Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 5 of 208
Found at i:1567225 original size:138 final size:139
Alignment explanation
Indices: 1566886--1567278 Score: 410
Period size: 138 Copynumber: 2.8 Consensus size: 139
1566876 GAGGACACAT
*
1566886 ATATAATTAATATATGAATTTGATTCATACAAAATATT--AAT-TGTAAATATTTTACCGAATTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAAAATAT-TAAATA-TTTACTGAATTT
* * * *
1566948 ATTAATATAAACTGTTATATTAATTAATACTGCTCAGAATATAAAAGAAATGAAAATTAATATTA
64 ATTAATATAAACAGTTATATTAATTAATACTGATCAAAATATAAAAGAAATGAAAAATAATATTA
* *
1567013 TTTTGGAAATA
129 TTTTGAAAAGA
* * *
1567024 ATATAATTAATATATAAATTTGATTCATACAAAATATT--AAT-TGTATATGTTTTACTGAATTT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAAAATAT-TAAAT-ATTTACTGAATTT
* *
1567086 ATTAATATAAACAGTTATATTAATTAATA-TCGATCAAAATATAAAAGATATGAAAAATATTATT
64 ATTAATATAAACAGTTATATTAATTAATACT-GATCAAAATATAAAAGAAATGAAAAATAATATT
1567150 -TGTTTGAAAAGA
128 AT-TTTGAAAAGA
1567162 ATAT-ATTAATATATGAATTTGATTCATACAAAATATTACAAAATATTAACTATATATGTTTTA-
1 ATATAATTAATATATGAATTTGATTCATACAAAATATT--AAAATATT-A--A-ATA---TTTAC
* * * ** *
1567225 TCGAATTTATTAATATAAATAATTATATTAATTCATTTTAATCAAAATATAAAA
57 T-GAATTTATTAATATAAACAGTTATATTAATTAATACTGATCAAAATATAAAA
1567279 TACATTAAAA
Statistics
Matches: 218, Mismatches: 20, Indels: 25
0.83 0.08 0.10
Matches are distributed among these distances:
137 34 0.16
138 125 0.57
141 4 0.02
142 2 0.01
145 2 0.01
146 1 0.00
147 49 0.22
148 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (139 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAAAATATTAAATATTTACTGAATTTAT
TAATATAAACAGTTATATTAATTAATACTGATCAAAATATAAAAGAAATGAAAAATAATATTATT
TTGAAAAGA
Found at i:1570460 original size:138 final size:137
Alignment explanation
Indices: 1570311--1570626 Score: 528
Period size: 138 Copynumber: 2.3 Consensus size: 137
1570301 GAGAACATAG
1570311 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
1570376 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACATAGAAATTAATATTA-TT
66 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACAT-GAAA--AATATTATTT
*
1570440 -TTGGAAATA
128 CTTGGAAAGA
* * **
1570449 ATATAATTAATATATAAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTTATT
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
*
1570514 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGATATGAAAAATATTATTTGCT
66 AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACATGAAAAATATTATTT-CT
1570579 TGGAAAGA
130 TGGAAAGA
1570587 ATATAATTAATATATGAATTTGATTCATACAAAATATTAA
1 ATATAATTAATATATGAATTTGATTCATACAAAATATTAA
1570627 CTATTCATTA
Statistics
Matches: 168, Mismatches: 7, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
135 7 0.04
136 2 0.01
137 4 0.02
138 155 0.92
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (137 bp):
ATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTAAATATTTTACCGAATTTATT
AATATAAACAGTTATATTAATTAATATCGGTCAAAATATAAAAGACATGAAAAATATTATTTCTT
GGAAAGA
Found at i:1578551 original size:6 final size:6
Alignment explanation
Indices: 1578540--1578574 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1578530 TTTTGATGTA
1578540 TATATC TATATC TATATC TATATC TATATC TATAT
1 TATATC TATATC TATATC TATATC TATATC TATAT
1578575 AATATATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (6 bp):
TATATC
Found at i:1579651 original size:3 final size:3
Alignment explanation
Indices: 1579643--1579699 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
1579633 TCCGCAACCG
1579643 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1579691 TAA TAA TAA
1 TAA TAA TAA
1579700 AAGAAACTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1582163 original size:21 final size:21
Alignment explanation
Indices: 1582137--1582176 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1582127 AGCGACGGAG
1582137 AAAATGATTTAGTGACGAATA
1 AAAATGATTTAGTGACGAATA
1582158 AAAATGATTTAGTGACGAA
1 AAAATGATTTAGTGACGAA
1582177 AGATATTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.20, T:0.28
Consensus pattern (21 bp):
AAAATGATTTAGTGACGAATA
Found at i:1585822 original size:30 final size:31
Alignment explanation
Indices: 1585781--1585840 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
1585771 ACATTAAATT
1585781 TTGAGGGATCTAATTAAAATTTTAAAAAAAA
1 TTGAGGGATCTAATTAAAATTTTAAAAAAAA
*
1585812 TTGA-GGATCTAATTAAAATTTTAAGAAAA
1 TTGAGGGATCTAATTAAAATTTTAAAAAAA
1585841 TTAATGAGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (31 bp):
TTGAGGGATCTAATTAAAATTTTAAAAAAAA
Found at i:1585855 original size:30 final size:30
Alignment explanation
Indices: 1585786--1585855 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
1585776 AAATTTTGAG
* *
1585786 GGATCTAATTAAAATTTTAAAAAAAATTGA
1 GGATATAATTAAAATTTTAAAAAAAATTAA
* *
1585816 GGATCTAATTAAAATTTT-AAGAAAATTAA
1 GGATATAATTAAAATTTTAAAAAAAATTAA
*
1585845 TGAGTATAATT
1 GGA-TATAATT
1585856 TTAGAGGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 11 0.31
30 24 0.69
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.36
Consensus pattern (30 bp):
GGATATAATTAAAATTTTAAAAAAAATTAA
Found at i:1588511 original size:30 final size:31
Alignment explanation
Indices: 1588465--1588528 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
1588455 TTAACAACCC
*
1588465 GACTTAAATAAAAACTTCCGAATAGTTCAGT
1 GACTTAAATAAAAACTTCAGAATAGTTCAGT
* * *
1588496 GACTT-AATGAAAACTTTAGAATAGTTTAGT
1 GACTTAAATAAAAACTTCAGAATAGTTCAGT
1588526 GAC
1 GAC
1588529 CATTTTGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (31 bp):
GACTTAAATAAAAACTTCAGAATAGTTCAGT
Found at i:1601118 original size:2 final size:2
Alignment explanation
Indices: 1601111--1601175 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
1601101 AAATAGTTAG
1601111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1601153 TA TA TA TA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1601176 GATTTTGTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1601420 original size:39 final size:42
Alignment explanation
Indices: 1601350--1601432 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 42
1601340 TATTTTCATA
1601350 TTGGAACTTAAAATTTTTTTTTATCCAAAGTTAGACCTTGAT
1 TTGGAACTTAAAATTTTTTTTTATCCAAAGTTAGACCTTGAT
*
1601392 TTGGAACTT-AAA-TTTTTTTTATCC-AAGTTAGACTTTGAT
1 TTGGAACTTAAAATTTTTTTTTATCCAAAGTTAGACCTTGAT
1601431 TT
1 TT
1601433 TACAGTTTGA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 16 0.40
40 12 0.30
41 3 0.08
42 9 0.22
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (42 bp):
TTGGAACTTAAAATTTTTTTTTATCCAAAGTTAGACCTTGAT
Found at i:1609422 original size:13 final size:13
Alignment explanation
Indices: 1609401--1609464 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
1609391 ACACTCAAAT
1609401 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
1609414 TTCTCAAAATCAC
1 TTTTCAAAAGCAC
*
1609427 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
1609440 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
1609453 ATTTT-AAAAGCA
1 -TTTTCAAAAGCA
1609465 AAAAAGAACT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
12 4 0.09
13 31 0.72
14 8 0.19
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:1609913 original size:54 final size:54
Alignment explanation
Indices: 1609844--1609946 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
1609834 CATGCACATG
*
1609844 ATCAAACTAGGAATCACTTTAATTTAGTGGCAATTAGT-TTATATATTATCTTAC
1 ATCAAACTAGCAATCACTTTAATTTAGTGGCAATTAGTCTT-TATATTATCTTAC
* **
1609898 ATCAAACTAGCAATCACTTTCATTTAGTTTCAATTAGTCTTTATATTAT
1 ATCAAACTAGCAATCACTTTAATTTAGTGGCAATTAGTCTTTATATTAT
1609947 ATTAGAAGTG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (54 bp):
ATCAAACTAGCAATCACTTTAATTTAGTGGCAATTAGTCTTTATATTATCTTAC
Found at i:1611856 original size:31 final size:30
Alignment explanation
Indices: 1611787--1611875 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 30
1611777 TTTGTCCAAT
* * * *
1611787 TTAATACTTAAACTTAACACTTTTCCTAAT
1 TTAATACCTAAACTTGACACTTTTCTTAAG
1611817 TTAATACCTAAACTTGACACATTTTCTTAAG
1 TTAATACCTAAACTTGACAC-TTTTCTTAAG
* *
1611848 TTAGTACCTAAGCTTGACACCTTTTCTT
1 TTAATACCTAAACTTGACA-CTTTTCTT
1611876 TTTGGGATTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 18 0.35
31 32 0.63
32 1 0.02
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (30 bp):
TTAATACCTAAACTTGACACTTTTCTTAAG
Found at i:1612432 original size:31 final size:31
Alignment explanation
Indices: 1612388--1612495 Score: 80
Period size: 31 Copynumber: 3.5 Consensus size: 31
1612378 GGGCTAAAAA
* *
1612388 AAGTTTAGGTACCAAATTAGAAAAAAATATC
1 AAGTTCAGATACCAAATTAGAAAAAAATATC
* **
1612419 AAGTTCAGATACCAAATTTGGCCAAAAA-A--
1 AAGTTCAGATACCAAA-TTAGAAAAAAATATC
* * *
1612448 AAGTTGA-AGTACCAAATTAAAAAAAAATGTC
1 AAGTTCAGA-TACCAAATTAGAAAAAAATATC
* *
1612479 AAATTCAAATACCAAAT
1 AAGTTCAGATACCAAAT
1612496 GTTATATTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
28 8 0.14
29 13 0.22
31 28 0.48
32 9 0.16
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (31 bp):
AAGTTCAGATACCAAATTAGAAAAAAATATC
Found at i:1612439 original size:60 final size:60
Alignment explanation
Indices: 1612307--1612495 Score: 213
Period size: 60 Copynumber: 3.1 Consensus size: 60
1612297 TAAATTTAGG
* * *
1612307 TACCAAA-TTGGACCTAAAAAAGGCTTAGGTACCAAATTAGAAAAAAAAGAGTCAAGTTCATG-
1 TACCAAATTTGG-CCTAAAAAAAGTTTAGGTACCAAATTAG-AAAAAAATA-TCAAGTTCA-GA
* *
1612369 TA-CTAATTTGGGCTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAGTTCAGA
1 TACCAAATTTGGCCTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAGTTCAGA
* * * * * * *
1612428 TACCAAATTTGGCCAAAAAAAAGTTGAAGTACCAAATTAAAAAAAAATGTCAAATTCAAA
1 TACCAAATTTGGCCTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAGTTCAGA
1612488 TACCAAAT
1 TACCAAAT
1612496 GTTATATTAA
Statistics
Matches: 110, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.01
59 11 0.10
60 64 0.58
61 28 0.25
62 6 0.05
ACGTcount: A:0.50, C:0.13, G:0.14, T:0.23
Consensus pattern (60 bp):
TACCAAATTTGGCCTAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATATCAAGTTCAGA
Found at i:1619685 original size:16 final size:17
Alignment explanation
Indices: 1619661--1619701 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
1619651 AGTAGACTCG
1619661 TATAAAATAT-AAAATT
1 TATAAAATATGAAAATT
*
1619677 TATATAATATGAAAA-T
1 TATAAAATATGAAAATT
1619693 TA-AAAATAT
1 TATAAAATAT
1619702 TATATAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 12 0.55
17 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (17 bp):
TATAAAATATGAAAATT
Found at i:1619714 original size:23 final size:23
Alignment explanation
Indices: 1619661--1619714 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
1619651 AGTAGACTCG
1619661 TATAAAATATAAAATTTATATAA
1 TATAAAATATAAAATTTATATAA
1619684 TATGAAAAT-TAAAAATATTATATAA
1 TAT-AAAATAT-AAAAT-TTATATAA
1619709 T-TAAAA
1 TATAAAA
1619715 AGTATGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 8 0.29
24 11 0.39
25 9 0.32
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TATAAAATATAAAATTTATATAA
Found at i:1627152 original size:394 final size:389
Alignment explanation
Indices: 1626417--1627190 Score: 999
Period size: 394 Copynumber: 2.0 Consensus size: 389
1626407 TTAAAACCAG
* * * * *
1626417 AGATGAAGGTGATGTTATCGATGTTGTAGGAGGTATATTTCTTTTATGTTCTGCACTCGTTCATG
1 AGATGAAGGTGATGCTACCGATGTTGTAGCAGGTATATTTCTTTTATATTCTGCACCCGTTCATG
* ** *
1626482 CTTTAATTAACCCTAAATCTACGTATTCATATGTTAATCTAACTTTATGAAATTGAGAAATTTGA
66 CTTTAATTAACCCTAAATCTACGTATCCATATGTTAATCTAACTTTATGAAATCAAGAAAATTGA
* * *
1626547 AATCTAAATTGTCAAGCATCGCAATAGTTGTCACAAGTCCTTTAGGACAATCTGCGCTCGTTAAC
131 AATCTAAATTATCAAGCATCGCAATAATTGTCACAAGTCCCTTAGGACAATCTGCGCTCGTTAAC
* **
1626612 CAAGTCTGTAGGCACTGTCCATTAGAGATCCAAAAAAAAATCATTCCCGGTTGATCATGCCATTT
196 CAAATCTGTAGGCACTGTCCATTAGAGATCCAAAAAAAAATCATTCCCAATTGATCATGCCATTT
* *
1626677 GGAGATTTGGGTTTTTGTATTGTTTTTTTTCAAGCTAAGGTAATAATGTTATGGTCATTCTCTGG
261 GGAGATTTGGG----TG-AGTGTTTTTTTTCAAGCTAAGGTAATAATGTTATGGTCATACTCTGG
1626742 ACCACATTTTATGTTGTTATAACGTTGTAAAGTCAAGTTATGTTCCTTTTTTCCTAAAGTTCAAA
321 ACCACATTTTATGTTGTTATAACGTTGTAAAGTCAAGTTATGTTCCTTTTTTCCTAAAGTTCAAA
1626807 TCAA
386 TCAA
* *
1626811 AGATGAGGGTGATGCTACCGATGTTGTAGCAGGTATAATTT-TTTTATATTTTGCACCCGTTCAT
1 AGATGAAGGTGATGCTACCGATGTTGTAGCAGGTAT-ATTTCTTTTATATTCTGCACCCGTTCAT
* * *** * *
1626875 GCTTTAATTGACCTTGGTTCTATGTATCCATATGTTAATTCTAGCTTTATGAAATCAAGAAAATT
65 GCTTTAATTAACCCTAAATCTACGTATCCATATGTTAA-TCTAACTTTATGAAATCAAGAAAATT
* ** * * *
1626940 GAAATGTGTATTATCAAGCAT-GACAATAATTGTCACAAGTCCCTTAGGACAATTTGTGTTCGTT
129 GAAATCTAAATTATCAAGCATCG-CAATAATTGTCACAAGTCCCTTAGGACAATCTGCGCTCGTT
* *** *
1627004 AACCAAATGTGTAGGTGTTGTCCATTAGAGATCC-AAAATAAATCATTCCCAATTGATCATGCCA
193 AACCAAATCTGTAGGCACTGTCCATTAGAGATCCAAAAAAAAATCATTCCCAATTGATCATGCCA
* * *
1627068 TTTGGAGATTTGGG-G-GT-TTTTTTTTCAAGCTAAGGTAATGATGTTATGGTCATAGTTTGGAC
258 TTTGGAGATTTGGGTGAGTGTTTTTTTTCAAGCTAAGGTAATAATGTTATGGTCATACTCTGGAC
* * * * *
1627130 CACA-TTTA--ATGTTATAATGTTGTAAGGTCAAGTTATGTTCCTTTTTTTTCTAAAGTCCAAA
323 CACATTTTATGTTGTTATAACGTTGTAAAGTCAAGTTATGTTCC-TTTTTTCCTAAAGTTCAAA
1627191 GACTTTATGG
Statistics
Matches: 331, Mismatches: 45, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
383 30 0.09
384 17 0.05
385 4 0.01
386 45 0.14
387 1 0.00
389 1 0.00
394 125 0.38
395 108 0.33
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (389 bp):
AGATGAAGGTGATGCTACCGATGTTGTAGCAGGTATATTTCTTTTATATTCTGCACCCGTTCATG
CTTTAATTAACCCTAAATCTACGTATCCATATGTTAATCTAACTTTATGAAATCAAGAAAATTGA
AATCTAAATTATCAAGCATCGCAATAATTGTCACAAGTCCCTTAGGACAATCTGCGCTCGTTAAC
CAAATCTGTAGGCACTGTCCATTAGAGATCCAAAAAAAAATCATTCCCAATTGATCATGCCATTT
GGAGATTTGGGTGAGTGTTTTTTTTCAAGCTAAGGTAATAATGTTATGGTCATACTCTGGACCAC
ATTTTATGTTGTTATAACGTTGTAAAGTCAAGTTATGTTCCTTTTTTCCTAAAGTTCAAATCAA
Found at i:1629091 original size:51 final size:50
Alignment explanation
Indices: 1628973--1629151 Score: 166
Period size: 51 Copynumber: 3.5 Consensus size: 50
1628963 TATCACTTAA
* * * * *
1628973 TAGCCTACGCATAGTACTACACACGTGATCAAGCTTTCTAGTTCACGTAG
1 TAGCCTACACATAGTACTACACACGTGACCAAGCATTCTAGTACACATAG
* *
1629023 TAGCCTAAACATAGTACTACACACGTGACCAAGGCCATT-TGGTACACATAG
1 TAGCCTACACATAGTACTACACACGTGACCAA-G-CATTCTAGTACACATAG
* * * * *
1629074 TAGCCTGCACATAGTACTACACATGTGACCATTATC-TATC-AATACACGTAG
1 TAGCCTACACATAGTACTACACACGTGACCA--AGCAT-TCTAGTACACATAG
* *
1629125 TAGCCTGCACTTAGTACTACACACGTG
1 TAGCCTACACATAGTACTACACACGTG
1629152 TTCATAGGTA
Statistics
Matches: 107, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
50 30 0.28
51 73 0.68
52 3 0.03
53 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (50 bp):
TAGCCTACACATAGTACTACACACGTGACCAAGCATTCTAGTACACATAG
Found at i:1632874 original size:27 final size:28
Alignment explanation
Indices: 1632839--1632892 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
1632829 AAACTCTTCC
* *
1632839 AAAAGAAACTCA-AGAGAAATTATTAAA
1 AAAAGAAACCCAGAAAGAAATTATTAAA
*
1632866 AAAAGAAACCCAGAAAGAATTTATTAA
1 AAAAGAAACCCAGAAAGAAATTATTAA
1632893 CTCAAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (28 bp):
AAAAGAAACCCAGAAAGAAATTATTAAA
Found at i:1636386 original size:16 final size:17
Alignment explanation
Indices: 1636365--1636397 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1636355 TAAATTTATT
1636365 TTTTAAAAT-TTTTTAA
1 TTTTAAAATATTTTTAA
1636381 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
1636398 AATACTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:1636437 original size:22 final size:22
Alignment explanation
Indices: 1636412--1636454 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1636402 CTTTTTTTTA
1636412 TTTTT-TATTT-TTAAAATAAAT
1 TTTTTGTATTTATTAAAA-AAAT
*
1636433 TTTTTGTGTTTATTAAAAAAAT
1 TTTTTGTATTTATTAAAAAAAT
1636455 GGGCCGGGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 8 0.42
23 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
TTTTTGTATTTATTAAAAAAAT
Found at i:1639400 original size:3 final size:3
Alignment explanation
Indices: 1639392--1639419 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1639382 TACGGTTCCT
1639392 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1639420 ACTTTATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1645819 original size:2 final size:2
Alignment explanation
Indices: 1645814--1645852 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1645804 ATATATATAT
1645814 AG AG AG AG AG 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 AG AG AG AG AG A
1645853 TTGGCTTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1649036 original size:108 final size:108
Alignment explanation
Indices: 1648871--1649082 Score: 379
Period size: 108 Copynumber: 2.0 Consensus size: 108
1648861 CTCTCTCTCC
1648871 GTCACCTGCTAGGTCCACATTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTTACCTG
1 GTCACCTGCTAGGTCCACATTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTTACCTG
* * **
1648936 TCCAGTCCATAATACAACCCCCTTCTCCTATGCCTTCCCCTAT
66 CCCAGTCCACAATACAACCCCCTTCTCCTACACCTTCCCCTAT
*
1648979 GTCACCTGCTAGGTCCACGTTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTTACCTG
1 GTCACCTGCTAGGTCCACATTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTTACCTG
1649044 CCCAGTCCACAATACAACCCCCTTCTCCTACACCTTCCC
66 CCCAGTCCACAATACAACCCCCTTCTCCTACACCTTCCC
1649083 ATAATTCCCC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 99 1.00
ACGTcount: A:0.21, C:0.42, G:0.08, T:0.30
Consensus pattern (108 bp):
GTCACCTGCTAGGTCCACATTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTTACCTG
CCCAGTCCACAATACAACCCCCTTCTCCTACACCTTCCCCTAT
Found at i:1649043 original size:57 final size:56
Alignment explanation
Indices: 1648874--1649044 Score: 139
Period size: 57 Copynumber: 3.1 Consensus size: 56
1648864 TCTCTCCGTC
1648874 ACCTGCTAGGTCCACATTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTT
1 ACCTGCTAGGTCCAC-TTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTT
* * * * **
1648931 ACCTGTCCA-GTCCA--TA-ATACAAC-C-C-CCTTCTCCTATGCCTTCCCCT-ATGTC---
1 ACCTG-CTAGGTCCACTTACCTAC-TCTCACACCTTCCCCTATG---TCAACTAAT-TCTTT
1648982 ACCTGCTAGGTCCACGTTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTT
1 ACCTGCTAGGTCCAC-TTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTT
1649039 ACCTGC
1 ACCTGC
1649045 CCAGTCCACA
Statistics
Matches: 84, Mismatches: 12, Indels: 36
0.64 0.09 0.27
Matches are distributed among these distances:
50 2 0.02
51 21 0.25
52 1 0.01
53 6 0.07
54 18 0.21
55 6 0.07
56 1 0.01
57 27 0.32
58 2 0.02
ACGTcount: A:0.21, C:0.39, G:0.08, T:0.32
Consensus pattern (56 bp):
ACCTGCTAGGTCCACTTACCTACTCTCACACCTTCCCCTATGTCAACTAATTCTTT
Found at i:1652379 original size:2 final size:2
Alignment explanation
Indices: 1652372--1652396 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1652362 TATAGAATAG
1652372 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1652397 GTAGACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1661688 original size:22 final size:22
Alignment explanation
Indices: 1661669--1661712 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1661659 TAACAACTTG
1661669 CTTCTCTTAACAAACTAACTAA
1 CTTCTCTTAACAAACTAACTAA
1661691 CTTCTCTTAACAAACTAACTAA
1 CTTCTCTTAACAAACTAACTAA
1661713 TCTGCTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.32
Consensus pattern (22 bp):
CTTCTCTTAACAAACTAACTAA
Found at i:1665470 original size:48 final size:48
Alignment explanation
Indices: 1665418--1665609 Score: 314
Period size: 48 Copynumber: 4.0 Consensus size: 48
1665408 TAGCCTACTT
* * * *
1665418 CAGCACCCCAATTTTGACCAAATTCTTTTCCATTTTGACCAGGTCTAA
1 CAGCACACCAATTTTGACCAAAGTCTTTTGCATTTTGACCAGGTCCAA
1665466 CAGCACACCAATTTTGACCAACA-TCTTTTGCATTTTGACCAGGTCCAA
1 CAGCACACCAATTTTGACCAA-AGTCTTTTGCATTTTGACCAGGTCCAA
*
1665514 CAGCACCCCAATTTTGACCAAAGTCTTTTGCATTTTGACCAGGTCCAA
1 CAGCACACCAATTTTGACCAAAGTCTTTTGCATTTTGACCAGGTCCAA
*
1665562 CAGCACACCAATTTTGACCAAAGTCTTTTGCATTTTGACTAGGTCCAA
1 CAGCACACCAATTTTGACCAAAGTCTTTTGCATTTTGACCAGGTCCAA
1665610 AATAATTTTG
Statistics
Matches: 136, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
47 1 0.01
48 134 0.99
49 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (48 bp):
CAGCACACCAATTTTGACCAAAGTCTTTTGCATTTTGACCAGGTCCAA
Found at i:1666611 original size:12 final size:12
Alignment explanation
Indices: 1666594--1666631 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1666584 AAGATGCCTT
1666594 CCTGGAAAGATG
1 CCTGGAAAGATG
*
1666606 CCTGG-AAGAGG
1 CCTGGAAAGATG
*
1666617 ACTGGAAAGATG
1 CCTGGAAAGATG
1666629 CCT
1 CCT
1666632 TCAAGGAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.32, C:0.18, G:0.34, T:0.16
Consensus pattern (12 bp):
CCTGGAAAGATG
Found at i:1670780 original size:16 final size:15
Alignment explanation
Indices: 1670744--1670779 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1670734 ATTTCACTTG
*
1670744 AAAAAAGGGGCATTC
1 AAAAAAGGGGCACTC
1670759 AAAAAAGGGGCACTC
1 AAAAAAGGGGCACTC
1670774 AAAAAA
1 AAAAAA
1670780 AACAAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.14, G:0.22, T:0.08
Consensus pattern (15 bp):
AAAAAAGGGGCACTC
Found at i:1670790 original size:14 final size:14
Alignment explanation
Indices: 1670773--1670800 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1670763 AAGGGGCACT
1670773 CAAAAAAAACAAAA
1 CAAAAAAAACAAAA
1670787 CAAAAAAAACAAAA
1 CAAAAAAAACAAAA
1670801 AACAACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (14 bp):
CAAAAAAAACAAAA
Found at i:1670800 original size:19 final size:18
Alignment explanation
Indices: 1670774--1670813 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
1670764 AGGGGCACTC
*
1670774 AAAAAAAACAA-AACAAA
1 AAAAAAAAAAACAACAAA
1670791 AAAAACAAAAAACAACAAA
1 AAAAA-AAAAAACAACAAA
1670810 AAAA
1 AAAA
1670814 GAGGGAGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
19 10 0.50
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAACAAA
Found at i:1673037 original size:14 final size:15
Alignment explanation
Indices: 1673013--1673051 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1673003 GAGCTCTCTG
*
1673013 TTCTCTTTTCTTGTT
1 TTCTTTTTTCTTGTT
*
1673028 TT-TTTTTTCTTTTT
1 TTCTTTTTTCTTGTT
1673042 TTCTTTTTTC
1 TTCTTTTTTC
1673052 ATTAGAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (15 bp):
TTCTTTTTTCTTGTT
Found at i:1673489 original size:3 final size:3
Alignment explanation
Indices: 1673481--1673602 Score: 172
Period size: 3 Copynumber: 40.3 Consensus size: 3
1673471 GAATTAGTCC
1673481 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
1673529 TAT TAT TGT TGT TGT TGT TGT TGT TGT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1673577 TAT TAT TAT TAT TAT TAT TACT TAT T
1 TAT TAT TAT TAT TAT TAT TA-T TAT T
1673603 TATTTATATT
Statistics
Matches: 116, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
3 113 0.97
4 3 0.03
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:1677898 original size:19 final size:19
Alignment explanation
Indices: 1677874--1677916 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
1677864 CCCCATACAT
1677874 TGTTTTGGTCTTTGAAAAC
1 TGTTTTGGTCTTTGAAAAC
1677893 TGTTTTGGTCTTTGAAAAC
1 TGTTTTGGTCTTTGAAAAC
1677912 TGTTT
1 TGTTT
1677917 GCTTCTACGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (19 bp):
TGTTTTGGTCTTTGAAAAC
Found at i:1678257 original size:31 final size:31
Alignment explanation
Indices: 1678220--1678279 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1678210 TTTTTCGTCC
*
1678220 AATTTAATATCTAAACTTAACACTTTTTTCT
1 AATTTAATACCTAAACTTAACACTTTTTTCT
*
1678251 AATTTAATACCTAAACTTCACACTTTTTT
1 AATTTAATACCTAAACTTAACACTTTTTT
1678280 TTAAGTTAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (31 bp):
AATTTAATACCTAAACTTAACACTTTTTTCT
Found at i:1678779 original size:29 final size:29
Alignment explanation
Indices: 1678727--1678782 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1678717 TGTAATAAAT
**
1678727 TTAGGTACCAAATTGAACCTAAAAAAGGC
1 TTAGGTACCAAATTGAACAAAAAAAAGGC
1678756 TTAGGTACCAAATTAGAA-AAAAAAAAG
1 TTAGGTACCAAATT-GAACAAAAAAAAG
1678783 TCAAGTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (29 bp):
TTAGGTACCAAATTGAACAAAAAAAAGGC
Found at i:1678918 original size:58 final size:58
Alignment explanation
Indices: 1678809--1678918 Score: 150
Period size: 58 Copynumber: 1.9 Consensus size: 58
1678799 ATTTGGGCTA
* * * *
1678809 AAAAAAAGTTTAGGTACCAAATTAGAAAAAATTGTTAATCCAGATACCAAATTTAGCC
1 AAAAAAAGTTTAAGTACCAAATTAGAAAAAAATGTAAATCCAAATACCAAATTTAGCC
* *
1678867 AAAAAAAGTTTAAGTACCAAATTA-AAAAAAATGTCAAATTCAAATATCAAAT
1 AAAAAAAGTTTAAGTACCAAATTAGAAAAAAATGT-AAATCCAAATACCAAAT
1678919 GTTATATTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
57 9 0.20
58 36 0.80
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (58 bp):
AAAAAAAGTTTAAGTACCAAATTAGAAAAAAATGTAAATCCAAATACCAAATTTAGCC
Found at i:1685383 original size:22 final size:22
Alignment explanation
Indices: 1685359--1685442 Score: 132
Period size: 22 Copynumber: 3.8 Consensus size: 22
1685349 TCAATTCTCC
*
1685359 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
1685381 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
1685403 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * *
1685425 ACGAACTAAACCCTCATG
1 ACGTACTAAGCTCTCATG
1685443 GCTCTACACA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:1685706 original size:63 final size:63
Alignment explanation
Indices: 1685607--1685739 Score: 266
Period size: 63 Copynumber: 2.1 Consensus size: 63
1685597 TTTACAACAT
1685607 ATACCCCCATCCTGATAAGAATACAATGAATACAGATTATCCTTATCTCTCATAGTTGCCATC
1 ATACCCCCATCCTGATAAGAATACAATGAATACAGATTATCCTTATCTCTCATAGTTGCCATC
1685670 ATACCCCCATCCTGATAAGAATACAATGAATACAGATTATCCTTATCTCTCATAGTTGCCATC
1 ATACCCCCATCCTGATAAGAATACAATGAATACAGATTATCCTTATCTCTCATAGTTGCCATC
1685733 ATACCCC
1 ATACCCC
1685740 AAGCTAGACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.29
Consensus pattern (63 bp):
ATACCCCCATCCTGATAAGAATACAATGAATACAGATTATCCTTATCTCTCATAGTTGCCATC
Found at i:1694517 original size:31 final size:29
Alignment explanation
Indices: 1694482--1694549 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
1694472 CCGACCTTAA
*
1694482 ATAATCA-ACTCCTACACAAACAAACAAATAC
1 ATAATCACACCCCT-CA-AAAC-AACAAATAC
*
1694513 ATAATCATCACCCCTCAAAACAGCAAATAC
1 ATAATCA-CACCCCTCAAAACAACAAATAC
1694543 ATAATCA
1 ATAATCA
1694550 TAAGAGCGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
30 15 0.45
31 11 0.33
32 2 0.06
33 5 0.15
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.18
Consensus pattern (29 bp):
ATAATCACACCCCTCAAAACAACAAATAC
Found at i:1696471 original size:51 final size:51
Alignment explanation
Indices: 1696391--1696529 Score: 244
Period size: 51 Copynumber: 2.7 Consensus size: 51
1696381 TGTAAAAAAA
* *
1696391 AAAATTAAATT-ACACAATGTGTAAATGTTGAGGGTTAGATTTTTTAGAAC
1 AAAACTAAATTGACATAATGTGTAAATGTTGAGGGTTAGATTTTTTAGAAC
*
1696441 AAAACTAAATTGACATAATGTGTAAATGTTGAGTGTTAGATTTTTTAGAAC
1 AAAACTAAATTGACATAATGTGTAAATGTTGAGGGTTAGATTTTTTAGAAC
1696492 AAAACTAAATTGACATAATGTGTAAATGTTGAGGGTTA
1 AAAACTAAATTGACATAATGTGTAAATGTTGAGGGTTA
1696530 AAGTTCCTAT
Statistics
Matches: 84, Mismatches: 4, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
50 10 0.12
51 74 0.88
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (51 bp):
AAAACTAAATTGACATAATGTGTAAATGTTGAGGGTTAGATTTTTTAGAAC
Found at i:1700657 original size:29 final size:29
Alignment explanation
Indices: 1700625--1700687 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
1700615 AATTTAATTT
1700625 TTATTTTTTATTTAAAAATACAAGTTCAA
1 TTATTTTTTATTTAAAAATACAAGTTCAA
1700654 TTATTTTTTATTTAAAAATACAAGTTCAA
1 TTATTTTTTATTTAAAAATACAAGTTCAA
1700683 TTATT
1 TTATT
1700688 AACATAGTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (29 bp):
TTATTTTTTATTTAAAAATACAAGTTCAA
Found at i:1700703 original size:29 final size:29
Alignment explanation
Indices: 1700636--1700700 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1700626 TATTTTTTAT
*** *
1700636 TTAAAAATACAAGTTCAATTATTTTTTAT
1 TTAAAAATACAAGTTCAATTATTACATAG
1700665 TTAAAAATACAAGTTCAATTATTAACATAG
1 TTAAAAATACAAGTTCAATTATT-ACATAG
1700695 TTAAAA
1 TTAAAA
1700701 TACTCTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 23 0.74
30 8 0.26
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.40
Consensus pattern (29 bp):
TTAAAAATACAAGTTCAATTATTACATAG
Found at i:1700924 original size:2 final size:2
Alignment explanation
Indices: 1700919--1700951 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1700909 ATATATATAT
1700919 AG AG 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 AG AG A
1700952 TTGGCTTGAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1711629 original size:5 final size:5
Alignment explanation
Indices: 1711588--1711628 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
1711578 CTCGCCCTTA
*
1711588 ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT AATTT A
1 ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT ACTTT A
1711629 AGGCTATACC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (5 bp):
ACTTT
Found at i:1720873 original size:19 final size:19
Alignment explanation
Indices: 1720849--1720885 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1720839 GATTGATGCC
*
1720849 AAATGTTTATATCTACTAA
1 AAATGTTAATATCTACTAA
*
1720868 AAATGTTAATTTCTACTA
1 AAATGTTAATATCTACTA
1720886 TCAGTCCTTG
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:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (19 bp):
AAATGTTAATATCTACTAA
Found at i:1724224 original size:22 final size:20
Alignment explanation
Indices: 1724198--1724253 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 20
1724188 GGCCTGGCCC
1724198 ATTTTATACATTTGTAATATAT
1 ATTTTATA-ATTT-TAATATAT
*
1724220 ATTTTTTAATTTTAATTTATAT
1 ATTTTATAATTTTAA--TATAT
*
1724242 ATTATATAATTT
1 ATTTTATAATTT
1724254 ATATCACATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 22 0.76
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTTATAATTTTAATATAT
Found at i:1730260 original size:22 final size:22
Alignment explanation
Indices: 1730235--1730276 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1730225 TCTTTATACA
*
1730235 CTTTGTACATTTAGAATTTAGT
1 CTTTCTACATTTAGAATTTAGT
* *
1730257 CTTTCTACTTTTTGAATTTA
1 CTTTCTACATTTAGAATTTA
1730277 AAATTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.10, T:0.55
Consensus pattern (22 bp):
CTTTCTACATTTAGAATTTAGT
Found at i:1730596 original size:29 final size:30
Alignment explanation
Indices: 1730563--1730621 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
1730553 CTATGGTTTA
* *
1730563 TGTGCAATTGTGTAC-ATAAATTTTGATTT
1 TGTGCAATTGTATACAAGAAATTTTGATTT
*
1730592 TGTGCAATTTTATACAAGAAATTTTGATTT
1 TGTGCAATTGTATACAAGAAATTTTGATTT
1730622 GATTCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (30 bp):
TGTGCAATTGTATACAAGAAATTTTGATTT
Found at i:1748650 original size:13 final size:13
Alignment explanation
Indices: 1748632--1748664 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1748622 GTAACTATTT
1748632 TATTAAAAAAATA
1 TATTAAAAAAATA
*
1748645 TATTAAATAAATA
1 TATTAAAAAAATA
1748658 -ATTAAAA
1 TATTAAAA
1748665 TGATTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
TATTAAAAAAATA
Found at i:1748824 original size:20 final size:18
Alignment explanation
Indices: 1748782--1748824 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1748772 GTTTTTATAT
*
1748782 TTAAAAAAAAATTGTTAA
1 TTAATAAAAAATTGTTAA
*
1748800 ATAATAAAAAATATGTTACA
1 TTAATAAAAAAT-TGTTA-A
1748820 TTAAT
1 TTAAT
1748825 CATCCAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 10 0.50
19 5 0.25
20 5 0.25
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAATAAAAAATTGTTAA
Found at i:1748842 original size:7 final size:7
Alignment explanation
Indices: 1748830--1748855 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1748820 TTAATCATCC
1748830 AATAGGA
1 AATAGGA
1748837 AATAGGA
1 AATAGGA
1748844 AATAGGA
1 AATAGGA
1748851 AATAG
1 AATAG
1748856 TTGATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (7 bp):
AATAGGA
Found at i:1750564 original size:11 final size:11
Alignment explanation
Indices: 1750548--1750575 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1750538 TATTAATTTA
1750548 TAATAATAAAG
1 TAATAATAAAG
1750559 TAATAATAAAG
1 TAATAATAAAG
1750570 TAATAA
1 TAATAA
1750576 AACCATCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (11 bp):
TAATAATAAAG
Found at i:1750743 original size:3 final size:3
Alignment explanation
Indices: 1750735--1750759 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1750725 AGTAATCAAT
1750735 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1750760 AAGTGGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1751033 original size:5 final size:5
Alignment explanation
Indices: 1751023--1751048 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1751013 ACATTTTACT
1751023 ATATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA ATATA ATATA ATATA A
1751049 GTTTTACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATATA
Found at i:1754557 original size:8 final size:8
Alignment explanation
Indices: 1754544--1754577 Score: 68
Period size: 8 Copynumber: 4.2 Consensus size: 8
1754534 AAAGAACCTG
1754544 TTTGATGT
1 TTTGATGT
1754552 TTTGATGT
1 TTTGATGT
1754560 TTTGATGT
1 TTTGATGT
1754568 TTTGATGT
1 TTTGATGT
1754576 TT
1 TT
1754578 GGTTGTGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.12, C:0.00, G:0.24, T:0.65
Consensus pattern (8 bp):
TTTGATGT
Found at i:1756389 original size:20 final size:20
Alignment explanation
Indices: 1756364--1756405 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1756354 AAATTCTGAT
1756364 CATATCTACTTTTTAAGATA
1 CATATCTACTTTTTAAGATA
1756384 CATATCTACTTTTTAAGATA
1 CATATCTACTTTTTAAGATA
1756404 CA
1 CA
1756406 ATGCTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.43
Consensus pattern (20 bp):
CATATCTACTTTTTAAGATA
Found at i:1757847 original size:26 final size:26
Alignment explanation
Indices: 1757790--1757848 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1757780 ACCTTTTTTT
* *
1757790 TAAAAAGATTGATGGTCAAATTCGAC
1 TAAAAAGATTGATGATCAAATTAGAC
* *
1757816 TAAAAAGATTGATGATTAAATTTAGCC
1 TAAAAAGATTGATGATCAAA-TTAGAC
1757843 TAAAAA
1 TAAAAA
1757849 AGGCCAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 18 0.64
27 10 0.36
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.29
Consensus pattern (26 bp):
TAAAAAGATTGATGATCAAATTAGAC
Found at i:1761884 original size:20 final size:20
Alignment explanation
Indices: 1761859--1761897 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1761849 TAAAAAAATT
1761859 TAAAGTTAAAATATATTATC
1 TAAAGTTAAAATATATTATC
1761879 TAAAGTTAAAATATATTAT
1 TAAAGTTAAAATATATTAT
1761898 AATATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAAAGTTAAAATATATTATC
Found at i:1762754 original size:2 final size:2
Alignment explanation
Indices: 1762747--1762805 Score: 95
Period size: 2 Copynumber: 30.0 Consensus size: 2
1762737 TTGAATTGGA
1762747 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
1762789 AT AT -T AT GA- AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT
1762806 TTGTAAATGT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 51 0.94
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1762976 original size:25 final size:25
Alignment explanation
Indices: 1762948--1763049 Score: 92
Period size: 22 Copynumber: 4.3 Consensus size: 25
1762938 GCGCTCTCTA
1762948 ATTATTAGCACGTCAGTGCTATCTG
1 ATTATTAGCACGTCAGTGCTATCTG
*
1762973 ATTATTAGCACGTCAATGCTATCTG
1 ATTATTAGCACGTCAGTGCTATCTG
* * *
1762998 --T-TTAGCACATCTGTGCTCTCTG
1 ATTATTAGCACGTCAGTGCTATCTG
* *
1763020 --TA-TAGCACTTCAGTGCTCTCT-
1 ATTATTAGCACGTCAGTGCTATCTG
1763041 ATTCATTAG
1 ATT-ATTAG
1763050 TGCATAATAA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
22 35 0.54
23 2 0.03
24 1 0.02
25 27 0.42
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.38
Consensus pattern (25 bp):
ATTATTAGCACGTCAGTGCTATCTG
Found at i:1763005 original size:22 final size:24
Alignment explanation
Indices: 1762950--1763005 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
1762940 GCTCTCTAAT
*
1762950 TATTAGCACGTCAGTGCTATCTGA
1 TATTAGCACGTCAATGCTATCTGA
1762974 TTATTAGCACGTCAATGCTATCTG-
1 -TATTAGCACGTCAATGCTATCTGA
1762998 T-TTAGCAC
1 TATTAGCAC
1763006 ATCTGTGCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 7 0.23
23 1 0.03
25 22 0.73
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (24 bp):
TATTAGCACGTCAATGCTATCTGA
Found at i:1763169 original size:31 final size:31
Alignment explanation
Indices: 1763133--1763191 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1763123 AAGAATATGA
1763133 GATAGTGAATTGAAAATAGAATGTGAAAAAC
1 GATAGTGAATTGAAAATAGAATGTGAAAAAC
*
1763164 GATAGTGAATTGAAAATAGGATGTGAAA
1 GATAGTGAATTGAAAATAGAATGTGAAA
1763192 TATGTTGTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (31 bp):
GATAGTGAATTGAAAATAGAATGTGAAAAAC
Found at i:1770906 original size:9 final size:10
Alignment explanation
Indices: 1770894--1770944 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
1770884 CAAAAAAATT
1770894 AAAATATT-A
1 AAAATATTAA
*
1770903 AAAAT-TTGA
1 AAAATATTAA
1770912 AAAAT-TTAAA
1 AAAATATT-AA
1770922 AAAATATTACA
1 AAAATATTA-A
1770933 AAAATATTAA
1 AAAATATTAA
1770943 AA
1 AA
1770945 TTATGGAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 2 0.05
9 13 0.35
10 10 0.27
11 12 0.32
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAATATTAA
Found at i:1770935 original size:11 final size:11
Alignment explanation
Indices: 1770911--1770944 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1770901 TAAAAATTTG
1770911 AAAAAT-TTAA
1 AAAAATATTAA
*
1770921 AAAAATATTAC
1 AAAAATATTAA
1770932 AAAAATATTAA
1 AAAAATATTAA
1770943 AA
1 AA
1770945 TTATGGAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAAATATTAA
Found at i:1771016 original size:18 final size:18
Alignment explanation
Indices: 1770995--1771030 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1770985 TTTAAAAATT
*
1770995 TATTAAAAAATGAATAAA
1 TATTAAAAAATAAATAAA
1771013 TATTAAAAAATAAATAAA
1 TATTAAAAAATAAATAAA
1771031 ATCATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TATTAAAAAATAAATAAA
Found at i:1785140 original size:5 final size:5
Alignment explanation
Indices: 1785130--1785156 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
1785120 ATCAAGAAAG
1785130 TTGGA TTGGA TTGGA TTGGA TTGGA TT
1 TTGGA TTGGA TTGGA TTGGA TTGGA TT
1785157 AGATCGGACC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.44
Consensus pattern (5 bp):
TTGGA
Found at i:1787641 original size:10 final size:10
Alignment explanation
Indices: 1787622--1787658 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
1787612 TTTAAAAAAT
1787622 ATTTTT-ATA
1 ATTTTTAATA
1787631 ATTTTTAATA
1 ATTTTTAATA
*
1787641 A-TTTTAATG
1 ATTTTTAATA
1787650 ATTTTTAAT
1 ATTTTTAAT
1787659 TTTTCAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 14 0.56
10 11 0.44
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:1804009 original size:11 final size:11
Alignment explanation
Indices: 1803995--1804021 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1803985 AATAAATATT
1803995 ATTTTATTAAG
1 ATTTTATTAAG
1804006 ATTTTATTAAG
1 ATTTTATTAAG
1804017 ATTTT
1 ATTTT
1804022 TAGTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
ATTTTATTAAG
Found at i:1805591 original size:5 final size:5
Alignment explanation
Indices: 1805581--1805612 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1805571 AAATGATAAT
*
1805581 ATTGA ATTGA ATTGA ATTAA ATTGA ATTGA AT
1 ATTGA ATTGA ATTGA ATTGA ATTGA ATTGA AT
1805613 GAAGAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.41
Consensus pattern (5 bp):
ATTGA
Found at i:1815929 original size:69 final size:69
Alignment explanation
Indices: 1815812--1815940 Score: 177
Period size: 69 Copynumber: 1.9 Consensus size: 69
1815802 ATTCGCAAAT
* * * *
1815812 ATTTGGACAGCAGTAAAAACATTTGGACAGCATTGACTTGTACCAAAAATGGACAGCATTTAAGC
1 ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATTTAAGC
1815877 ACTA
66 ACTA
* * * **
1815881 ATTTGGACAACATTAATAACATTCGGACAACATAGATTTGTATGAAAAATGGACAGCATT
1 ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATT
1815941 AATATGCTCA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 51 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (69 bp):
ATTTGGACAACAGTAAAAACATTCGGACAACATAGACTTGTACCAAAAATGGACAGCATTTAAGC
ACTA
Found at i:1815997 original size:34 final size:35
Alignment explanation
Indices: 1815954--1816023 Score: 99
Period size: 34 Copynumber: 2.0 Consensus size: 35
1815944 ATGCTCAAAA
* *
1815954 TGGACAACATT-TATACATG-CAAAGCAACCACATT
1 TGGACAACATTATA-ACATGTAAAAACAACCACATT
1815988 TGGACAACATTATAACATGTAAAAACAACCACATT
1 TGGACAACATTATAACATGTAAAAACAACCACATT
1816023 T
1 T
1816024 TAATACCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.24
Consensus pattern (35 bp):
TGGACAACATTATAACATGTAAAAACAACCACATT
Found at i:1816773 original size:41 final size:41
Alignment explanation
Indices: 1816703--1816879 Score: 191
Period size: 40 Copynumber: 4.3 Consensus size: 41
1816693 ACTCAATGTT
* * *
1816703 TCGCACACTAAATGCCATTGCATAGCCGAAGCTAT-T-ATAA
1 TCGCACACTAAGTGCCA-TACATAGCCGAAGCTATCTCACAA
* * ***
1816743 TCCCGCACACTAAGTGCCTTACATAGCCGAATCTATCTCAGTC
1 T--CGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
* *
1816786 TCGCACACTAAGTGCCATATATAGCCGAAGCTAT-TCCCAA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
* *
1816826 TCGCACACTAAGTGCCATAAATAGCCGAATCTATCTCA-AA
1 TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
1816866 TCGCACACTAAGTG
1 TCGCACACTAAGTG
1816880 ATAAACATAG
Statistics
Matches: 115, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
40 51 0.44
41 47 0.41
42 15 0.13
43 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATACATAGCCGAAGCTATCTCACAA
Found at i:1816850 original size:81 final size:80
Alignment explanation
Indices: 1816703--1816879 Score: 232
Period size: 81 Copynumber: 2.2 Consensus size: 80
1816693 ACTCAATGTT
* * * *
1816703 TCGCACACTAAATGCCATTGCATAGCCGAAGCTATTATAATCCCGCACACTAAGTGCCTTACATA
1 TCGCACACTAAGTGCCATT-CATAGCCGAAGCTATTACAAT-CCGCACACTAAGTGCCATAAATA
**
1816768 GCCGAATCTATCTCAGTC
64 GCCGAATCTATCTCA-AA
*
1816786 TCGCACACTAAGTGCCATAT-ATAGCCGAAGCTATTCCCAAT-CGCACACTAAGTGCCATAAATA
1 TCGCACACTAAGTGCCAT-TCATAGCCGAAGCTATT-ACAATCCGCACACTAAGTGCCATAAATA
1816849 GCCGAATCTATCTCAAA
64 GCCGAATCTATCTCAAA
1816866 TCGCACACTAAGTG
1 TCGCACACTAAGTG
1816880 ATAAACATAG
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
80 14 0.16
81 35 0.41
82 15 0.18
83 20 0.24
84 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (80 bp):
TCGCACACTAAGTGCCATTCATAGCCGAAGCTATTACAATCCGCACACTAAGTGCCATAAATAGC
CGAATCTATCTCAAA
Found at i:1819427 original size:61 final size:61
Alignment explanation
Indices: 1819304--1819429 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 61
1819294 TTTGATCCTA
* * * **
1819304 AATTTTAAAAAAATCAACAAATTTAACTATCAATATTTATAAAATTTATCATTTTAGTTTT
1 AATTCTAAAAAAATCAACAAATTTAACCATCAATATTTATAAAATTTATCAATTTAAATTT
* * *
1819365 AATTCTAAAAAAATCAACAAATTTAACCCTTAGTATTTACT-AAATGTT-TCAATTTAAATTT
1 AATTCTAAAAAAATCAACAAATTTAACCATCAATATTTA-TAAAAT-TTATCAATTTAAATTT
1819426 AATT
1 AATT
1819430 TTAATTCTAA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 52 0.95
62 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (61 bp):
AATTCTAAAAAAATCAACAAATTTAACCATCAATATTTATAAAATTTATCAATTTAAATTT
Found at i:1821349 original size:61 final size:61
Alignment explanation
Indices: 1821254--1821375 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
1821244 TGTTGATGGG
1821254 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
1 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
1821315 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
1 CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
1821376 TCTTCTTCTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.38
Consensus pattern (61 bp):
CCGCATTTATGATGGTTTGTACCAGTTTGATCTATTAGACACTCAGAGTTTCAAAACTTCT
Found at i:1824552 original size:18 final size:18
Alignment explanation
Indices: 1824529--1824584 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
1824519 AATAGACTCA
1824529 TTTGCTTACTCCACTTCT
1 TTTGCTTACTCCACTTCT
1824547 TTTGCTTACTCCACTTCT
1 TTTGCTTACTCCACTTCT
1824565 TTTGCTTACTCCACTTCT
1 TTTGCTTACTCCACTTCT
1824583 TT
1 TT
1824585 CCTATGAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.11, C:0.32, G:0.05, T:0.52
Consensus pattern (18 bp):
TTTGCTTACTCCACTTCT
Found at i:1825420 original size:45 final size:46
Alignment explanation
Indices: 1825366--1825476 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
1825356 ATCACTTGTC
*
1825366 CTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTACCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
*
1825411 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTATCA
1 CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
1825457 CTTGATCAGATAAGTGTAGC
1 CTTGATCAGATAAGTGTAGC
1825477 CACTTATCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
45 21 0.33
46 42 0.67
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (46 bp):
CTTGATCAGATAAGTGTAGCTGAAGCTACCACTTATCACTTTACCA
Found at i:1825459 original size:46 final size:45
Alignment explanation
Indices: 1825353--1825623 Score: 207
Period size: 37 Copynumber: 6.6 Consensus size: 45
1825343 CATATGACCT
* *
1825353 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
1825396 CTTATCACTTTACCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
1825442 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* ** *
1825479 CTTATCACTTTGTTTCTTGATCAAATAA--GT-G-T-A---ACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* **
1825516 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
* ** *
1825553 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGCTAAAACTACCA
1 CTTATCACTTTATCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
1825599 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTATCACTTGATCAGA
1825624 AGTACTCAAA
Statistics
Matches: 204, Mismatches: 11, Indels: 23
0.86 0.05 0.10
Matches are distributed among these distances:
37 99 0.49
39 2 0.01
40 3 0.01
41 1 0.00
42 1 0.00
43 10 0.05
44 5 0.02
45 21 0.10
46 62 0.30
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTATCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:1825480 original size:37 final size:37
Alignment explanation
Indices: 1825438--1825585 Score: 251
Period size: 37 Copynumber: 4.0 Consensus size: 37
1825428 AGCTGAAGCT
* **
1825438 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
1825475 GCCACTTATCACTTTGTTTCTTGATCAAATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1825512 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1825549 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1825586 GCTAAAACTA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 104 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:1840196 original size:17 final size:17
Alignment explanation
Indices: 1840174--1840209 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1840164 GATATTAAAA
1840174 AATAATGAATTAAATGT
1 AATAATGAATTAAATGT
* *
1840191 AATAATGAGTTAGATGT
1 AATAATGAATTAAATGT
1840208 AA
1 AA
1840210 AAATTGTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (17 bp):
AATAATGAATTAAATGT
Found at i:1847924 original size:137 final size:136
Alignment explanation
Indices: 1847678--1847953 Score: 543
Period size: 137 Copynumber: 2.0 Consensus size: 136
1847668 CTGAACTAGA
1847678 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1847743 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGGAT
66 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAA-GAT
1847808 TCAAGGT
130 TCAAGGT
1847815 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1 ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
1847880 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
66 ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
1847945 CAAGGT
131 CAAGGT
1847951 ACA
1 ACA
1847954 TTAGACCAAA
Statistics
Matches: 139, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
136 13 0.09
137 126 0.91
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (136 bp):
ACAAATTTAAGGTTGGAAGCGATTTCTGGGCTCTTGGCTGTCTAGGCTTTGTTTTTTACTATTTA
ATTTTCAACGACTTTTAGCCCTTGAGTAGGCCCAGAGTCGATTTTGGAAGAAAAAAAAAAAGATT
CAAGGT
Found at i:1871221 original size:6 final size:6
Alignment explanation
Indices: 1871170--1871204 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
1871160 AGAATGTTCT
1871170 TTTACA TTTACA TTTACA TTTACA TTTACA TTTAC
1 TTTACA TTTACA TTTACA TTTACA TTTACA TTTAC
1871205 TTGACTCACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTACA
Found at i:1882816 original size:15 final size:16
Alignment explanation
Indices: 1882796--1882825 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1882786 TATTTAAAGC
1882796 AAAAAAAAA-AATTTG
1 AAAAAAAAATAATTTG
1882811 AAAAAAAAATAATTT
1 AAAAAAAAATAATTT
1882826 TCTTTCTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAAAAAAATAATTTG
Found at i:1884738 original size:40 final size:40
Alignment explanation
Indices: 1884666--1884741 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
1884656 GAAGCCTGCG
* * *
1884666 GGAGAGCTCGCGTAAGCCTCGCAGAAATGAGGCCGCAAGA
1 GGAGAGCTCGAGTAAACCTCGCAGAAACGAGGCCGCAAGA
* **
1884706 GGAGAGCTCGAGTAAACCTCGTAGGGACGAGGCCGC
1 GGAGAGCTCGAGTAAACCTCGCAGAAACGAGGCCGC
1884742 GAGCTATGTC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.28, C:0.25, G:0.37, T:0.11
Consensus pattern (40 bp):
GGAGAGCTCGAGTAAACCTCGCAGAAACGAGGCCGCAAGA
Found at i:1891754 original size:3 final size:3
Alignment explanation
Indices: 1891746--1891810 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
1891736 AATGTTTTAG
1891746 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1891794 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
1891811 AAAGATTTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:1892737 original size:18 final size:18
Alignment explanation
Indices: 1892697--1892737 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
1892687 CTTTTTTTCT
1892697 TTTTTACTTTCCTTTAAA
1 TTTTTACTTTCCTTTAAA
*
1892715 GTTTTACTTTCCTTTAAA
1 TTTTTACTTTCCTTTAAA
1892733 TTTTT
1 TTTTT
1892738 TTAATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTTACTTTCCTTTAAA
Found at i:1893992 original size:2 final size:2
Alignment explanation
Indices: 1893985--1894014 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1893975 TGGAAACTCA
1893985 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
1894015 TACAGCATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1894570 original size:19 final size:18
Alignment explanation
Indices: 1894548--1894584 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
1894538 AATAAAAAAT
1894548 AAAATTCTAAATATTTATA
1 AAAATTCTAAAT-TTTATA
1894567 AAAATTCTAAATTTTATA
1 AAAATTCTAAATTTTATA
1894585 TTTTTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
AAAATTCTAAATTTTATA
Found at i:1899197 original size:8 final size:8
Alignment explanation
Indices: 1899186--1899227 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
1899176 TTTAATCTTT
1899186 TAAAATTA
1 TAAAATTA
1899194 T-AAATATA
1 TAAAAT-TA
*
1899202 TAAAATAA
1 TAAAATTA
*
1899210 TAAAATAA
1 TAAAATTA
1899218 TAAAATTA
1 TAAAATTA
1899226 TA
1 TA
1899228 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 4 0.13
8 22 0.73
9 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
TAAAATTA
Found at i:1899207 original size:16 final size:16
Alignment explanation
Indices: 1899186--1899227 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1899176 TTTAATCTTT
1899186 TAAAATTAT-AAATATA
1 TAAAATTATAAAATA-A
*
1899202 TAAAATAATAAAATAA
1 TAAAATTATAAAATAA
1899218 TAAAATTATA
1 TAAAATTATA
1899228 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATTATAAAATAA
Found at i:1900328 original size:22 final size:22
Alignment explanation
Indices: 1900303--1900344 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1900293 AGTTACTTTC
*
1900303 ATTAATT-TTACAAATAATATAT
1 ATTAATTATTA-AAAAAATATAT
1900325 ATTAATTATTAAAAAAATAT
1 ATTAATTATTAAAAAAATAT
1900345 TTAAAATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAATTATTAAAAAAATATAT
Found at i:1901877 original size:14 final size:15
Alignment explanation
Indices: 1901847--1901879 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1901837 CTCCCCTCAC
1901847 TTGTAATTCATTTCA
1 TTGTAATTCATTTCA
*
1901862 TTGTACTTCA-TTCA
1 TTGTAATTCATTTCA
1901876 TTGT
1 TTGT
1901880 TTCATGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (15 bp):
TTGTAATTCATTTCA
Found at i:1904867 original size:30 final size:31
Alignment explanation
Indices: 1904810--1904872 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1904800 AAAGTACTCC
1904810 TGTCTATGAGGCTATTACATCCAGAGATCGG
1 TGTCTATGAGGCTATTACATCCAGAGATCGG
1904841 TGTCTATGAGGCTATTACAT-CAGAGATCGG
1 TGTCTATGAGGCTATTACATCCAGAGATCGG
1904871 TG
1 TG
1904873 AAAGTATCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 12 0.38
31 20 0.62
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (31 bp):
TGTCTATGAGGCTATTACATCCAGAGATCGG
Found at i:1905293 original size:33 final size:33
Alignment explanation
Indices: 1905251--1905319 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
1905241 ATGAAAAAAA
1905251 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
1 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
*
1905284 ACAAAGAAATAACTCAGCATAGTCATGTTGGGC
1 ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
1905317 ACA
1 ACA
1905320 TACACACTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (33 bp):
ACAAAGAAATAACTAAGCATAGTCATGTTGGGC
Found at i:1924912 original size:15 final size:17
Alignment explanation
Indices: 1924892--1924923 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1924882 TTAGATTTAA
1924892 TTTAAA-ATTAT-ATCT
1 TTTAAACATTATCATCT
1924907 TTTAAACATTATCATCT
1 TTTAAACATTATCATCT
1924924 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (17 bp):
TTTAAACATTATCATCT
Found at i:1934546 original size:26 final size:25
Alignment explanation
Indices: 1934509--1934575 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
1934499 TCTACAAAAC
* *
1934509 AAAAGAACAAAGAACAGCAGAAGCAT
1 AAAAGAAAAAAGAA-AGCAGAAGCAA
* *
1934535 AGAAGAAGAAAGCAAAGCAGAAGCAA
1 AAAAGAAAAAAG-AAAGCAGAAGCAA
1934561 AAAAGAAAAAAGAAA
1 AAAAGAAAAAAGAAA
1934576 TATTGTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 3 0.09
26 30 0.86
27 2 0.06
ACGTcount: A:0.67, C:0.10, G:0.21, T:0.01
Consensus pattern (25 bp):
AAAAGAAAAAAGAAAGCAGAAGCAA
Found at i:1937077 original size:42 final size:40
Alignment explanation
Indices: 1937030--1937167 Score: 137
Period size: 42 Copynumber: 3.5 Consensus size: 40
1937020 AGTAATTCGG
1937030 GGAATCAGCACTTAGCAACCCTTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCC--TTCACATTTAAAATACGGT
* * *
1937072 GGAATCAGCACTTAGCAA--CTAC-CA-AT-GAAT-CGG-
1 GGAATCAGCACTTAGCAACCCTTCACATTTAAAATACGGT
*
1937105 GGAATCATCACTTAGCAATCCCCCTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAA---CCCTTCACATTTAAAATACGGT
*
1937148 GGAATCAGCGCTTAGCAACC
1 GGAATCAGCACTTAGCAACC
1937168 ACCAATGAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 22
0.71 0.08 0.20
Matches are distributed among these distances:
33 17 0.22
34 3 0.04
35 3 0.04
36 1 0.01
37 2 0.03
38 5 0.06
39 2 0.03
40 4 0.05
41 3 0.04
42 21 0.27
43 16 0.21
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
GGAATCAGCACTTAGCAACCCTTCACATTTAAAATACGGT
Found at i:1937162 original size:76 final size:75
Alignment explanation
Indices: 1936993--1937202 Score: 314
Period size: 76 Copynumber: 2.8 Consensus size: 75
1936983 TATCTGTTGT
* * * **
1936993 CGGTGGATTCAGCAATTAGCAACCACCAGT-AATTCGGGGAATCAGCACTTAGCAACCCTTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACTTAGCAACCCCCTTCA
1937057 CATTTAAAATA
65 CATTTAAAATA
* *
1937068 CGGTGGAATCAGCACTTAGCAACTACCAATGAATCGGGGAATCATCACTTAGCAATCCCCCTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCCTTCA
1937133 CATTTAAAATA
65 CATTTAAAATA
* *
1937144 CGGTGGAATCAGCGCTTAGCAACCACCAATGAATCGGGGAATCAGCGCTTAGCAACCCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
1937203 TTGGGGGAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 51 0.42
76 71 0.58
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTTAAAATA
Found at i:1938595 original size:5 final size:5
Alignment explanation
Indices: 1938585--1938614 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1938575 ATTTCATGTT
1938585 AGAAG AGAAG AGAAG AGAAG AGAAG A-AAG A
1 AGAAG AGAAG AGAAG AGAAG AGAAG AGAAG A
1938615 AAGTTTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:1940439 original size:45 final size:45
Alignment explanation
Indices: 1940382--1940530 Score: 174
Period size: 45 Copynumber: 3.3 Consensus size: 45
1940372 ATATACTGAC
1940382 TACTGTTACTGTTACCGATTTGACACTTTGTGTGTTAAATACTGT
1 TACTGTTACTGTTACCGATTTGACACTTTGTGTGTTAAATACTGT
* * **
1940427 TACTATTACTGTTACCGATTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACCGATTTGACACTTTGTGTGTTAAATACTGT
* * * * **
1940472 TACCGTTAATGTTACAGA-TTCAGCACTTTGTGTACTAAATACTGT
1 TACTGTTACTGTTACCGATTTGA-CACTTTGTGTGTTAAATACTGT
* *
1940517 TACTGCTACCGTTA
1 TACTGTTACTGTTA
1940531 TTGATTACTG
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
44 2 0.02
45 83 0.98
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (45 bp):
TACTGTTACTGTTACCGATTTGACACTTTGTGTGTTAAATACTGT
Found at i:1940725 original size:19 final size:20
Alignment explanation
Indices: 1940703--1940745 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1940693 CGTGATTGTA
* *
1940703 GAATAT-AATTTGAAAATGT
1 GAATATGAATATGAAAATAT
1940722 GAAT-TGAATATGAAAATAT
1 GAATATGAATATGAAAATAT
1940741 GAATA
1 GAATA
1940746 GAAAGCATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.33
Consensus pattern (20 bp):
GAATATGAATATGAAAATAT
Found at i:1943135 original size:25 final size:26
Alignment explanation
Indices: 1943071--1943156 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 26
1943061 CAGACACACC
*
1943071 ACAGCTCGTATGAGCTT-CTTGATTT
1 ACAGCTCGTATGAGCTTACTCGATTT
*
1943096 ACAGCTCATGA-GAGCTTAC-CGATTCT
1 ACAGCTCGT-ATGAGCTTACTCGATT-T
*
1943122 -CAGCTCGTATGAGCTTA-TTGATTT
1 ACAGCTCGTATGAGCTTACTCGATTT
*
1943146 ATAGCTCGTAT
1 ACAGCTCGTAT
1943157 AAGCATATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 2 0.04
25 45 0.90
26 3 0.06
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (26 bp):
ACAGCTCGTATGAGCTTACTCGATTT
Found at i:1946148 original size:21 final size:21
Alignment explanation
Indices: 1946124--1946166 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1946114 AAATCCCAAA
1946124 TTTTCTTCCTTTCCTTCCCTT
1 TTTTCTTCCTTTCCTTCCCTT
* * * *
1946145 TTTTTTTCTTTTTCTTTCCTT
1 TTTTCTTCCTTTCCTTCCCTT
1946166 T
1 T
1946167 CCTTCTTTCC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCTTCCTTTCCTTCCCTT
Found at i:1946418 original size:14 final size:13
Alignment explanation
Indices: 1946392--1946442 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
1946382 GTTTATTTGA
1946392 AATATAATAATAT
1 AATATAATAATAT
1946405 AATATAATTAATAT
1 AATATAA-TAATAT
* *
1946419 AAT-TTACAATAT
1 AATATAATAATAT
*
1946431 AATAAAATAATA
1 AATATAATAATA
1946443 ATATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:1948954 original size:24 final size:26
Alignment explanation
Indices: 1948903--1948971 Score: 72
Period size: 27 Copynumber: 2.7 Consensus size: 26
1948893 ACATATATTC
**
1948903 TCAATTCAATCACAATTTCTCACACTT
1 TCAATTCAATCA-TTTTTCTCACACTT
1948930 TCAATTCAATCATTTTTC-CAC-CTT
1 TCAATTCAATCATTTTTCTCACACTT
*
1948954 TCAA-TCAATAATTATTTC
1 TCAATTCAATCATT-TTTC
1948972 ACAAATTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
23 8 0.21
24 11 0.29
25 3 0.08
26 4 0.11
27 12 0.32
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (26 bp):
TCAATTCAATCATTTTTCTCACACTT
Found at i:1949123 original size:3 final size:3
Alignment explanation
Indices: 1949115--1949177 Score: 92
Period size: 3 Copynumber: 21.0 Consensus size: 3
1949105 ATTCCCACTC
1949115 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATAA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
* *
1949163 ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA
1949178 CTTACCTCAC
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:1950224 original size:5 final size:5
Alignment explanation
Indices: 1950216--1950282 Score: 79
Period size: 5 Copynumber: 14.2 Consensus size: 5
1950206 TATTTAATTT
* * *
1950216 ATATA ATATA AAACA ATATA ATATA ATATA ATATA ATAT- ATATT ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1950265 ATA-A A-ATA ATAT- ATATA A
1 ATATA ATATA ATATA ATATA A
1950283 AACATAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
3 1 0.02
4 12 0.23
5 40 0.75
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:1950262 original size:7 final size:7
Alignment explanation
Indices: 1950215--1950279 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
1950205 CTATTTAATT
1950215 TATATAA
1 TATATAA
*
1950222 TATAAAA
1 TATATAA
*
1950229 CAATATAA
1 -TATATAA
1950237 TATA-ATA
1 TATATA-A
1950244 TAATATAA
1 T-ATATAA
*
1950252 TATATAT
1 TATATAA
1950259 TATATAA
1 TATATAA
*
1950266 TAAAATAA
1 T-ATATAA
1950274 TATATA
1 TATATA
1950280 TAAAACATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 27 0.60
8 16 0.36
9 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (7 bp):
TATATAA
Found at i:1950280 original size:22 final size:22
Alignment explanation
Indices: 1950214--1950280 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1950204 TCTATTTAAT
* *
1950214 TTATATAATATAA-AACA-ATA
1 TTATATAATAAAATAATATATA
*
1950234 TAATATAATATAATATAATATATA
1 TTATATAATA-AA-ATAATATATA
1950258 TTATATAATAAAATAATATATA
1 TTATATAATAAAATAATATATA
1950280 T
1 T
1950281 AAAACATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.23
21 1 0.03
22 12 0.31
23 5 0.13
24 12 0.31
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATATAATAAAATAATATATA
Found at i:1955318 original size:29 final size:30
Alignment explanation
Indices: 1955271--1955327 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
1955261 TTGATATAAT
* *
1955271 ATACAATTATATATATG-AACTTTAATTTG
1 ATACAATTATACACATGAAACTTTAATTTG
*
1955300 ATACAATTATACACGTGAAACTTTAATT
1 ATACAATTATACACATGAAACTTTAATT
1955328 GTTGTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.40
Consensus pattern (30 bp):
ATACAATTATACACATGAAACTTTAATTTG
Found at i:1955522 original size:30 final size:31
Alignment explanation
Indices: 1955502--1955581 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
1955492 AGAATTGGAT
1955502 AAATTAAAATTT-TATATATAAAAATATACA
1 AAATTAAAATTTATATATATAAAAATATACA
* ** * **
1955532 AAATTAAAATTTATGTATATAATTACATATT
1 AAATTAAAATTTATATATATAAAAATATACA
*
1955563 AAATTATAATTTATATATA
1 AAATTAAAATTTATATATA
1955582 ATTTTAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
30 12 0.29
31 29 0.71
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (31 bp):
AAATTAAAATTTATATATATAAAAATATACA
Found at i:1963710 original size:18 final size:20
Alignment explanation
Indices: 1963687--1963733 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
1963677 AATTCATATA
1963687 TATAATTACATATT-AAA-T
1 TATAATTACATATTAAAATT
1963705 TATAATT-CAT-TTAAAATT
1 TATAATTACATATTAAAATT
1963723 TATAA-TACATA
1 TATAATTACATA
1963734 AAAAAATCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
16 2 0.08
17 7 0.28
18 16 0.64
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAATTACATATTAAAATT
Found at i:1985559 original size:22 final size:19
Alignment explanation
Indices: 1985534--1985580 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
1985524 TCTTCCAGTT
1985534 CTTGAATCATTATCTTTTTGCA
1 CTTGAATC-TTA-CTTTTT-CA
1985556 CTTGTAATCTTACTTTTTCA
1 CTTG-AATCTTACTTTTTCA
1985576 -TTGAA
1 CTTGAA
1985581 ACTTTCCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 2 0.08
21 6 0.25
22 7 0.29
23 4 0.17
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (19 bp):
CTTGAATCTTACTTTTTCA
Found at i:1994154 original size:30 final size:29
Alignment explanation
Indices: 1994114--1994266 Score: 105
Period size: 30 Copynumber: 5.2 Consensus size: 29
1994104 CAAATTTCAT
*
1994114 ATTTTTTAAAATTATATTTTAACCTCTAAA
1 ATTTTCTAAAATTATATTTTAACC-CTAAA
* *
1994144 ATTTTCTAAAATTATAGTTTGACCCCT-AA
1 ATTTTCTAAAATTATA-TTTTAACCCTAAA
* * * *
1994173 CTTTCCTAAAATTACATTTTGAATCCTAAA
1 ATTTTCTAAAATTATATTTT-AACCCTAAA
* * * * *
1994203 CTTTTTCT--ATTTACATTTTGACCCTTAA
1 -ATTTTCTAAAATTATATTTTAACCCTAAA
* *
1994231 ATTTTCCTAAAATTATATTTTGACCCCAAA
1 ATTTT-CTAAAATTATATTTTAACCCTAAA
1994261 AGTTTT
1 A-TTTT
1994267 GCATACCCTA
Statistics
Matches: 95, Mismatches: 20, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
27 4 0.04
28 11 0.12
29 29 0.31
30 36 0.38
31 15 0.16
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (29 bp):
ATTTTCTAAAATTATATTTTAACCCTAAA
Found at i:1994193 original size:29 final size:30
Alignment explanation
Indices: 1994120--1994257 Score: 129
Period size: 29 Copynumber: 4.7 Consensus size: 30
1994110 TCATATTTTT
* * * *
1994120 TAAAATTATATTTTAACCTCTAAAATTTTC
1 TAAAATTATATTTTGACCCCTAAACTTTCC
*
1994150 TAAAATTATAGTTTGACCCCT-AACTTTCC
1 TAAAATTATATTTTGACCCCTAAACTTTCC
* ** *
1994179 TAAAATTACATTTTGAATCCTAAACTTTTTC
1 TAAAATTATATTTTGACCCCTAAAC-TTTCC
* * * *
1994210 T--ATTTACATTTTGACCCTTAAATTTTCC
1 TAAAATTATATTTTGACCCCTAAACTTTCC
1994238 TAAAATTATATTTTGACCCC
1 TAAAATTATATTTTGACCCC
1994258 AAAAGTTTTG
Statistics
Matches: 85, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
28 5 0.06
29 40 0.47
30 35 0.41
31 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (30 bp):
TAAAATTATATTTTGACCCCTAAACTTTCC
Found at i:1994734 original size:4 final size:4
Alignment explanation
Indices: 1994725--1994772 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
1994715 GGGTTAGGGT
* * *
1994725 GAAA GAAA GAAA G-AA GAAA GGAA GAAA AAAA GAAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA
1994773 AAAAAGAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:1994743 original size:11 final size:10
Alignment explanation
Indices: 1994730--1994783 Score: 58
Period size: 9 Copynumber: 5.3 Consensus size: 10
1994720 AGGGTGAAAG
1994730 AAAGAAAGAA
1 AAAGAAAGAA
*
1994740 GAAAGGAAGAAAA
1 -AAA-GAA-AGAA
1994753 AAAGAAA-AA
1 AAAGAAAGAA
1994762 AAAGAAAGAA
1 AAAGAAAGAA
1994772 AAA-AAAGAA
1 AAAGAAAGAA
1994781 AAA
1 AAA
1994784 AATAAAAGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
9 18 0.46
10 6 0.15
11 6 0.15
12 6 0.15
13 3 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Done.