Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 76 of 144
Found at i:16804418 original size:89 final size:88
Alignment explanation
Indices: 16804288--16804606 Score: 340
Period size: 89 Copynumber: 3.6 Consensus size: 88
16804278 ATTTGAGGTC
* * * *
16804288 AAAATGTAA-TTTATGGAAAATTTAGGGGGTGAAATGTAATTTTTAGAAAGGTTTGAGGGTTAAA
1 AAAATATAATTTTA-GGAAAATTTAAGGGTTAAAATGTAA-TTTTAGAAA-GTTTGAGGG-TAAA
16804352 ATATAATTTTAGGAAAGTTTAGGGG-T
62 ATATAATTTTAGGAAAGTTTAGGGGTT
* * * * *
16804378 CAAATATAATTTT-GGAAAGTTTAAGGGTTAAAATGTAATTTTAGGAAGTTTGGGAGGCAAAATA
1 AAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTTAGAAAGTTTGAG-GGTAAAATA
16804442 TAATTTTAGGAAAGTTTAGGGGTT
65 TAATTTTAGGAAAGTTTAGGGGTT
* * * * * * *
16804466 AAAATGTAATTTTAAGTAAGTTTAAGGGTTAAAATGCAATTTTGGAAAAGTTTGAGGGTAAAATG
1 AAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTTAG-AAAGTTTGAGGGTAAAATA
16804531 TAATTTTA-GAAATGTTTAGGGGTT
65 TAATTTTAGGAAA-GTTTAGGGGTT
* * * * * *
16804555 AAAACAAAATTTTAGAAAAATTTAGGGGTCAAAATGTAATTTTGGAAGAGTT
1 AAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTTAGAA-AGTT
16804607 CAAAGGCTCT
Statistics
Matches: 193, Mismatches: 29, Indels: 15
0.81 0.12 0.06
Matches are distributed among these distances:
87 34 0.18
88 28 0.15
89 113 0.59
90 15 0.08
91 3 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (88 bp):
AAAATATAATTTTAGGAAAATTTAAGGGTTAAAATGTAATTTTAGAAAGTTTGAGGGTAAAATAT
AATTTTAGGAAAGTTTAGGGGTT
Found at i:16804474 original size:59 final size:59
Alignment explanation
Indices: 16804288--16804602 Score: 283
Period size: 59 Copynumber: 5.3 Consensus size: 59
16804278 ATTTGAGGTC
* * *
16804288 AAAATGTAA-TTTATGGAAAATTTAGGGGGT-GAAATGTAATTTTTA-GAAAGGTTT-GAGGGTT
1 AAAATGTAATTTTA-GG-AAGTTTA-GGGGTCAAAATATAA-TTTTAGGAAA-GTTTAG-GGGTT
* *
16804349 AAAATATAATTTTAGGAAAGTTTAGGGGTC-AAATATAATTTT-GGAAAGTTTAAGGGTT
1 AAAATGTAATTTTAGG-AAGTTTAGGGGTCAAAATATAATTTTAGGAAAGTTTAGGGGTT
*
16804407 AAAATGTAATTTTAGGAAGTTT-GGGAGGCAAAATATAATTTTAGGAAAGTTTAGGGGTT
1 AAAATGTAATTTTAGGAAGTTTAGGG-GTCAAAATATAATTTTAGGAAAGTTTAGGGGTT
* * * **
16804466 AAAATGTAATTTTAAGTAAGTTTAAGGGTTAAAATGCAATTTT-GGAAAAGTTT-GAGGG-T
1 AAAATGTAATTTT-AGGAAGTTTAGGGGTCAAAATATAATTTTAGG-AAAGTTTAG-GGGTT
* * * * * * *
16804525 AAAATGTAATTTTAGAAATGTTTAGGGGTTAAAACAAAATTTTAGAAAAATTTAGGGGTC
1 AAAATGTAATTTTAGGAA-GTTTAGGGGTCAAAATATAATTTTAGGAAAGTTTAGGGGTT
16804585 AAAATGTAATTTT-GGAAG
1 AAAATGTAATTTTAGGAAG
16804603 AGTTCAAAGG
Statistics
Matches: 217, Mismatches: 22, Indels: 33
0.80 0.08 0.12
Matches are distributed among these distances:
56 3 0.01
57 8 0.04
58 41 0.19
59 85 0.39
60 57 0.26
61 19 0.09
62 4 0.02
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (59 bp):
AAAATGTAATTTTAGGAAGTTTAGGGGTCAAAATATAATTTTAGGAAAGTTTAGGGGTT
Found at i:16809552 original size:48 final size:48
Alignment explanation
Indices: 16809499--16809598 Score: 200
Period size: 48 Copynumber: 2.1 Consensus size: 48
16809489 TAAAAGTTAA
16809499 ATTACATTTTATTTTTTCTATTAAAAATAAGTAAATTAGTCTTTATAC
1 ATTACATTTTATTTTTTCTATTAAAAATAAGTAAATTAGTCTTTATAC
16809547 ATTACATTTTATTTTTTCTATTAAAAATAAGTAAATTAGTCTTTATAC
1 ATTACATTTTATTTTTTCTATTAAAAATAAGTAAATTAGTCTTTATAC
16809595 ATTA
1 ATTA
16809599 GATTAAAGAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (48 bp):
ATTACATTTTATTTTTTCTATTAAAAATAAGTAAATTAGTCTTTATAC
Found at i:16810065 original size:182 final size:182
Alignment explanation
Indices: 16809728--16810092 Score: 518
Period size: 182 Copynumber: 2.0 Consensus size: 182
16809718 TGACTAGACC
* * *
16809728 TGTTCATGGGTCGGGCTACTCGTCCAGGCATGAAAGTTCGCCCGAAATTTGGGAGGGTTTGAGTA
1 TGTTCATGGGTCGGGCTACTCGTCCAGGCATAAAAGTTCACCCGAAATTTGGGAGGATTTGAGTA
* * ** **
16809793 AAAATATTAAGCCTGAAAAGTGGGCTTGGGCAAAAATTTGGCTTGTTTAAAATATGGGTCAAACT
66 AAAATATTAAGCCTGAAAAATGGGCTTGGACAAAAATTAAGCTTGTTTAAAATATGGACCAAACT
* * * *
16809858 TAGGCTTGAACATTCAAGTCTCGAGCTTGGCCCGGCCTAACCCGTTTTTAAG
131 TAGGCTTAAACATTCAAGGCTCGAGCTTGACCCGGCCTAACCCATTTTTAAG
* *
16809910 TGTTCATGGGTCGGGCTACTCG-CCAGGCCTAAAAGTTTACCCGAAATTTGGGAGGATTTGAGTA
1 TGTTCATGGGTCGGGCTACTCGTCCAGGCATAAAAGTTCACCCGAAATTTGGGAGGATTTGAGTA
* *
16809974 AAAATATTAATCCTGAAAAATGGGCTTGGACAAAAAATTAAGCTTGTTTAAAATATGGACCGAAC
66 AAAATATTAAGCCTGAAAAATGGGCTTGGAC-AAAAATTAAGCTTGTTTAAAATATGGACCAAAC
* * *
16810039 -TCGGACTTAAACTTTCAAGGCTCGAGCTTGACCCGGCCTGACCCATTTTTAAG
130 TTAGG-CTTAAACATTCAAGGCTCGAGCTTGACCCGGCCTAACCCATTTTTAAG
16810092 T
1 T
16810093 TTATAATACT
Statistics
Matches: 161, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
181 68 0.42
182 93 0.58
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (182 bp):
TGTTCATGGGTCGGGCTACTCGTCCAGGCATAAAAGTTCACCCGAAATTTGGGAGGATTTGAGTA
AAAATATTAAGCCTGAAAAATGGGCTTGGACAAAAATTAAGCTTGTTTAAAATATGGACCAAACT
TAGGCTTAAACATTCAAGGCTCGAGCTTGACCCGGCCTAACCCATTTTTAAG
Found at i:16823924 original size:19 final size:19
Alignment explanation
Indices: 16823896--16823937 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
16823886 ACCCGACCCG
* *
16823896 TTGACTATTGGTCATTGAC
1 TTGACCATTGATCATTGAC
*
16823915 TTGACCATTGATCGTTGAC
1 TTGACCATTGATCATTGAC
16823934 TTGA
1 TTGA
16823938 TCGTTGACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (19 bp):
TTGACCATTGATCATTGAC
Found at i:16823937 original size:12 final size:12
Alignment explanation
Indices: 16823922--16823947 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16823912 GACTTGACCA
16823922 TTGATCGTTGAC
1 TTGATCGTTGAC
16823934 TTGATCGTTGAC
1 TTGATCGTTGAC
16823946 TT
1 TT
16823948 TTTTGACCAA
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:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (12 bp):
TTGATCGTTGAC
Found at i:16847179 original size:25 final size:25
Alignment explanation
Indices: 16847127--16847180 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
16847117 TAGTACTTAT
**
16847127 AAATAAATTTCAAGTTTTTGCCAAA
1 AAATAAATTTCAAGTTTTTGAAAAA
16847152 AAATAAATTTCAAGTTTTT-AAAATA
1 AAATAAATTTCAAGTTTTTGAAAA-A
16847177 AAAT
1 AAAT
16847181 GGAAAGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (25 bp):
AAATAAATTTCAAGTTTTTGAAAAA
Found at i:16849802 original size:19 final size:17
Alignment explanation
Indices: 16849778--16849812 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
16849768 TTTTATTGGA
16849778 TATTGTATAATTCTTGTTT
1 TATTGT-TAATT-TTGTTT
16849797 TATTGTTAATTTTGTT
1 TATTGTTAATTTTGTT
16849813 ACTATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 5 0.31
19 6 0.38
ACGTcount: A:0.20, C:0.03, G:0.11, T:0.66
Consensus pattern (17 bp):
TATTGTTAATTTTGTTT
Found at i:16849818 original size:18 final size:19
Alignment explanation
Indices: 16849778--16849818 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
16849768 TTTTATTGGA
*
16849778 TATTGTATAATTCTTGTTT
1 TATTGTATAATTCTTGTTC
16849797 TATTGT-TAATT-TTGTTAC
1 TATTGTATAATTCTTGTT-C
16849815 TATT
1 TATT
16849819 TTAGAAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.22, C:0.05, G:0.10, T:0.63
Consensus pattern (19 bp):
TATTGTATAATTCTTGTTC
Found at i:16853781 original size:22 final size:21
Alignment explanation
Indices: 16853756--16853803 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
16853746 ATAATCCGTT
*
16853756 TCATCTCAATTCTATTTTCATA
1 TCATCTC-ATTCTAGTTTCATA
* *
16853778 TCATTCTCATTTTAGTTTCATT
1 TCA-TCTCATTCTAGTTTCATA
16853800 TCAT
1 TCAT
16853804 AACCAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (21 bp):
TCATCTCATTCTAGTTTCATA
Found at i:16861074 original size:22 final size:21
Alignment explanation
Indices: 16861049--16861096 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
16861039 ATAATCCGTT
*
16861049 TCATCTCAATTCTATTTTCATA
1 TCATCTC-ATTCTAGTTTCATA
* *
16861071 TCATTCTCATTTTAGTTTCATT
1 TCA-TCTCATTCTAGTTTCATA
16861093 TCAT
1 TCAT
16861097 AACCAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
21 1 0.05
22 17 0.77
23 4 0.18
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.54
Consensus pattern (21 bp):
TCATCTCATTCTAGTTTCATA
Found at i:16866987 original size:18 final size:18
Alignment explanation
Indices: 16866964--16867000 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16866954 GAAGAAAGCC
16866964 TAACATAAGCCATTTTCA
1 TAACATAAGCCATTTTCA
16866982 TAACATAAGCCATTTTCA
1 TAACATAAGCCATTTTCA
16867000 T
1 T
16867001 CCTTTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (18 bp):
TAACATAAGCCATTTTCA
Found at i:16869772 original size:2 final size:2
Alignment explanation
Indices: 16869762--16869814 Score: 54
Period size: 2 Copynumber: 26.0 Consensus size: 2
16869752 ATATAAATTT
* * *
16869762 TA TA CA TA TA TA TA TA TA TA TA TA TT TA TA AA CTGA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A TA TA TA TA
16869805 TA TA TA TA TA
1 TA TA TA TA TA
16869815 CATGTGTTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 1 0.02
2 39 0.93
3 1 0.02
4 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:16875159 original size:28 final size:28
Alignment explanation
Indices: 16875123--16875192 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
16875113 GCTCCTTTAT
* *
16875123 GAGCTAGAAACAGATTAACGCTCTACCC
1 GAGCAAGAAACAGAATAACGCTCTACCC
* *
16875151 GAGCAAGAAACAGAATATCGTTCTACCC
1 GAGCAAGAAACAGAATAACGCTCTACCC
*
16875179 GAGCCAGAAACAGA
1 GAGCAAGAAACAGA
16875193 GTACTCCTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (28 bp):
GAGCAAGAAACAGAATAACGCTCTACCC
Found at i:16875471 original size:25 final size:25
Alignment explanation
Indices: 16875411--16875527 Score: 126
Period size: 25 Copynumber: 4.6 Consensus size: 25
16875401 CAGAGTTTAA
* * * *
16875411 CTCTTACGAGCCCAGAAAAAATATCA
1 CTCTTACAAG-CCAGACAGAATATCG
* * *
16875437 CTCTTACAAGCTAGTCAGAACATCG
1 CTCTTACAAGCCAGACAGAATATCG
16875462 CTCTTACAAGCCAGACAGAATATCG
1 CTCTTACAAGCCAGACAGAATATCG
* *
16875487 CTCTTACGAGCCAGACAGAATATTG
1 CTCTTACAAGCCAGACAGAATATCG
* *
16875512 CTCTTACGAGGCAGAC
1 CTCTTACAAGCCAGAC
16875528 CTTAGTAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
25 69 0.88
26 9 0.12
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.21
Consensus pattern (25 bp):
CTCTTACAAGCCAGACAGAATATCG
Found at i:16880200 original size:17 final size:17
Alignment explanation
Indices: 16880161--16880207 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
16880151 GACAATGTAG
*
16880161 ATGCACTGACAATAAAA
1 ATGCAGTGACAATAAAA
16880178 ATGCAGTGACAATAAAA
1 ATGCAGTGACAATAAAA
*
16880195 ATGCAGGGACAAT
1 ATGCAGTGACAAT
16880208 TATACTATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (17 bp):
ATGCAGTGACAATAAAA
Found at i:16880819 original size:12 final size:12
Alignment explanation
Indices: 16880802--16880826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16880792 TTTGCCTTGA
16880802 CATCTATTTCTT
1 CATCTATTTCTT
16880814 CATCTATTTCTT
1 CATCTATTTCTT
16880826 C
1 C
16880827 CTTCACACGA
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:0.16, C:0.28, G:0.00, T:0.56
Consensus pattern (12 bp):
CATCTATTTCTT
Found at i:16882798 original size:21 final size:22
Alignment explanation
Indices: 16882774--16882818 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
16882764 ACCCTTTTGA
*
16882774 AATTGAACCAAACCCAA-ACCT
1 AATTAAACCAAACCCAATACCT
16882795 AATTAAACCAAACCCAATACCT
1 AATTAAACCAAACCCAATACCT
16882817 AA
1 AA
16882819 ACCATGTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.51, C:0.31, G:0.02, T:0.16
Consensus pattern (22 bp):
AATTAAACCAAACCCAATACCT
Found at i:16882903 original size:27 final size:27
Alignment explanation
Indices: 16882852--16882903 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
16882842 CCCGAACCCA
** *
16882852 TTGACCGTTGACTGTTTATCATTGACT
1 TTGACCGTTGACCATTGATCATTGACT
*
16882879 TTGACCGTTGACCATTGATCGTTGA
1 TTGACCGTTGACCATTGATCATTGA
16882904 TTGTTGACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (27 bp):
TTGACCGTTGACCATTGATCATTGACT
Found at i:16884145 original size:6 final size:6
Alignment explanation
Indices: 16884125--16884154 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
16884115 AATTGTAGAC
16884125 TTTATA TTATATA TTTATA TTTATA TTTAT
1 TTTATA TT-TATA TTTATA TTTATA TTTAT
16884155 GAATGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:16894033 original size:29 final size:29
Alignment explanation
Indices: 16893914--16894073 Score: 101
Period size: 29 Copynumber: 5.3 Consensus size: 29
16893904 TGTAAATAAG
16893914 TATGCAT-AG-TTTAGTTATATATAATAGTTA
1 TATGCATGAGCTTTA-TTATATATAATA--TA
* * *
16893944 TATGCATGAGTCTTGTGTTATTATATTATATG
1 TATGCATGAG-CTT-TATTA-TATATAATATA
* * **
16893976 TAGGCGT-AAATTTATTATATAGATAATATA
1 TATGCATGAGCTTTATTATAT--ATAATATA
** * *
16894006 TATGTGTGAGCTTTATTTTATGTAATATA
1 TATGCATGAGCTTTATTATATATAATATA
*
16894035 TATGCATGGGCTTTATTATATATAGTATATA
1 TATGCATGAGCTTTATTATATATA--ATATA
16894066 TATGCATG
1 TATGCATG
16894074 GGTTTTGGTG
Statistics
Matches: 99, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
28 3 0.03
29 30 0.30
30 20 0.20
31 26 0.26
32 6 0.06
33 5 0.05
34 9 0.09
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (29 bp):
TATGCATGAGCTTTATTATATATAATATA
Found at i:16894065 original size:31 final size:32
Alignment explanation
Indices: 16893986--16894075 Score: 109
Period size: 31 Copynumber: 3.0 Consensus size: 32
16893976 TAGGCGTAAA
* ** *
16893986 TTTATTATATAGA-TAATATATATGTGTGAGC
1 TTTATTATATATAGTAATATATATGCATGGGC
16894017 TTTATT-T-TAT-GTAATATATATGCATGGGC
1 TTTATTATATATAGTAATATATATGCATGGGC
16894046 TTTATTATATATAGT-ATATATATGCATGGG
1 TTTATTATATATAGTAATATATATGCATGGG
16894076 TTTTGGTGTT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
29 23 0.45
30 2 0.04
31 24 0.47
32 2 0.04
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (32 bp):
TTTATTATATATAGTAATATATATGCATGGGC
Found at i:16912591 original size:51 final size:51
Alignment explanation
Indices: 16912526--16912753 Score: 368
Period size: 51 Copynumber: 4.5 Consensus size: 51
16912516 GAATCTATAA
16912526 ACTCACGATGACACTTAATCATCGAACC-TCTAATCCATACAGGATTCATTT
1 ACTCACGATGACACTTAATCATCGAACCAT-TAATCCATACAGGATTCATTT
* * *
16912577 ACTCACAATGACACTTAGTCATCGGACCATTAATCCATACAGGATTCATTT
1 ACTCACGATGACACTTAATCATCGAACCATTAATCCATACAGGATTCATTT
* *
16912628 ACTCACGATGACACTTAATCATCGGACCATTAATCCATATAGGATTCATTT
1 ACTCACGATGACACTTAATCATCGAACCATTAATCCATACAGGATTCATTT
*
16912679 ACTCACGATGAAACTTAATCATCGAACCATTAATCCATACAGGATTCATTT
1 ACTCACGATGACACTTAATCATCGAACCATTAATCCATACAGGATTCATTT
* *
16912730 ACTCACGATGACATTTAGTCATCG
1 ACTCACGATGACACTTAATCATCG
16912754 GACCCCTTTC
Statistics
Matches: 164, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
51 163 0.99
52 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (51 bp):
ACTCACGATGACACTTAATCATCGAACCATTAATCCATACAGGATTCATTT
Found at i:16912752 original size:153 final size:155
Alignment explanation
Indices: 16912472--16912757 Score: 429
Period size: 153 Copynumber: 1.9 Consensus size: 155
16912462 TTTCTTTTAA
* **
16912472 TACTCACGATGACATATAATCATCGGACTTGTCGTTCCATATAGGAATCTATAAACTCACGATGA
1 TACTCACGATGACATATAATCATCGGACATGTCAATCCATATAGGAATCTATAAACTCACGATGA
*
16912537 CACTTAATCATCGAACCTCTAATCCATACAGGATTCATTTACTCACAATGACACTTAGTCATCGG
66 AACTTAATCATCGAACCTCTAATCCATACAGGATTCATTTACTCACAATGACACTTAGTCATCGG
16912602 ACCATTAATCCATACAGGATTCATT
131 ACCATTAATCCATACAGGATTCATT
* **
16912627 TACTCACGATGACACT-TAATCATCGGACCAT-T-AATCCATATAGGATTC-ATTTACTCACGAT
1 TACTCACGATGACA-TATAATCATCGGA-CATGTCAATCCATATAGGAATCTATAAACTCACGAT
* *
16912688 GAAACTTAATCATCGAACCAT-TAATCCATACAGGATTCATTTACTCACGATGACATTTAGTCAT
64 GAAACTTAATCATCGAACC-TCTAATCCATACAGGATTCATTTACTCACAATGACACTTAGTCAT
16912752 CGGACC
128 CGGACC
16912758 CCTTTCGTTT
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
153 76 0.64
154 14 0.12
155 26 0.22
156 3 0.03
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (155 bp):
TACTCACGATGACATATAATCATCGGACATGTCAATCCATATAGGAATCTATAAACTCACGATGA
AACTTAATCATCGAACCTCTAATCCATACAGGATTCATTTACTCACAATGACACTTAGTCATCGG
ACCATTAATCCATACAGGATTCATT
Found at i:16919137 original size:21 final size:23
Alignment explanation
Indices: 16919099--16919153 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 23
16919089 CCTGCAACTT
16919099 CTACCGATACAAGCATAC-A-AA
1 CTACCGATACAAGCATACAACAA
*
16919120 CTACCGATAC-ATCTATACATACAA
1 CTACCGATACAAGC-ATACA-ACAA
16919144 CTACCGATAC
1 CTACCGATAC
16919154 TCACACTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.07
21 14 0.48
23 1 0.03
24 12 0.41
ACGTcount: A:0.42, C:0.31, G:0.07, T:0.20
Consensus pattern (23 bp):
CTACCGATACAAGCATACAACAA
Found at i:16923456 original size:17 final size:18
Alignment explanation
Indices: 16923436--16923483 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
16923426 ACTACAATGC
16923436 AAATGCGATGACAAAT-A
1 AAATGCGATGACAAATAA
* *
16923453 AAATGCAATGA-TAATAA
1 AAATGCGATGACAAATAA
*
16923470 AAATGTGATGACAA
1 AAATGCGATGACAA
16923484 CTACATTATA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.54, C:0.08, G:0.17, T:0.21
Consensus pattern (18 bp):
AAATGCGATGACAAATAA
Found at i:16930029 original size:18 final size:18
Alignment explanation
Indices: 16930008--16930054 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
16929998 TGCAGTCTGC
*
16930008 TGTGGCTGCATAC-GAGCA
1 TGTGACTGCAT-CTGAGCA
*
16930026 TGTGACTGCATCTGAGTA
1 TGTGACTGCATCTGAGCA
16930044 TGTGACTGCAT
1 TGTGACTGCAT
16930055 TTGATCGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 1 0.04
18 25 0.96
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (18 bp):
TGTGACTGCATCTGAGCA
Found at i:16937122 original size:51 final size:51
Alignment explanation
Indices: 16937060--16937295 Score: 384
Period size: 51 Copynumber: 4.6 Consensus size: 51
16937050 CTATAAACAA
*
16937060 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
16937111 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
16937162 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
*
16937213 AAAGGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
16937264 AAAAGTCTGATGTCTATA-TGTCTTCGTGAGTA
1 AAAGGTCCGATGACTA-AGTGTCATCGTGAGTA
16937296 TTAAATGAAA
Statistics
Matches: 173, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
51 172 0.99
52 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:16944402 original size:51 final size:51
Alignment explanation
Indices: 16944321--16944506 Score: 273
Period size: 51 Copynumber: 3.6 Consensus size: 51
16944311 CTATAAACGA
** *
16944321 AAAGGTCCGATGACTAAGTGTCATTGTGAGTAAATGGATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
*
16944372 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACAGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
** *
16944423 AAAGGTTTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
* * **
16944474 AAGGGTCCGATGAATTTGTGTCATCATGAGTAA
1 AAAGGTCCGATGACTAAGTGTCATCATGAGTAA
16944507 GAAATGCGAG
Statistics
Matches: 120, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 120 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCATGAGTAAATGAATCCTTTACGGATT
Found at i:16948792 original size:46 final size:43
Alignment explanation
Indices: 16948721--16948808 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 43
16948711 TATTGCTTCC
*
16948721 TCGGGTTTTCTTGGTGCCTTTGTTATGAGGGAAGCATGGTCAA
1 TCGGGTTTTCTTGGTACCTTTGTTATGAGGGAAGCATGGTCAA
16948764 TCGGGTTTATCTTGGTACCTATTTGTTATGAGGGAAGCATGGTCA
1 TCGGGTTT-TCTTGGTACC--TTTGTTATGAGGGAAGCATGGTCA
16948809 GACAGGTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
43 8 0.20
44 9 0.22
46 24 0.59
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.38
Consensus pattern (43 bp):
TCGGGTTTTCTTGGTACCTTTGTTATGAGGGAAGCATGGTCAA
Found at i:16948817 original size:46 final size:44
Alignment explanation
Indices: 16948724--16948818 Score: 131
Period size: 46 Copynumber: 2.1 Consensus size: 44
16948714 TGCTTCCTCG
* *
16948724 GGTTT-TCTTGGTGCCTTTGTTATGAGGGAAGCATGGTCAATCG
1 GGTTTATCTTGGTACCTTTGTTATGAGGGAAGCATGGTCAATCA
16948767 GGTTTATCTTGGTACCTATTTGTTATGAGGGAAGCATGGTCAGA-CA
1 GGTTTATCTTGGTACC--TTTGTTATGAGGGAAGCATGGTCA-ATCA
16948813 GGTTTA
1 GGTTTA
16948819 CTGTATTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
43 5 0.11
44 9 0.20
46 31 0.67
47 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.31, T:0.37
Consensus pattern (44 bp):
GGTTTATCTTGGTACCTTTGTTATGAGGGAAGCATGGTCAATCA
Found at i:16953387 original size:30 final size:30
Alignment explanation
Indices: 16953343--16953402 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16953333 ATGTGTAATC
*
16953343 ATATACACAAACTTTAATTTTG-TTCAATT
1 ATATACAAAAACTTTAATTTTGATTCAATT
16953372 ATATACATAAAACTTTAATTTTGATTCAATT
1 ATATACA-AAAACTTTAATTTTGATTCAATT
16953403 TTCCCGTATC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 7 0.25
30 14 0.50
31 7 0.25
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (30 bp):
ATATACAAAAACTTTAATTTTGATTCAATT
Found at i:16960989 original size:16 final size:14
Alignment explanation
Indices: 16960954--16960983 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16960944 TTATCATTTT
16960954 TATATTATAAAAAA
1 TATATTATAAAAAA
*
16960968 TATATTTTAAAAAA
1 TATATTATAAAAAA
16960982 TA
1 TA
16960984 AATATTCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATTATAAAAAA
Found at i:16962215 original size:2 final size:2
Alignment explanation
Indices: 16962208--16962240 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16962198 AAAACAAAAT
16962208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16962241 GAAATAATTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16966881 original size:52 final size:52
Alignment explanation
Indices: 16966786--16966890 Score: 131
Period size: 52 Copynumber: 2.0 Consensus size: 52
16966776 ATTAAATCTG
* * * **
16966786 AACAACATAATAATTAACTATTTAAAATTAAATAATTTGATAATACT-TTCTT
1 AACAACATAATAATTAACGAATTAAAATTAAATAAATAAATAATA-TGTTCTT
* *
16966838 AACATCATAATTATTAACGAATTAAAATTAAATAAATAAATAATATGTTCTT
1 AACAACATAATAATTAACGAATTAAAATTAAATAAATAAATAATATGTTCTT
16966890 A
1 A
16966891 CCATTTGTAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
51 1 0.02
52 44 0.98
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (52 bp):
AACAACATAATAATTAACGAATTAAAATTAAATAAATAAATAATATGTTCTT
Found at i:16967049 original size:21 final size:21
Alignment explanation
Indices: 16967011--16967055 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16967001 TTGGAATTGG
* *
16967011 GAATTTAGATTAAAAAATCGA
1 GAATTGAGAATAAAAAATCGA
*
16967032 GAATTGAGAATAACAAATCGA
1 GAATTGAGAATAAAAAATCGA
16967053 GAA
1 GAA
16967056 CAAGAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (21 bp):
GAATTGAGAATAAAAAATCGA
Found at i:16967732 original size:17 final size:17
Alignment explanation
Indices: 16967701--16967760 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
16967691 TTGAAAAGAT
16967701 TTTTTTTATAATTTTATAA
1 TTTTTTTAT--TTTTATAA
16967720 TTTTTTTATTTTTA-ATA
1 TTTTTTTATTTTTATA-A
*
16967737 TTTTATTATTCTATT-TAA
1 TTTTTTTATT-T-TTATAA
16967755 TTTTTT
1 TTTTTT
16967761 AAATTTAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 1 0.03
17 15 0.43
18 7 0.20
19 12 0.34
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTATTTTTATAA
Found at i:16967897 original size:14 final size:15
Alignment explanation
Indices: 16967870--16967904 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
16967860 GTTGTTTGCA
16967870 ATTTTTTATAAAATT
1 ATTTTTTATAAAATT
*
16967885 ATTTTTTA-CAAATT
1 ATTTTTTATAAAATT
16967899 ATTTTT
1 ATTTTT
16967905 AATGAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTTATAAAATT
Found at i:16968071 original size:2 final size:2
Alignment explanation
Indices: 16968064--16968090 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16968054 TAATTTAAAT
16968064 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16968091 GAAAGTAGAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16969582 original size:35 final size:35
Alignment explanation
Indices: 16969535--16969605 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
16969525 TTTATGTGTC
*
16969535 ATCTCAAAGTTAAAACAAATTTAGGGGCAAAAGTA
1 ATCTCAAAGTTAAAACAAATTTAGAGGCAAAAGTA
*
16969570 ATCTCAATGTTAAAACAAATTTAGAGGCAAAAGTA
1 ATCTCAAAGTTAAAACAAATTTAGAGGCAAAAGTA
16969605 A
1 A
16969606 ATATCATTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.24
Consensus pattern (35 bp):
ATCTCAAAGTTAAAACAAATTTAGAGGCAAAAGTA
Found at i:16971329 original size:13 final size:13
Alignment explanation
Indices: 16971311--16971335 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16971301 AAAAGCCCAA
16971311 TTCTTTTTTCTTC
1 TTCTTTTTTCTTC
16971324 TTCTTTTTTCTT
1 TTCTTTTTTCTT
16971336 TCCATCTGTT
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTCTTTTTTCTTC
Found at i:16972253 original size:8 final size:8
Alignment explanation
Indices: 16972237--16972266 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16972227 AAAAAAAAAG
16972237 AATCCTTA
1 AATCCTTA
*
16972245 AATCATTA
1 AATCCTTA
16972253 AATCCTTA
1 AATCCTTA
16972261 AATCCT
1 AATCCT
16972267 CATTGCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.40, C:0.23, G:0.00, T:0.37
Consensus pattern (8 bp):
AATCCTTA
Found at i:16972694 original size:19 final size:20
Alignment explanation
Indices: 16972652--16972695 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
16972642 GGGTGTATGG
*
16972652 TTTTAACTTTTATAATAATG
1 TTTTAACTTTTATAATAATA
16972672 TTTTAA-TTTTAT-ATAAATA
1 TTTTAACTTTTATAAT-AATA
16972691 TTTTA
1 TTTTA
16972696 TATTATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 6 0.27
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAACTTTTATAATAATA
Found at i:16973676 original size:11 final size:11
Alignment explanation
Indices: 16973660--16973684 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16973650 GTTTAATTTT
16973660 AATAATTATTA
1 AATAATTATTA
16973671 AATAATTATTA
1 AATAATTATTA
16973682 AAT
1 AAT
16973685 TGATAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATAATTATTA
Found at i:16974255 original size:19 final size:19
Alignment explanation
Indices: 16974227--16974275 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
16974217 TTACAAAAAA
16974227 CAAAAA-TCAAATAATTTT
1 CAAAAATTCAAATAATTTT
16974245 CAAAAATTCAAAATAATTTT
1 CAAAAATTC-AAATAATTTT
*
16974265 -TAAAATTCAAA
1 CAAAAATTCAAA
16974276 ATATTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 9 0.32
19 9 0.32
20 10 0.36
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (19 bp):
CAAAAATTCAAATAATTTT
Found at i:16974260 original size:20 final size:20
Alignment explanation
Indices: 16974227--16974278 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
16974217 TTACAAAAAA
16974227 CAAAAA-TC-AAATAATTTT
1 CAAAAATTCAAAATAATTTT
16974245 CAAAAATTCAAAATAATTTT
1 CAAAAATTCAAAATAATTTT
*
16974265 -TAAAATTCAAAATA
1 CAAAAATTCAAAATA
16974279 TTTATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 6 0.19
19 15 0.48
20 10 0.32
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
CAAAAATTCAAAATAATTTT
Found at i:16974288 original size:19 final size:19
Alignment explanation
Indices: 16974235--16974288 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
16974225 AACAAAAATC
16974235 AAATAATTTTCAAAAATTCA
1 AAATAATTTT-AAAAATTCA
*
16974255 AAATAATTTTTAAAATTCA
1 AAATAATTTTAAAAATTCA
16974274 AAAT-ATTTATAAAAA
1 AAATAATTT-TAAAAA
16974289 AATTCTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 4 0.13
19 17 0.55
20 10 0.32
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (19 bp):
AAATAATTTTAAAAATTCA
Found at i:16974301 original size:20 final size:21
Alignment explanation
Indices: 16974246--16974304 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 21
16974236 AATAATTTTC
16974246 AAAAATTCAAAATAATTT-T--
1 AAAAATTCAAAAT-ATTTATAA
*
16974265 TAAAATTCAAAATATTTATAA
1 AAAAATTCAAAATATTTATAA
*
16974286 AAAAATTCTAAA-ATTTATA
1 AAAAATTCAAAATATTTATA
16974305 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 4 0.12
19 13 0.38
20 7 0.21
21 10 0.29
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATTCAAAATATTTATAA
Found at i:16974320 original size:17 final size:18
Alignment explanation
Indices: 16974295--16974331 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16974285 AAAAAATTCT
16974295 AAAATT-TATATTTTTAAA
1 AAAATTATAT-TTTTTAAA
16974313 AAAATTATATTTTTTAAA
1 AAAATTATATTTTTTAAA
16974331 A
1 A
16974332 TCTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAATTATATTTTTTAAA
Found at i:16985494 original size:36 final size:37
Alignment explanation
Indices: 16985414--16985495 Score: 132
Period size: 36 Copynumber: 2.3 Consensus size: 37
16985404 TAGGTTAGGG
*
16985414 AAAGTAAAGGAAGTTGAGTATCTTTGCTATCTTTTAA
1 AAAGTAAAAGAAGTTGAGTATCTTTGCTATCTTTTAA
*
16985451 ATA-TAAAAGAAGTTGAGTATCTTTGCTATC-TTTAA
1 AAAGTAAAAGAAGTTGAGTATCTTTGCTATCTTTTAA
16985486 AAAGTAAAAG
1 AAAGTAAAAG
16985496 GATTAAATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
35 7 0.17
36 32 0.78
37 2 0.05
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.35
Consensus pattern (37 bp):
AAAGTAAAAGAAGTTGAGTATCTTTGCTATCTTTTAA
Found at i:16988981 original size:11 final size:11
Alignment explanation
Indices: 16988967--16989005 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
16988957 AAAAAGCATG
16988967 AAAAATGAAGA
1 AAAAATGAAGA
16988978 AAAAAT-AGAGA
1 AAAAATGA-AGA
16988989 AAAAATGAAGA
1 AAAAATGAAGA
16989000 AAAAAT
1 AAAAAT
16989006 AGATAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.04
11 24 0.92
12 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.10
Consensus pattern (11 bp):
AAAAATGAAGA
Found at i:16988982 original size:22 final size:22
Alignment explanation
Indices: 16988967--16989008 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
16988957 AAAAAGCATG
16988967 AAAAATGAAGAAAAAATAGAGA
1 AAAAATGAAGAAAAAATAGAGA
16988989 AAAAATGAAGAAAAAATAGA
1 AAAAATGAAGAAAAAATAGA
16989009 TAGAATCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (22 bp):
AAAAATGAAGAAAAAATAGAGA
Found at i:16991052 original size:52 final size:52
Alignment explanation
Indices: 16990957--16991337 Score: 489
Period size: 52 Copynumber: 7.3 Consensus size: 52
16990947 TTGATACACA
* * ** *
16990957 ATGACATAGAGTCATCGGACC-C-TCAATCCGTATTGGAAATCATATACTCACG
1 ATGACACATAGTCATCGGACCTCAT-AATCCGTAAAGG-ATTCATATACTCACG
* **
16991009 ATGACACATAGTCATCAGATTTCATAATCCGTAAAGGATTCATATACTCACG
1 ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACG
* *
16991061 ATGACACATAGTCATCGGACCTCATAATTCGTAAAGGATTTATATACTCACG
1 ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACG
* ** ** * *
16991113 ATAACACATAGTCATCAAACCTCATAATCTATAAATGATTTATATACTCACG
1 ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACG
* *
16991165 ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTTATATACTCATG
1 ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACG
*
16991217 ATGACACATAGTCATC-GAGCCTCATAATCCGTAAATGATTCATATACTCACG
1 ATGACACATAGTCATCGGA-CCTCATAATCCGTAAAGGATTCATATACTCACG
* * * *
16991269 ATGACACATAATCATTGGACCTCATAATCTGTAAAGGATTCATATACTCATG
1 ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACG
*
16991321 ATGACACATAATCATCG
1 ATGACACATAGTCATCG
16991338 AACTTATTTC
Statistics
Matches: 289, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
51 2 0.01
52 273 0.94
53 13 0.04
54 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.28
Consensus pattern (52 bp):
ATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACG
Found at i:16994362 original size:23 final size:23
Alignment explanation
Indices: 16994336--16994428 Score: 143
Period size: 23 Copynumber: 4.1 Consensus size: 23
16994326 TTTACAAATT
* **
16994336 AATCATATTAACTGCTAAGCATA
1 AATCACATTAACTTTTAAGCATA
*
16994359 AATCACATTAACTTTTAAGCGTA
1 AATCACATTAACTTTTAAGCATA
16994382 AATCACATTAACTTTTAAGCATA
1 AATCACATTAACTTTTAAGCATA
16994405 AATCACATTAACTTTTAA-CATA
1 AATCACATTAACTTTTAAGCATA
16994427 AA
1 AA
16994429 ACGAATTACT
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
22 6 0.09
23 59 0.91
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.33
Consensus pattern (23 bp):
AATCACATTAACTTTTAAGCATA
Found at i:16994815 original size:36 final size:36
Alignment explanation
Indices: 16994766--16994927 Score: 236
Period size: 36 Copynumber: 4.5 Consensus size: 36
16994756 ATATTCACTA
**
16994766 TCACATGAAATGAATAACATACCCACATATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTATTG
* * **
16994802 TCTCATGGCATGAATAACATGCTAACATATTTACTT-
1 TCACATGGCATGAATAACATACCCACATATTTA-TTG
16994838 TCACATGGCATGAATAACATACCCACATATTTATTG
1 TCACATGGCATGAATAACATACCCACATATTTATTG
* *
16994874 TCTCATGGCATGAATAACATACCCACATATTTACTG
1 TCACATGGCATGAATAACATACCCACATATTTATTG
16994910 TCACATGGCATGAATAAC
1 TCACATGGCATGAATAAC
16994928 GTATTCATAT
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
35 2 0.02
36 107 0.96
37 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (36 bp):
TCACATGGCATGAATAACATACCCACATATTTATTG
Found at i:16994873 original size:72 final size:72
Alignment explanation
Indices: 16994756--16994927 Score: 272
Period size: 72 Copynumber: 2.4 Consensus size: 72
16994746 TTAGCACAAT
* **
16994756 ATATTCACTATCACATGAAATGAATAACATACCCACATATTTATTGTCTCATGGCATGAATAACA
1 ATATTTACTATCACATGGCATGAATAACATACCCACATATTTATTGTCTCATGGCATGAATAACA
* *
16994821 TGCTAAC
66 TACCAAC
*
16994828 ATATTTACTTTCACATGGCATGAATAACATACCCACATATTTATTGTCTCATGGCATGAATAACA
1 ATATTTACTATCACATGGCATGAATAACATACCCACATATTTATTGTCTCATGGCATGAATAACA
*
16994893 TACCCAC
66 TACCAAC
*
16994900 ATATTTACTGTCACATGGCATGAATAAC
1 ATATTTACTATCACATGGCATGAATAAC
16994928 GTATTCATAT
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
72 92 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (72 bp):
ATATTTACTATCACATGGCATGAATAACATACCCACATATTTATTGTCTCATGGCATGAATAACA
TACCAAC
Found at i:16998143 original size:36 final size:33
Alignment explanation
Indices: 16998061--16998143 Score: 87
Period size: 36 Copynumber: 2.4 Consensus size: 33
16998051 TTTTTCAATA
*
16998061 TCAATTTC-TTTTCTCTCACACTTTCTTTCTTT
1 TCAATTTCTTTTTCTCTCACACTCTCTTTCTTT
* *
16998093 TCAGTTTCTTTTTTCTTCTTCACACTCTCTTTTTATT
1 TCAATTTC-TTTTTC-TC-TCACACTCTCTTTCT-TT
*
16998130 TTAATTTCTTTTTC
1 TCAATTTCTTTTTC
16998144 GCACTTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
32 7 0.17
34 5 0.12
35 2 0.05
36 19 0.46
37 8 0.20
ACGTcount: A:0.12, C:0.24, G:0.01, T:0.63
Consensus pattern (33 bp):
TCAATTTCTTTTTCTCTCACACTCTCTTTCTTT
Found at i:17005154 original size:60 final size:59
Alignment explanation
Indices: 17005078--17005189 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 59
17005068 CTTAATAAAC
17005078 ATTTGGACATGAACTTGACACT-TTTTCCTAATTTGGTACTTAAACTTTTTTTGGACCCA
1 ATTTGGACATGAACTTGACA-TATTTTCCTAATTTGGTACTTAAACTTTTTTTGGACCCA
* *
17005137 ATTTGGTACCTGAACTTGACATATTTTCCTAATTTGGTACTTAAGCTTTTTTT
1 ATTTGG-ACATGAACTTGACATATTTTCCTAATTTGGTACTTAAACTTTTTTT
17005190 TAAGATTCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
59 7 0.14
60 42 0.86
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (59 bp):
ATTTGGACATGAACTTGACATATTTTCCTAATTTGGTACTTAAACTTTTTTTGGACCCA
Found at i:17005448 original size:30 final size:31
Alignment explanation
Indices: 17005412--17005488 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
17005402 GAACCCCAAA
** *
17005412 AAGTTTAAGTACCAACTTAA-AAAAAGTGTC
1 AAGTTTAAGTACCAAAATAAGAAAAAGTATC
* *
17005442 AAGTTTAGGTACCAAAATAAGAAAAAGTATT
1 AAGTTTAAGTACCAAAATAAGAAAAAGTATC
* *
17005473 AAGTTTGAGTATCAAA
1 AAGTTTAAGTACCAAA
17005489 TTGGACAAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
30 17 0.45
31 21 0.55
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAAATAAGAAAAAGTATC
Found at i:17005516 original size:28 final size:27
Alignment explanation
Indices: 17005476--17005528 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
17005466 AAGTATTAAG
*
17005476 TTTGAGTATCAAATT-GGACAAAAAAAT
1 TTTGAGTACCAAATTAGGA-AAAAAAAT
17005503 TTTGAAGTACCAAATTAGGAAAAAAA
1 TTTG-AGTACCAAATTAGGAAAAAAA
17005529 TGTCAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 16 0.70
29 3 0.13
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (27 bp):
TTTGAGTACCAAATTAGGAAAAAAAAT
Found at i:17005626 original size:9 final size:9
Alignment explanation
Indices: 17005612--17005674 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
17005602 TTGTAGTATT
17005612 TTTTTATAA
1 TTTTTATAA
*
17005621 TTTTTAAATA
1 TTTTTATA-A
17005631 TTTTATATAA
1 TTTT-TATAA
* *
17005641 CTTTTATGA
1 TTTTTATAA
*
17005650 TTTATAT-A
1 TTTTTATAA
17005658 TTTTT-TAA
1 TTTTTATAA
17005666 TTTTT-TAA
1 TTTTTATAA
17005674 T
1 T
17005675 AGAAAATATC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
7 1 0.02
8 15 0.34
9 16 0.36
10 9 0.20
11 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17005853 original size:60 final size:60
Alignment explanation
Indices: 17005760--17005882 Score: 228
Period size: 60 Copynumber: 2.0 Consensus size: 60
17005750 GTTACTTTTT
*
17005760 AATGGTTGGCTTTAATAATTAAAAAGTTTAATTGATTGAAATTTTAACATACAATAACTC
1 AATGGTTGGCTTTAACAATTAAAAAGTTTAATTGATTGAAATTTTAACATACAATAACTC
*
17005820 AATGGTTGGCTTTAACAATTAAAAAGTTTAATTGATTGAAATTTTAACATACAATAGCTC
1 AATGGTTGGCTTTAACAATTAAAAAGTTTAATTGATTGAAATTTTAACATACAATAACTC
17005880 AAT
1 AAT
17005883 AGCTCAATTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (60 bp):
AATGGTTGGCTTTAACAATTAAAAAGTTTAATTGATTGAAATTTTAACATACAATAACTC
Found at i:17006991 original size:2 final size:2
Alignment explanation
Indices: 17006984--17007028 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17006974 ACCAAAAATA
17006984 AT AT AT 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 AT AT AT
17007026 AT A
1 AT A
17007029 AATAATTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17007482 original size:29 final size:29
Alignment explanation
Indices: 17007425--17007482 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
17007415 TTTTTAAATT
* * *
17007425 TTTAAAAAAGTTAAAATTATAATTTTTTA
1 TTTAAAAAAGTTAAAATAAAAATTATTTA
17007454 TTTAAAAAAGTTAAAA-AAAAGATTATTTA
1 TTTAAAAAAGTTAAAATAAAA-ATTATTTA
17007483 CATTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTAAAAAAGTTAAAATAAAAATTATTTA
Found at i:17009558 original size:29 final size:30
Alignment explanation
Indices: 17009501--17009579 Score: 79
Period size: 31 Copynumber: 2.6 Consensus size: 30
17009491 ATATCAAAAT
* * * *
17009501 TATACATAAACTTTGATTTAATAAGCAATTG
1 TATACATGAATTTTAATTTAAT-AGCAATTA
17009532 TATACATGAATTTTAATTTAAT-GCAATTA
1 TATACATGAATTTTAATTTAATAGCAATTA
* *
17009561 TACACATGAAATTCTAATT
1 TATACATG-AATTTTAATT
17009580 GTGATTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 13 0.32
30 9 0.22
31 19 0.46
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.41
Consensus pattern (30 bp):
TATACATGAATTTTAATTTAATAGCAATTA
Found at i:17010842 original size:24 final size:24
Alignment explanation
Indices: 17010815--17010873 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
17010805 ATTAAAATAC
17010815 ACGAGCATAAACGTATAGTGACTG
1 ACGAGCATAAACGTATAGTGACTG
*
17010839 ACGAGCATAAACGTATAGTGGCTG
1 ACGAGCATAAACGTATAGTGACTG
*
17010863 ACAAGCATAAA
1 ACGAGCATAAA
17010874 TGTACGCTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.19
Consensus pattern (24 bp):
ACGAGCATAAACGTATAGTGACTG
Found at i:17011596 original size:21 final size:22
Alignment explanation
Indices: 17011570--17011619 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
17011560 TTGGGAAGTT
**
17011570 TCGGTAGTATCATCT-AGAGTA
1 TCGGTAGTATCAAATGAGAGTA
*
17011591 TCGGTAGTATGAAATGAGAGTA
1 TCGGTAGTATCAAATGAGAGTA
17011613 TCGGTAG
1 TCGGTAG
17011620 AAGCTATAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (22 bp):
TCGGTAGTATCAAATGAGAGTA
Found at i:17016378 original size:25 final size:27
Alignment explanation
Indices: 17016311--17016382 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 27
17016301 TATCATTTAT
*
17016311 TATTATAT-TTAATT-TTTTA-AAATA
1 TATTATGTATTAATTATTTTACAAATA
*
17016335 TTTTATGTATT-ATTAATTTTACAAATA
1 TATTATGTATTAATT-ATTTTACAAATA
17016362 -ATT-TGTATTAATTA-TTTACAA
1 TATTATGTATTAATTATTTTACAA
17016383 GTTATTGAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
24 16 0.40
25 9 0.22
26 10 0.25
27 5 0.12
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (27 bp):
TATTATGTATTAATTATTTTACAAATA
Found at i:17017355 original size:31 final size:30
Alignment explanation
Indices: 17017289--17017347 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
17017279 GAATTGGATC
*
17017289 AAATCAAAATTTCATGTATAAAATTGCACA
1 AAATCAAAATTTCATGTATAAAATTACACA
*
17017319 AAATCAAAA-TTCATGTATATAATTACACA
1 AAATCAAAATTTCATGTATAAAATTACACA
17017348 TTAAATCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATCAAAATTTCATGTATAAAATTACACA
Found at i:17017827 original size:21 final size:21
Alignment explanation
Indices: 17017803--17017849 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17017793 TAGCATAATT
17017803 CAAATATAAAGTTTAGAAATC
1 CAAATATAAAGTTTAGAAATC
* *
17017824 CAAACATAAAGTTTATAAATC
1 CAAATATAAAGTTTAGAAATC
17017845 CAAAT
1 CAAAT
17017850 TACATAATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (21 bp):
CAAATATAAAGTTTAGAAATC
Found at i:17019038 original size:28 final size:25
Alignment explanation
Indices: 17018998--17019058 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 25
17018988 TTCTGTCTCA
17018998 TGAGCTGGAGGAACTAATCATCATTGTG
1 TGAGCTGGAGGAA-T--TCATCATTGTG
* *
17019026 TGAGTTGGAGGAATTTATCATTGTG
1 TGAGCTGGAGGAATTCATCATTGTG
17019051 TGAGCTGG
1 TGAGCTGG
17019059 TCCTCATCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.57
27 1 0.03
28 12 0.40
ACGTcount: A:0.25, C:0.10, G:0.33, T:0.33
Consensus pattern (25 bp):
TGAGCTGGAGGAATTCATCATTGTG
Found at i:17020840 original size:51 final size:51
Alignment explanation
Indices: 17020764--17020865 Score: 168
Period size: 51 Copynumber: 2.0 Consensus size: 51
17020754 TGTGTTGTTA
* *
17020764 AGGATGAAACCACGGGTCAAGTACTCTTACATAGCATAGAGCAAGATGGTC
1 AGGATGAAACCACGGGTCAAGTACTCCTACATAGCATAGAGCAAAATGGTC
* *
17020815 AGGATGAAACCATGGGTCAAGTACTCCTACATAGCGTAGAGCAAAATGGTC
1 AGGATGAAACCACGGGTCAAGTACTCCTACATAGCATAGAGCAAAATGGTC
17020866 TTTACTGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (51 bp):
AGGATGAAACCACGGGTCAAGTACTCCTACATAGCATAGAGCAAAATGGTC
Found at i:17022932 original size:52 final size:52
Alignment explanation
Indices: 17022840--17023078 Score: 318
Period size: 52 Copynumber: 4.6 Consensus size: 52
17022830 TAAATGAAAA
* *
17022840 AGGTCCGATGATTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
* * * *
17022892 AGGTTTTATGACTTTGTGTCATCGTGAGCT-TATGAATCCTTTACAGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAG-TATATGAATCCTTTACAGATTAAG
* ** *
17022944 AGGTCTGATAACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
* * * *
17022996 AGGTCCGATGACTATGTGTCATCGTGAGTATATGATTTCTTTACGGATTAAG
1 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
* *
17023048 AGGTTTGATGACTATTTGTCATCGTGAGTAT
1 AGGTCTGATGACTATGTGTCATCGTGAGTAT
17023079 TAAATGAAAT
Statistics
Matches: 164, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
51 1 0.01
52 162 0.99
53 1 0.01
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (52 bp):
AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTAAG
Found at i:17025736 original size:52 final size:52
Alignment explanation
Indices: 17025653--17025836 Score: 253
Period size: 52 Copynumber: 3.5 Consensus size: 52
17025643 TGCATTTTTT
17025653 TATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCA
* * *
17025705 TATATTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGAATTCA
1 TATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCA
* * * * *
17025757 TATACTCACGATAACACACAGTCATCAGACCTTATAAT-TCGTAAATGATTCA
1 TATACTCACGATGACACATAGTCATCGGACCTCATAATCT-GTAAAGGATTCA
** *
17025809 TATACTCATAATGACACAAAGTCATCGG
1 TATACTCACGATGACACATAGTCATCGG
17025837 GCCCTTTTTC
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 115 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
TATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATTCA
Found at i:17030770 original size:19 final size:18
Alignment explanation
Indices: 17030723--17030772 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 18
17030713 TGCAAATTCT
*
17030723 ACCGATACAAGTGTTCAA
1 ACCGATACTAGTGTTCAA
17030741 ACTATCGATACTAGTGTTCAGA
1 AC---CGATACTAGTGTTCA-A
17030763 ACCGATACTA
1 ACCGATACTA
17030773 CTATGAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.07
19 8 0.30
21 14 0.52
22 3 0.11
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (18 bp):
ACCGATACTAGTGTTCAA
Found at i:17031437 original size:26 final size:26
Alignment explanation
Indices: 17031397--17031461 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
17031387 CAATAAATCA
* * *
17031397 CTCTTATGAGTCAGTACAGTATGTTG
1 CTCTTACGAGCCAGTACAGTATATTG
**
17031423 CTCTTACGAGCCAGTGTAGTATATTG
1 CTCTTACGAGCCAGTACAGTATATTG
17031449 CTCTTACGAGCCA
1 CTCTTACGAGCCA
17031462 ATGCAGAATC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.34
Consensus pattern (26 bp):
CTCTTACGAGCCAGTACAGTATATTG
Found at i:17036204 original size:28 final size:27
Alignment explanation
Indices: 17036160--17036212 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 27
17036150 GCATTTTATC
17036160 TATTTTATTTCATTTTATA-TATCATT
1 TATTTTATTTCATTTTATATTATCATT
*
17036186 TATTTTTTCTTCATTTTTATATTATCA
1 TATTTTAT-TTCA-TTTTATATTATCA
17036213 CCTCTTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 7 0.30
27 4 0.17
28 7 0.30
29 5 0.22
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (27 bp):
TATTTTATTTCATTTTATATTATCATT
Found at i:17036911 original size:109 final size:109
Alignment explanation
Indices: 17036717--17036924 Score: 326
Period size: 109 Copynumber: 1.9 Consensus size: 109
17036707 AAAATCAAGG
* * * *
17036717 TAATGTTCTTTTATTTTAGGAAACTCGAGAAATTGTACCCTAATGTGCTGGGTATGGTTTTTCTT
1 TAATGTTCTATTATTTTAGGAAACTCGAGAAATTGTACCCTAACGTACTGGGTATGATTTTTCTT
*
17036782 TAAACCTAAGTAATTCAATATCCTATTTAAAATCGACAAATGTT
66 TAAACCTAAGTAACTCAATATCCTATTTAAAATCGACAAATGTT
* *
17036826 TAATGTTCTATTATTTTAGGGAACTCGAGAAATTGTACCCTAACGTATTGGGTATGATTTTTCTT
1 TAATGTTCTATTATTTTAGGAAACTCGAGAAATTGTACCCTAACGTACTGGGTATGATTTTTCTT
* * *
17036891 TGAACTTAAGTAACTGAATATCCTATTTAAAATC
66 TAAACCTAAGTAACTCAATATCCTATTTAAAATC
17036925 AATAAGTGTT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
109 89 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (109 bp):
TAATGTTCTATTATTTTAGGAAACTCGAGAAATTGTACCCTAACGTACTGGGTATGATTTTTCTT
TAAACCTAAGTAACTCAATATCCTATTTAAAATCGACAAATGTT
Found at i:17041314 original size:29 final size:29
Alignment explanation
Indices: 17041215--17041314 Score: 94
Period size: 29 Copynumber: 3.3 Consensus size: 29
17041205 TTAAAATATG
* *
17041215 AATAAAATAAATATATATAATTGTTTAAAAA
1 AATAAAA-AAA-ATACATAATTTTTTAAAAA
* * *
17041246 AATAAAAATATTACAGAATTTTTTAAAAA
1 AATAAAAAAAATACATAATTTTTTAAAAA
* *
17041275 AATTTAAAAAAAT-GATAATTTTTTAAAAA
1 AA-TAAAAAAAATACATAATTTTTTAAAAA
17041304 ATATAAAAAAA
1 A-ATAAAAAAA
17041315 TTATTAGGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 39 0.70
30 10 0.18
31 7 0.12
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (29 bp):
AATAAAAAAAATACATAATTTTTTAAAAA
Found at i:17041776 original size:12 final size:12
Alignment explanation
Indices: 17041759--17041788 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
17041749 GAGATAAATA
17041759 ATTTAAAATATT
1 ATTTAAAATATT
17041771 ATTTAAAATATT
1 ATTTAAAATATT
17041783 ATTTAA
1 ATTTAA
17041789 TTGAAATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAAAATATT
Found at i:17042170 original size:4 final size:4
Alignment explanation
Indices: 17042161--17042190 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
17042151 GATATATGTC
*
17042161 TTAT TTAT TTAT TTAT TTAT TTAT ATAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
17042191 TCATTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:17045093 original size:17 final size:17
Alignment explanation
Indices: 17045071--17045127 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
17045061 TGGGCGTGAG
*
17045071 TATTAAATATATAATTA
1 TATTAAATATATTATTA
*
17045088 TATTAAAAATATTATTA
1 TATTAAATATATTATTA
* *
17045105 AATT--ATATATTATTT
1 TATTAAATATATTATTA
17045120 TATTAAAT
1 TATTAAAT
17045128 TGTATTTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
15 12 0.38
17 20 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTAAATATATTATTA
Found at i:17045124 original size:20 final size:20
Alignment explanation
Indices: 17045099--17045189 Score: 64
Period size: 20 Copynumber: 4.7 Consensus size: 20
17045089 ATTAAAAATA
17045099 TTATTAAATTATATATTATT
1 TTATTAAATTATATATTATT
*
17045119 TTATTAAATTGTAT-TTA--
1 TTATTAAATTATATATTATT
* * * ** *
17045136 ATAAT-AATTATGTTAAAATA
1 TTATTAAATTAT-ATATTATT
* *
17045156 TAATTAAATTATTTATTATT
1 TTATTAAATTATATATTATT
17045176 TTATTAAATTATAT
1 TTATTAAATTATAT
17045190 TTAATAATAA
Statistics
Matches: 51, Mismatches: 15, Indels: 10
0.67 0.20 0.13
Matches are distributed among these distances:
16 5 0.10
17 4 0.08
18 1 0.02
19 3 0.06
20 32 0.63
21 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TTATTAAATTATATATTATT
Found at i:17045164 original size:57 final size:58
Alignment explanation
Indices: 17045070--17045210 Score: 205
Period size: 57 Copynumber: 2.4 Consensus size: 58
17045060 GTGGGCGTGA
* *
17045070 GTATTAAATATATAATTATATTAAAAATATTATTAAATTATATATTATTTTATTAAATT
1 GTATTTAATA-ATAATTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATT
* *
17045129 GTATTTAATAATAATTATGTT-AAAATATAATTAAATTATTTATTATTTTATTAAATT
1 GTATTTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATT
*
17045186 ATATTTAATAATAATCT-TATTAAAA
1 GTATTTAATAATAAT-TATATTAAAA
17045211 TTTAATAATG
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
57 51 0.69
58 14 0.19
59 9 0.12
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (58 bp):
GTATTTAATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTATTAAATT
Found at i:17045393 original size:16 final size:16
Alignment explanation
Indices: 17045372--17045426 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
17045362 TGAATTACTG
17045372 ATTACAGTCCTATTCC
1 ATTACAGTCCTATTCC
* *
17045388 ATTACAATTCTATTCC
1 ATTACAGTCCTATTCC
* *
17045404 ATTATA-ACTCTATTCC
1 ATTACAGTC-CTATTCC
17045420 ATTACAG
1 ATTACAG
17045427 CAAACTAAAC
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACAGTCCTATTCC
Found at i:17048935 original size:31 final size:30
Alignment explanation
Indices: 17048900--17048991 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
17048890 TAATTTATAT
17048900 TGTATTATTAGATTAAATTATTTAAATATTA
1 TGTATTATTA-ATTAAATTATTTAAATATTA
* * *
17048931 TGTATCATTAAGTTAATTTATTT-AATATAA
1 TGTATTATTAA-TTAAATTATTTAAATATTA
* * *
17048961 TGAATTATTATATTTAATTTTTTATAATATT
1 TGTATTATTA-ATTAAATTATTTA-AATATT
17048992 TTATGATACA
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
30 23 0.48
31 20 0.42
32 5 0.10
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.54
Consensus pattern (30 bp):
TGTATTATTAATTAAATTATTTAAATATTA
Found at i:17056481 original size:27 final size:28
Alignment explanation
Indices: 17056430--17056490 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
17056420 AAGATTTAAG
* *
17056430 AAAAATAAAATAAAAGGACTTAATTTTTA
1 AAAAATAAAACAAAAGGAC-AAATTTTTA
17056459 AAAAATAAAACAAAAGGA-AAATTTTTA
1 AAAAATAAAACAAAAGGACAAATTTTTA
17056486 AAAAA
1 AAAAA
17056491 GAATAAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.43
29 17 0.57
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.25
Consensus pattern (28 bp):
AAAAATAAAACAAAAGGACAAATTTTTA
Found at i:17056490 original size:29 final size:30
Alignment explanation
Indices: 17056424--17056498 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 30
17056414 AAGATTAAGA
* * *
17056424 TTTAAGAAAAATAAAATAAAAGGACTTAATT
1 TTTAAAAAAAATAAAACAAAAGGAC-AAATT
17056455 TTT--AAAAAATAAAACAAAAGGA-AAATT
1 TTTAAAAAAAATAAAACAAAAGGACAAATT
17056482 TTTAAAAAAGAATAAAA
1 TTTAAAAAA-AATAAAA
17056499 TGATTTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 7 0.18
29 21 0.55
30 7 0.18
31 3 0.08
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (30 bp):
TTTAAAAAAAATAAAACAAAAGGACAAATT
Found at i:17056588 original size:82 final size:81
Alignment explanation
Indices: 17056467--17056618 Score: 252
Period size: 82 Copynumber: 1.9 Consensus size: 81
17056457 TAAAAAATAA
17056467 AACAAAAGGAAAATTTTTAAAAAAGAATAAAATGATTTAATTAAAA-AACATAATAAAAAGGTTA
1 AACAAAAGGAAAATTTTTAAAAAAGAATAAAATGATTTAATTAAAAGAACATAATAAAAAGGTTA
17056531 AATTTGTTTTAAATGG
66 AATTTGTTTTAAATGG
* * *
17056547 AACAAAAGGATTAATTTTTTAAAAAAGAATAAAATGATTTAATTAAAAGAATATAATAAAAGGGT
1 AACAAAAGGA--AAATTTTTAAAAAAGAATAAAATGATTTAATTAAAAGAACATAATAAAAAGGT
17056612 TAAATTT
64 TAAATTT
17056619 AAAAAGGAAA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
80 10 0.15
82 35 0.53
83 21 0.32
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (81 bp):
AACAAAAGGAAAATTTTTAAAAAAGAATAAAATGATTTAATTAAAAGAACATAATAAAAAGGTTA
AATTTGTTTTAAATGG
Found at i:17056639 original size:17 final size:17
Alignment explanation
Indices: 17056612--17056649 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
17056602 ATAAAAGGGT
17056612 TAAATTTAAAAAGGAAAA
1 TAAATTTAAAAAGG-AAA
17056630 TAAA-TTAAAAAGGAAA
1 TAAATTTAAAAAGGAAA
17056646 TAAA
1 TAAA
17056650 ACTATGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 9 0.45
18 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (17 bp):
TAAATTTAAAAAGGAAA
Found at i:17060426 original size:49 final size:49
Alignment explanation
Indices: 17060334--17060550 Score: 263
Period size: 49 Copynumber: 4.4 Consensus size: 49
17060324 GGAAACGTTA
* ** * * *
17060334 AATCATATACCCTAGAAGACATGAAGGGGAAGATTGAAGCCGCAACGATG
1 AATCTTATACCCTA-AAGATGTGAAGGGAAAGATTGAAGCCACAACGACG
* * * * * **
17060384 AATATTATACCCTAAAGATGTGGAGGGAAAGGTTGAAACCGCAACGGTG
1 AATCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCACAACGACG
* * *
17060433 AACCTTATACCCTATAGATGTGAAGGGAAAGATTGAAGCCACAATGACG
1 AATCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCACAACGACG
* *
17060482 AATCTTATACCCTAGAGATGTAAAGGGAAAGATTGAAGCCACAACGACG
1 AATCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCACAACGACG
17060531 AATCTTATACCCTAAAGATG
1 AATCTTATACCCTAAAGATG
17060551 AGGAGAAGTA
Statistics
Matches: 143, Mismatches: 24, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 131 0.92
50 12 0.08
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.20
Consensus pattern (49 bp):
AATCTTATACCCTAAAGATGTGAAGGGAAAGATTGAAGCCACAACGACG
Found at i:17060467 original size:98 final size:96
Alignment explanation
Indices: 17060339--17060574 Score: 258
Period size: 98 Copynumber: 2.4 Consensus size: 96
17060329 CGTTAAATCA
* *
17060339 TATACCCTAGAAGACATGAAGGGGAAGATTGAAGCCGCAACGATGAATATTATACCCTAAAGATG
1 TATACCCTA-AAG--ATGAAGGGAAAGATTGAAGCCGCAACGACGAATATTATACCCTAAAGATG
** * * **
17060404 TGGAGGGAAAGGTTGAAACCGCAACGGTGAACCT
63 TAAAGGGAAAGATTGAAACCACAACGACGAACCT
* * * * *
17060438 TATACCCTATAGATGTGAAGGGAAAGATTGAAGCCACAATGACGAATCTTATACCCTAGAGATGT
1 TATACCCTAAAGA--TGAAGGGAAAGATTGAAGCCGCAACGACGAATATTATACCCTAAAGATGT
* *
17060503 AAAGGGAAAGATTGAAGCCACAACGACGAATCT
64 AAAGGGAAAGATTGAAACCACAACGACGAACCT
17060536 TATACCCTAAAGATG-AGGAGAAGTAGATTGAAGCCGCAA
1 TATACCCTAAAGATGAAGG-GAA--AGATTGAAGCCGCAA
17060575 AGGCAAATCT
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
95 3 0.03
96 6 0.05
98 97 0.84
99 9 0.08
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (96 bp):
TATACCCTAAAGATGAAGGGAAAGATTGAAGCCGCAACGACGAATATTATACCCTAAAGATGTAA
AGGGAAAGATTGAAACCACAACGACGAACCT
Found at i:17060584 original size:49 final size:47
Alignment explanation
Indices: 17060334--17060576 Score: 200
Period size: 49 Copynumber: 4.9 Consensus size: 47
17060324 GGAAACGTTA
* * * * *
17060334 AATCATATACCCTAGAAGACATGAAGGGGAAGATTGAAGCCGCAACGATG
1 AATCTTATACCCTA-AAG--ATGAAGGGAAAGATTGAAGCCACAAAGACG
* * * * * * **
17060384 AATATTATACCCTAAAGATGTGGAGGGAAAGGTTGAAACCGCAACGGTG
1 AATCTTATACCCTAAAGA--TGAAGGGAAAGATTGAAGCCACAAAGACG
* * *
17060433 AACCTTATACCCTATAGATGTGAAGGGAAAGATTGAAGCCACAATGACG
1 AATCTTATACCCTAAAGA--TGAAGGGAAAGATTGAAGCCACAAAGACG
* *
17060482 AATCTTATACCCTAGAGATGTAAAGGGAAAGATTGAAGCCACAACGACG
1 AATCTTATACCCTAAAGATG--AAGGGAAAGATTGAAGCCACAAAGACG
*
17060531 AATCTTATACCCTAAAGATG-AGGAGAAGTAGATTGAAGCCGCAAAG
1 AATCTTATACCCTAAAGATGAAGG-GAA--AGATTGAAGCCACAAAG
17060577 GCAAATCTCA
Statistics
Matches: 163, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
46 3 0.02
47 6 0.04
49 142 0.87
50 12 0.07
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.19
Consensus pattern (47 bp):
AATCTTATACCCTAAAGATGAAGGGAAAGATTGAAGCCACAAAGACG
Found at i:17060659 original size:42 final size:43
Alignment explanation
Indices: 17060554--17060668 Score: 132
Period size: 42 Copynumber: 2.7 Consensus size: 43
17060544 AAAGATGAGG
*
17060554 AGAAG-TAGATTGAAGCCGCAAAGGCAAATCTCAAGACTGTAG
1 AGAAGCTAGATTGAAGCCGCAAAGGCAAATCTCAAGACTGTAA
17060596 AGAAGC-ATG-TTGAAGCCGCAAAGGCAAATCTCAA-AGCTGTAA
1 AGAAGCTA-GATTGAAGCCGCAAAGGCAAATCTCAAGA-CTGTAA
* * * *
17060638 AG-GGCTAGATTAAAGCTGCAAAGGCGAATCT
1 AGAAGCTAGATTGAAGCCGCAAAGGCAAATCT
17060669 TACGTCTCTA
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
41 4 0.06
42 58 0.92
43 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (43 bp):
AGAAGCTAGATTGAAGCCGCAAAGGCAAATCTCAAGACTGTAA
Found at i:17061160 original size:189 final size:189
Alignment explanation
Indices: 17060752--17061357 Score: 775
Period size: 189 Copynumber: 3.2 Consensus size: 189
17060742 AGTAACGAAT
* * *
17060752 CTCAACGTCCTTGAGGTTATAGTGGAGTGGAGTGAAACTTTAAATCCCATCTTCCTAGTGAGGTA
1 CTCAACATCCCTGAGGTTATAGTGGAGTGGAGTGAGACTTTAAATCCCATCTTCCTAGTGAGGTA
* * *
17060817 CAGAGAAGTGGGTCAAAACAGGTAGCAGATCTCAACATCCCCTGAGGTTACATTGGAGTGGAGTG
66 CAGAGAAGTGGGTCAAAACAAGTAGCAGATCTCAACAT-CCTTGAGGTTACAATGGAGTGGAGTG
* * * * * *
17060882 TAGCGCCAAAATCTTATACCCTTGAGTTGCAGTGGGTCAAATTAAAACAACGAAGCAGAG
130 AAGCGCCAAAATCTTATACCCTTGAGTTGCAGTGGGTCAGATGAAAATAATGAAGTAGAG
* * *
17060942 CTCAACATCCTTGAGGTTATAGAGGAGTGGAATGAGACTTTAAATCCCATCTTCCTAGTGAGGTA
1 CTCAACATCCCTGAGGTTATAGTGGAGTGGAGTGAGACTTTAAATCCCATCTTCCTAGTGAGGTA
* * * * * * * *
17061007 TAGAGAAGTGAGTTAAAACATGTAACAGATCTCAATATCCTTAAGGTTACAGTGGAGTGGAGTGA
66 CAGAGAAGTGGGTCAAAACAAGTAGCAGATCTCAACATCCTTGAGGTTACAATGGAGTGGAGTGA
* * * * *
17061072 AGTGCTAAAATCTTATACCCCTAAGTCGCAGTGGGTCAGATGAAAATAATGAAGTAGAG
131 AGCGCCAAAATCTTATACCCTTGAGTTGCAGTGGGTCAGATGAAAATAATGAAGTAGAG
* * * * *
17061131 CTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGTCTTCAAATCCCA-CTTCCTTGTGAGGTA
1 CTCAACATCCCTGAGGTTATAGTGGAGTGGAGTGAGACTTTAAATCCCATCTTCCTAGTGAGGTA
* * * *
17061195 CAGAGAAGTGGGTCAAAACAAGTAGTAGATC-AAACATCCTTGATGTTACAATGGAGTGGAATGA
66 CAGAGAAGTGGGTCAAAACAAGTAGCAGATCTCAACATCCTTGAGGTTACAATGGAGTGGAGTGA
* * * *
17061259 AGCGCCACAATTTTATACCCTTGAGTTGCAATGGGTCGGATGAAAATAATGAAGTAGAG
131 AGCGCCAAAATCTTATACCCTTGAGTTGCAGTGGGTCAGATGAAAATAATGAAGTAGAG
* * * * *
17061318 CTAAAAATCCCTAAGGTTATAGTGGAGTGAAGTGAAACTT
1 CTCAACATCCCTGAGGTTATAGTGGAGTGGAGTGAGACTT
17061358 CAAAATCTCG
Statistics
Matches: 355, Mismatches: 61, Indels: 3
0.85 0.15 0.01
Matches are distributed among these distances:
187 109 0.31
188 39 0.11
189 114 0.32
190 93 0.26
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (189 bp):
CTCAACATCCCTGAGGTTATAGTGGAGTGGAGTGAGACTTTAAATCCCATCTTCCTAGTGAGGTA
CAGAGAAGTGGGTCAAAACAAGTAGCAGATCTCAACATCCTTGAGGTTACAATGGAGTGGAGTGA
AGCGCCAAAATCTTATACCCTTGAGTTGCAGTGGGTCAGATGAAAATAATGAAGTAGAG
Found at i:17061222 original size:94 final size:94
Alignment explanation
Indices: 17060752--17061254 Score: 274
Period size: 94 Copynumber: 5.3 Consensus size: 94
17060742 AGTAACGAAT
* * * *
17060752 CTCAACGTCCTTGAGGTTATAGTGGAGTGGAGTGAAACTTTAAATCCCATCTTCCTAGTGAGGTA
1 CTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCA-CTTCCTAGTGAGGTA
* *
17060817 CAGAGAAGTGGGTCAAAACAGGTAGCAGAT
65 CAGAGAAGTGGGTCAAAACAAGTAGCAGAG
* * ** ** *
17060847 CTCAACATCCCCTGAGGTTACATTGGAGTGGAGTGTAG-CGCCAAAATCTTA-TACCCT--TGAG
1 CTCAACAT-CCTTGAGGTTACAGTGGAGTGGAGTG-AGACTTC-AAATCCCACT-TCCTAGTGAG
* * * * *** * *
17060908 TTGCAGTG-GGTCAAATTAAAACAACGAAGCAGAG
62 GTACAGAGAAGT-GGGTCAAAACAA-GTAGCAGAG
* * * *
17060942 CTCAACATCCTTGAGGTTATAGAGGAGTGGAATGAGACTTTAAATCCCATCTTCCTAGTGAGGTA
1 CTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCA-CTTCCTAGTGAGGTA
* * * * * *
17061007 TAGAGAAGTGAGTTAAAACATGTAACAGAT
65 CAGAGAAGTGGGTCAAAACAAGTAGCAGAG
* * * * ** * ** *
17061037 CTCAATATCCTTAAGGTTACAGTGGAGTGGAGTGA-AGTGCTAAAATCTTA-TACC-CCT-AAGT
1 CTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACT--TCAAATCCCACTTCCTAGTGAGGT
* * * * * * * * *
17061098 CGCAGTG-GGTCAGATGAAAATAATGAAGTAGAG
64 -ACAGAGAAGT-GGGTCAAAACAA-GTAGCAGAG
* * * *
17061131 CTCAACGTCCCTGAGGTTACAGTGGAGTGGAGTGAGTCTTCAAATCCCACTTCCTTGTGAGGTAC
1 CTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCACTTCCTAGTGAGGTAC
*
17061196 AGAGAAGTGGGTCAAAACAAGTAGTAGA-
66 AGAGAAGTGGGTCAAAACAAGTAGCAGAG
* *
17061224 -TCAAACATCCTTGATGTTACAATGGAGTGGA
1 CTC-AACATCCTTGAGGTTACAGTGGAGTGGA
17061255 ATGAAGCGCC
Statistics
Matches: 289, Mismatches: 96, Indels: 48
0.67 0.22 0.11
Matches are distributed among these distances:
92 7 0.02
93 51 0.18
94 92 0.32
95 74 0.26
96 56 0.19
97 9 0.03
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (94 bp):
CTCAACATCCTTGAGGTTACAGTGGAGTGGAGTGAGACTTCAAATCCCACTTCCTAGTGAGGTAC
AGAGAAGTGGGTCAAAACAAGTAGCAGAG
Found at i:17063151 original size:32 final size:30
Alignment explanation
Indices: 17063105--17063181 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 30
17063095 ATTTATTCTG
* *
17063105 TTTTTTAAATTTAAATCCTTCTATTTTTAAT
1 TTTTTTAAAATTAAACCCTTCTATTTTT-AT
*
17063136 TTTTGTTAAAATTAAACCCTTTTATTTTTAT
1 TTTT-TTAAAATTAAACCCTTCTATTTTTAT
17063167 TCCTTTTTAAAATTA
1 T--TTTTTAAAATTA
17063182 CCCTTTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
31 7 0.17
32 30 0.75
33 3 0.08
ACGTcount: A:0.30, C:0.10, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTTTTAAAATTAAACCCTTCTATTTTTAT
Found at i:17063245 original size:16 final size:16
Alignment explanation
Indices: 17063224--17063260 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
17063214 CCTTTTACAT
17063224 CTTTTTTAATTAAATC
1 CTTTTTTAATTAAATC
*
17063240 CTTTTTTAATTTAATC
1 CTTTTTTAATTAAATC
17063256 CTTTT
1 CTTTT
17063261 ATGACTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (16 bp):
CTTTTTTAATTAAATC
Found at i:17077214 original size:27 final size:27
Alignment explanation
Indices: 17077184--17077244 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
17077174 AAATGAATGT
17077184 CTTTGTGGAAATATATGAAAGGAACGC
1 CTTTGTGGAAATATATGAAAGGAACGC
*** * *
17077211 CTTTGTGGCGGTATATGAAAGGAATGT
1 CTTTGTGGAAATATATGAAAGGAACGC
17077238 CTTTGTG
1 CTTTGTG
17077245 ACAAACTCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (27 bp):
CTTTGTGGAAATATATGAAAGGAACGC
Found at i:17077993 original size:12 final size:12
Alignment explanation
Indices: 17077972--17078002 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
17077962 ATGATGACTA
*
17077972 ACACACACACAC
1 ACACATACACAC
17077984 ACACATACACAC
1 ACACATACACAC
17077996 ACACATA
1 ACACATA
17078003 TATATAGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.52, C:0.42, G:0.00, T:0.06
Consensus pattern (12 bp):
ACACATACACAC
Found at i:17086015 original size:21 final size:21
Alignment explanation
Indices: 17085985--17086040 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
17085975 CAGTACAGAA
* * *
17085985 TTCTATCGATACAAGGGATAG
1 TTCTACCGATACAAGGGACAC
* *
17086006 TTCTACCGATAAAAGTGACAC
1 TTCTACCGATACAAGGGACAC
17086027 TTCTACCGATACAA
1 TTCTACCGATACAA
17086041 ATCATGCTTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (21 bp):
TTCTACCGATACAAGGGACAC
Found at i:17088668 original size:21 final size:23
Alignment explanation
Indices: 17088644--17088693 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
17088634 GTTGAGAAAG
* *
17088644 TTATTTAATTTAA-AAATTA-AT
1 TTATTTAATTAAATAAATAATAT
*
17088665 TTATGTAATTAAATAAATAATAT
1 TTATTTAATTAAATAAATAATAT
17088688 TTATTT
1 TTATTT
17088694 GAGGAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 11 0.48
22 5 0.22
23 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTATTTAATTAAATAAATAATAT
Found at i:17092306 original size:31 final size:30
Alignment explanation
Indices: 17092270--17092340 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
17092260 TATGTTAAGC
*
17092270 TTTATTTAGATATAAAAATAAAAACAAAAGA
1 TTTATTTAGATAGAAAAA-AAAAACAAAAGA
* * * *
17092301 TTTATTTTTGATGGAAAAAAAAACCGAAAGA
1 TTTA-TTTAGATAGAAAAAAAAAACAAAAGA
17092332 TTTATTTAG
1 TTTATTTAG
17092341 TCATATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 4 0.12
31 18 0.55
32 11 0.33
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.34
Consensus pattern (30 bp):
TTTATTTAGATAGAAAAAAAAAACAAAAGA
Found at i:17100914 original size:15 final size:15
Alignment explanation
Indices: 17100891--17100924 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
17100881 AATTTATATA
* *
17100891 TTCTTGCACTTTACT
1 TTCTCGCACTTTACC
17100906 TTCTCGCACTTTACC
1 TTCTCGCACTTTACC
17100921 TTCT
1 TTCT
17100925 TGCATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.32, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCTCGCACTTTACC
Found at i:17101202 original size:4 final size:4
Alignment explanation
Indices: 17101193--17101227 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
17101183 TTTATATAAA
17101193 TATC TATC TATC TATC TATC TATC TATC TATC TAT
1 TATC TATC TATC TATC TATC TATC TATC TATC TAT
17101228 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:17104440 original size:2 final size:2
Alignment explanation
Indices: 17104433--17104465 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17104423 CTTTATTCTT
17104433 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17104466 TAATACGCAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17104506 original size:18 final size:18
Alignment explanation
Indices: 17104474--17104547 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
17104464 ATTAATACGC
17104474 ATTATTATTTCTATTACTT
1 ATTA-TATTTCTATTACTT
*
17104493 ATTATATTTTTATT-CTT
1 ATTATATTTCTATTACTT
*
17104510 -TATATATTTCTAATACTT
1 AT-TATATTTCTATTACTT
*
17104528 ATTATAATTT-TATTATTT
1 ATTAT-ATTTCTATTACTT
17104546 AT
1 AT
17104548 ATAAATATCT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.02
17 13 0.28
18 23 0.50
19 9 0.20
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.64
Consensus pattern (18 bp):
ATTATATTTCTATTACTT
Found at i:17104517 original size:17 final size:17
Alignment explanation
Indices: 17104495--17104550 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
17104485 TATTACTTAT
17104495 TATATTTTTATTCTTTA
1 TATATTTTTATTCTTTA
* *
17104512 TATATTTCTAATAC-TTA
1 TATATTT-TTATTCTTTA
* *
17104529 TTATAATTTTATTATTTA
1 -TATATTTTTATTCTTTA
17104547 TATA
1 TATA
17104551 AATATCTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTTTTATTCTTTA
Found at i:17104519 original size:35 final size:35
Alignment explanation
Indices: 17104475--17104550 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
17104465 TTAATACGCA
* * *
17104475 TTAT-TATTTCTATTACTTATTATATTTTTATTCT
1 TTATATATTTCTAATACTTATTATAATTTTATTAT
17104509 TTATATATTTCTAATACTTATTATAATTTTATTAT
1 TTATATATTTCTAATACTTATTATAATTTTATTAT
17104544 TTATATA
1 TTATATA
17104551 AATATCTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 4 0.11
35 34 0.89
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (35 bp):
TTATATATTTCTAATACTTATTATAATTTTATTAT
Found at i:17119303 original size:26 final size:25
Alignment explanation
Indices: 17119250--17119419 Score: 93
Period size: 25 Copynumber: 6.7 Consensus size: 25
17119240 CCCAACAAAG
* * * *
17119250 TTTAGCTCTTACGAGCCCAAACATAA
1 TTTAGCTCTTATGAG-CCAGATAGAA
17119276 TTTAGCTCTTATGAGCCCAGATAGAA
1 TTTAGCTCTTATGAG-CCAGATAGAA
*
17119302 TTTTA-CTCTCT-CGAGCCAGATAGAA
1 -TTTAGCTCT-TATGAGCCAGATAGAA
** * *
17119327 TTGCGCTCTTATGAGCCAAACAGAA
1 TTTAGCTCTTATGAGCCAGATAGAA
17119352 -TTACGCTCTT-TCGAGCCAGATA-AA
1 TTTA-GCTCTTAT-GAGCCAGATAGAA
* * * *
17119376 ATTATGCTCTTTTGAGCTAGACAGAA
1 TTTA-GCTCTTATGAGCCAGATAGAA
17119402 -TTACGCTCTT-TCGAGCCA
1 TTTA-GCTCTTAT-GAGCCA
17119420 AACTTCGGAG
Statistics
Matches: 115, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
24 8 0.07
25 70 0.61
26 32 0.28
27 5 0.04
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (25 bp):
TTTAGCTCTTATGAGCCAGATAGAA
Found at i:17119335 original size:25 final size:25
Alignment explanation
Indices: 17119292--17119419 Score: 132
Period size: 25 Copynumber: 5.1 Consensus size: 25
17119282 TCTTATGAGC
*** *
17119292 CCAGATAGAATTTTACTCTCTCGAG
1 CCAGATAGAATTACGCTCTTTCGAG
*
17119317 CCAGATAGAATTGCGCTCTTAT-GAG
1 CCAGATAGAATTACGCTCTT-TCGAG
* *
17119342 CCAAACAGAATTACGCTCTTTCGAG
1 CCAGATAGAATTACGCTCTTTCGAG
* * *
17119367 CCAGATAAAATTATGCTCTTTTGAG
1 CCAGATAGAATTACGCTCTTTCGAG
* *
17119392 CTAGACAGAATTACGCTCTTTCGAG
1 CCAGATAGAATTACGCTCTTTCGAG
17119417 CCA
1 CCA
17119420 AACTTCGGAG
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
24 1 0.01
25 81 0.98
26 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (25 bp):
CCAGATAGAATTACGCTCTTTCGAG
Found at i:17119368 original size:50 final size:50
Alignment explanation
Indices: 17119280--17119419 Score: 172
Period size: 50 Copynumber: 2.8 Consensus size: 50
17119270 ACATAATTTA
* *** * * *
17119280 GCTCTTATGAGCCCAGATAGAATTTTACTCTCTCGAGCCAGATAGAATTGC
1 GCTCTTATGAG-CCAGACAGAATTACGCTCTTTCGAGCCAGATAAAATTAC
* *
17119331 GCTCTTATGAGCCAAACAGAATTACGCTCTTTCGAGCCAGATAAAATTAT
1 GCTCTTATGAGCCAGACAGAATTACGCTCTTTCGAGCCAGATAAAATTAC
* *
17119381 GCTCTTTTGAGCTAGACAGAATTACGCTCTTTCGAGCCA
1 GCTCTTATGAGCCAGACAGAATTACGCTCTTTCGAGCCA
17119420 AACTTCGGAG
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 66 0.86
51 11 0.14
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (50 bp):
GCTCTTATGAGCCAGACAGAATTACGCTCTTTCGAGCCAGATAAAATTAC
Found at i:17119409 original size:75 final size:76
Alignment explanation
Indices: 17119254--17119422 Score: 184
Period size: 75 Copynumber: 2.2 Consensus size: 76
17119244 ACAAAGTTTA
* * * *
17119254 GCTCTTACGAGCCCAAACATAATTTAGCTCTTATGAGCCCAGATAGAATTTTACTCTCTCGAGCC
1 GCTCTTATGAG-CCAAACAGAATTTAGCTCTTATGAGCCCAGATAAAATTATACTCTCTCGAGCC
* *
17119319 AGATAGAATTGC
65 AGACAGAATTAC
* * *
17119331 GCTCTTATGAGCCAAACAGAA-TTACGCTCTT-TCGAG-CCAGATAAAATTATGCTCTTTTGAGC
1 GCTCTTATGAGCCAAACAGAATTTA-GCTCTTAT-GAGCCCAGATAAAATTATACTCTCTCGAGC
*
17119393 TAGACAGAATTAC
64 CAGACAGAATTAC
17119406 GCTCTT-TCGAGCCAAAC
1 GCTCTTAT-GAGCCAAAC
17119423 TTCGGAGTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
74 1 0.01
75 50 0.63
76 18 0.23
77 10 0.13
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (76 bp):
GCTCTTATGAGCCAAACAGAATTTAGCTCTTATGAGCCCAGATAAAATTATACTCTCTCGAGCCA
GACAGAATTAC
Found at i:17124179 original size:18 final size:18
Alignment explanation
Indices: 17124153--17124197 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
17124143 AAGGTTTGCG
*
17124153 AACATCATAGGTTCGCAT
1 AACAACATAGGTTCGCAT
*
17124171 AACAACATAGGTTTGCAT
1 AACAACATAGGTTCGCAT
17124189 AACAACATA
1 AACAACATA
17124198 AAAGGGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (18 bp):
AACAACATAGGTTCGCAT
Found at i:17125309 original size:27 final size:27
Alignment explanation
Indices: 17125274--17125325 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17125264 AGTAACTTGC
* *
17125274 AAAAACACTTATTCGTATAAAGCTCAA
1 AAAAACACTTATTCATACAAAGCTCAA
*
17125301 AAAAACACTTGTTCATACAAAGCTC
1 AAAAACACTTATTCATACAAAGCTC
17125326 GCATAGCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (27 bp):
AAAAACACTTATTCATACAAAGCTCAA
Found at i:17126683 original size:25 final size:25
Alignment explanation
Indices: 17126634--17126682 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
17126624 TATTAATATT
*
17126634 TATTTTAAAATCTAAAAATATAAAA
1 TATTATAAAATCTAAAAATATAAAA
17126659 TATTATAAAAT-T-AAAATATGAAAA
1 TATTATAAAATCTAAAAATAT-AAAA
17126683 AAAATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 5 0.23
25 10 0.45
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
TATTATAAAATCTAAAAATATAAAA
Found at i:17126684 original size:16 final size:17
Alignment explanation
Indices: 17126647--17126684 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17126637 TTTAAAATCT
*
17126647 AAAAATATAAAATATTA
1 AAAAATATAAAATATGA
*
17126664 TAAAAT-TAAAATATGA
1 AAAAATATAAAATATGA
17126680 AAAAA
1 AAAAA
17126685 AATATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAAATATAAAATATGA
Found at i:17126846 original size:9 final size:9
Alignment explanation
Indices: 17126832--17126907 Score: 52
Period size: 9 Copynumber: 8.7 Consensus size: 9
17126822 AAATGTGTAT
17126832 TTTTATTAA
1 TTTTATTAA
17126841 TTTTA-TAA
1 TTTTATTAA
*
17126849 TTTTTATAAA
1 -TTTTATTAA
*
17126859 TTATTAATAA
1 TT-TTATTAA
*
17126869 TTTTTTTAA
1 TTTTATTAA
*
17126878 TTTT-TTCA
1 TTTTATTAA
**
17126886 CGTT-TTAA
1 TTTTATTAA
17126894 TTTT-TTAA
1 TTTTATTAA
17126902 TTTTAT
1 TTTTAT
17126908 ATTTTTTTCA
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
8 21 0.40
9 22 0.42
10 9 0.17
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (9 bp):
TTTTATTAA
Found at i:17126898 original size:7 final size:8
Alignment explanation
Indices: 17126832--17126914 Score: 51
Period size: 8 Copynumber: 9.8 Consensus size: 8
17126822 AAATGTGTAT
17126832 TTTTATTAA
1 TTTT-TTAA
*
17126841 TTTTATAA
1 TTTTTTAA
17126849 TTTTTATAAA
1 TTTTT-T-AA
*
17126859 TTATTAATAA
1 TT-TT-TTAA
17126869 TTTTTTTAA
1 -TTTTTTAA
*
17126878 TTTTTTCA
1 TTTTTTAA
**
17126886 CGTTTTAA
1 TTTTTTAA
17126894 TTTTTTAA
1 TTTTTTAA
*
17126902 TTTTAT-A
1 TTTTTTAA
17126909 TTTTTT
1 TTTTTT
17126915 TCACATTTTC
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
7 6 0.11
8 30 0.53
9 8 0.14
10 8 0.14
11 5 0.09
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (8 bp):
TTTTTTAA
Found at i:17127429 original size:15 final size:16
Alignment explanation
Indices: 17127399--17127432 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17127389 AAAATATTTT
17127399 TTTATCATTTTAATAA
1 TTTATCATTTTAATAA
*
17127415 TTTAT-ATTTTTATAA
1 TTTATCATTTTAATAA
17127430 TTT
1 TTT
17127433 TTAAAAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTATCATTTTAATAA
Done.