 1386890--1386965 Score: 61
Period size: 11 Copynumber: 7.2 Consensus size: 11
1386880 AAAGTTAATT
1386890 AAATTTTATCA
1 AAATTTTATCA
* *
1386901 AAA-GTTATTA
1 AAATTTTATCA
*
1386911 AAATTTTATTA
1 AAATTTTATCA
*
1386922 AAATTTGA-CA
1 AAATTTTATCA
1386932 AAATTATTAT--
1 AAATT-TTATCA
**
1386942 AAATGCTATCA
1 AAATTTTATCA
1386953 AAATTTTATCA
1 AAATTTTATCA
1386964 AA
1 AA
1386966 GTTTGCTAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
9 3 0.06
10 18 0.36
11 29 0.58
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.41
Consensus pattern (11 bp):
AAATTTTATCA
Found at i:1387158 original size:21 final size:20
Alignment explanation
Indices: 1387134--1387201 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
1387124 TTAGATTACC
*
1387134 AAAATAAGTATAAAAGTTATT
1 AAAAT-AGTATAAAAGTTATA
* * *
1387155 AAAATTGTATAAAATATTATC
1 AAAATAGTATAAAA-GTTATA
1387176 AAAATCA-TATCAAAAGTTATA
1 AAAAT-AGTAT-AAAAGTTATA
1387197 AAAAT
1 AAAAT
1387202 TATATTAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 8 0.21
21 26 0.68
22 4 0.11
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (20 bp):
AAAATAGTATAAAAGTTATA
Found at i:1387191 original size:42 final size:41
Alignment explanation
Indices: 1387128--1387288 Score: 144
Period size: 42 Copynumber: 3.8 Consensus size: 41
1387118 AATTGTTTAG
* *
1387128 ATTACCAAAATAAGTATAAAAGTTATTAAAATTGTATAAAAT
1 ATTACCAAAATTA-TATAAAAGTTATTAAAATTATATAAAAT
* * *
1387170 ATTATCAAAATCATATCAAAAGTTATAAAAATTATATTAAAA-
1 ATTACCAAAATTATAT-AAAAGTTATTAAAATTATA-TAAAAT
** * * *
1387212 CCTGCTAAAATTATATAAAATGTTATTAAAATTATATCAAAT
1 ATTACCAAAATTATATAAAA-GTTATTAAAATTATATAAAAT
* * * *
1387254 GTTACCAAAATTATACAAAAAATTATCAAAATTAT
1 ATTACCAAAATTATA-TAAAAGTTATTAAAATTAT
1387289 TTCAAAATTC
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 11 0.12
42 75 0.79
43 9 0.09
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.34
Consensus pattern (41 bp):
ATTACCAAAATTATATAAAAGTTATTAAAATTATATAAAAT
Found at i:1387206 original size:21 final size:21
Alignment explanation
Indices: 1387145--1387337 Score: 134
Period size: 21 Copynumber: 9.4 Consensus size: 21
1387135 AAATAAGTAT
* *
1387145 AAAAGTTATTAAAATTGTAT-
1 AAAAGTTATCAAAATTATATC
* *
1387165 AAAATATTATCAAAATCATATC
1 AAAA-GTTATCAAAATTATATC
* *
1387187 AAAAGTTATAAAAATTATATT
1 AAAAGTTATCAAAATTATATC
** *
1387208 AAAACCT-GCTAAAATTATAT-
1 AAAAGTTATC-AAAATTATATC
*
1387228 AAAATGTTATTAAAATTATATC
1 AAAA-GTTATCAAAATTATATC
* *
1387250 AAATGTTACCAAAATTATA-C
1 AAAAGTTATCAAAATTATATC
* *
1387270 AAAAAATTATCAAAATTATTTC
1 -AAAAGTTATCAAAATTATATC
*
1387292 AAAA--T-TC--ATTTATATC
1 AAAAGTTATCAAAATTATATC
* *
1387308 GAAGGTTATCAAAATTATATC
1 AAAAGTTATCAAAATTATATC
1387329 AAAAGTTAT
1 AAAAGTTAT
1387338 TAAGTTATGT
Statistics
Matches: 130, Mismatches: 30, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
16 9 0.07
18 3 0.02
19 3 0.02
20 9 0.07
21 98 0.75
22 8 0.06
ACGTcount: A:0.51, C:0.08, G:0.05, T:0.36
Consensus pattern (21 bp):
AAAAGTTATCAAAATTATATC
Found at i:1393839 original size:19 final size:19
Alignment explanation
Indices: 1393811--1393847 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1393801 TCCAAAACTT
1393811 TTTTAAAAATTGAATAAAA
1 TTTTAAAAATTGAATAAAA
* *
1393830 TTTTATAAATTGATTAAA
1 TTTTAAAAATTGAATAAA
1393848 TAAGATGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TTTTAAAAATTGAATAAAA
Found at i:1394340 original size:11 final size:12
Alignment explanation
Indices: 1394318--1394381 Score: 56
Period size: 11 Copynumber: 6.1 Consensus size: 12
1394308 AGATTATTAT
*
1394318 TATAAAAGATAA
1 TATAAAATATAA
1394330 T-TAAAATATAA
1 TATAAAATATAA
1394341 TAT-AAA-ATAA
1 TATAAAATATAA
1394351 -A-AAAAT-T-A
1 TATAAAATATAA
1394359 TAT-AAATATAA
1 TATAAAATATAA
1394370 TAT-AAATATAA
1 TATAAAATATAA
1394381 T
1 T
1394382 CTGATCAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
8 1 0.02
9 10 0.23
10 5 0.11
11 26 0.59
12 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
TATAAAATATAA
Found at i:1394353 original size:18 final size:19
Alignment explanation
Indices: 1394332--1394369 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1394322 AAAGATAATT
*
1394332 AAAATATAATATAAA-ATA
1 AAAAAATAATATAAATATA
*
1394350 AAAAAATTATATAAATATA
1 AAAAAATAATATAAATATA
1394369 A
1 A
1394370 TATAAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAATAATATAAATATA
Found at i:1398510 original size:15 final size:15
Alignment explanation
Indices: 1398488--1398538 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
1398478 AGCATCTTGA
1398488 ACATGAATTGCAGTT
1 ACATGAATTGCAGTT
* * *
1398503 AAATGAATAGCATTT
1 ACATGAATTGCAGTT
*
1398518 ACATGAACTGCAGTT
1 ACATGAATTGCAGTT
1398533 ACATGA
1 ACATGA
1398539 GCTGCAGTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (15 bp):
ACATGAATTGCAGTT
Found at i:1398543 original size:15 final size:15
Alignment explanation
Indices: 1398516--1398607 Score: 69
Period size: 15 Copynumber: 6.1 Consensus size: 15
1398506 TGAATAGCAT
*
1398516 TTACATGAACTGCAG
1 TTACATGAGCTGCAG
1398531 TTACATGAGCTGCAG
1 TTACATGAGCTGCAG
* * *
1398546 TTGCAGGA-CTCACAG
1 TTACATGAGCT-GCAG
* *
1398561 TTACATAATCTGCAG
1 TTACATGAGCTGCAG
* * * *
1398576 ATGCATAAGCTGCAT
1 TTACATGAGCTGCAG
*
1398591 TTACATGACCTGCAG
1 TTACATGAGCTGCAG
1398606 TT
1 TT
1398608 GCAGGACTCA
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
14 2 0.03
15 54 0.93
16 2 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (15 bp):
TTACATGAGCTGCAG
Found at i:1398562 original size:30 final size:30
Alignment explanation
Indices: 1398528--1398627 Score: 112
Period size: 30 Copynumber: 3.3 Consensus size: 30
1398518 ACATGAACTG
*
1398528 CAGTTACATGAGCTGCAGTTGCAGGACTCA
1 CAGTTACATGACCTGCAGTTGCAGGACTCA
* * * ** *
1398558 CAGTTACATAATCTGCAGATGCATAAGCT-G
1 CAGTTACATGACCTGCAGTTGCAGGA-CTCA
*
1398588 CATTTACATGACCTGCAGTTGCAGGACTCA
1 CAGTTACATGACCTGCAGTTGCAGGACTCA
1398618 CAGTTACATG
1 CAGTTACATG
1398628 GTCCGCAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
29 2 0.04
30 50 0.93
31 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (30 bp):
CAGTTACATGACCTGCAGTTGCAGGACTCA
Found at i:1398598 original size:60 final size:60
Alignment explanation
Indices: 1398525--1398652 Score: 193
Period size: 60 Copynumber: 2.1 Consensus size: 60
1398515 TTTACATGAA
* * *
1398525 CTGCAGTTACATGAGCTGCAGTTGCAGGACTCACAGTTACATAATCTGCAGATGCATAAG
1 CTGCAGTTACATGACCTGCAGTTGCAGGACTCACAGTTACATAATCCGCAAATGCATAAG
* ** *
1398585 CTGCATTTACATGACCTGCAGTTGCAGGACTCACAGTTACATGGTCCGCAAATGCATGAG
1 CTGCAGTTACATGACCTGCAGTTGCAGGACTCACAGTTACATAATCCGCAAATGCATAAG
1398645 CTGCAGTT
1 CTGCAGTT
1398653 GCATAAATTG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.26
Consensus pattern (60 bp):
CTGCAGTTACATGACCTGCAGTTGCAGGACTCACAGTTACATAATCCGCAAATGCATAAG
Found at i:1398655 original size:15 final size:15
Alignment explanation
Indices: 1398519--1398656 Score: 66
Period size: 15 Copynumber: 9.2 Consensus size: 15
1398509 ATAGCATTTA
* *
1398519 CATGAACTGCAGTTA
1 CATGAGCTGCAGTTG
1398534 CATGAGCTGCAGTTG
1 CATGAGCTGCAGTTG
* * *
1398549 CAGGA-CTCACAGTTA
1 CATGAGCT-GCAGTTG
* * *
1398564 CATAATCTGCAGATG
1 CATGAGCTGCAGTTG
* * *
1398579 CATAAGCTGCATTTA
1 CATGAGCTGCAGTTG
*
1398594 CATGACCTGCAGTTG
1 CATGAGCTGCAGTTG
* * *
1398609 CAGGA-CTCACAGTTA
1 CATGAGCT-GCAGTTG
* **
1398624 CATG-GTCCGCAAATG
1 CATGAG-CTGCAGTTG
1398639 CATGAGCTGCAGTTG
1 CATGAGCTGCAGTTG
1398654 CAT
1 CAT
1398657 AAATTGCAGT
Statistics
Matches: 87, Mismatches: 30, Indels: 12
0.67 0.23 0.09
Matches are distributed among these distances:
14 4 0.05
15 79 0.91
16 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (15 bp):
CATGAGCTGCAGTTG
Found at i:1404011 original size:42 final size:42
Alignment explanation
Indices: 1403965--1404046 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1403955 AAAGAAGATT
*
1403965 TTTTTTTACTTTCTTAATAATTAATTAAGAGAGAGAAAAATA
1 TTTTTTTACTTTCTTAATAATTAATTAAAAGAGAGAAAAATA
*
1404007 TTTTTTTACTTTCTTGATAATTAATTAAAAGAGAGAAAAA
1 TTTTTTTACTTTCTTAATAATTAATTAAAAGAGAGAAAAA
1404047 ATAGTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (42 bp):
TTTTTTTACTTTCTTAATAATTAATTAAAAGAGAGAAAAATA
Found at i:1404058 original size:42 final size:42
Alignment explanation
Indices: 1403970--1404058 Score: 117
Period size: 42 Copynumber: 2.1 Consensus size: 42
1403960 AGATTTTTTT
* * **
1403970 TTACTTTCTTAATAATTAATTAAGAGAGAGAAAAATATTTTT
1 TTACTTTCTTAATAATTAATTAAAAGAGAGAAAAATATGTAA
*
1404012 TTACTTTCTTGATAATTAATTAAAAGAGAGAAAAA-ATAGTAA
1 TTACTTTCTTAATAATTAATTAAAAGAGAGAAAAATAT-GTAA
1404054 TTACT
1 TTACT
1404059 AAAAAAAGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (42 bp):
TTACTTTCTTAATAATTAATTAAAAGAGAGAAAAATATGTAA
Found at i:1405068 original size:2 final size:2
Alignment explanation
Indices: 1405063--1405089 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1405053 AAGGATGCAA
1405063 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1405090 AGATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1405949 original size:2 final size:2
Alignment explanation
Indices: 1405942--1405970 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1405932 ACACAAGGAT
1405942 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1405971 TACAGACGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1406701 original size:75 final size:76
Alignment explanation
Indices: 1406578--1406727 Score: 257
Period size: 75 Copynumber: 2.0 Consensus size: 76
1406568 CACCAAACTC
*
1406578 AATGGCTTATTCAGGTTAACAAACACATGATCCTAATCACAAGTTCATATATAACAT-TAAAAAA
1 AATGGCTTATTCAGGTTAACAAACACATGATCCTAATCACAAGTTCATATATAACATGAAAAAAA
*
1406642 ATTTGTCACAA
66 AATTGTCACAA
* *
1406653 AATGGTTTATTCAGGTTAGCAAACACATGATCCTAATCACAAGTTCATATATAACATGAAAAAAA
1 AATGGCTTATTCAGGTTAACAAACACATGATCCTAATCACAAGTTCATATATAACATGAAAAAAA
1406718 AATTGTCACA
66 AATTGTCACA
1406728 TATTAAGCAT
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
75 55 0.79
76 15 0.21
ACGTcount: A:0.44, C:0.17, G:0.11, T:0.29
Consensus pattern (76 bp):
AATGGCTTATTCAGGTTAACAAACACATGATCCTAATCACAAGTTCATATATAACATGAAAAAAA
AATTGTCACAA
Found at i:1409490 original size:21 final size:21
Alignment explanation
Indices: 1409466--1409509 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1409456 ATTGTCAAAA
*
1409466 TATAAATATTATTAAAATTAT
1 TATAAATATTATCAAAATTAT
* *
1409487 TATAAATGTTATCAAAGTTAT
1 TATAAATATTATCAAAATTAT
1409508 TA
1 TA
1409510 CAAAAAGTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (21 bp):
TATAAATATTATCAAAATTAT
Found at i:1409725 original size:24 final size:24
Alignment explanation
Indices: 1409697--1409744 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
1409687 TTTTTGACCA
1409697 ATTAAAT-TAATTTTATACTAATTC
1 ATTAAATATAATTTTATA-TAATTC
1409721 ATTAAATAAATAATTTTATATAAT
1 ATTAAAT--ATAATTTTATATAAT
1409745 ATATCGAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 7 0.33
26 4 0.19
27 10 0.48
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
ATTAAATATAATTTTATATAATTC
Found at i:1409834 original size:15 final size:15
Alignment explanation
Indices: 1409811--1409858 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1409801 AAAATTTTTT
1409811 AATTATAATTTTTAAA
1 AATT-TAATTTTTAAA
* *
1409827 AATTTAATTATAAAA
1 AATTTAATTTTTAAA
*
1409842 AATATAATATTTTAAA
1 AATTTAAT-TTTTAAA
1409858 A
1 A
1409859 TTATCATTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAATTTTTAAA
Found at i:1412381 original size:51 final size:51
Alignment explanation
Indices: 1412283--1412382 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
1412273 GAGTGAAGTA
* *
1412283 ATAAATAATGAAGAAGAACATCTTCTGGATAAGACACCTTCGACTGATATC
1 ATAAATAACGAAGAAGAACATCTTCTGGATAAGACACATTCGACTGATATC
* * * *
1412334 ATAAATAACGAAGAGGAACATTTTGTGGATGAGACACATTCTG-CTGATA
1 ATAAATAACGAAGAAGAACATCTTCTGGATAAGACACATTC-GACTGATA
1412383 CTGCTGAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 41 0.98
52 1 0.02
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (51 bp):
ATAAATAACGAAGAAGAACATCTTCTGGATAAGACACATTCGACTGATATC
Found at i:1415706 original size:16 final size:18
Alignment explanation
Indices: 1415666--1415710 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1415656 TATATATGAA
*
1415666 TTATTAATATATTAAAAT
1 TTATAAATATATTAAAAT
*
1415684 TTATAAATATA-TAATAT
1 TTATAAATATATTAAAAT
1415701 TT-TAAATATA
1 TTATAAATATA
1415711 ATATTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.32
17 7 0.28
18 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTATAAATATATTAAAAT
Found at i:1416778 original size:18 final size:16
Alignment explanation
Indices: 1416736--1416778 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
1416726 TTTTAAAAAA
1416736 TTATAATATTTATTTT
1 TTATAATATTTATTTT
1416752 TATATTAATATTTATATATT
1 T-TA-TAATATTTAT-T-TT
1416772 TTATAAT
1 TTATAAT
1416779 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 2 0.09
18 14 0.61
19 3 0.13
20 3 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATAATATTTATTTT
Found at i:1417061 original size:23 final size:23
Alignment explanation
Indices: 1417022--1417065 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1417012 AAATTATAAA
*
1417022 TATTAAAATTTTAATTTTAAATT
1 TATTAAAATTATAATTTTAAATT
1417045 TATTAAAATTCAT-ATTTTAAA
1 TATTAAAATT-ATAATTTTAAA
1417066 AAAATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTAAAATTATAATTTTAAATT
Found at i:1418710 original size:21 final size:20
Alignment explanation
Indices: 1418678--1418716 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1418668 CTTAAATCTC
1418678 AATCTGTATAATATTTTTTTT
1 AATCTGTATAAT-TTTTTTTT
1418699 AATCT-TATTAATTTTTTT
1 AATCTGTA-TAATTTTTTT
1418717 GTACCGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
AATCTGTATAATTTTTTTTT
Found at i:1420866 original size:2 final size:2
Alignment explanation
Indices: 1420854--1420883 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
1420844 ATGTAAGTTC
1420854 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT A
1420884 GCAGTTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1422745 original size:4 final size:4
Alignment explanation
Indices: 1422736--1422767 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1422726 TTTTCCATTG
*
1422736 AGAA AGAA AGAA AGAA GGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
1422768 TCAATTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:1422758 original size:16 final size:16
Alignment explanation
Indices: 1422737--1422767 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1422727 TTTCCATTGA
1422737 GAAAGAAAGAAAGAAG
1 GAAAGAAAGAAAGAAG
1422753 GAAAGAAAGAAAGAA
1 GAAAGAAAGAAAGAA
1422768 TCAATTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
GAAAGAAAGAAAGAAG
Found at i:1438899 original size:12 final size:12
Alignment explanation
Indices: 1438884--1438908 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1438874 TTTTTTTTTA
1438884 ATTTATATATAT
1 ATTTATATATAT
1438896 ATTTATATATAT
1 ATTTATATATAT
1438908 A
1 A
1438909 ATCAAGGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTATATATAT
Found at i:1441368 original size:2 final size:2
Alignment explanation
Indices: 1441361--1441394 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1441351 CTTAGCTTCA
1441361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1441395 TTGGGAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1443773 original size:30 final size:32
Alignment explanation
Indices: 1443730--1443811 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 32
1443720 ATATTTTTTT
* *
1443730 TATTTTAA-ATATAAAATATCAAT-ATCATTA
1 TATTATAATATATAAAATATCAATAATAATTA
* *
1443760 -ATTATAATATATAAAACATTAATAATAATTA
1 TATTATAATATATAAAATATCAATAATAATTA
*
1443791 TTATTATATTATAATAAAATA
1 -TATTATAATAT-ATAAAATA
1443812 ATAAATAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
29 6 0.15
30 13 0.32
31 6 0.15
33 9 0.22
34 7 0.17
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (32 bp):
TATTATAATATATAAAATATCAATAATAATTA
Found at i:1443952 original size:30 final size:31
Alignment explanation
Indices: 1443896--1443955 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
1443886 ATTCAGTTTG
* *
1443896 TTTAATAATCAAACTTTTAAAATTTTGTTCA
1 TTTAATAATCAAACCTATAAAATTTTGTTCA
*
1443927 TTTAATAATC-AACCTATAGAATTTTGTTC
1 TTTAATAATCAAACCTATAAAATTTTGTTC
1443956 TAATAAACGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 16 0.62
31 10 0.38
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.47
Consensus pattern (31 bp):
TTTAATAATCAAACCTATAAAATTTTGTTCA
Found at i:1445988 original size:14 final size:14
Alignment explanation
Indices: 1445969--1445995 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1445959 TATTAAGAAT
1445969 TATTTTATTAATTA
1 TATTTTATTAATTA
1445983 TATTTTATTAATT
1 TATTTTATTAATT
1445996 TTTAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTATTAATTA
Found at i:1446053 original size:30 final size:29
Alignment explanation
Indices: 1445973--1446054 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 29
1445963 AAGAATTATT
1445973 TTATTAATTATATTTTATTAATTTTTAAAA
1 TTATT-ATTATATTTTATTAATTTTTAAAA
* * *
1446003 TTATTATAATAATTTAATTAATTTTATTAAA
1 TTATTATTAT-ATTTTATTAATTTT-TAAAA
1446034 -TATTATTACTATTTTATTAAT
1 TTATTATTA-TATTTTATTAAT
1446055 AAGTGTCTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 4 0.09
30 35 0.80
31 5 0.11
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (29 bp):
TTATTATTATATTTTATTAATTTTTAAAA
Found at i:1446317 original size:16 final size:16
Alignment explanation
Indices: 1446296--1446347 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1446286 AATTATTTTA
*
1446296 ATTTAATAAATGTAAT
1 ATTTAATAAATATAAT
*
1446312 ATTTAAAAAATATAA-
1 ATTTAATAAATATAAT
*
1446327 ATTT-TTAAA-ATAAT
1 ATTTAATAAATATAAT
1446341 ATTTAAT
1 ATTTAAT
1446348 TGAGATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
13 4 0.14
14 7 0.24
15 5 0.17
16 13 0.45
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTTAATAAATATAAT
Found at i:1446770 original size:2 final size:2
Alignment explanation
Indices: 1446763--1446796 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1446753 TCTCCTATTT
1446763 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
1446797 AAATTTCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1446967 original size:18 final size:19
Alignment explanation
Indices: 1446933--1446968 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1446923 AAAAAATTTG
*
1446933 AATAATAATATTTAATAAA
1 AATAATAATATTAAATAAA
1446952 AATAAT-ATATTAAATAA
1 AATAATAATATTAAATAA
1446969 TATTTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAATAATATTAAATAAA
Found at i:1451650 original size:20 final size:20
Alignment explanation
Indices: 1451613--1451649 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1451603 ATTATTATTT
*
1451613 TTTTATTTTTTTAATTTTGA
1 TTTTAATTTTTTAATTTTGA
1451633 TTTTAATTTTTT-ATTTT
1 TTTTAATTTTTTAATTTT
1451650 TTTAATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (20 bp):
TTTTAATTTTTTAATTTTGA
Found at i:1453322 original size:3 final size:3
Alignment explanation
Indices: 1453314--1453346 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1453304 TGTTTTCATA
1453314 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1453347 GTTATAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1455909 original size:2 final size:2
Alignment explanation
Indices: 1455902--1455930 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1455892 GTTGAGAAGA
1455902 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1455931 CTGGAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1457617 original size:25 final size:24
Alignment explanation
Indices: 1457546--1457617 Score: 67
Period size: 25 Copynumber: 3.0 Consensus size: 24
1457536 ATACATGATG
*
1457546 TAAATATAATATCAA-AAATAATTA
1 TAAATATAATAT-AATAAATAAATA
* *
1457570 -AAATATAGTATAATAAAAAAAATA
1 TAAATATAATATAAT-AAATAAATA
*
1457594 TAAATATAATATGAATATATAAAT
1 TAAATATAATAT-AATAAATAAAT
1457618 TTATCAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
22 2 0.05
23 10 0.26
24 7 0.18
25 16 0.42
26 3 0.08
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (24 bp):
TAAATATAATATAATAAATAAATA
Found at i:1457940 original size:18 final size:19
Alignment explanation
Indices: 1457896--1457943 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
1457886 TATTATATGA
1457896 AAAAATAATATGAATACGAT
1 AAAAAT-ATATGAATACGAT
*
1457916 AAAAATATATGAATATG-T
1 AAAAATATATGAATACGAT
*
1457934 CAAAATATAT
1 AAAAATATAT
1457944 ATAATTCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 10 0.38
20 6 0.23
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (19 bp):
AAAAATATATGAATACGAT
Found at i:1457945 original size:20 final size:20
Alignment explanation
Indices: 1457897--1457945 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1457887 ATTATATGAA
1457897 AAAATA-ATATGAATACGAT
1 AAAATATATATGAATACGAT
*
1457916 AAAA-ATATATGAATATG-T
1 AAAATATATATGAATACGAT
1457934 CAAAATATATAT
1 -AAAATATATAT
1457946 AATTCTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 18 0.69
20 6 0.23
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (20 bp):
AAAATATATATGAATACGAT
Found at i:1459716 original size:20 final size:22
Alignment explanation
Indices: 1459673--1459722 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1459663 AAATATGATT
*
1459673 TAATTTTTATATCTTATCAAAA
1 TAATTTTTATATCATATCAAAA
1459695 TAATTTTTATA-CATAT-AAAA
1 TAATTTTTATATCATATCAAAA
1459715 T-ATTTTTA
1 TAATTTTTA
1459723 ATATTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 7 0.26
20 5 0.19
21 4 0.15
22 11 0.41
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATTTTTATATCATATCAAAA
Found at i:1459727 original size:9 final size:10
Alignment explanation
Indices: 1459713--1459762 Score: 54
Period size: 9 Copynumber: 5.4 Consensus size: 10
1459703 ATACATATAA
1459713 AATATT-TTT
1 AATATTATTT
1459722 AATATTATTT
1 AATATTATTT
*
1459732 AATAATATTT
1 AATATTATTT
*
1459742 -ATATAATTT
1 AATATTATTT
1459751 AAT-TTA-TT
1 AATATTATTT
1459759 AATA
1 AATA
1459763 ATAAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 5 0.15
9 15 0.44
10 14 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
AATATTATTT
Found at i:1459735 original size:19 final size:19
Alignment explanation
Indices: 1459713--1459762 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 19
1459703 ATACATATAA
*
1459713 AATATTTTTAATATTATTT
1 AATATTTTTAATATAATTT
*
1459732 AATAATATTT-ATATAATTT
1 AAT-ATTTTTAATATAATTT
*
1459751 AAT-TTATTAATA
1 AATATTTTTAATA
1459763 ATAAAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
17 3 0.12
18 3 0.12
19 14 0.56
20 5 0.20
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AATATTTTTAATATAATTT
Found at i:1459748 original size:24 final size:22
Alignment explanation
Indices: 1459713--1459762 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
1459703 ATACATATAA
1459713 AATATTTTTAATATT-ATTTAAT
1 AATATTTTTAAT-TTAATTTAAT
*
1459735 AATATTTATATAATTTAATTTATT
1 AATATTT-T-TAATTTAATTTAAT
1459759 AATA
1 AATA
1459763 ATAAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.29
23 3 0.12
24 14 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
AATATTTTTAATTTAATTTAAT
Found at i:1461586 original size:29 final size:29
Alignment explanation
Indices: 1461545--1461629 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 29
1461535 TTTTGAAAAT
* *
1461545 TATAAGATATTAATTTATTAATAAGTAAA
1 TATAAAATTTTAATTTATTAATAAGTAAA
* *
1461574 TATAAAATTTTAAAATTT-TTAA-AAATATA
1 TATAAAATTTT--AATTTATTAATAAGTAAA
*
1461603 TA-AAAATAATTTTATTTATTAATAAGT
1 TATAAAAT--TTTAATTTATTAATAAGT
1461630 GATATTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
28 9 0.20
29 20 0.45
30 10 0.23
31 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (29 bp):
TATAAAATTTTAATTTATTAATAAGTAAA
Found at i:1461675 original size:23 final size:22
Alignment explanation
Indices: 1461642--1461685 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
1461632 TATTTTAAAA
1461642 TTTATTAATAATAT-ATAAATT
1 TTTATTAATAATATGATAAATT
*
1461663 TTTATATAGATAATGTGATAAAT
1 TTTAT-TA-ATAATATGATAAAT
1461686 ATAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 6 0.32
24 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTATTAATAATATGATAAATT
Found at i:1462483 original size:26 final size:27
Alignment explanation
Indices: 1462452--1462519 Score: 84
Period size: 26 Copynumber: 2.6 Consensus size: 27
1462442 TGGTGGATTT
1462452 AATTAATTTATTTTATTTTAAT-TAAA
1 AATTAATTTATTTTATTTTAATATAAA
* * *
1462478 AATTAATTTAATTAATTTTAATATTAA
1 AATTAATTTATTTTATTTTAATATAAA
* *
1462505 AATTGATTGATTTTA
1 AATTAATTTATTTTA
1462520 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (27 bp):
AATTAATTTATTTTATTTTAATATAAA
Found at i:1462486 original size:22 final size:22
Alignment explanation
Indices: 1462456--1462532 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 22
1462446 GGATTTAATT
*
1462456 AATTTATTTTATTTTAATTAAA
1 AATTAATTTTATTTTAATTAAA
*
1462478 AATTAATTTAATTAATTTTAATATTAA
1 AATTAA-TT--TT-ATTTTAAT-TAAA
* *
1462505 AATTGA-TTGATTTTAAATTAAA
1 AATTAATTTTATTTT-AATTAAA
1462527 AATTAA
1 AATTAA
1462533 AATAATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
22 18 0.42
23 6 0.14
25 3 0.07
26 8 0.19
27 8 0.19
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
AATTAATTTTATTTTAATTAAA
Found at i:1462552 original size:48 final size:48
Alignment explanation
Indices: 1462466--1462560 Score: 138
Period size: 48 Copynumber: 2.0 Consensus size: 48
1462456 AATTTATTTT
** *
1462466 ATTTTAATTAAAAATTAATTTAATTAATTTTAATATTAAAATTGATTG
1 ATTTTAATTAAAAATTAAAATAATTAATATTAATATTAAAATTGATTG
*
1462514 ATTTTAAATTAAAAATTAAAATAATTAA-ATTGATATTAAAATTGATT
1 ATTTT-AATTAAAAATTAAAATAATTAATATTAATATTAAAATTGATT
1462561 AATCCGGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 22 0.52
49 20 0.48
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (48 bp):
ATTTTAATTAAAAATTAAAATAATTAATATTAATATTAAAATTGATTG
Found at i:1462683 original size:23 final size:23
Alignment explanation
Indices: 1462657--1462725 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
1462647 TTATTTTAAT
*
1462657 TGAGTTTTTAATTTAAGTTTATA
1 TGAGTTTTTAATTTAAATTTATA
** *
1462680 TGAGTTTTTTGTTTAAATTTAAA
1 TGAGTTTTTAATTTAAATTTATA
* *
1462703 TG-GGTTTAAATTTAAATTTATA
1 TGAGTTTTTAATTTAAATTTATA
1462725 T
1 T
1462726 TTTATTAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 16 0.43
23 21 0.57
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (23 bp):
TGAGTTTTTAATTTAAATTTATA
Found at i:1463126 original size:30 final size:30
Alignment explanation
Indices: 1463006--1463119 Score: 89
Period size: 28 Copynumber: 3.8 Consensus size: 30
1462996 ACGCCTAAAC
*
1463006 AAAATTTACTATAAA-A-ATAAAATTTTAA-T
1 AAAA-TTA-TATAAATATATAAAATATTAATT
* *
1463035 AAAATT-TATGAA-ATATAAATTATTAATATAT
1 AAAATTATATAAATATATAAAATATT-A-AT-T
*
1463066 CAAAATTATATAAATTTATAAAATATTAATT
1 -AAAATTATATAAATATATAAAATATTAATT
1463097 AAAATTAT-T-AATATATAAAATAT
1 AAAATTATATAAATATATAAAATAT
1463120 ATTAATTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
26 6 0.09
27 8 0.11
28 16 0.23
29 6 0.09
30 8 0.11
31 2 0.03
32 8 0.11
33 6 0.09
34 10 0.14
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAATTATATAAATATATAAAATATTAATT
Found at i:1463669 original size:15 final size:15
Alignment explanation
Indices: 1463651--1463697 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 15
1463641 AAAAAGCAAT
*
1463651 TAAAATATATATGAA
1 TAAAATATATATAAA
1463666 T-AAAT-TATATAAA
1 TAAAATATATATAAA
*
1463679 TATAAATATATATATA
1 TA-AAATATATATAAA
1463695 TAA
1 TAA
1463698 TTTATATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 8 0.30
14 4 0.15
15 6 0.22
16 9 0.33
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
TAAAATATATATAAA
Found at i:1463724 original size:29 final size:29
Alignment explanation
Indices: 1463653--1463713 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
1463643 AAAGCAATTA
1463653 AAATATATATGA-ATAAATTATATAAATAT
1 AAATATATAT-ATATAAATTATATAAATAT
*
1463682 AAATATATATATATAATTTATAT-AATAT
1 AAATATATATATATAAATTATATAAATAT
1463710 AAAT
1 AAAT
1463714 TATTAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (29 bp):
AAATATATATATATAAATTATATAAATAT
Found at i:1463765 original size:27 final size:27
Alignment explanation
Indices: 1463708--1463774 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 27
1463698 TTTATATAAT
* * * *
1463708 ATAAATTATTAATATATTACAATTTTT
1 ATAAATAAATAATATATTACAATTATA
* *
1463735 ATAAATAAATAATATTTTACTATTATA
1 ATAAATAAATAATATATTACAATTATA
1463762 ATAAA-AATATAAT
1 ATAAATAA-ATAAT
1463775 GTAAATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 2 0.06
27 31 0.94
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
ATAAATAAATAATATATTACAATTATA
Found at i:1470397 original size:27 final size:29
Alignment explanation
Indices: 1470367--1470436 Score: 72
Period size: 30 Copynumber: 2.3 Consensus size: 29
1470357 TGTTGTTGCT
*
1470367 GCTGCTGCTGCTGTAG-AG-GTGGCTGTG
1 GCTGCTGCTGCTGAAGAAGAGTGGCTGTG
*
1470394 GCTGAGGCTGCTGTTGAAGAAGATGTGGCTGTG
1 GCT---GCTGCTGCTGAAGAAGA-GTGGCTGTG
1470427 GCTGCTGCTG
1 GCTGCTGCTG
1470437 TGGCTGTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 3 0.09
30 18 0.51
31 2 0.06
33 12 0.34
ACGTcount: A:0.11, C:0.17, G:0.43, T:0.29
Consensus pattern (29 bp):
GCTGCTGCTGCTGAAGAAGAGTGGCTGTG
Found at i:1470404 original size:33 final size:33
Alignment explanation
Indices: 1470367--1470430 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1470357 TGTTGTTGCT
** *
1470367 GCTGCTGCTGCTGTAGAGGTGGCTGTGGCTGAG
1 GCTGCTGCTGAAGAAGAGGTGGCTGTGGCTGAG
* *
1470400 GCTGCTGTTGAAGAAGATGTGGCTGTGGCTG
1 GCTGCTGCTGAAGAAGAGGTGGCTGTGGCTG
1470431 CTGCTGTGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.12, C:0.16, G:0.44, T:0.28
Consensus pattern (33 bp):
GCTGCTGCTGAAGAAGAGGTGGCTGTGGCTGAG
Found at i:1472043 original size:4 final size:4
Alignment explanation
Indices: 1472034--1472059 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1472024 ATTCTATCAA
1472034 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
1472060 GCACACGCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:1472092 original size:2 final size:2
Alignment explanation
Indices: 1472087--1472132 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1472077 CGCACGCGCG
1472087 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1472129 CA CA
1 CA CA
1472133 TATGTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1476550 original size:28 final size:29
Alignment explanation
Indices: 1476519--1476574 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1476509 GCATCATTAT
* *
1476519 AAATTGTTTAAT-TATCATTTAAATAAAA
1 AAATTATTTAATATATAATTTAAATAAAA
*
1476547 AAATTATTTAATATATAATTTTAATAAA
1 AAATTATTTAATATATAATTTAAATAAA
1476575 TTTCAAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (29 bp):
AAATTATTTAATATATAATTTAAATAAAA
Found at i:1476712 original size:22 final size:22
Alignment explanation
Indices: 1476669--1476712 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1476659 AGCAAAAGGC
* *
1476669 TTGCTCAACTAATTAGATAAGT
1 TTGCTCAACGAATTAGAGAAGT
* *
1476691 TTGCTCAAGGAATTTGAGAAGT
1 TTGCTCAACGAATTAGAGAAGT
1476713 AAAGGTATAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (22 bp):
TTGCTCAACGAATTAGAGAAGT
Found at i:1477363 original size:28 final size:26
Alignment explanation
Indices: 1477332--1477410 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 26
1477322 TTAAATTTAA
* *
1477332 TTTTATAAATATTAATTATTTTTAATAT
1 TTTTATAAATA-AAATTAATTTTAA-AT
1477360 TTTTA-ATAATAAAATTAATTTTAAAT
1 TTTTATA-AATAAAATTAATTTTAAAT
*
1477386 TTTAATAAATTAAATATTAATTTTA
1 TTTTATAAA-TAAA-ATTAATTTTA
1477411 CTCACAGTTG
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
26 8 0.18
27 17 0.39
28 19 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTATAAATAAAATTAATTTTAAAT
Found at i:1477367 original size:25 final size:24
Alignment explanation
Indices: 1477345--1477410 Score: 60
Period size: 27 Copynumber: 2.5 Consensus size: 24
1477335 TATAAATATT
*
1477345 AATTATTTTTAATATTTTTAATAATAA
1 AATTAATTTTAA-A-TTTTAAT-ATAA
1477372 AATTAATTTTAAATTTTAATAAATTAA
1 AATTAATTTTAAATTTTAAT--A-TAA
1477399 ATATTAATTTTA
1 A-ATTAATTTTA
1477411 CTCACAGTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
25 7 0.20
26 3 0.09
27 15 0.43
28 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
AATTAATTTTAAATTTTAATATAA
Found at i:1477407 original size:21 final size:22
Alignment explanation
Indices: 1477366--1477410 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1477356 ATATTTTTAA
*
1477366 TAATAAAATTAATTTTAAATTT
1 TAATAAAATTAATATTAAATTT
1477388 TAAT-AAATTAAATATT-AATTT
1 TAATAAAATT-AATATTAAATTT
1477409 TA
1 TA
1477411 CTCACAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATAAAATTAATATTAAATTT
Found at i:1477781 original size:17 final size:19
Alignment explanation
Indices: 1477744--1477781 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
1477734 ATATATACTT
1477744 TTAAATATAATTATATCAA
1 TTAAATATAATTATATCAA
*
1477763 TTAAAT-TAA-TATATTAA
1 TTAAATATAATTATATCAA
1477780 TT
1 TT
1477782 TTTATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 3 0.17
19 6 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAATATAATTATATCAA
Found at i:1480795 original size:20 final size:20
Alignment explanation
Indices: 1480741--1480801 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
1480731 AAAATTAAGT
* *
1480741 ATTATTTTTA-ATAATTTAA
1 ATTATATTTATATAATTAAA
* *
1480760 GTTA-ATTTAATTTAATTAAA
1 ATTATATTT-ATATAATTAAA
*
1480780 ATTATATTTATATAATAAAA
1 ATTATATTTATATAATTAAA
1480800 AT
1 AT
1480802 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
18 3 0.09
19 4 0.12
20 21 0.66
21 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTATATTTATATAATTAAA
Found at i:1480857 original size:24 final size:24
Alignment explanation
Indices: 1480828--1480875 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
1480818 AATTATAAAT
1480828 ATATATTATTAATATAAAAATTAATG
1 ATAT-TTATTAATA-AAAAATTAATG
* *
1480854 ATATTTTTTAATAATAAATTAA
1 ATATTTATTAATAAAAAATTAA
1480876 GTTTACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 8 0.40
26 4 0.20
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATTTATTAATAAAAAATTAATG
Found at i:1482168 original size:30 final size:30
Alignment explanation
Indices: 1482132--1482192 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
1482122 GGCGATAGAT
1482132 AGTAAGAAATTAGATATCTAATATTATTTG
1 AGTAAGAAATTAGATATCTAATATTATTTG
1482162 AGTAAGAAATTAGATATCTAATATTATTTG
1 AGTAAGAAATTAGATATCTAATATTATTTG
1482192 A
1 A
1482193 TTTAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.13, T:0.39
Consensus pattern (30 bp):
AGTAAGAAATTAGATATCTAATATTATTTG
Found at i:1482692 original size:22 final size:23
Alignment explanation
Indices: 1482646--1482692 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1482636 GAAAATTCTA
*
1482646 TTTGCAAAACAATGTTTTTAGTT
1 TTTGCAAAACAATATTTTTAGTT
*
1482669 TTTGCAAAATAA-ATTTTTA-TT
1 TTTGCAAAACAATATTTTTAGTT
1482690 TTT
1 TTT
1482693 ATTTGTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.32, C:0.06, G:0.09, T:0.53
Consensus pattern (23 bp):
TTTGCAAAACAATATTTTTAGTT
Found at i:1483677 original size:20 final size:20
Alignment explanation
Indices: 1483654--1483701 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
1483644 ATTAATAACT
1483654 AAAATATTACTA-ATTATTAA
1 AAAATATTACTATATT-TTAA
1483674 AAAATATT--TATATTTTAA
1 AAAATATTACTATATTTTAA
*
1483692 TAAATATTAC
1 AAAATATTAC
1483702 GTGTTAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 8 0.33
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATATTACTATATTTTAA
Found at i:1485817 original size:2 final size:2
Alignment explanation
Indices: 1485810--1485839 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1485800 TCAATAATGG
*
1485810 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1485840 TAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1487190 original size:38 final size:38
Alignment explanation
Indices: 1487147--1487245 Score: 153
Period size: 38 Copynumber: 2.6 Consensus size: 38
1487137 CAGCCACCGA
* * * *
1487147 CCAATTCCAAATTGAATTCTCTAGTCGTCAGCTGCCGG
1 CCAATTTCAAATTGAATTCTCTAGCCGTCAGCCGCCAG
*
1487185 TCAATTTCAAATTGAATTCTCTAGCCGTCAGCCGCCAG
1 CCAATTTCAAATTGAATTCTCTAGCCGTCAGCCGCCAG
1487223 CCAATTTCAAATTGAATTCTCTA
1 CCAATTTCAAATTGAATTCTCTA
1487246 ACTGTCAACT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.31
Consensus pattern (38 bp):
CCAATTTCAAATTGAATTCTCTAGCCGTCAGCCGCCAG
Found at i:1490865 original size:38 final size:38
Alignment explanation
Indices: 1490822--1490919 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 38
1490812 ATCCACCGGC
* * * *
1490822 CAATTTCAAATTGAATTTTTTAGTCGTCAGCCGCC-GAT
1 CAATTTCAAATTGAATTCTCTAGCCGTCAACCGCCAG-T
* *
1490860 CAATTTCAAATTGAATTCTCTAGCCGTTAACCGTCAGT
1 CAATTTCAAATTGAATTCTCTAGCCGTCAACCGCCAGT
1490898 CAATTTCAAATTGAATTCTCTA
1 CAATTTCAAATTGAATTCTCTA
1490920 ACTGTCAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
38 52 0.98
39 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (38 bp):
CAATTTCAAATTGAATTCTCTAGCCGTCAACCGCCAGT
Found at i:1491376 original size:3 final size:3
Alignment explanation
Indices: 1491368--1491397 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1491358 GCTTATTCAA
1491368 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1491398 GACGCATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1493817 original size:2 final size:2
Alignment explanation
Indices: 1493810--1493842 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1493800 TGGTACCCTT
1493810 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1493843 TTCAATGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1494963 original size:21 final size:22
Alignment explanation
Indices: 1494938--1494990 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 22
1494928 TAAAATATAA
1494938 TATAAATATATATTTAAAT-TT
1 TATAAATATATATTTAAATATT
1494959 TATAAA-A-ATA-TTAAATATT
1 TATAAATATATATTTAAATATT
1494978 T-TAAATATA-ATTT
1 TATAAATATATATTT
1494991 CAGCATAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
18 10 0.36
19 8 0.29
20 4 0.14
21 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TATAAATATATATTTAAATATT
Found at i:1500790 original size:17 final size:17
Alignment explanation
Indices: 1500768--1500802 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1500758 ACGTTAAAAT
* *
1500768 AATACCAATAGAAAAGA
1 AATACCAAGAAAAAAGA
1500785 AATACCAAGAAAAAAGA
1 AATACCAAGAAAAAAGA
1500802 A
1 A
1500803 GCAATGAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.11, G:0.11, T:0.09
Consensus pattern (17 bp):
AATACCAAGAAAAAAGA
Found at i:1502705 original size:26 final size:27
Alignment explanation
Indices: 1502676--1502726 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1502666 AATTATTATT
*
1502676 TTAAATAAAAATATAAT-GAATTATAA
1 TTAAATAAAAATAAAATCGAATTATAA
* *
1502702 TTAATTAAATATAAAATCGAATTAT
1 TTAAATAAAAATAAAATCGAATTAT
1502727 GATATAGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
TTAAATAAAAATAAAATCGAATTATAA
Found at i:1504358 original size:18 final size:19
Alignment explanation
Indices: 1504335--1504372 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1504325 TAATATCTTG
1504335 TATTTATAAATT-TTAATA
1 TATTTATAAATTATTAATA
*
1504353 TATTTATACATTATTAATA
1 TATTTATAAATTATTAATA
1504372 T
1 T
1504373 TATTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (19 bp):
TATTTATAAATTATTAATA
Found at i:1506519 original size:2 final size:2
Alignment explanation
Indices: 1506512--1506546 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1506502 TGGTCGCTTA
1506512 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1506547 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1507441 original size:11 final size:10
Alignment explanation
Indices: 1507419--1507452 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
1507409 TATATATATA
*
1507419 TCTTCTTTTT
1 TCTTTTTTTT
1507429 TCTTTTATTTT
1 TCTTTT-TTTT
1507440 TCTTTTTTTT
1 TCTTTTTTTT
1507450 TCT
1 TCT
1507453 ATGTGATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:1507491 original size:21 final size:23
Alignment explanation
Indices: 1507450--1507492 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1507440 TCTTTTTTTT
1507450 TCTATGTGATAATGAGTGCAATA
1 TCTATGTGATAATGAGTGCAATA
*
1507473 TCTA-GTGATAAT-TGTGCAAT
1 TCTATGTGATAATGAGTGCAAT
1507493 CGAATCAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.37
Consensus pattern (23 bp):
TCTATGTGATAATGAGTGCAATA
Found at i:1511551 original size:2 final size:2
Alignment explanation
Indices: 1511544--1511579 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1511534 ATAAACACTA
1511544 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1511580 TCTCTTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1517620 original size:20 final size:22
Alignment explanation
Indices: 1517580--1517645 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 22
1517570 TATGTATTCG
* *
1517580 ATAAAAATATATTTA-AAATTT
1 ATAAAATTATATTTATATATTT
1517601 ATAAAATT-T-TTTATATATTT
1 ATAAAATTATATTTATATATTT
* *
1517621 AAAAAATTATATTTATATAATT
1 ATAAAATTATATTTATATATTT
1517643 ATA
1 ATA
1517646 TTTAAATATA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 4 0.11
20 13 0.35
21 8 0.22
22 12 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATTATATTTATATATTT
Found at i:1517631 original size:14 final size:14
Alignment explanation
Indices: 1517614--1517651 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1517604 AAATTTTTTA
1517614 TATATTTAAAAAAT
1 TATATTTAAAAAAT
* *
1517628 TATATTTATATAAT
1 TATATTTAAAAAAT
1517642 TATATTTAAA
1 TATATTTAAA
1517652 TATATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATTTAAAAAAT
Found at i:1517783 original size:15 final size:17
Alignment explanation
Indices: 1517745--1517784 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
1517735 TATTTTTAAA
1517745 ATTAATA-AAATAATAT
1 ATTAATATAAATAATAT
1517761 ATTAAATATAAATAAT-T
1 ATT-AATATAAATAATAT
1517778 -TTAATAT
1 ATTAATAT
1517785 TTATAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 5 0.23
16 5 0.23
17 5 0.23
18 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTAATATAAATAATAT
Found at i:1519194 original size:22 final size:24
Alignment explanation
Indices: 1519150--1519203 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 24
1519140 TCCTGCTTAA
* *
1519150 AAATAAATATAGTATATAAATA-T
1 AAATAAATTTAATATATAAATATT
*
1519173 AAATAAATTTAAT-TATATATATT
1 AAATAAATTTAATATATAAATATT
1519196 AAA-AAATT
1 AAATAAATT
1519204 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATAAATTTAATATATAAATATT
Found at i:1519918 original size:30 final size:30
Alignment explanation
Indices: 1519900--1519976 Score: 145
Period size: 30 Copynumber: 2.6 Consensus size: 30
1519890 AAATAAACAC
1519900 TTAACTTTTAATTTATATTCAAATACATCT
1 TTAACTTTTAATTTATATTCAAATACATCT
1519930 TTAACTTTTAATTTATATTCAAATACATCT
1 TTAACTTTTAATTTATATTCAAATACATCT
*
1519960 TTAACTTTAAATTTATA
1 TTAACTTTTAATTTATA
1519977 CGTAAATGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.51
Consensus pattern (30 bp):
TTAACTTTTAATTTATATTCAAATACATCT
Found at i:1521435 original size:2 final size:2
Alignment explanation
Indices: 1521430--1521454 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1521420 ATACATATAT
1521430 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1521455 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1521459 original size:2 final size:2
Alignment explanation
Indices: 1521454--1521480 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1521444 ACACACACAC
1521454 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1521481 ACTCTTTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1531435 original size:2 final size:2
Alignment explanation
Indices: 1531428--1531465 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1531418 CACATCTTAA
*
1531428 CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1531466 TTTCCTTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:1533747 original size:25 final size:26
Alignment explanation
Indices: 1533719--1533772 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
1533709 AAGTTTTTAA
1533719 AATAAATAAAAATAAATTT-ATTT-TT
1 AATAAA-AAAAATAAATTTAATTTATT
* *
1533744 AATAAAAAAATTTAATTTAATTTATT
1 AATAAAAAAAATAAATTTAATTTATT
1533770 AAT
1 AAT
1533773 GATAGTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 10 0.40
26 5 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
AATAAAAAAAATAAATTTAATTTATT
Found at i:1533802 original size:11 final size:11
Alignment explanation
Indices: 1533778--1533816 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1533768 TTAATGATAG
*
1533778 TATATAAATTA
1 TATATTAATTA
1533789 TATATT-ATTAA
1 TATATTAATT-A
1533800 TATATTAATTA
1 TATATTAATTA
1533811 TATATT
1 TATATT
1533817 TTTTTACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 3 0.12
11 19 0.76
12 3 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TATATTAATTA
Found at i:1535858 original size:31 final size:31
Alignment explanation
Indices: 1535820--1535887 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
1535810 AATAATATTT
1535820 TAATATTTTTAA-AATTA-TAAAAAATATTAAG
1 TAATA-TTTTAAGAATTATTAAAAAATA-TAAG
*
1535851 TAATA-TTTAAGGTATTATTAAAAAATATAAG
1 TAATATTTTAA-GAATTATTAAAAAATATAAG
1535882 TAATAT
1 TAATAT
1535888 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 5 0.16
31 18 0.56
32 9 0.28
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (31 bp):
TAATATTTTAAGAATTATTAAAAAATATAAG
Found at i:1536716 original size:23 final size:25
Alignment explanation
Indices: 1536690--1536742 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1536680 GACTCTCCAA
* *
1536690 TTATT-AATTTTA-TTTTTTTATAT
1 TTATTCAATTTAACTTTTGTTATAT
*
1536713 TTATTCAATTTAACTTTTGTTATCT
1 TTATTCAATTTAACTTTTGTTATAT
1536738 TTATT
1 TTATT
1536743 TTATAATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (25 bp):
TTATTCAATTTAACTTTTGTTATAT
Found at i:1540561 original size:2 final size:2
Alignment explanation
Indices: 1540549--1540588 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1540539 ATTGAGTTAA
* *
1540549 AT AT AT CT AT AT AT AT AT AT AT AT AG AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1540589 GCGAAGGAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1541602 original size:20 final size:19
Alignment explanation
Indices: 1541569--1541627 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 19
1541559 ATAATTATAG
1541569 TTAAAAT-T-TTATATATT
1 TTAAAATATATTATATATT
*
1541586 TTAATAATTTATTATATAAATT
1 TTAA-AATATATTATAT--ATT
1541608 TTAAAATATATATATATATT
1 TTAAAATATAT-TATATATT
1541628 ATATGATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
17 4 0.11
18 3 0.09
19 1 0.03
20 9 0.26
21 6 0.17
22 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTAAAATATATTATATATT
Found at i:1541608 original size:22 final size:22
Alignment explanation
Indices: 1541578--1541625 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1541568 GTTAAAATTT
* *
1541578 TATATATTTTAATAATTTAT-TA
1 TATAAATTTTAA-AATATATATA
1541600 TATAAATTTTAAAATATATATA
1 TATAAATTTTAAAATATATATA
1541622 TATA
1 TATA
1541626 TTATATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TATAAATTTTAAAATATATATA
Found at i:1542077 original size:2 final size:2
Alignment explanation
Indices: 1542070--1542113 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
1542060 TTATTTAAAA
* *
1542070 AT AT AT AT TT AT AT GT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1542111 AT A
1 AT A
1542114 AAATCTTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1551830 original size:15 final size:15
Alignment explanation
Indices: 1551798--1551832 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1551788 ATATTTAAAA
*
1551798 TAATTATATTAATAT
1 TAATTATATAAATAT
*
1551813 TAATTATATAAATTT
1 TAATTATATAAATAT
1551828 TAATT
1 TAATT
1551833 TATTTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAATTATATAAATAT
Found at i:1551849 original size:28 final size:28
Alignment explanation
Indices: 1551798--1551871 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 28
1551788 ATATTTAAAA
*
1551798 TAATTATATTA-ATATTAATTATATAAATTT
1 TAATTAT-TTATATA-TAAATAT-TAAATTT
*
1551828 TAATTTATTTATATATAAATATTATATTT
1 TAA-TTATTTATATATAAATATTAAATTT
* *
1551857 TTATTATTTTTATAT
1 TAATTATTTATATAT
1551872 TATATATACA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 11 0.29
29 8 0.21
30 12 0.32
31 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
TAATTATTTATATATAAATATTAAATTT
Found at i:1552390 original size:27 final size:29
Alignment explanation
Indices: 1552352--1552410 Score: 104
Period size: 27 Copynumber: 2.1 Consensus size: 29
1552342 AAAAATTATA
1552352 AATTAATTTAATCAAAT-TT-TTTAAATT
1 AATTAATTTAATCAAATCTTATTTAAATT
1552379 AATTAATTTAATCAAATCTTATTTAAATT
1 AATTAATTTAATCAAATCTTATTTAAATT
1552408 AAT
1 AAT
1552411 CAAAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 17 0.57
28 2 0.07
29 11 0.37
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (29 bp):
AATTAATTTAATCAAATCTTATTTAAATT
Found at i:1553691 original size:20 final size:20
Alignment explanation
Indices: 1553666--1553716 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1553656 AGTCCAATAA
*
1553666 AAAAATTTAATTGAATTGAT
1 AAAAATTTAATTAAATTGAT
*
1553686 AAAAATTAAATTAAATTGAT
1 AAAAATTTAATTAAATTGAT
1553706 AAAAA-TTAATT
1 AAAAATTTAATT
1553717 TTATTATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (20 bp):
AAAAATTTAATTAAATTGAT
Found at i:1553744 original size:29 final size:26
Alignment explanation
Indices: 1553705--1553762 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 26
1553695 ATTAAATTGA
** *
1553705 TAAAAATTAATTTTATTATTTATTTTT
1 TAAAAATTAATTGAATT-TTTAATTTT
1553732 TAAAAATAATAATTGAATTTTTAATTTT
1 TAAAAAT--TAATTGAATTTTTAATTTT
1553760 TAA
1 TAA
1553763 TTTTATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 11 0.42
29 8 0.31
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (26 bp):
TAAAAATTAATTGAATTTTTAATTTT
Found at i:1553828 original size:18 final size:18
Alignment explanation
Indices: 1553785--1553829 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
1553775 AGTTATATCA
1553785 TTAA-ATTAAATATATAT
1 TTAATATTAAATATATAT
* *
1553802 TT-TTATTAAATATTTAT
1 TTAATATTAAATATATAT
1553819 TTAATATTAAA
1 TTAATATTAAA
1553830 AATTATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATATTAAATATATAT
Found at i:1553845 original size:21 final size:18
Alignment explanation
Indices: 1553805--1553847 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
1553795 TATATATTTT
*
1553805 TATTAAATATTTATTTAA
1 TATTAAAAATTTATTTAA
1553823 TATTAAAAATTATATATTCAA
1 TATTAAAAATT-TAT-TT-AA
1553844 TATT
1 TATT
1553848 CTATTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 3 0.14
20 2 0.10
21 6 0.29
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAAAAATTTATTTAA
Found at i:1565166 original size:13 final size:13
Alignment explanation
Indices: 1565098--1565166 Score: 50
Period size: 13 Copynumber: 5.2 Consensus size: 13
1565088 TAAATTAATT
* *
1565098 ATTAAATTTAATA
1 ATTAATTTTATTA
*
1565111 ATTTATTTTTATTA
1 A-TTAATTTTATTA
* * *
1565125 TTTAAATATATTA
1 ATTAATTTTATTA
1565138 TATTAATATTTA-TA
1 -ATTAAT-TTTATTA
1565152 ATTAATTTTATTA
1 ATTAATTTTATTA
1565165 AT
1 AT
1565167 AAATAATAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
12 4 0.10
13 20 0.48
14 15 0.36
15 3 0.07
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (13 bp):
ATTAATTTTATTA
Found at i:1565182 original size:42 final size:42
Alignment explanation
Indices: 1565097--1565186 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
1565087 TTAAATTAAT
* *
1565097 TATTAA-ATTTAATAATTTATTTTTATTATTTAAATATATTA
1 TATTAATATTTAATAATTTAATTTTATTATATAAATATATTA
1565138 TATTAATATTT-ATAA-TTAATTTTATTA-ATAAATAATAATTTA
1 TATTAATATTTAATAATTTAATTTTATTATATAAAT-AT-A-TTA
1565180 TATTAAT
1 TATTAAT
1565187 TAAATAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
39 5 0.12
40 13 0.30
41 11 0.26
42 14 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (42 bp):
TATTAATATTTAATAATTTAATTTTATTATATAAATATATTA
Found at i:1565203 original size:20 final size:19
Alignment explanation
Indices: 1565159--1565203 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
1565149 ATAATTAATT
* *
1565159 TTATTAATAAATAATAATT
1 TTATTAATAAATAAAAATA
1565178 TATATTAATTAAATAAAAATA
1 T-TATTAA-TAAATAAAAATA
1565199 TTATT
1 TTATT
1565204 TTTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 10 0.45
21 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATTAATAAATAAAAATA
Done.