Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 4 of 54
Found at i:1634966 original size:34 final size:34
Alignment explanation
Indices: 1634915--1635015 Score: 132
Period size: 34 Copynumber: 3.0 Consensus size: 34
1634905 AAAAAAAAAA
*
1634915 AATTTAATGGA-GTCAACAGCCGAAGGAAAGAATC
1 AATTTAATGAACG-CAACAGCCGAAGGAAAGAATC
* *
1634949 AGTTTAATGAACGCAACAGCCGAAGGAAAGAATT
1 AATTTAATGAACGCAACAGCCGAAGGAAAGAATC
* **
1634983 AATTTAATGAAGGCAACAGGGGAAGGAAAGAAT
1 AATTTAATGAACGCAACAGCCGAAGGAAAGAAT
1635016 GGAGAGGTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 58 0.98
35 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.26, T:0.17
Consensus pattern (34 bp):
AATTTAATGAACGCAACAGCCGAAGGAAAGAATC
Found at i:1635927 original size:14 final size:15
Alignment explanation
Indices: 1635908--1635944 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1635898 TATTTATTTT
1635908 ATTAATTAATA-AAA
1 ATTAATTAATATAAA
1635922 ATTAA-TAATATAAA
1 ATTAATTAATATAAA
*
1635936 AATAATTAA
1 ATTAATTAA
1635945 AATTTATCCG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATTAATATAAA
Found at i:1645145 original size:2 final size:2
Alignment explanation
Indices: 1645132--1645187 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
1645122 AATTTTGGCC
*
1645132 AT AT AC 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
1645174 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1645188 TTAAAGCTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1654671 original size:24 final size:23
Alignment explanation
Indices: 1654627--1654676 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
1654617 TGTTAAATAA
1654627 AAAAAAATAAACATAGAAAAAATG
1 AAAAAAATAAACATAGAAAAAA-G
1654651 AAAAAAATAATA-ATA-ACAAAAAG
1 AAAAAAATAA-ACATAGA-AAAAAG
1654674 AAA
1 AAA
1654677 GAGAATAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.21
24 18 0.75
25 1 0.04
ACGTcount: A:0.78, C:0.04, G:0.06, T:0.12
Consensus pattern (23 bp):
AAAAAAATAAACATAGAAAAAAG
Found at i:1658763 original size:61 final size:61
Alignment explanation
Indices: 1658689--1658813 Score: 223
Period size: 61 Copynumber: 2.0 Consensus size: 61
1658679 GGTGAGACAA
* *
1658689 GTGCAGGCAAAATCTAGTGCTTCACCAATTTTAACTAGGATACTAAACAATGCATGTGTGT
1 GTGCAGGCAAAATCTAGCGCTTCACCAATTTTAACTAGGATACTAAACAATGCATGTGTAT
*
1658750 GTGCAGGCAAAATCTAGCGCTTCACCAATTTTAGCTAGGATACTAAACAATGCATGTGTAT
1 GTGCAGGCAAAATCTAGCGCTTCACCAATTTTAACTAGGATACTAAACAATGCATGTGTAT
1658811 GTG
1 GTG
1658814 TATATATACA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (61 bp):
GTGCAGGCAAAATCTAGCGCTTCACCAATTTTAACTAGGATACTAAACAATGCATGTGTAT
Found at i:1666672 original size:3 final size:3
Alignment explanation
Indices: 1666664--1666694 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1666654 GATTAAAAAG
1666664 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1666695 CATGTAAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1667446 original size:21 final size:22
Alignment explanation
Indices: 1667422--1667462 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1667412 TTCTTTCTCT
*
1667422 ATTTTTTAAAAT-AAATTATTA
1 ATTTTATAAAATAAAATTATTA
*
1667443 ATTTTATCAAATAAAATTAT
1 ATTTTATAAAATAAAATTAT
1667463 CAAAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTTATAAAATAAAATTATTA
Found at i:1671404 original size:24 final size:22
Alignment explanation
Indices: 1671359--1671412 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
1671349 TTTATTTCTT
1671359 ATATAAAAATATTAAATATTTA
1 ATATAAAAATATTAAATATTTA
* *
1671381 TATTATAAAAATTTTTTAAT-TTTA
1 -A-TATAAAAA-TATTAAATATTTA
1671405 ATATAAAA
1 ATATAAAA
1671413 TATCCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 7 0.26
23 2 0.07
24 12 0.44
25 6 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATAAAAATATTAAATATTTA
Found at i:1674423 original size:20 final size:22
Alignment explanation
Indices: 1674384--1674429 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1674374 TATTTAACTA
*
1674384 TTTATATTTTATGCATTATAGG
1 TTTATATTTTATGCATTATAAG
*
1674406 TTTATA-TTTA-GTATTATAAG
1 TTTATATTTTATGCATTATAAG
1674426 TTTA
1 TTTA
1674430 GATAGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 12 0.55
21 4 0.18
22 6 0.27
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (22 bp):
TTTATATTTTATGCATTATAAG
Found at i:1698795 original size:197 final size:200
Alignment explanation
Indices: 1698329--1698848 Score: 762
Period size: 197 Copynumber: 2.6 Consensus size: 200
1698319 ATTTTGGGAG
** ** * *
1698329 ATGAAAATTTTCACTTGTTCACACACTGTTTTTACAAGGGACTAATAGCAAATTCATGGCTATTA
1 ATGAAAA--TTCACTTGTTCACACTTTCATTTTACAAGGGACTAATTGCAAATTCATGGCTATAA
* * * *
1698394 TAGTTTG-AATCCATTTTCCCAATCAAAGATTGAAAGTTGAATCCATTTTCCAGTCAATCTGATC
64 TAGTTTGAAATCCATTTTCCCAATCCAAGATTGATAGTTGAATCCATTTCCCAATCAATCTGATC
* * *
1698458 AAGAAAAACTATGGGATTTTTTTGTCTTTTCTTCTCTGCCAATGTTCATCCTATTGCTACAAAGT
129 AAGAAAAACTATGGGATTTTTTTGTCTTTCCTTCTCTGCCAATGATCATCCTATTGCCACAAAGT
*
1698523 CTGGCAT
194 CTGGCAA
* *
1698530 ATGAAAATTCACTTGTTCACACTTTCATTTTACAAGGGACTAATTGCAAATTCACGGCTATGATA
1 ATGAAAATTCACTTGTTCACACTTTCATTTTACAAGGGACTAATTGCAAATTCATGGCTATAATA
*
1698595 GTTTGAAACCCATTTTCCCAATCCAAGATTGATAGTTGAATCCAATTTCCCAATCAATCTGATCA
66 GTTTGAAATCCATTTTCCCAATCCAAGATTGATAGTTGAATCC-ATTTCCCAATCAATCTGATCA
* * *
1698660 AG-AAAATTATGGG-TTTTTTTGTCTTTCCTTCTCTGCCAATGATCATCCTATTGCCACATA-TT
130 AGAAAAACTATGGGATTTTTTTGTCTTTCCTTCTCTGCCAATGATCATCCTATTGCCACAAAGTC
*
1698722 TGGGAA
195 TGGCAA
*
1698728 ATG-AAATTCACTTGTTCACACTTTCATTTTACAAGGGACTACTTGCAAATTCATGGCTATAATA
1 ATGAAAATTCACTTGTTCACACTTTCATTTTACAAGGGACTAATTGCAAATTCATGGCTATAATA
*
1698792 GTTTGAAATCCATTTTCCCAATCCAAGATTGATAGTTGAATCCTTTTTCCCAATCAA
66 GTTTGAAATCCATTTTCCCAATCCAAGATTGATAGTTGAATCC-ATTTCCCAATCAA
1698849 AGATTGATAA
Statistics
Matches: 291, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
197 112 0.38
198 8 0.03
199 99 0.34
200 44 0.15
201 28 0.10
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (200 bp):
ATGAAAATTCACTTGTTCACACTTTCATTTTACAAGGGACTAATTGCAAATTCATGGCTATAATA
GTTTGAAATCCATTTTCCCAATCCAAGATTGATAGTTGAATCCATTTCCCAATCAATCTGATCAA
GAAAAACTATGGGATTTTTTTGTCTTTCCTTCTCTGCCAATGATCATCCTATTGCCACAAAGTCT
GGCAA
Found at i:1698840 original size:32 final size:32
Alignment explanation
Indices: 1698789--1698912 Score: 160
Period size: 32 Copynumber: 3.8 Consensus size: 32
1698779 CATGGCTATA
*
1698789 ATAGTTTGAAATCCATTTTCCCAATCCAAGATTG
1 ATAG-TTG-AATCCATTTTCCCAATCAAAGATTG
*
1698823 ATAGTTGAATCCTTTTTCCCAATCAAAGATTG
1 ATAGTTGAATCCATTTTCCCAATCAAAGATTG
* * *
1698855 ATAATTGACTCCATTTTCCCAATCAAAGATTC
1 ATAGTTGAATCCATTTTCCCAATCAAAGATTG
*
1698887 ACT-GTTGAATCCAATTTCCCAATCAA
1 A-TAGTTGAATCCATTTTCCCAATCAA
1698913 TCTGATCAAG
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
32 72 0.90
33 4 0.05
34 4 0.05
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.35
Consensus pattern (32 bp):
ATAGTTGAATCCATTTTCCCAATCAAAGATTG
Found at i:1704436 original size:6 final size:6
Alignment explanation
Indices: 1704425--1704450 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1704415 TCTTCAAGAC
1704425 TCTATT TCTATT TCTATT TCTATT TC
1 TCTATT TCTATT TCTATT TCTATT TC
1704451 ACAACTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (6 bp):
TCTATT
Found at i:1710201 original size:2 final size:2
Alignment explanation
Indices: 1710194--1710232 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1710184 CTCTTGGTGC
1710194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1710233 GAGGATTAAG
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:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1710877 original size:171 final size:173
Alignment explanation
Indices: 1710347--1710815 Score: 500
Period size: 178 Copynumber: 2.7 Consensus size: 173
1710337 TATATAGATC
* * * **
1710347 TTTTTCTT-TCTTGTTTCTTTGTTAATTTTAGTTTTATGAATAATACCCAGAGTTGAAATAGTGT
1 TTTTTCTTGT-TT-TTTGTTTGTTAATTTGAGTTTTATGAATAATACCCAGAGTCGAAATAGAAT
* * * ** **
1710411 TTATTTTTCCGATCGTGCAATAAATATTTTCTCCTTTATGT-TCCAAAATAATAAATCTTCTTTT
64 TTATTTTTCCAACCCTATAATAAATATTTTCTCCTTTAT-TATCCAAAATAATAAATCTTCTCCT
** * * * * **
1710475 C-AAGGAAATTAAAAGATTTTAAGGAACTATACTAATAGCATTCCTTT
128 CGAAAAAAATTCAAAGATTTTACGAAACTATACTAAAAGCACACC--T
* * *
1710522 TTTTTCTTCTTTTATTTTATTTTATTAATTTGAGTTTTATGAATAATACCCAGAGTCGAAATAGA
1 TTTTTC-T-TGTT-TTTT-GTTTGTTAATTTGAGTTTTATGAATAATACCCAGAGTCGAAATAGA
** * *
1710587 ATTTATTTTTCCGGCCCTGTAATAAATATTTTCTCCTTTATTATGCAAAATAATAAATCTTCTCC
62 ATTTATTTTTCCAACCCTATAATAAATATTTTCTCCTTTATTATCCAAAATAATAAATCTTCTCC
1710652 TCGAAAAAAATTCAAAGATTTTACGAAACTATACTAAAAGCACACCT
127 TCGAAAAAAATTCAAAGATTTTACGAAACTATACTAAAAGCACACCT
** * * **
1710699 TTTTTCTTGTTTTTTGTTTGTTAATTTGAGTTTTATGAATAATACTTAGAGTGGGAATAGTGTTT
1 TTTTTCTTGTTTTTTGTTTGTTAATTTGAGTTTTATGAATAATACCCAGAGTCGAAATAGAATTT
*
1710764 A-TTTTCCAACCC-ATAATAAGTATTTT-TCCTTTTATTATCCAAAATAATAAAT
66 ATTTTTCCAACCCTATAATAAATATTTTCTCC-TTTATTATCCAAAATAATAAAT
1710816 TTTTTCTTTA
Statistics
Matches: 251, Mismatches: 35, Indels: 20
0.82 0.11 0.07
Matches are distributed among these distances:
170 3 0.01
171 33 0.13
172 9 0.04
173 43 0.17
174 4 0.02
175 9 0.04
176 2 0.01
177 13 0.05
178 100 0.40
179 35 0.14
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.45
Consensus pattern (173 bp):
TTTTTCTTGTTTTTTGTTTGTTAATTTGAGTTTTATGAATAATACCCAGAGTCGAAATAGAATTT
ATTTTTCCAACCCTATAATAAATATTTTCTCCTTTATTATCCAAAATAATAAATCTTCTCCTCGA
AAAAAATTCAAAGATTTTACGAAACTATACTAAAAGCACACCT
Found at i:1710885 original size:12 final size:13
Alignment explanation
Indices: 1710868--1710896 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1710858 AAAGGCATAC
1710868 TCTTTTT-CTTTT
1 TCTTTTTCCTTTT
1710880 TCTTTTTCCTTTT
1 TCTTTTTCCTTTT
1710893 TCTT
1 TCTT
1710897 ATACTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (13 bp):
TCTTTTTCCTTTT
Found at i:1717102 original size:218 final size:216
Alignment explanation
Indices: 1716523--1717399 Score: 1125
Period size: 218 Copynumber: 4.1 Consensus size: 216
1716513 CAGTTTTTAG
* * * * * * *
1716523 TTAAGTGAAGATTAACTGTTTGAGTTTGATTAAGAGTGTTTTGGAACTTGGATTTGTTTGATTTA
1 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATT-AATT-
* ** ** * * *
1716588 TAATTGAGTTGATTAGGCGATTTTCGAAGTTGTGATTATCTTTTTTAAGTTTCTAATAA-----T
64 TAGTTGAGTTGACCATACGATTTTTGAAGTTGTGATTAT-TCTTTTAAGTTTCTAGTAATTGTTT
* * * *
1716648 T-GT-TTTT-TGTTTGGTTGAGTGAGGTGTTGTGGGATTTTTAGTGTTTTGGGATCCGTGAAAAG
128 TAGTGTTTTCTGTTCGGTTGAGTGAGATATTGTGGGATTTTTAGTGTTTTGGGATCTGTGAAAAG
1716710 TGAAATTTCCTGGAAATTTGAATT
193 TGAAATTTCCTGGAAATTTGAATT
* * *
1716734 TTAAGTGAAGGTTAACTGTTTGACTATGATTAA-AGTGCTTTGGAACTTCGA-TTGATTACTTTA
1 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTAATTTA
1716797 GTTGAGTTGACCATACGATTTTTGAAGTTGTGATTATCTCTTTTAAGTTTCTAGTAATTGTTTTC
66 GTTGAGTTGACCATACGATTTTTGAAGTTGTGATTAT-TCTTTTAAGTTTCTAGTAATTGTTTT-
* *
1716862 AGTGTTTTCTGTTTGGTTGAGTGAGATATTGTGGGATTTTTAGTGTTTTGGGATCTTTGAAAAGT
129 AGTGTTTTCTGTTCGGTTGAGTGAGATATTGTGGGATTTTTAGTGTTTTGGGATCTGTGAAAAGT
*
1716927 AAAATTTCCTGGAAATTTGAATT
194 GAAATTTCCTGGAAATTTGAATT
1716950 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTAATTTA
1 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTAATTTA
* *
1717015 GTTGAGTTGACCATTCGATTTTTGAAGTTGTGATTATTACTTTTAAGTTCCTAGTAATTGTTTCT
66 GTTGAGTTGACCATACGATTTTTGAAGTTGTGATTATT-CTTTTAAGTTTCTAGTAATTGTTT-T
* * * * *
1717080 AGTGTTTTCTGTTCGGTTGAGTGAGATGTTGTGCGACTTTTAGTGTTTTGGGATCTGAGAAAGGT
129 AGTGTTTTCTGTTCGGTTGAGTGAGATATTGTGGGATTTTTAGTGTTTTGGGATCTGTGAAAAGT
* *
1717145 GAAATTTCCGGGAGATTTGAATT
194 GAAATTTCCTGGAAATTTGAATT
* * *
1717168 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGCAACTTCTATTTGTTTAATTTA
1 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTAATTTA
* ** * *
1717233 ATTGAGTTGATTATGCGA-TTTTGGAGTTGTGATTATTCCTTTTAAGTTTCTAGTAATTGTTTTT
66 GTTGAGTTGACCATACGATTTTTGAAGTTGTGATTATT-CTTTTAAGTTTCTAGTAATTG-TTTT
* * ** *
1717297 AGTGTTTTCTGTTC-ATTGATTGAGATATTGCT-AAATTTTTAGTGTTTTGGGATCTAAT-AAAA
129 AGTGTTTTCTGTTCGGTTGAGTGAGATATTG-TGGGATTTTTAGTGTTTTGGGATCT-GTGAAAA
1717359 GTGAAATTTCCTGGAAATTTGAATT
192 GTGAAATTTCCTGGAAATTTGAATT
*
1717384 GTAAGTGAAGGTTAAC
1 TTAAGTGAAGGTTAAC
1717400 AAGTTGACTT
Statistics
Matches: 593, Mismatches: 57, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
207 51 0.09
208 3 0.01
209 5 0.01
210 16 0.03
211 30 0.05
212 2 0.00
214 2 0.00
215 4 0.01
216 179 0.30
217 73 0.12
218 227 0.38
219 1 0.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (216 bp):
TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTAATTTA
GTTGAGTTGACCATACGATTTTTGAAGTTGTGATTATTCTTTTAAGTTTCTAGTAATTGTTTTAG
TGTTTTCTGTTCGGTTGAGTGAGATATTGTGGGATTTTTAGTGTTTTGGGATCTGTGAAAAGTGA
AATTTCCTGGAAATTTGAATT
Found at i:1717324 original size:434 final size:427
Alignment explanation
Indices: 1716523--1717399 Score: 1158
Period size: 434 Copynumber: 2.0 Consensus size: 427
1716513 CAGTTTTTAG
* * * * * * *
1716523 TTAAGTGAAGATTAACTGTTTGAGTTTGATTAAGAGTGTTTTGGAACTTGGATTTGTTTGATTTA
1 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTGAATTA
** * *
1716588 TAATTGAGTTGATTAGGCGATTTTCGAAGTTGTGATTATCTTTTTTAAGTTTCTAATAATTGTTT
66 TAATTGAGTTGACCAGGCGATTTTCGAAGTTGTGATTATCTCTTTTAAGTTCCTAATAATTGTTT
* * * * *
1716653 TTTGTTTGGTTGAGTGAGGTGTTGTGGGATTTTTAGTGTTTTGGGATCCGTGAAAAGTGAAATTT
131 TTTGTTCGGTTGAGTGAGATGTTGTGCGACTTTTAGTGTTTTGGGATCCGAGAAAAGTGAAATTT
* * *
1716718 CCTGGAAATTTGAATTTTAAGTGAAGGTTAACTGTTTGACTATGATTAAAGTGCTTTGGAACTTC
196 CCGGGAAATTTGAATTTTAAGTGAAGGTTAACTGTTTAACTATGATTAAAGTGCTTTGCAACTTC
* *
1716783 GATTGATTACTTTAGTTGAGTTGACCATACGATTTTTGAAGTTGTGATTATCTCTTTTAAGTTTC
261 GATTGATTAATTTAATTGAGTTGACCATACGATTTTTGAAGTTGTGATTATCTCTTTTAAGTTTC
** **
1716848 TAGTAATTGTTTTCAGTGTTTTCTGTTTGGTTGAGTGAGATATTG-TGGGATTTTTAGTGTTTTG
326 TAGTAATTGTTTTCAGTGTTTTCTGTTTCATTGAGTGAGATATTGCT-AAATTTTTAGTGTTTTG
*
1716912 GGATCT-TTGAAAAGTAAAATTTCCTGGAAATTTGAATT
390 GGATCTAAT-AAAAGTAAAATTTCCTGGAAATTTGAATT
1716950 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATT-AATT-
1 TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTGAATTA
* ** * *
1717013 TAGTTGAGTTGACCATTCGATTTTTGAAGTTGTGATTAT-TACTTTTAAGTTCCTAGTAATTGTT
66 TAATTGAGTTGACCAGGCGATTTTCGAAGTTGTGATTATCT-CTTTTAAGTTCCTAATAA-----
*
1717077 TCTAGTGTTTTCTGTTCGGTTGAGTGAGATGTTGTGCGACTTTTAGTGTTTTGGGATCTGAGAAA
125 T-T-GT-TTTT-TGTTCGGTTGAGTGAGATGTTGTGCGACTTTTAGTGTTTTGGGATCCGAGAAA
* * *
1717142 GGTGAAATTTCCGGGAGATTTGAATTTTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGC
186 AGTGAAATTTCCGGGAAATTTGAATTTTAAGTGAAGGTTAACTGTTTAACTATGATTAA-AGTGC
* * ** * *
1717207 TTTGCAACTTCTATTTGTTTAATTTAATTGAGTTGATTATGCGA-TTTTGGAGTTGTGATTAT-T
250 TTTGCAACTTCGA-TTGATTAATTTAATTGAGTTGACCATACGATTTTTGAAGTTGTGATTATCT
* *
1717270 CCTTTTAAGTTTCTAGTAATTGTTTTTAGTGTTTTCTG-TTCATTGATTGAGATATTGCTAAATT
314 -CTTTTAAGTTTCTAGTAATTGTTTTCAGTGTTTTCTGTTTCATTGAGTGAGATATTGCTAAATT
*
1717334 TTTAGTGTTTTGGGATCTAATAAAAGTGAAATTTCCTGGAAATTTGAATT
378 TTTAGTGTTTTGGGATCTAATAAAAGTAAAATTTCCTGGAAATTTGAATT
*
1717384 GTAAGTGAAGGTTAAC
1 TTAAGTGAAGGTTAAC
1717400 AAGTTGACTT
Statistics
Matches: 390, Mismatches: 45, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
424 1 0.00
425 48 0.12
426 3 0.01
427 53 0.14
430 1 0.00
431 1 0.00
432 2 0.01
433 4 0.01
434 182 0.47
435 71 0.18
436 24 0.06
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (427 bp):
TTAAGTGAAGGTTAACTGTTTAACTTTGATTAAGAGTGCTTTGGAACTTCGATTTGATTGAATTA
TAATTGAGTTGACCAGGCGATTTTCGAAGTTGTGATTATCTCTTTTAAGTTCCTAATAATTGTTT
TTTGTTCGGTTGAGTGAGATGTTGTGCGACTTTTAGTGTTTTGGGATCCGAGAAAAGTGAAATTT
CCGGGAAATTTGAATTTTAAGTGAAGGTTAACTGTTTAACTATGATTAAAGTGCTTTGCAACTTC
GATTGATTAATTTAATTGAGTTGACCATACGATTTTTGAAGTTGTGATTATCTCTTTTAAGTTTC
TAGTAATTGTTTTCAGTGTTTTCTGTTTCATTGAGTGAGATATTGCTAAATTTTTAGTGTTTTGG
GATCTAATAAAAGTAAAATTTCCTGGAAATTTGAATT
Found at i:1720127 original size:23 final size:23
Alignment explanation
Indices: 1720097--1720145 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
1720087 TCCTTTCTGT
1720097 GATAGTTTCTCATGGAAACATTG
1 GATAGTTTCTCATGGAAACATTG
1720120 GATAGTTTCTCATGGAAACATTG
1 GATAGTTTCTCATGGAAACATTG
1720143 GAT
1 GAT
1720146 GTATAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (23 bp):
GATAGTTTCTCATGGAAACATTG
Found at i:1725623 original size:2 final size:2
Alignment explanation
Indices: 1725616--1725686 Score: 79
Period size: 2 Copynumber: 35.0 Consensus size: 2
1725606 CCAAAGTTTC
* * * * * *
1725616 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA CA CTA TT TN
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
1725659 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
1725687 CACACACACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 62 0.98
3 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1730078 original size:15 final size:15
Alignment explanation
Indices: 1730051--1730088 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1730041 GCCAAAGGTC
*
1730051 TAACAAGTTACTAAA
1 TAACAAATTACTAAA
*
1730066 TAGCAAATTACTAAA
1 TAACAAATTACTAAA
1730081 TAACAAAT
1 TAACAAAT
1730089 GAGTTGATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (15 bp):
TAACAAATTACTAAA
Found at i:1738967 original size:53 final size:53
Alignment explanation
Indices: 1738895--1738999 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
1738885 CCTTAATGAG
*
1738895 ATTAAGGTACTAATAAGCAAATTAGGGATCATCATAATTGTCATATTAATACT
1 ATTAAGGTACTAATAAGCAAATTAGAGATCATCATAATTGTCATATTAATACT
*
1738948 ATTATGGTACTAATAAGCAAATTAGAGATCATCATAATTGTCATATTAATAC
1 ATTAAGGTACTAATAAGCAAATTAGAGATCATCATAATTGTCATATTAATAC
1739000 GTGTTTGACT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (53 bp):
ATTAAGGTACTAATAAGCAAATTAGAGATCATCATAATTGTCATATTAATACT
Found at i:1739680 original size:14 final size:14
Alignment explanation
Indices: 1739661--1739694 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1739651 AGAAGTACAT
*
1739661 ATTAGATCAGATGG
1 ATTAGATCAGACGG
1739675 ATTAGATCAGACGG
1 ATTAGATCAGACGG
1739689 ATTAGA
1 ATTAGA
1739695 GTAAGATCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (14 bp):
ATTAGATCAGACGG
Found at i:1740319 original size:30 final size:30
Alignment explanation
Indices: 1740249--1740328 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 30
1740239 TGGGATTCCT
* * *
1740249 CCAAGGCCACCACCTGCACCAGCTCCGCCA
1 CCAAGCCCACCACCAGCACCAGCTCCACCA
* * * *
1740279 CCAAACCCACCGCCAGCGCCAGCTCCACCG
1 CCAAGCCCACCACCAGCACCAGCTCCACCA
* *
1740309 CCAAGTCCACCACCACCACC
1 CCAAGCCCACCACCAGCACC
1740329 GAACCCGCCT
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.25, C:0.56, G:0.14, T:0.05
Consensus pattern (30 bp):
CCAAGCCCACCACCAGCACCAGCTCCACCA
Found at i:1740371 original size:18 final size:18
Alignment explanation
Indices: 1740314--1740373 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
1740304 CACCGCCAAG
*
1740314 TCCACCACCACCACCGAA
1 TCCACCACCACCACCTAA
* * * * **
1740332 CCCGCCTCCACCTCCTGC
1 TCCACCACCACCACCTAA
1740350 TCCACCACCACCACCTAA
1 TCCACCACCACCACCTAA
1740368 TCCACC
1 TCCACC
1740374 TCCTGCTCCA
Statistics
Matches: 29, Mismatches: 13, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.23, C:0.60, G:0.05, T:0.12
Consensus pattern (18 bp):
TCCACCACCACCACCTAA
Found at i:1740376 original size:36 final size:36
Alignment explanation
Indices: 1740301--1740391 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 36
1740291 CCAGCGCCAG
* *
1740301 CTCCACCGCCAAG-TCCACCACCACCACCGAACCCGC
1 CTCCACCTCC-AGCTCCACCACCACCACCGAACCCAC
* * *
1740337 CTCCACCTCCTGCTCCACCACCACCACCTAATCCAC
1 CTCCACCTCCAGCTCCACCACCACCACCGAACCCAC
**
1740373 CTCCTGCTCCAGCTCCACC
1 CTCCACCTCCAGCTCCACC
1740392 TCCGAACCCT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
35 1 0.02
36 45 0.98
ACGTcount: A:0.21, C:0.58, G:0.08, T:0.13
Consensus pattern (36 bp):
CTCCACCTCCAGCTCCACCACCACCACCGAACCCAC
Found at i:1740417 original size:24 final size:24
Alignment explanation
Indices: 1740381--1740436 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
1740371 ACCTCCTGCT
* * *
1740381 CCAGCTCCACCTCCGAACCCTCCA
1 CCAGCACCACCTCCAAACCCACCA
* *
1740405 CCAGCACCGCCTCCAAATCCACCA
1 CCAGCACCACCTCCAAACCCACCA
*
1740429 CCACCACC
1 CCAGCACC
1740437 TAGTCCACCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.25, C:0.59, G:0.07, T:0.09
Consensus pattern (24 bp):
CCAGCACCACCTCCAAACCCACCA
Found at i:1740489 original size:24 final size:24
Alignment explanation
Indices: 1740456--1740503 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1740446 GCCGCCTCCG
*
1740456 AACCCTCCACC-GCCACCTCCACCT
1 AACCCACCACCAG-CACCTCCACCT
*
1740480 AACCCACCACCAGCACCTGCACCT
1 AACCCACCACCAGCACCTCCACCT
1740504 GCACCTGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.25, C:0.58, G:0.06, T:0.10
Consensus pattern (24 bp):
AACCCACCACCAGCACCTCCACCT
Found at i:1740550 original size:18 final size:18
Alignment explanation
Indices: 1740529--1740575 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1740519 CCAAATCCAG
*
1740529 CTCCACCACCTAACCCTC
1 CTCCACCACCTAACCCAC
*
1740547 CTCCACCTCCTAACCCAC
1 CTCCACCACCTAACCCAC
1740565 CTCCACCACCT
1 CTCCACCACCT
1740576 CCTCCTAAGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.21, C:0.62, G:0.00, T:0.17
Consensus pattern (18 bp):
CTCCACCACCTAACCCAC
Found at i:1751269 original size:31 final size:31
Alignment explanation
Indices: 1751234--1751292 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
1751224 ACTCTTATAC
*
1751234 TTTTATTTTAAATTAAATAAATTTTTATTTT
1 TTTTATTTTAAATCAAATAAATTTTTATTTT
*
1751265 TTTTATTTTGAATCAAATAAATTTTTAT
1 TTTTATTTTAAATCAAATAAATTTTTAT
1751293 AATTAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTTATTTTAAATCAAATAAATTTTTATTTT
Found at i:1751501 original size:22 final size:21
Alignment explanation
Indices: 1751474--1751552 Score: 63
Period size: 22 Copynumber: 3.7 Consensus size: 21
1751464 ATAAATATAA
1751474 AATAATAAATAATATTTTAATT
1 AATAATAAA-AATATTTTAATT
** *
1751496 AATAATAATTAT-TTATTTATT
1 AATAATAAAAATATT-TTAATT
* *
1751517 AATTATAAAAATTTATTTAATTT
1 AATAATAAAAATAT-TTTAA-TT
1751540 AA-AATAAAAATAT
1 AATAATAAAAATAT
1751553 AAAAGATTGA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
20 2 0.05
21 16 0.36
22 21 0.48
23 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAATAAAAATATTTTAATT
Found at i:1751518 original size:25 final size:26
Alignment explanation
Indices: 1751490--1751540 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1751480 AAATAATATT
*
1751490 TTAATTAATAATAA-TTATTT-ATTTA
1 TTAATT-ATAAAAATTTATTTAATTTA
1751515 TTAATTATAAAAATTTATTTAATTTA
1 TTAATTATAAAAATTTATTTAATTTA
1751541 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 6 0.26
25 12 0.52
26 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TTAATTATAAAAATTTATTTAATTTA
Found at i:1751519 original size:21 final size:21
Alignment explanation
Indices: 1751474--1751550 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
1751464 ATAAATATAA
*
1751474 AATAATAAATAATATT-TTAATT
1 AATAATAAA-AAT-TTATTTATT
**
1751496 AATAATAATTATTTATTTATT
1 AATAATAAAAATTTATTTATT
*
1751517 AATTATAAAAATTTATTTAATTT
1 AATAATAAAAATTTATTT-A-TT
1751540 AA-AATAAAAAT
1 AATAATAAAAAT
1751551 ATAAAAGATT
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 2 0.04
21 22 0.49
22 17 0.38
23 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AATAATAAAAATTTATTTATT
Found at i:1751532 original size:17 final size:17
Alignment explanation
Indices: 1751510--1751543 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1751500 ATAATTATTT
1751510 ATTTA-TTAATTATAAAA
1 ATTTATTTAATT-TAAAA
1751527 ATTTATTTAATTTAAAA
1 ATTTATTTAATTTAAAA
1751544 TAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTATTTAATTTAAAA
Found at i:1763123 original size:77 final size:80
Alignment explanation
Indices: 1762985--1763139 Score: 235
Period size: 77 Copynumber: 2.0 Consensus size: 80
1762975 ACCGCATTAT
* * * * *
1762985 ATTATTTTATTTTGAGTTTCTATTTAAAGGTCCAGTGGGCTAATATCCAAAGAAATTGGGCCCAC
1 ATTATTTTATTTTAAATTTATATTTAAAGGCCCAGTGGGCTAAAATCCAAAGAAATTGGGCCCAC
1763050 CAAATCCAGAAGCTA
66 CAAATCCAGAAGCTA
*
1763065 ATTATTTTATTTTAAATTTATA-TTAAAGGCCCAGT-TGCTAAAATCC-AAGAAATTGGGCCCAC
1 ATTATTTTATTTTAAATTTATATTTAAAGGCCCAGTGGGCTAAAATCCAAAGAAATTGGGCCCAC
1763127 CAAATCCAGAAGC
66 CAAATCCAGAAGC
1763140 CAACATTGGG
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
77 29 0.42
78 9 0.13
79 12 0.17
80 19 0.28
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (80 bp):
ATTATTTTATTTTAAATTTATATTTAAAGGCCCAGTGGGCTAAAATCCAAAGAAATTGGGCCCAC
CAAATCCAGAAGCTA
Found at i:1763704 original size:2 final size:2
Alignment explanation
Indices: 1763697--1763788 Score: 93
Period size: 2 Copynumber: 46.5 Consensus size: 2
1763687 TGCAAAAACA
1763697 AT AT AT AT AT AT AT -T AT AT AT AT -T 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
* * * *
1763737 AT -T AT AT AT AG AC AT ANC AT AT TT CAT AT AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT -AT AT AT AT AT AT AT AT AT
1763779 AT AT AGT AT A
1 AT AT A-T AT A
1763789 GTCTAATTAA
Statistics
Matches: 76, Mismatches: 7, Indels: 14
0.78 0.07 0.14
Matches are distributed among these distances:
1 4 0.05
2 68 0.89
3 4 0.05
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1767138 original size:87 final size:83
Alignment explanation
Indices: 1767029--1767255 Score: 267
Period size: 87 Copynumber: 2.7 Consensus size: 83
1767019 ATTTCACAAT
* * * * *
1767029 ATTCTATGATTGTATATGAAATTTATTAACTGCGTAATTTTAATTCGAAAAATGTTAATATAAGA
1 ATTCTGTGATTGTATATGAAATTCATTAACTGTGTAATTCTAATTCGAAAAATGTTAAGATAAGA
*
1767094 GCAATACGAGAATTTGAA
66 ACAATACGAGAATTTGAA
* * *
1767112 ACTCTCTGATTGATTGTATGTAAAATTCATTAACTGTATAATTCTAATTTC-AAAAATGTTAAGA
1 A-T-TCTG--TGATTGTATATGAAATTCATTAACTGTGTAATTCTAA-TTCGAAAAATGTTAAGA
*
1767176 TAAGAATAATACGAGAATTTGAA
61 TAAGAACAATACGAGAATTTGAA
* * * *
1767199 ATTCTGTGATCGTATCTGAAATTCATTAACCGTGTAATTCTAGATCCGAAAAATGTT
1 ATTCTGTGATTGTATATGAAATTCATTAACTGTGTAATTCTA-ATTCGAAAAATGTT
1767256 GAAAAAAACA
Statistics
Matches: 121, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
83 34 0.28
84 11 0.09
85 7 0.06
86 1 0.01
87 65 0.54
88 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (83 bp):
ATTCTGTGATTGTATATGAAATTCATTAACTGTGTAATTCTAATTCGAAAAATGTTAAGATAAGA
ACAATACGAGAATTTGAA
Found at i:1774156 original size:64 final size:64
Alignment explanation
Indices: 1773999--1774165 Score: 190
Period size: 64 Copynumber: 2.6 Consensus size: 64
1773989 TCGCCGGTTC
* * * * * * * *
1773999 CTTAATGCCATTATCCGAGTTACCAATCTTAATCGTACGATTAAGTACGTATAAATTCTTGTTT
1 CTTAATGCTATTATCAGAGTTAACAATCTTAATCGTACCATTAAATACATATAAATTCTTGCTG
* * * *
1774063 TTTAACGTTATTTTCAGAGTTAACAATCTTAATCGTACCATTAAATACATATAAATTCTTGCTG
1 CTTAATGCTATTATCAGAGTTAACAATCTTAATCGTACCATTAAATACATATAAATTCTTGCTG
* * * *
1774127 CTTAATGCTATTATCGGACTTAGCGATCTTAATCGTACC
1 CTTAATGCTATTATCAGAGTTAACAATCTTAATCGTACC
1774166 TATAAGTCTC
Statistics
Matches: 83, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 83 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.39
Consensus pattern (64 bp):
CTTAATGCTATTATCAGAGTTAACAATCTTAATCGTACCATTAAATACATATAAATTCTTGCTG
Found at i:1778786 original size:20 final size:20
Alignment explanation
Indices: 1778746--1778782 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
1778736 AATCTACCGT
1778746 ATGAAAAATCAAGTACAACA
1 ATGAAAAATCAAGTACAACA
*
1778766 ATGAAAAA-GAAGTACAA
1 ATGAAAAATCAAGTACAA
1778783 ACAAAACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.11, G:0.14, T:0.14
Consensus pattern (20 bp):
ATGAAAAATCAAGTACAACA
Found at i:1780230 original size:14 final size:14
Alignment explanation
Indices: 1780208--1780251 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1780198 TTAATCACTA
1780208 TTAATAATTTAAAT
1 TTAATAATTTAAAT
*
1780222 TTAAAAATTTTAAA-
1 TTAATAA-TTTAAAT
1780236 TTATATAATTTAAAT
1 TTA-ATAATTTAAAT
1780251 T
1 T
1780252 CGAAAATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTAATAATTTAAAT
Found at i:1783418 original size:20 final size:20
Alignment explanation
Indices: 1783365--1783442 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
1783355 CCTTTCTCTC
* *
1783365 TCTACTTCTCTTTCTATATA
1 TCTATTTCTCTCTCTATATA
* *
1783385 TCTATCTATCTCTCTATATA
1 TCTATTTCTCTCTCTATATA
* *
1783405 TCTATTTCTCTCTCTCTAACCA
1 TCTATTTCTCTCTCTAT-A-TA
*
1783427 ACTATTTCTCTCTCTA
1 TCTATTTCTCTCTCTA
1783443 AATCTATGTC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
20 30 0.65
21 1 0.02
22 15 0.33
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (20 bp):
TCTATTTCTCTCTCTATATA
Found at i:1783418 original size:22 final size:22
Alignment explanation
Indices: 1783371--1783441 Score: 76
Period size: 22 Copynumber: 3.3 Consensus size: 22
1783361 TCTCTCTACT
*
1783371 TCTCTTTCTATATATCTA--TC
1 TCTCTCTCTATATATCTATTTC
*
1783391 TATCTCTCTATATATCTATTTC
1 TCTCTCTCTATATATCTATTTC
* *
1783413 TCTCTCTCTA-ACCAACTATTTC
1 TCTCTCTCTATA-TATCTATTTC
1783435 TCTCTCT
1 TCTCTCT
1783442 AAATCTATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
20 16 0.37
21 1 0.02
22 26 0.60
ACGTcount: A:0.20, C:0.30, G:0.00, T:0.51
Consensus pattern (22 bp):
TCTCTCTCTATATATCTATTTC
Found at i:1784840 original size:20 final size:20
Alignment explanation
Indices: 1784775--1784840 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
1784765 AATTTAAAAA
*
1784775 TTAATTAAAATTATTAAT-AT
1 TTAAATAAAA-TATTAATAAT
* *
1784795 TTTAATAATAATATTTA-AAT
1 TTAAATAA-AATATTAATAAT
1784815 TATAAATAAAATATTAATAAT
1 T-TAAATAAAATATTAATAAT
1784836 TTAAA
1 TTAAA
1784841 ATGTTAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 25 0.68
21 12 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATAAAATATTAATAAT
Found at i:1784866 original size:42 final size:42
Alignment explanation
Indices: 1784803--1784898 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
1784793 ATTTTAATAA
* * *
1784803 TAATATTTAAATTATAAATAAAATATTAATAATTTAAAATGT
1 TAATATTTAAATCAAAAATAAAATATTAATAATTTAAAATGC
*
1784845 TAATGA-TTAAATCAAAAATAAAATATTAATATTTTAAAATGC
1 TAAT-ATTTAAATCAAAAATAAAATATTAATAATTTAAAATGC
1784887 TAATATTTAAAT
1 TAATATTTAAAT
1784899 AATCAATTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (42 bp):
TAATATTTAAATCAAAAATAAAATATTAATAATTTAAAATGC
Found at i:1784958 original size:27 final size:27
Alignment explanation
Indices: 1784894--1784952 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
1784884 TGCTAATATT
*
1784894 TAAATAATCAATTATTAATATTTTAAA
1 TAAATAATAAATTATTAATATTTTAAA
*
1784921 TAAATTATAAATTATTAATA-TTTAAA
1 TAAATAATAAATTATTAATATTTTAAA
1784947 -AAATAA
1 TAAATAA
1784953 AATAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 5 0.17
26 6 0.21
27 18 0.62
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAATAATAAATTATTAATATTTTAAA
Found at i:1790578 original size:12 final size:13
Alignment explanation
Indices: 1790561--1790589 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1790551 ATATATATAA
1790561 TATAATTAT-TTT
1 TATAATTATGTTT
1790573 TATAATTATGTTT
1 TATAATTATGTTT
1790586 TATA
1 TATA
1790590 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (13 bp):
TATAATTATGTTT
Found at i:1796485 original size:47 final size:47
Alignment explanation
Indices: 1796416--1796531 Score: 144
Period size: 47 Copynumber: 2.4 Consensus size: 47
1796406 TCAGACTTTC
*
1796416 CCACTTTTCTTGCTCATTTCCTTCGACGGAATATAAA-GTCACCCAGT
1 CCACTTTTCTTGC-CATTTCCTTCGACAGAATATAAAGGTCACCCAGT
* ** *
1796463 CCACTTTTCTTGACCTTTTCCTTCGACAGCGTGTAAAGGTCACCCAGT
1 CCACTTTTCTTG-CCATTTCCTTCGACAGAATATAAAGGTCACCCAGT
*
1796511 CCACTTGTCTTGTCCATTTCC
1 CCACTTTTCTTG-CCATTTCC
1796532 AAATCTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
47 30 0.51
48 29 0.49
ACGTcount: A:0.19, C:0.32, G:0.14, T:0.35
Consensus pattern (47 bp):
CCACTTTTCTTGCCATTTCCTTCGACAGAATATAAAGGTCACCCAGT
Found at i:1796994 original size:23 final size:21
Alignment explanation
Indices: 1796952--1796995 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
1796942 AAAAGCACAC
**
1796952 ATATATAAATATATTTAATAA
1 ATATATAAATATATAAAATAA
1796973 ATATATAACATGATATAAAATAA
1 ATATATAA-AT-ATATAAAATAA
1796996 TTAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 2 0.11
23 9 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATATAAATATATAAAATAA
Found at i:1797745 original size:30 final size:30
Alignment explanation
Indices: 1797694--1797759 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1797684 ATAAAAGTGA
*
1797694 CATGAAGGAATGCAGAACACTAATGGGTGG
1 CATGAAGGAATGCAGAACACTAATGGGAGG
* * *
1797724 CATGAAGGAATGCATACCACTACTGGGAGG
1 CATGAAGGAATGCAGAACACTAATGGGAGG
*
1797754 GATGAA
1 CATGAA
1797760 AAAAAGGTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.32, T:0.17
Consensus pattern (30 bp):
CATGAAGGAATGCAGAACACTAATGGGAGG
Found at i:1804382 original size:23 final size:23
Alignment explanation
Indices: 1804331--1804397 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 23
1804321 GTCATATATT
*
1804331 TTAATTTATTTTTTATTATTATC
1 TTAATATATTTTTTATTATTATC
*
1804354 TT-ATATATTTTATTTTTATT-TC
1 TTAATATATTTT-TTATTATTATC
1804376 TTAATATAATTTTTTA-TATTAT
1 TTAATAT-ATTTTTTATTATTAT
1804398 ATATTTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
22 16 0.43
23 16 0.43
24 5 0.14
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (23 bp):
TTAATATATTTTTTATTATTATC
Found at i:1804394 original size:33 final size:33
Alignment explanation
Indices: 1804324--1804408 Score: 91
Period size: 33 Copynumber: 2.6 Consensus size: 33
1804314 TTTTCATGTC
* * * *
1804324 ATATATTTTA-ATTTATTTTTTATTATTATCTT
1 ATATATTTTATTTTTATTTCTTAATATAATCTT
*
1804356 ATATATTTTATTTTTATTTCTTAATATAATTTT
1 ATATATTTTATTTTTATTTCTTAATATAATCTT
* *
1804389 TTATATTATATATTTTATTT
1 ATATATTTTAT-TTTTATTT
1804409 TAATTTCTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 10 0.23
33 26 0.59
34 8 0.18
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTCTTAATATAATCTT
Found at i:1804419 original size:14 final size:13
Alignment explanation
Indices: 1804327--1804421 Score: 52
Period size: 14 Copynumber: 7.3 Consensus size: 13
1804317 TCATGTCATA
*
1804327 TATTTTAATTTAT
1 TATTTTAATTTTT
*
1804340 T-TTTT-A-TTAT
1 TATTTTAATTTTT
* *
1804350 TATCTTATATATTT
1 TATTTTA-ATTTTT
* *
1804364 TATTTTTATTTCT
1 TATTTTAATTTTT
* *
1804377 TAATATAATTTTT
1 TATTTTAATTTTT
* *
1804390 TATATTATATATTT
1 TATTTTA-ATTTTT
1804404 TATTTTAATTTCTT
1 TATTTTAATTT-TT
1804418 TATT
1 TATT
1804422 CTTTAATGAA
Statistics
Matches: 59, Mismatches: 17, Indels: 11
0.68 0.20 0.13
Matches are distributed among these distances:
10 5 0.08
11 4 0.07
12 4 0.07
13 22 0.37
14 24 0.41
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TATTTTAATTTTT
Found at i:1808053 original size:7 final size:7
Alignment explanation
Indices: 1808041--1808065 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1808031 TATTCACGTT
1808041 AAATGTG
1 AAATGTG
1808048 AAATGTG
1 AAATGTG
1808055 AAATGTG
1 AAATGTG
1808062 AAAT
1 AAAT
1808066 ATCATAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (7 bp):
AAATGTG
Found at i:1808802 original size:28 final size:28
Alignment explanation
Indices: 1808740--1808809 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
1808730 TATATTTAAC
*
1808740 ATTATTTATTTATTTATATATGTTTGGTT
1 ATTATTTATTTATTTATATATATTT-GTT
* *
1808769 -TAATTTATTTGTTTATAATATATTT-TT
1 ATTATTTATTTATTTAT-ATATATTTGTT
1808796 ATTATTTAATTTAT
1 ATTATTT-ATTTAT
1808810 AAATTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.06
28 19 0.58
29 12 0.36
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.66
Consensus pattern (28 bp):
ATTATTTATTTATTTATATATATTTGTT
Found at i:1810000 original size:30 final size:30
Alignment explanation
Indices: 1809964--1810059 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
1809954 GTATATTAAA
* *
1809964 ATTTTTTCAAATATGGTGTGCAACAATAAT
1 ATTTTTTCAAATATGATGTACAACAATAAT
*
1809994 ATTTTTTCAACATA--ACT-TACAACAACAAT
1 ATTTTTTCAA-ATATGA-TGTACAACAATAAT
* *
1810023 ATTTTTTTC-AATATGAAGTATAACAATAAT
1 A-TTTTTTCAAATATGATGTACAACAATAAT
1810053 ATTTTTT
1 ATTTTTT
1810060 TTAACCATAG
Statistics
Matches: 54, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
28 3 0.06
29 18 0.33
30 30 0.56
31 3 0.06
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (30 bp):
ATTTTTTCAAATATGATGTACAACAATAAT
Found at i:1810060 original size:30 final size:30
Alignment explanation
Indices: 1809984--1810060 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
1809974 ATATGGTGTG
*
1809984 CAACAATAATA-TTTTTTCAACATAACTTA
1 CAACAATAATATTTTTTTCAACATAACGTA
* *
1810013 CAACAACAATATTTTTTTCAATATGAA-GTA
1 CAACAATAATATTTTTTTCAACAT-AACGTA
*
1810043 TAACAATAATATTTTTTT
1 CAACAATAATATTTTTTT
1810061 TAACCATAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 10 0.24
30 29 0.71
31 2 0.05
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.42
Consensus pattern (30 bp):
CAACAATAATATTTTTTTCAACATAACGTA
Found at i:1813770 original size:2 final size:2
Alignment explanation
Indices: 1813763--1813800 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
1813753 AAACAGAATG
* *
1813763 AC AC AC AC AC AC AC AC AC GC AC AC AT AC AC AC A- AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1813801 GGCCTGCAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.45, G:0.03, T:0.03
Consensus pattern (2 bp):
AC
Found at i:1820489 original size:2 final size:2
Alignment explanation
Indices: 1820484--1820508 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1820474 TATGTGTGTG
1820484 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 T
1820509 NNNNNNNNNN
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1827992 original size:11 final size:11
Alignment explanation
Indices: 1827978--1828002 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1827968 AAAAATTTAA
1827978 GATTTTTTCAT
1 GATTTTTTCAT
1827989 GATTTTTTCAT
1 GATTTTTTCAT
1828000 GAT
1 GAT
1828003 GTTTACGATC
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:0.20, C:0.08, G:0.12, T:0.60
Consensus pattern (11 bp):
GATTTTTTCAT
Found at i:1830535 original size:7 final size:7
Alignment explanation
Indices: 1830525--1830551 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1830515 AAATTAATAA
1830525 TTCTAAT
1 TTCTAAT
1830532 TTCTAAT
1 TTCTAAT
1830539 TTCTAAT
1 TTCTAAT
1830546 TTCTAA
1 TTCTAA
1830552 CTAATTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (7 bp):
TTCTAAT
Found at i:1831390 original size:19 final size:19
Alignment explanation
Indices: 1831337--1831395 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
1831327 AACTTCTAAC
*
1831337 TAATTCTAAGAAATTTCAT
1 TAATTCTAAGAAATTTAAT
1831356 TAATT-TATAG---TTTAAT
1 TAATTCTA-AGAAATTTAAT
1831372 TAATTCTAAGAAATTTAAT
1 TAATTCTAAGAAATTTAAT
1831391 TAATT
1 TAATT
1831396 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
16 12 0.35
17 2 0.06
18 2 0.06
19 18 0.53
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TAATTCTAAGAAATTTAAT
Found at i:1833103 original size:27 final size:26
Alignment explanation
Indices: 1833073--1833166 Score: 95
Period size: 27 Copynumber: 3.6 Consensus size: 26
1833063 TTTTACATAT
* *
1833073 TAATATATTATAATTATTAAATTTTA
1 TAATATATTATAATTATAAAATATTA
*
1833099 GTAATATTTTATAA-TATAAAATATTA
1 -TAATATATTATAATTATAAAATATTA
*
1833125 TGAATATATATATAATTATATAATCATTA
1 T-AATATAT-TATAATTATAAAAT-ATTA
1833154 T-ATATATT-TAATT
1 TAATATATTATAATT
1833167 TATACGTAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
25 6 0.10
26 17 0.29
27 23 0.40
28 7 0.12
29 5 0.09
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (26 bp):
TAATATATTATAATTATAAAATATTA
Found at i:1833782 original size:49 final size:49
Alignment explanation
Indices: 1833708--1833801 Score: 161
Period size: 49 Copynumber: 1.9 Consensus size: 49
1833698 CAACTTCTCC
*
1833708 AAACTTTTAATAATATTTATTAATTAATTCTTTTAAGAAAAAAAAACTA
1 AAACTTTTAATAATATTTATCAATTAATTCTTTTAAGAAAAAAAAACTA
* *
1833757 AAACTTTTAATAATATTTATCAATTAATTGTTTTAAGAGAAAAAA
1 AAACTTTTAATAATATTTATCAATTAATTCTTTTAAGAAAAAAAA
1833802 TATAAATTAG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (49 bp):
AAACTTTTAATAATATTTATCAATTAATTCTTTTAAGAAAAAAAAACTA
Found at i:1836289 original size:177 final size:177
Alignment explanation
Indices: 1835984--1836317 Score: 605
Period size: 177 Copynumber: 1.9 Consensus size: 177
1835974 TTGTCCTATG
*
1835984 TGATGAGTGATAGTTTTCCAGGATTTGAACAATGAAGAGAAGTGGGTGTGGATCAAATAATCTTG
1 TGATCAGTGATAGTTTTCCAGGATTTGAACAATGAAGAGAAGTGGGTGTGGATCAAATAATCTTG
* **
1836049 TTAATGAATTTGTTCACATTTTGTAGCTTGTGGAAGGCTTAATCTTAGACCAATACCATGATGTT
66 TTAATGAATTTGTTCACATTTTGTAGCTTGTGGAACGCAAAATCTTAGACCAATACCATGATGTT
1836114 TCTGATTCACAAGAACAAATGATTGTTGTGTGGTTTGAGTTCCAATT
131 TCTGATTCACAAGAACAAATGATTGTTGTGTGGTTTGAGTTCCAATT
*
1836161 TGATCAGTGATAGTTTTTCAGGATTTGAACAATGAAGAGAAGTGGGTGTGGATCAAATAATCTTG
1 TGATCAGTGATAGTTTTCCAGGATTTGAACAATGAAGAGAAGTGGGTGTGGATCAAATAATCTTG
*
1836226 TTAATGAATTTGTTCACATTTTGTAGCTTGTGGAACGCAAAATCTTAGACCAATACTATGATGTT
66 TTAATGAATTTGTTCACATTTTGTAGCTTGTGGAACGCAAAATCTTAGACCAATACCATGATGTT
*
1836291 TCTGGTTCACAAGAACAAATGATTGTT
131 TCTGATTCACAAGAACAAATGATTGTT
1836318 ATTGTGTGAT
Statistics
Matches: 150, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
177 150 1.00
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (177 bp):
TGATCAGTGATAGTTTTCCAGGATTTGAACAATGAAGAGAAGTGGGTGTGGATCAAATAATCTTG
TTAATGAATTTGTTCACATTTTGTAGCTTGTGGAACGCAAAATCTTAGACCAATACCATGATGTT
TCTGATTCACAAGAACAAATGATTGTTGTGTGGTTTGAGTTCCAATT
Found at i:1838223 original size:15 final size:15
Alignment explanation
Indices: 1838205--1838237 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1838195 TGGCCATAGC
1838205 CATCATCCC-CATCAT
1 CATCA-CCCTCATCAT
1838220 CATCACCCTCATCAT
1 CATCACCCTCATCAT
1838235 CAT
1 CAT
1838238 GCCATGGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.27, C:0.45, G:0.00, T:0.27
Consensus pattern (15 bp):
CATCACCCTCATCAT
Found at i:1849734 original size:29 final size:29
Alignment explanation
Indices: 1849690--1849754 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
1849680 TCCGTGTATG
1849690 TGCAGTTGCTGATTATTTGGATAAAAACA
1 TGCAGTTGCTGATTATTTGGATAAAAACA
* ** *
1849719 TGCAGTTGCTGGTTATTTGGATTTAGACA
1 TGCAGTTGCTGATTATTTGGATAAAAACA
1849748 TGCAGTT
1 TGCAGTT
1849755 ACTTATAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (29 bp):
TGCAGTTGCTGATTATTTGGATAAAAACA
Found at i:1849821 original size:20 final size:21
Alignment explanation
Indices: 1849785--1849823 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1849775 AAACTTCCTT
1849785 TTAACACTTGTAATCCATGCC
1 TTAACACTTGTAATCCATGCC
1849806 TTAACACTTG-AATCCATG
1 TTAACACTTGTAATCCATG
1849824 TCTTGACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (21 bp):
TTAACACTTGTAATCCATGCC
Found at i:1854202 original size:21 final size:20
Alignment explanation
Indices: 1854173--1854215 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1854163 AAACTTCCTT
*
1854173 TTAACACTTGTAATCCATGTC
1 TTAACACTT-AAATCCATGTC
*
1854194 TTAATACTTAAATCCATGTC
1 TTAACACTTAAATCCATGTC
1854214 TT
1 TT
1854216 GACAAGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (20 bp):
TTAACACTTAAATCCATGTC
Found at i:1856064 original size:5 final size:5
Alignment explanation
Indices: 1856048--1856079 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
1856038 GGCCTCAGAG
1856048 TTTTC ATTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC T
1856080 ACATCAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:1864949 original size:59 final size:57
Alignment explanation
Indices: 1864851--1864963 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 57
1864841 TATTAGAAAG
*
1864851 TAAACGTTTAAACATTTTGAACATTTTGGAGTAGTTTTTGATACATGAAGAAAATTT
1 TAAACGTTTAAACATTTTAAACATTTTGGAGTAGTTTTTGATACATGAAGAAAATTT
* * * *
1864908 TAAACGTTTTAAATATTTTAAAATATTTTTGAGT-GATTTTTGATATATGAAGAAAA
1 TAAACG-TTTAAACATTTT-AAACATTTTGGAGTAG-TTTTTGATACATGAAGAAAA
1864964 ACTTTTGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 6 0.12
58 12 0.25
59 30 0.62
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.42
Consensus pattern (57 bp):
TAAACGTTTAAACATTTTAAACATTTTGGAGTAGTTTTTGATACATGAAGAAAATTT
Found at i:1865148 original size:21 final size:21
Alignment explanation
Indices: 1865118--1865189 Score: 83
Period size: 21 Copynumber: 3.4 Consensus size: 21
1865108 TAATTTTTAA
*
1865118 ACATTACGTGACTGACTTTGG
1 ACATTGCGTGACTGACTTTGG
*
1865139 ACATTGCGTGACTGA-TTTTG
1 ACATTGCGTGACTGACTTTGG
* *
1865159 AGCATTGTGTGATTGACTTTGG
1 A-CATTGCGTGACTGACTTTGG
*
1865181 GCATTGCGT
1 ACATTGCGT
1865190 AACTAGTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 5 0.12
21 33 0.79
22 4 0.10
ACGTcount: A:0.19, C:0.15, G:0.28, T:0.38
Consensus pattern (21 bp):
ACATTGCGTGACTGACTTTGG
Found at i:1865394 original size:22 final size:22
Alignment explanation
Indices: 1865369--1865431 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
1865359 TTAAGTCACG
1865369 CAATACTTAAAAATCAGTCTCA
1 CAATACTTAAAAATCAGTCTCA
*
1865391 CAATACTTAAAAATCAGTCTCG
1 CAATACTTAAAAATCAGTCTCA
1865413 CAATACTTAAAAATCAGTC
1 CAATACTTAAAAATCAGTC
1865432 AAATTAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.27
Consensus pattern (22 bp):
CAATACTTAAAAATCAGTCTCA
Found at i:1867793 original size:60 final size:59
Alignment explanation
Indices: 1867687--1867845 Score: 187
Period size: 60 Copynumber: 2.7 Consensus size: 59
1867677 TAACATCATC
* * * *
1867687 ACCTACTCGTGGGAACTGCCTACGCCACC-ATATGAATCGGGGCTTCAGGT-TCCCCTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCAATATAAATCGGGACTTCAGGTCT-CCCTTT
* * **
1867745 ACCTACTCGTGGAAACTACCCACGTCACTCAATATAAATCGGGACTTCAGGTCTCTTTTT
1 ACCTACTCGTGGGAACTACCCACGCCAC-CAATATAAATCGGGACTTCAGGTCTCCCTTT
* *
1867805 ACCTACTTGTGGGAACTATCCACGCCACCCAATATAAATCG
1 ACCTACTCGTGGGAACTACCCACGCCA-CCAATATAAATCG
1867846 AGGCTTTAGA
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
58 24 0.28
59 1 0.01
60 58 0.68
61 2 0.02
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (59 bp):
ACCTACTCGTGGGAACTACCCACGCCACCAATATAAATCGGGACTTCAGGTCTCCCTTT
Found at i:1867865 original size:60 final size:59
Alignment explanation
Indices: 1867687--1867866 Score: 186
Period size: 60 Copynumber: 3.0 Consensus size: 59
1867677 TAACATCATC
* * * *
1867687 ACCTACTCGTGGGAACTGCCTACGCCA-CC-ATATGAATCGGGGCTTCAGGTTCCCC-TTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATC-GGGCTTCA-GATCCCCTTTT
* * * * * *
1867745 ACCTACTCGTGGAAACTACCCACGTCACTCAATATAAATCGGGACTTCAGGTCTCTTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGG-CTTCAGATCCCCTTTT
* * *
1867805 ACCTACTTGTGGGAACTATCCACGCCACCCAATATAAATCGAGGCTTTAGATCCCCTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCG-GGCTTCAGATCCCCTTTT
1867865 AC
1 AC
1867867 AATCAAATAT
Statistics
Matches: 99, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
58 23 0.23
59 8 0.08
60 66 0.67
61 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (59 bp):
ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGCTTCAGATCCCCTTTT
Found at i:1868751 original size:8 final size:8
Alignment explanation
Indices: 1868734--1868791 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
1868724 ACTCTCCAAA
*
1868734 CTTTTCCT
1 CTTTTTCT
1868742 CTTTTTCT
1 CTTTTTCT
*
1868750 CTCTTT-T
1 CTTTTTCT
1868757 CTTTTTCT
1 CTTTTTCT
1868765 CTTTCTT-T
1 CTTT-TTCT
*
1868773 CTTCTTCT
1 CTTTTTCT
1868781 -TTTATTCT
1 CTTT-TTCT
1868789 CTT
1 CTT
1868792 GGCGGGGCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
7 10 0.25
8 26 0.65
9 4 0.10
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.71
Consensus pattern (8 bp):
CTTTTTCT
Found at i:1868759 original size:15 final size:16
Alignment explanation
Indices: 1868741--1868780 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1868731 AAACTTTTCC
1868741 TCTTTTTCTCTCT-TT
1 TCTTTTTCTCTCTCTT
*
1868756 TCTTTTTCTCTTTCTT
1 TCTTTTTCTCTCTCTT
*
1868772 TCTTCTTCT
1 TCTTTTTCT
1868781 TTTATTCTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (16 bp):
TCTTTTTCTCTCTCTT
Found at i:1868778 original size:24 final size:25
Alignment explanation
Indices: 1868745--1868791 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1868735 TTTTCCTCTT
*
1868745 TTTCTCTCTT-TTCTTTTTCTCTTTC
1 TTTCTCTCTTCTT-TTATTCTCTTTC
1868770 TTTCT-TCTTCTTTTATTCTCTT
1 TTTCTCTCTTCTTTTATTCTCTT
1868792 GGCGGGGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (25 bp):
TTTCTCTCTTCTTTTATTCTCTTTC
Found at i:1874138 original size:13 final size:12
Alignment explanation
Indices: 1874122--1874177 Score: 60
Period size: 13 Copynumber: 4.4 Consensus size: 12
1874112 GCTAATGCAA
1874122 TTATTTAATTTTT
1 TTATTT-ATTTTT
1874135 TTATTTATTATTT
1 TTATTTATT-TTT
*
1874148 ATTA-TTATTATT
1 -TTATTTATTTTT
1874160 TTATTTTATTTTT
1 TTA-TTTATTTTT
1874173 TTATT
1 TTATT
1874178 ATCACATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
11 3 0.08
12 7 0.19
13 24 0.65
14 3 0.08
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTATTTTT
Found at i:1874713 original size:15 final size:15
Alignment explanation
Indices: 1874695--1874735 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1874685 AGTTAATGTC
1874695 ATTATATTTTATTTT
1 ATTATATTTTATTTT
1874710 ATTATATTATT-TTTT
1 ATTATATT-TTATTTT
*
1874725 -TTATGTTTTAT
1 ATTATATTTTAT
1874736 GTATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 2 0.09
14 7 0.30
15 12 0.52
16 2 0.09
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (15 bp):
ATTATATTTTATTTT
Found at i:1874733 original size:29 final size:32
Alignment explanation
Indices: 1874696--1874754 Score: 79
Period size: 29 Copynumber: 1.9 Consensus size: 32
1874686 GTTAATGTCA
*
1874696 TTATATTTTAT-TTTAT-TATAT-TATTTTTT
1 TTATATTTTATGTATATATATATATATTTTTT
*
1874725 TTATGTTTTATGTATATATATATATATTTT
1 TTATATTTTATGTATATATATATATATTTT
1874755 AAGAGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 4 0.16
31 5 0.20
32 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (32 bp):
TTATATTTTATGTATATATATATATATTTTTT
Found at i:1875446 original size:60 final size:60
Alignment explanation
Indices: 1875353--1875549 Score: 207
Period size: 60 Copynumber: 3.1 Consensus size: 60
1875343 TTTCTTCTCT
*
1875353 CTTT-TCTCTCTCTGGCCGCCGACCGATCTCCCTTGGCCCGATCGGTCCTCCCTCTATCA
1 CTTTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCGGTCCTCCCTCTATCA
* *
1875412 CTTTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCTGATCGGTCTTCCCTTTCTCACTCA
1 CTTTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCGGTCCTCCC--TCT-A-TCA
* * * * * *
1875476 CTCACACTCTCTCTCTCTCTAGCTGCTGATCGATCTCCCTTGGCCCGCTCAGTCCTCCCTCTTTC
1 CT-----T-TCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCGGTCCTCCCTCTATC
1875541 A
60 A
*
1875542 CTCTCTCT
1 CTTTCTCT
1875550 TTCACTCTTT
Statistics
Matches: 115, Mismatches: 12, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
59 4 0.03
60 50 0.43
62 3 0.03
63 1 0.01
64 5 0.04
66 5 0.04
68 3 0.03
69 1 0.01
70 43 0.37
ACGTcount: A:0.09, C:0.44, G:0.14, T:0.34
Consensus pattern (60 bp):
CTTTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCGGTCCTCCCTCTATCA
Found at i:1875535 original size:70 final size:70
Alignment explanation
Indices: 1875410--1875544 Score: 182
Period size: 70 Copynumber: 1.9 Consensus size: 70
1875400 CTCCCTCTAT
* * * *
1875410 CACTTTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCTGATCGGTCTTCCCT-TTCTCACT
1 CACTCTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCAGTCCTCCCTCTT-TCACT
1875474 CACTCA
65 CACTCA
* * * *
1875480 CACTCTCTCTCTCTCTAGCTGCTGATCGATCTCCCTTGGCCCGCTCAGTCCTCCCTCTTTCACTC
1 CACTCTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCAGTCCTCCCTCTTTCACTC
1875545 TCTCTTTCAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
70 54 0.96
71 2 0.04
ACGTcount: A:0.10, C:0.44, G:0.13, T:0.33
Consensus pattern (70 bp):
CACTCTCTCTCTCTCTAGCCGCCGACCGATCTCCCTTGGCCCGATCAGTCCTCCCTCTTTCACTC
ACTCA
Found at i:1876365 original size:22 final size:22
Alignment explanation
Indices: 1876340--1876417 Score: 95
Period size: 22 Copynumber: 3.6 Consensus size: 22
1876330 TAGTTTTTGG
*
1876340 GCATTGTGTGACTAATTTTTAA
1 GCATTGCGTGACTAATTTTTAA
* * **
1876362 GCATTGCGTGACTGA-CTTTGG
1 GCATTGCGTGACTAATTTTTAA
*
1876383 GCATTACGTGACTAATTTTTAA
1 GCATTGCGTGACTAATTTTTAA
1876405 GCATTGCGTGACT
1 GCATTGCGTGACT
1876418 GACTTTAGGC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 16 0.36
22 28 0.64
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (22 bp):
GCATTGCGTGACTAATTTTTAA
Found at i:1876392 original size:21 final size:21
Alignment explanation
Indices: 1876339--1876459 Score: 93
Period size: 21 Copynumber: 5.7 Consensus size: 21
1876329 GTAGTTTTTG
* * *
1876339 GGCATTGTGTGACTAATTTTTA
1 GGCATTGCGTGACTGA-CTTTA
* *
1876361 AGCATTGCGTGACTGACTTTG
1 GGCATTGCGTGACTGACTTTA
* * *
1876382 GGCATTACGTGACTAATTTTTA
1 GGCATTGCGTGACTGA-CTTTA
*
1876404 AGCATTGCGTGACTGACTTTA
1 GGCATTGCGTGACTGACTTTA
* *
1876425 GGCAATG-TTGACTGACTTT-
1 GGCATTGCGTGACTGACTTTA
*
1876444 GGATATTGCGTGACTG
1 GG-CATTGCGTGACTG
1876460 GTTGTATAAC
Statistics
Matches: 76, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.03
20 14 0.18
21 31 0.41
22 29 0.38
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (21 bp):
GGCATTGCGTGACTGACTTTA
Found at i:1876396 original size:43 final size:43
Alignment explanation
Indices: 1876335--1876428 Score: 161
Period size: 43 Copynumber: 2.2 Consensus size: 43
1876325 TTTTGTAGTT
**
1876335 TTTGGGCATTGTGTGACTAATTTTTAAGCATTGCGTGACTGAC
1 TTTGGGCATTACGTGACTAATTTTTAAGCATTGCGTGACTGAC
1876378 TTTGGGCATTACGTGACTAATTTTTAAGCATTGCGTGACTGAC
1 TTTGGGCATTACGTGACTAATTTTTAAGCATTGCGTGACTGAC
*
1876421 TTTAGGCA
1 TTTGGGCA
1876429 ATGTTGACTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.38
Consensus pattern (43 bp):
TTTGGGCATTACGTGACTAATTTTTAAGCATTGCGTGACTGAC
Found at i:1876475 original size:22 final size:22
Alignment explanation
Indices: 1876448--1876525 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
1876438 GACTTTGGAT
*
1876448 ATTGCGTGACTGGTTGTATA-AC
1 ATTGCGTGACTAGTTG-ATAGAC
**
1876470 ATTGCGTGACTAGTTGATAGGT
1 ATTGCGTGACTAGTTGATAGAC
* * *
1876492 ATTGCGTGACTTGTTAATAAGGC
1 ATTGCGTGACTAGTTGAT-AGAC
*
1876515 ATTGTGTGACT
1 ATTGCGTGACT
1876526 TAGGGCCTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
21 3 0.06
22 31 0.66
23 13 0.28
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (22 bp):
ATTGCGTGACTAGTTGATAGAC
Found at i:1876523 original size:23 final size:22
Alignment explanation
Indices: 1876469--1876526 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
1876459 GGTTGTATAA
* *
1876469 CATTGCGTGACTAGTTGATAGG
1 CATTGCGTGACTTGTTAATAGG
*
1876491 TATTGCGTGACTTGTTAATAAGG
1 CATTGCGTGACTTGTTAAT-AGG
*
1876514 CATTGTGTGACTT
1 CATTGCGTGACTT
1876527 AGGGCCTTGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (22 bp):
CATTGCGTGACTTGTTAATAGG
Found at i:1878525 original size:60 final size:59
Alignment explanation
Indices: 1878403--1878579 Score: 230
Period size: 60 Copynumber: 3.0 Consensus size: 59
1878393 CACCATCACT
* * * * *
1878403 TACTCGTGGGAACTGCCTACACCACC-ATATGAATCGGGGCTTCAGGTCCCCCTTTACT
1 TACTCGTGGGAACTACCCACACCACCAATATAAATCGGGGCTTCAGGTCCCCTTTTACC
*
1878461 TACTCGTGGGAACTACCCACACCACTCAATATAAATCGGGGCTTCAGGTCGCCTTTTACC
1 TACTCGTGGGAACTACCCACACCAC-CAATATAAATCGGGGCTTCAGGTCCCCTTTTACC
* * * * *
1878521 TACTCGTGAGAACTATCCACACCACCCAATATAAATCGAGGCTTTAGATCCCCTTTTAC
1 TACTCGTGGGAACTACCCACACCA-CCAATATAAATCGGGGCTTCAGGTCCCCTTTTAC
1878580 AATCAAATAT
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
58 23 0.22
59 1 0.01
60 79 0.76
61 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (59 bp):
TACTCGTGGGAACTACCCACACCACCAATATAAATCGGGGCTTCAGGTCCCCTTTTACC
Found at i:1891092 original size:29 final size:29
Alignment explanation
Indices: 1891050--1891120 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 29
1891040 TTTGGGTACT
1891050 ACATTGAACATTTTTTAAGTACAGATACC
1 ACATTGAACATTTTTTAAGTACAGATACC
* * *
1891079 ACATTGAACATTTTTTTAGTGCAGGTACC
1 ACATTGAACATTTTTTAAGTACAGATACC
1891108 ACATTCG-ACATTT
1 ACATT-GAACATTT
1891121 CTCTAATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 37 0.97
30 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (29 bp):
ACATTGAACATTTTTTAAGTACAGATACC
Found at i:1894007 original size:58 final size:57
Alignment explanation
Indices: 1893911--1894024 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 57
1893901 AATGGTGAGT
* *
1893911 GTTTGCATTGGTATTTAACAATTCATTGATTCAGCTTAGACTATAAGTACTAATAGG
1 GTTTGCATTCGTATTTAAAAATTCATTGATTCAGCTTAGACTATAAGTACTAATAGG
* *
1893968 GTTTAGCATTCGTATTTAAAAATTCATTGATTCATCTTAGACTATAATTACTAATAG
1 GTTT-GCATTCGTATTTAAAAATTCATTGATTCAGCTTAGACTATAAGTACTAATAG
1894025 TGAATATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
57 4 0.08
58 48 0.92
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.40
Consensus pattern (57 bp):
GTTTGCATTCGTATTTAAAAATTCATTGATTCAGCTTAGACTATAAGTACTAATAGG
Found at i:1900249 original size:20 final size:20
Alignment explanation
Indices: 1900226--1900264 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1900216 GAAAAAAAAG
1900226 GAGATTTAAGGCTCTAATGA
1 GAGATTTAAGGCTCTAATGA
1900246 GAGATTTAAGGCTCTAATG
1 GAGATTTAAGGCTCTAATG
1900265 TTCGAGAGTT
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:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (20 bp):
GAGATTTAAGGCTCTAATGA
Found at i:1902145 original size:93 final size:98
Alignment explanation
Indices: 1902030--1902233 Score: 251
Period size: 105 Copynumber: 2.1 Consensus size: 98
1902020 TCTCTGTCTC
*
1902030 TGATAGTTATGGAGGTAGTTTGGC-T-A-A-T-GACAGTGTTGTCGATTCCAGGTCAAAAG-TAA
1 TGATAGTAATGGAGGTAGTTTGGCATGATATTAGACAGTGTTGTCGATTCCAGGTCAAAAGAT-A
*
1902089 ATGAGGACTCTGAAACGGCTGTAGCC-GATGATGG
65 ATAAGGACTCTGAAACGGCTGTA-CCTGATGATGG
1902123 TGATAGTAATGGAGGTAGTTTGGCTAATGATAGTTTCAAAGACAGTGTTGTCGATTCCAGGTCAA
1 TGATAGTAATGGAGGTAGTTTGGC--ATGATA--TT---AGACAGTGTTGTCGATTCCAGGTCAA
*
1902188 AAGATGATAAGGACTCTGAAACGGCTGTACCTGATGATGG
59 AAGATAATAAGGACTCTGAAACGGCTGTACCTGATGATGG
1902228 TGATAG
1 TGATAG
1902234 CAGTGGAGAT
Statistics
Matches: 94, Mismatches: 3, Indels: 16
0.83 0.03 0.14
Matches are distributed among these distances:
93 23 0.24
96 1 0.01
97 1 0.01
98 1 0.01
101 1 0.01
104 2 0.02
105 64 0.68
106 1 0.01
ACGTcount: A:0.29, C:0.12, G:0.30, T:0.28
Consensus pattern (98 bp):
TGATAGTAATGGAGGTAGTTTGGCATGATATTAGACAGTGTTGTCGATTCCAGGTCAAAAGATAA
TAAGGACTCTGAAACGGCTGTACCTGATGATGG
Found at i:1902259 original size:105 final size:105
Alignment explanation
Indices: 1902058--1902260 Score: 295
Period size: 105 Copynumber: 1.9 Consensus size: 105
1902048 TTTGGCTAAT
*
1902058 GACAGTGTTGTCGATTCCAGGTCAAAAGTAAATGAGGACTCTGAAACGGCTGTAGCCGATGATGG
1 GACAGTGTTGTCGATTCCAGGTCAAAAGTAAATAAGGACTCTGAAACGGCTGTAGCCGATGATGG
* * *
1902123 TGATAGTAATGGAGGTAGTTTGGCTAATGATAGTTTCAAA
66 TGATAGCAATGGAGATAGTTTAGCTAATGATAGTTTCAAA
*
1902163 GACAGTGTTGTCGATTCCAGGTCAAAAG-ATGATAAGGACTCTGAAACGGCTGTA-CCTGATGAT
1 GACAGTGTTGTCGATTCCAGGTCAAAAGTA-AATAAGGACTCTGAAACGGCTGTAGCC-GATGAT
* *
1902226 GGTGATAGCAGTGGAGAT-GCTTTAGCTACTGATAG
64 GGTGATAGCAATGGAGATAG-TTTAGCTAATGATAG
1902261 CGCCAAGGAC
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
104 4 0.05
105 84 0.95
ACGTcount: A:0.30, C:0.14, G:0.30, T:0.27
Consensus pattern (105 bp):
GACAGTGTTGTCGATTCCAGGTCAAAAGTAAATAAGGACTCTGAAACGGCTGTAGCCGATGATGG
TGATAGCAATGGAGATAGTTTAGCTAATGATAGTTTCAAA
Found at i:1902574 original size:99 final size:99
Alignment explanation
Indices: 1902443--1902653 Score: 377
Period size: 99 Copynumber: 2.1 Consensus size: 99
1902433 GATTCCGGGG
* *
1902443 CTGAACAGAATGATGGTGTTCCTGTCTCTGTCTCTGATAGTAACGGGAATTGTTTACCTGCTGAT
1 CTGAACAGAATGATGGTGTTCCTGTCTCTGTCTCTGATACTAACGGGAATTGTTTACCTGCTGAA
1902508 AGTGTGGAAGATACTGTTTCAGAAGTTTCCAAGC
66 AGTGTGGAAGATACTGTTTCAGAAGTTTCCAAGC
* *
1902542 CTGAACAGAATGATGGTGTTCCTGTCTCTGTCTCTGATTCTAACGGGGATTGTTTACCTGCTGAA
1 CTGAACAGAATGATGGTGTTCCTGTCTCTGTCTCTGATACTAACGGGAATTGTTTACCTGCTGAA
*
1902607 AGTGTGGAGGATACTGTTTCAGAAGTTTCCAAGC
66 AGTGTGGAAGATACTGTTTCAGAAGTTTCCAAGC
1902641 CTGAACAGAATGA
1 CTGAACAGAATGA
1902654 GTCCTCTAAC
Statistics
Matches: 107, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 107 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (99 bp):
CTGAACAGAATGATGGTGTTCCTGTCTCTGTCTCTGATACTAACGGGAATTGTTTACCTGCTGAA
AGTGTGGAAGATACTGTTTCAGAAGTTTCCAAGC
Found at i:1903281 original size:39 final size:39
Alignment explanation
Indices: 1903238--1903316 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
1903228 CCATCTTCTA
* *
1903238 CTGTTGATGATGAGAAAGCTGAAACTGAAGTCGTAAAGT
1 CTGTTGATGATGAGAAAGCAGAAACTGAAGTCATAAAGT
*
1903277 CTGTTGATGATGAGAAGGCAGAAACTGAAGTCATAAAGT
1 CTGTTGATGATGAGAAAGCAGAAACTGAAGTCATAAAGT
1903316 C
1 C
1903317 AGATGAGAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (39 bp):
CTGTTGATGATGAGAAAGCAGAAACTGAAGTCATAAAGT
Found at i:1910028 original size:184 final size:184
Alignment explanation
Indices: 1909530--1910034 Score: 608
Period size: 188 Copynumber: 2.7 Consensus size: 184
1909520 TCTAGATATC
* * * * *
1909530 AAATTGGA-AACATATCCTTAAGCAATTCAACAATGGATAAACTACAATTCTCCTAACC-AAATA
1 AAATT-GATAACATATCATTAAGCAATTCAACAACGAATAAACTACCATTCTCCTAACCGAAA-G
* * ** *
1909593 AATCAAACTAAAACCCTAAGGAAACAAATGATAATGCATTA-ATCATTGATAAGATGGAACTATC
64 AATCAAACTATAACCCTAGGGAAACAAATGATAATGCA-TACATCATCCATAGGATGGAACTATC
* * * * ** *
1909657 AACATATGCAAAATGTTGTTTACAAATTCATCATCAACTTGAAAGGAACAAAAGGAT
128 AACCTAGGCAAAATATTGTTAACAAATTCATCATCAACCCGAAACGAACAAAAGGAT
* * * *
1909714 AAATTGATACAGATTCATCACTAAGCAATTCAACAACAAATAAACT-CCGATTCTACTAACCGGA
1 AAATTGATA-ACA-T-ATCATTAAGCAATTCAACAACGAATAAACTACC-ATTCTCCTAACC-GA
* * *
1909778 ATGAA-CTGAACTATAACCCTAGGGAAACAAATGATAATGCATTCATCATCCATAGGATGGAACT
61 AAGAATC-AAACTATAACCCTAGGGAAACAAATGATAATGCATACATCATCCATAGGATGGAACT
*
1909842 ATCAACCTAGGCAACAA-ATTGTTAACAAATTCATCATCAACCCGAAACGAACGAAAGGAT
125 ATCAACCTAGGCAA-AATATTGTTAACAAATTCATCATCAACCCGAAACGAACAAAAGGAT
*
1909902 GAATTGATAACATATCATTAAGCAATTCAACAACGAATAAACTACCATTCTCCTAACCGAAAGAA
1 AAATTGATAACATATCATTAAGCAATTCAACAACGAATAAACTACCATTCTCCTAACCGAAAGAA
* * * *
1909967 TCAAACTATAACCCTGGGGAAACGAATGATAATGCATACATCACCCATAGGATGTAACTATCAAC
66 TCAAACTATAACCCTAGGGAAACAAATGATAATGCATACATCATCCATAGGATGGAACTATCAAC
1910032 CTA
131 CTA
1910035 ATTCATCAAC
Statistics
Matches: 272, Mismatches: 37, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
183 2 0.01
184 72 0.26
185 42 0.15
186 5 0.02
187 40 0.15
188 107 0.39
189 4 0.01
ACGTcount: A:0.44, C:0.20, G:0.12, T:0.23
Consensus pattern (184 bp):
AAATTGATAACATATCATTAAGCAATTCAACAACGAATAAACTACCATTCTCCTAACCGAAAGAA
TCAAACTATAACCCTAGGGAAACAAATGATAATGCATACATCATCCATAGGATGGAACTATCAAC
CTAGGCAAAATATTGTTAACAAATTCATCATCAACCCGAAACGAACAAAAGGAT
Found at i:1914479 original size:81 final size:81
Alignment explanation
Indices: 1914376--1914539 Score: 310
Period size: 81 Copynumber: 2.0 Consensus size: 81
1914366 ACTCAACGAA
*
1914376 TTTCGATCACCAACCTATTGCTTGTTGTGTGCCATAGCTAAAATGTTCGTGTTGTTCCCTCTTCG
1 TTTCGATCACCAACCTATTGCTTGTTGTGTGCCATAGCTAAAATGTTCGTGTTGTTCCCTCTGCG
*
1914441 GAGGGATCACTCGTTT
66 GAGGAATCACTCGTTT
1914457 TTTCGATCACCAACCTATTGCTTGTTGTGTGCCATAGCTAAAATGTTCGTGTTGTTCCCTCTGCG
1 TTTCGATCACCAACCTATTGCTTGTTGTGTGCCATAGCTAAAATGTTCGTGTTGTTCCCTCTGCG
1914522 GAGGAATCACTCGTTT
66 GAGGAATCACTCGTTT
1914538 TT
1 TT
1914540 GAAAGCTTTT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (81 bp):
TTTCGATCACCAACCTATTGCTTGTTGTGTGCCATAGCTAAAATGTTCGTGTTGTTCCCTCTGCG
GAGGAATCACTCGTTT
Found at i:1929246 original size:23 final size:23
Alignment explanation
Indices: 1929189--1929246 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1929179 CTAATTAATT
1929189 TAATTTAATTAAATTCATTATTA
1 TAATTTAATTAAATTCATTATTA
** *
1929212 TAAAATATTTAAA-T-ATTATATCA
1 TAATTTAATTAAATTCATTAT-T-A
1929235 TAATTTAATTAA
1 TAATTTAATTAA
1929247 TTTATGTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 5 0.19
22 2 0.07
23 20 0.74
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTTAATTAAATTCATTATTA
Found at i:1933053 original size:26 final size:28
Alignment explanation
Indices: 1932995--1933053 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
1932985 TAAATTTTGA
*
1932995 AAAATTTTTGAAAAAAAAACTATAACAAT
1 AAAATTTTTGAAAAAAAAACTAT-ACAAG
1933024 AAAATTTTT-AAAAAAAGAACT-T-CAAG
1 AAAATTTTTGAAAAAAA-AACTATACAAG
1933050 AAAA
1 AAAA
1933054 GCTCCTCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 7 0.25
28 8 0.29
29 13 0.46
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.25
Consensus pattern (28 bp):
AAAATTTTTGAAAAAAAAACTATACAAG
Found at i:1934679 original size:24 final size:25
Alignment explanation
Indices: 1934647--1934695 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
1934637 ATCGACCTAT
1934647 ATTCAACTA-T-TTTTTTAGAAAAAA
1 ATTCAACTACTCTTTTTTA-AAAAAA
1934671 ATTCAACTACTCTTTTTTAAAAAAA
1 ATTCAACTACTCTTTTTTAAAAAAA
1934696 TCATAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.39
25 7 0.30
26 7 0.30
ACGTcount: A:0.45, C:0.12, G:0.02, T:0.41
Consensus pattern (25 bp):
ATTCAACTACTCTTTTTTAAAAAAA
Found at i:1934766 original size:35 final size:36
Alignment explanation
Indices: 1934726--1934814 Score: 126
Period size: 35 Copynumber: 2.5 Consensus size: 36
1934716 ATTTCAAGTC
*
1934726 AAGAAAATCCATACACCAACCTTACAAAAAA-AAAA
1 AAGAAAATTCATACACCAACCTTACAAAAAATAAAA
* *
1934761 AAGAAAATTCATGCACCGACCTTACAAAAAATAAAA
1 AAGAAAATTCATACACCAACCTTACAAAAAATAAAA
*
1934797 ATAAAAAATTCATACACC
1 A-AGAAAATTCATACACC
1934815 TAAATTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 28 0.60
36 5 0.11
37 14 0.30
ACGTcount: A:0.58, C:0.21, G:0.04, T:0.16
Consensus pattern (36 bp):
AAGAAAATTCATACACCAACCTTACAAAAAATAAAA
Found at i:1974711 original size:22 final size:22
Alignment explanation
Indices: 1974680--1974736 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1974670 AAAGAATAAT
*
1974680 TATATAAAATTATAAATATATA
1 TATATAAAATTAGAAATATATA
* *
1974702 TATATCAAATTAGATATATATA
1 TATATAAAATTAGAAATATATA
1974724 -ATAATAATAATTA
1 TAT-ATAA-AATTA
1974737 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TATATAAAATTAGAAATATATA
Found at i:1983752 original size:37 final size:35
Alignment explanation
Indices: 1983682--1983752 Score: 81
Period size: 35 Copynumber: 2.0 Consensus size: 35
1983672 GCATCAATTG
* *
1983682 ATTAAAACTAAATCCAATTTGGACTAGGCCTTCAA
1 ATTAAAACTAAATCCAATTTCGACTAAGCCTTCAA
*
1983717 ATTAAAACTGAAATTTCAATTTTCGACTAAG-CTTCA
1 ATTAAAACT-AAA-TCCAA-TTTCGACTAAGCCTTCA
1983753 TGATCATGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 9 0.30
36 3 0.10
37 9 0.30
38 9 0.30
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (35 bp):
ATTAAAACTAAATCCAATTTCGACTAAGCCTTCAA
Found at i:1988535 original size:25 final size:28
Alignment explanation
Indices: 1988475--1988533 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
1988465 GTCTACCTAG
1988475 ATAATAGTATTGTATAATAACTCTAACT
1 ATAATAGTATTGTATAATAACTCTAACT
*
1988503 ATAATAGTATTGTATAATAACTCTAATT
1 ATAATAGTATTGTATAATAACTCTAACT
1988531 ATA
1 ATA
1988534 GTTTAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (28 bp):
ATAATAGTATTGTATAATAACTCTAACT
Found at i:1996582 original size:12 final size:14
Alignment explanation
Indices: 1996552--1996580 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1996542 TTTTTTTTTC
1996552 TTTATTGTTAATTT
1 TTTATTGTTAATTT
1996566 TTTATTG-TAATTT
1 TTTATTGTTAATTT
1996579 TT
1 TT
1996581 ATCTTGTTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTATTGTTAATTT
Found at i:2003013 original size:29 final size:29
Alignment explanation
Indices: 2002967--2003023 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2002957 GGCTGCATAT
* *
2002967 TATAAGCATATATATAAAAATGCTGAAGC
1 TATAACCATATATATAAAAATGATGAAGC
* *
2002996 TATAACCATATATGTAAACATGATGAAG
1 TATAACCATATATATAAAAATGATGAAG
2003024 TTAGTAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (29 bp):
TATAACCATATATATAAAAATGATGAAGC
Found at i:2005136 original size:11 final size:10
Alignment explanation
Indices: 2005114--2005166 Score: 52
Period size: 10 Copynumber: 4.9 Consensus size: 10
2005104 TACTTTATTC
2005114 ATTTACCATT
1 ATTTACCATT
*
2005124 ATGTTACCTTT
1 AT-TTACCATT
2005135 ATTTACCCATTTT
1 ATTTA-CCA--TT
*
2005148 ATTTACCAAT
1 ATTTACCATT
2005158 ATTTACCAT
1 ATTTACCAT
2005167 AGAGATTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 14 0.40
11 11 0.31
12 3 0.09
13 7 0.20
ACGTcount: A:0.28, C:0.21, G:0.02, T:0.49
Consensus pattern (10 bp):
ATTTACCATT
Found at i:2010866 original size:30 final size:30
Alignment explanation
Indices: 2010823--2010929 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
2010813 AATAATTAAT
* *
2010823 TATAAAAACTTATTTAATGTAAAACAAAAA
1 TATAAAAATTTATTTAATGTAAAATAAAAA
* *
2010853 TATAAATATTTATTTAATTTAAAATAAAAA
1 TATAAAAATTTATTTAATGTAAAATAAAAA
* * *
2010883 TATAAGAATTTAATTGAGTGT--AATAAAAA
1 TATAAAAATTT-ATTTAATGTAAAATAAAAA
2010912 TATAAAAATTTTATTTAA
1 TATAAAAA-TTTATTTAA
2010930 ATTTTCATGA
Statistics
Matches: 63, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
29 19 0.30
30 38 0.60
31 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (30 bp):
TATAAAAATTTATTTAATGTAAAATAAAAA
Found at i:2013771 original size:19 final size:21
Alignment explanation
Indices: 2013721--2013773 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 21
2013711 CGAGCTTGTG
2013721 GAATTGATTAATAAATTTTACT
1 GAATTGATTAATAAATTTTA-T
* * *
2013743 AAATTTATTAATACA-TTT-T
1 GAATTGATTAATAAATTTTAT
2013762 GAATTGATTAAT
1 GAATTGATTAAT
2013774 TACTAATACA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.42
21 3 0.12
22 12 0.46
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (21 bp):
GAATTGATTAATAAATTTTAT
Found at i:2030351 original size:17 final size:16
Alignment explanation
Indices: 2030329--2030371 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
2030319 ATATATACAT
*
2030329 TACTATTGAATTATTTC
1 TACTATTGAA-AATTTC
2030346 TACTATTCGAAAATTTC
1 TACTATT-GAAAATTTC
*
2030363 TAATATTGA
1 TACTATTGA
2030372 TTACCATATG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 18 0.78
18 3 0.13
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (16 bp):
TACTATTGAAAATTTC
Found at i:2039751 original size:12 final size:12
Alignment explanation
Indices: 2039727--2039764 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
2039717 CAATCCAAGG
*
2039727 AAAAATAAA-AA
1 AAAAAAAAAGAA
2039738 AAAAAAAAAGAA
1 AAAAAAAAAGAA
2039750 AAAAAAAAAGAA
1 AAAAAAAAAGAA
2039762 AAA
1 AAA
2039765 GATGAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.92, C:0.00, G:0.05, T:0.03
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:2039751 original size:15 final size:15
Alignment explanation
Indices: 2039727--2039758 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2039717 CAATCCAAGG
*
2039727 AAAAATAAAAAAAAA
1 AAAAAGAAAAAAAAA
2039742 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
2039757 AA
1 AA
2039759 GAAAAAGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.94, C:0.00, G:0.03, T:0.03
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:2058199 original size:25 final size:25
Alignment explanation
Indices: 2058171--2058221 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2058161 TAATTACATG
2058171 TCTTTTACTTGGTGATTATTTAGTT
1 TCTTTTACTTGGTGATTATTTAGTT
* * *
2058196 TCTTTTATTTGGTGGTTATTTGGTT
1 TCTTTTACTTGGTGATTATTTAGTT
2058221 T
1 T
2058222 TTCATGTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.06, G:0.20, T:0.63
Consensus pattern (25 bp):
TCTTTTACTTGGTGATTATTTAGTT
Found at i:2076519 original size:21 final size:21
Alignment explanation
Indices: 2076495--2076552 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
2076485 ACTTAATCTG
2076495 TGAAGTTAGCTGACTAAAGCA
1 TGAAGTTAGCTGACTAAAGCA
* **
2076516 TGAAGTTAGCTAACTAAAGTG
1 TGAAGTTAGCTGACTAAAGCA
2076537 TGAAGTTAGCTGACTA
1 TGAAGTTAGCTGACTA
2076553 CAGTTATTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (21 bp):
TGAAGTTAGCTGACTAAAGCA
Found at i:2079750 original size:12 final size:12
Alignment explanation
Indices: 2079733--2079758 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2079723 ATATTTTCAG
2079733 GGTTCAGATAAA
1 GGTTCAGATAAA
2079745 GGTTCAGATAAA
1 GGTTCAGATAAA
2079757 GG
1 GG
2079759 AGAATATGAT
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:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (12 bp):
GGTTCAGATAAA
Found at i:2100345 original size:17 final size:16
Alignment explanation
Indices: 2100322--2100371 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
2100312 AACATAGATC
2100322 ATTTTTAAATTTATTT
1 ATTTTTAAATTTATTT
*
2100338 ATTTTTTAAATATCATTT
1 A-TTTTTAAAT-TTATTT
* *
2100356 AATTTTAATTTTATTT
1 ATTTTTAAATTTATTT
2100372 TTATCTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 16 0.57
18 6 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTTTAAATTTATTT
Found at i:2108492 original size:127 final size:128
Alignment explanation
Indices: 2108303--2108543 Score: 335
Period size: 127 Copynumber: 1.9 Consensus size: 128
2108293 TAAATAAATG
* * * *
2108303 TATATATCCATTAGATTTGTGTCATTTTTTTTTATGTTAAACTTGTAATTTTTACATCCAAATGT
1 TATATATCCATTAGATTTGTGTCATTTTTTTTCATATTAAACTTGTAATTTTAACATCCAAATAT
* * *
2108368 TGATATCG-TTTTTCCAAAAGTTACATTTTTCTTATTTAAAAGCCATAAATAAACATATATATA
66 TGATATCGCTTTTT-CAAAAATTACATTTCTCTTACTTAAAAGCCATAAATAAACATATATATA
* *
2108431 TATATATCCATTAGATTTGTG-C-TATTTTTTTCATATTAAACTTGTGATTTTAACATTCAAATA
1 TATATATCCATTAGATTTGTGTCAT-TTTTTTTCATATTAAACTTGTAATTTTAACATCCAAATA
* * *
2108494 TTGATATTGCTTTTTCAAAAATTATATTTCTCTTGCTTAAAAGCCATAAA
65 TTGATATCGCTTTTTCAAAAATTACATTTCTCTTACTTAAAAGCCATAAA
2108544 AGCATATTGA
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
126 1 0.01
127 72 0.73
128 26 0.26
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (128 bp):
TATATATCCATTAGATTTGTGTCATTTTTTTTCATATTAAACTTGTAATTTTAACATCCAAATAT
TGATATCGCTTTTTCAAAAATTACATTTCTCTTACTTAAAAGCCATAAATAAACATATATATA
Found at i:2108867 original size:16 final size:16
Alignment explanation
Indices: 2108845--2108892 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
2108835 TTATTAATAC
2108845 TAAAAATTTATTTAAA
1 TAAAAATTTATTTAAA
* * **
2108861 TATAAATTAAAATAAA
1 TAAAAATTTATTTAAA
2108877 TAAAAATTTATTTAAA
1 TAAAAATTTATTTAAA
2108893 ATTGTAATAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAAAATTTATTTAAA
Found at i:2112630 original size:55 final size:55
Alignment explanation
Indices: 2112527--2112845 Score: 186
Period size: 55 Copynumber: 5.9 Consensus size: 55
2112517 TGACACTGTA
* *
2112527 AAAACCCAAAAAACCAGTTTATCCACAACACGCCAGGAACAACCGTGACACACCC
1 AAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACACCC
* * * * ** *
2112582 AAAACCCAAAAAACCAGTTAACCCACGACACGCCAGGAATAGCTGTGACATGCCA
1 AAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACACCC
* ** ** * * ** * **
2112637 AAAACCCATAAATTCAGTT-------GTCATGCCAAGAACAATTGTGACACGCAA
1 AAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACACCC
* * ** * *****
2112685 AAAATCCATAAATTCAGTTAACCCACGACACGCCAGGAACAACCGTGACATGTTA
1 AAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACACCC
* ** * * * * *
2112740 AAAACCCATAAATTCAATTAACCCACGACACGCCAGGAACAGCCGTGACAC-GCT
1 AAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACACCC
* * * *
2112794 AACAACCAAAAAAACTAGTTAACCCACAACACGCTAGGAATAACCGTGACAC
1 AA-AACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACAC
2112846 GCTAAAATAA
Statistics
Matches: 210, Mismatches: 46, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
48 39 0.19
54 2 0.01
55 169 0.80
ACGTcount: A:0.42, C:0.30, G:0.14, T:0.14
Consensus pattern (55 bp):
AAAACCCAAAAAACCAGTTAACCCACAACACGCCAGGAACAACCGTGACACACCC
Found at i:2112846 original size:55 final size:55
Alignment explanation
Indices: 2112674--2112852 Score: 200
Period size: 55 Copynumber: 3.3 Consensus size: 55
2112664 AAGAACAATT
* * *
2112674 GTGACACGCAAAAAATCC-ATAAATTCAGTTAACCCACGACACGCCAGGAACAACC
1 GTGACACGCTAAAAA-CCAAAAAACTCAGTTAACCCACGACACGCCAGGAACAACC
* * * * * * *
2112729 GTGACATGTTAAAAACCCATAAATTCAATTAACCCACGACACGCCAGGAACAGCC
1 GTGACACGCTAAAAACCAAAAAACTCAGTTAACCCACGACACGCCAGGAACAACC
* * * *
2112784 GTGACACGCTAACAACCAAAAAAACT-AGTTAACCCACAACACGCTAGGAATAACC
1 GTGACACGCTAAAAACC-AAAAAACTCAGTTAACCCACGACACGCCAGGAACAACC
2112839 GTGACACGCTAAAA
1 GTGACACGCTAAAA
2112853 TAACGCTAAC
Statistics
Matches: 105, Mismatches: 17, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
54 2 0.02
55 98 0.93
56 5 0.05
ACGTcount: A:0.42, C:0.29, G:0.15, T:0.14
Consensus pattern (55 bp):
GTGACACGCTAAAAACCAAAAAACTCAGTTAACCCACGACACGCCAGGAACAACC
Found at i:2123769 original size:2 final size:2
Alignment explanation
Indices: 2123762--2123798 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2123752 AAAGCTCATG
* *
2123762 AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2123799 GTAGTCAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Done.