Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009461.1 Hibiscus syriacus cultivar Beakdansim tig00113724_pilon, whole genome shotgun sequence
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: 2346588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1457920 original size:31 final size:31
Alignment explanation
Indices: 1457875--1457975 Score: 143
Period size: 31 Copynumber: 3.3 Consensus size: 31
1457865 GCTTATATAA
*
1457875 TAATCTATCCATATGTCCTGAAGAACATAGG
1 TAATCTGTCCATATGTCCTGAAGAACATAGG
**
1457906 TAA-CATGTCCATATGTCCCAAAGAACATAGG
1 TAATC-TGTCCATATGTCCTGAAGAACATAGG
1457937 TAATCTGTCCATATGT-CTAGAAGAACATAGG
1 TAATCTGTCCATATGTCCT-GAAGAACATAGG
1457968 TAATCTGT
1 TAATCTGT
1457976 AACATATATA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
30 2 0.03
31 59 0.95
32 1 0.02
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (31 bp):
TAATCTGTCCATATGTCCTGAAGAACATAGG
Found at i:1458232 original size:31 final size:31
Alignment explanation
Indices: 1458194--1458359 Score: 260
Period size: 31 Copynumber: 5.4 Consensus size: 31
1458184 TCTATATGTC
1458194 AACATAGGTAAACAGTCCATATGTCCCGAAG
1 AACATAGGTAAACAGTCCATATGTCCCGAAG
* *
1458225 AACATAGGTAAACAGTCCATATTTCCCAAAG
1 AACATAGGTAAACAGTCCATATGTCCCGAAG
* * *
1458256 AACATAGGTAAACAATCCACATGTCTCGAAG
1 AACATAGGTAAACAGTCCATATGTCCCGAAG
1458287 AACATAGGTAAACAGTCCATATGTCCCGAAG
1 AACATAGGTAAACAGTCCATATGTCCCGAAG
* *
1458318 AACATAGGCAAACAATCCATATGTCCCGAAG
1 AACATAGGTAAACAGTCCATATGTCCCGAAG
*
1458349 AATATAGGTAA
1 AACATAGGTAA
1458360 CCCTCGACTC
Statistics
Matches: 121, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 121 1.00
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (31 bp):
AACATAGGTAAACAGTCCATATGTCCCGAAG
Found at i:1458799 original size:2 final size:2
Alignment explanation
Indices: 1458794--1458847 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
1458784 CTTATATAAC
1458794 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
1458836 TA T- TA TA TA TA T
1 TA TA TA TA TA TA T
1458848 TTCTATCATA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1461029 original size:21 final size:21
Alignment explanation
Indices: 1461001--1461046 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1460991 GATTTTGTAA
*
1461001 AAAT-TGAAAGTTCAAGTACT
1 AAATGTGAAACTTCAAGTACT
* *
1461021 AAATGTGAAACTTTAGGTACT
1 AAATGTGAAACTTCAAGTACT
1461042 AAATG
1 AAATG
1461047 CTTAGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.30
Consensus pattern (21 bp):
AAATGTGAAACTTCAAGTACT
Found at i:1461631 original size:18 final size:17
Alignment explanation
Indices: 1461603--1461639 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
1461593 AATATACTAA
*
1461603 TTATTAAATTTTTTGAG
1 TTATTAAATTTTTCGAG
1461620 TTATTCAAATTTTTCGAG
1 TTATT-AAATTTTTCGAG
1461638 TT
1 TT
1461640 TTATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (17 bp):
TTATTAAATTTTTCGAG
Found at i:1461632 original size:17 final size:18
Alignment explanation
Indices: 1461603--1461639 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1461593 AATATACTAA
1461603 TTATTAAATTTTTT-GAG
1 TTATTAAATTTTTTCGAG
1461620 TTATTCAAA-TTTTTCGAG
1 TTATT-AAATTTTTTCGAG
1461638 TT
1 TT
1461640 TTATTTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (18 bp):
TTATTAAATTTTTTCGAG
Found at i:1462413 original size:15 final size:16
Alignment explanation
Indices: 1462393--1462424 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1462383 ATTCATATAT
1462393 TCGGGTCGAG-TCGGG
1 TCGGGTCGAGTTCGGG
1462408 TCGGGTCGAGTTCGGG
1 TCGGGTCGAGTTCGGG
1462424 T
1 T
1462425 TTAGGGTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.06, C:0.19, G:0.50, T:0.25
Consensus pattern (16 bp):
TCGGGTCGAGTTCGGG
Found at i:1462512 original size:205 final size:208
Alignment explanation
Indices: 1462198--1462617 Score: 686
Period size: 205 Copynumber: 2.0 Consensus size: 208
1462188 ATTCGGGTCA
* * *
1462198 GGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCAGATCGACCCGAAAATATATATAATTTTA
1 GGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACCCGAAAATATATAT-ATTTTA
1462263 CCTTATATATTTAGGAATAATTACAATAATACCCATATATATATATTTTTTTCCAATTAAGTCAC
65 CCTTATATATTTAGGAATAATTACAATAATACCCATATATATATATTTTTTT-CAATTAAGTCAC
1462328 TGTTTTTATTAAATAAAAATAATTTTTTATTATTTC-A-GGTCGGGTCGGATTTCTAATTCATAT
129 TGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGAGGGTCGGGTCGGATTTCTAATTCATAT
1462391 ATTCGGGTCGAGTCG
194 ATTCGGGTCGAGTCG
*
1462406 GGTCGGGTCGAGTTCGGGTTTAGGGTG-AAAAAACCGGACCAACCCGAAAATATATAT-TTTTAC
1 GGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACCCGAAAATATATATATTTTAC
* * *
1462469 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTTCAATTAAGTCATTG
66 CTTATATATTTAGGAATAATTACAATAATACCCATATATATATATTTTTTTCAATTAAGTCACTG
1462534 TTTTTATTAAATAAAAATAATTTTTTATTATTTCGAGTCGGGTCGGGTCGGATTTCTAATTCATA
131 TTTTTATTAAATAAAAATAATTTTTTATTATTTCGA---GGGTCGGGTCGGATTTCTAATTCATA
* *
1462599 TATTCGGGTTGGGTCG
193 TATTCGGGTCGAGTCG
1462615 GGT
1 GGT
1462618 GAAACTTTAT
Statistics
Matches: 198, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
204 47 0.24
205 56 0.28
207 27 0.14
208 26 0.13
209 42 0.21
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (208 bp):
GGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAAAACCAGACCAACCCGAAAATATATATATTTTAC
CTTATATATTTAGGAATAATTACAATAATACCCATATATATATATTTTTTTCAATTAAGTCACTG
TTTTTATTAAATAAAAATAATTTTTTATTATTTCGAGGGTCGGGTCGGATTTCTAATTCATATAT
TCGGGTCGAGTCG
Found at i:1463286 original size:18 final size:16
Alignment explanation
Indices: 1463245--1463291 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
1463235 ATATGGAATT
1463245 AGATTCCAATTCCTAC
1 AGATTCCAATTCCTAC
* *
1463261 ATATTCCAATTCATTCAC
1 AGATTCCAATTC-CT-AC
1463279 AGATTCCAATTCC
1 AGATTCCAATTCC
1463292 CTCATAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
16 11 0.44
17 1 0.04
18 13 0.52
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (16 bp):
AGATTCCAATTCCTAC
Found at i:1468582 original size:23 final size:22
Alignment explanation
Indices: 1468554--1468612 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1468544 TAATTTTATT
*
1468554 TTTATGGTACGTTTTCCTCTAC
1 TTTATGGTACATTTTCCTCTAC
1468576 ATTTAT-G-ACATATTTCCTCTAC
1 -TTTATGGTACAT-TTTCCTCTAC
* *
1468598 TTTTTGGTACTTTTT
1 TTTATGGTACATTTT
1468613 TGTCGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
21 7 0.23
22 15 0.50
23 8 0.27
ACGTcount: A:0.17, C:0.19, G:0.10, T:0.54
Consensus pattern (22 bp):
TTTATGGTACATTTTCCTCTAC
Found at i:1474977 original size:6 final size:6
Alignment explanation
Indices: 1474966--1474997 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
1474956 ACATCACCTT
1474966 CCCCTC CCCCTC CCCCTC CCCCT- CCCCTC CCC
1 CCCCTC CCCCTC CCCCTC CCCCTC CCCCTC CCC
1474998 TCATCCTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.84, G:0.00, T:0.16
Consensus pattern (6 bp):
CCCCTC
Found at i:1475544 original size:42 final size:42
Alignment explanation
Indices: 1475470--1475586 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
1475460 ACCTCTATCT
* * * * *
1475470 CCACCGCCTCATTG-AGTCTGGTGTCCCACCTCCTTCACCTCCA
1 CCACC-CCT-ATTGAAGTCTAGTGCCCCTCCTCCTCCACCTCAA
1475513 CCACCCCTATTGAAGTCTAGTGCCCCTCCTCCTCCACCTCAA
1 CCACCCCTATTGAAGTCTAGTGCCCCTCCTCCTCCACCTCAA
* * * *
1475555 CTATTCCC-ATTGATGCCTAGTGCCCCTCCTCC
1 CCA-CCCCTATTGAAGTCTAGTGCCCCTCCTCC
1475587 ACCCCTTCTC
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 4 0.06
42 51 0.81
43 8 0.13
ACGTcount: A:0.15, C:0.46, G:0.12, T:0.26
Consensus pattern (42 bp):
CCACCCCTATTGAAGTCTAGTGCCCCTCCTCCTCCACCTCAA
Found at i:1475771 original size:33 final size:33
Alignment explanation
Indices: 1475734--1475831 Score: 115
Period size: 33 Copynumber: 3.0 Consensus size: 33
1475724 CCACGTGGAC
* *
1475734 CACCACCCCCACCTCTCGTGCGTGGATCACCTG
1 CACCACCCCCACCTCTCATGCGTGGAGCACCTG
* * *
1475767 CACCACCCCCATCTCCCATGCGTGGAGCACCAG
1 CACCACCCCCACCTCTCATGCGTGGAGCACCTG
** * *
1475800 CACTGCCTCCACCTCTTATGCGTGGAGCACCT
1 CACCACCCCCACCTCTCATGCGTGGAGCACCT
1475832 CCCCCACCTT
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.17, C:0.46, G:0.18, T:0.18
Consensus pattern (33 bp):
CACCACCCCCACCTCTCATGCGTGGAGCACCTG
Found at i:1477314 original size:2 final size:2
Alignment explanation
Indices: 1477309--1477369 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1477299 TCTTTGTGTG
1477309 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
1477351 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1477370 TCATAAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1479439 original size:19 final size:19
Alignment explanation
Indices: 1479415--1479458 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1479405 ACTGTCGGAT
1479415 CCAGCTTGATGGCTCGAAC
1 CCAGCTTGATGGCTCGAAC
1479434 CCAGCTTGATGGCTCGAAC
1 CCAGCTTGATGGCTCGAAC
1479453 CCAGCT
1 CCAGCT
1479459 AGATAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.20
Consensus pattern (19 bp):
CCAGCTTGATGGCTCGAAC
Found at i:1486658 original size:8 final size:8
Alignment explanation
Indices: 1486647--1486714 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
1486637 GACTCTCAAT
1486647 CTCTTAAA
1 CTCTTAAA
1486655 CTCTTAAA
1 CTCTTAAA
* *
1486663 TTCTTGAA
1 CTCTTAAA
1486671 CTCTCT-AA
1 CTCT-TAAA
*
1486679 CTCTGAAA
1 CTCTTAAA
* *
1486687 CTATCAAA
1 CTCTTAAA
*
1486695 CTCTCAAA
1 CTCTTAAA
1486703 CT-TTCAAA
1 CTCTT-AAA
1486711 CTCT
1 CTCT
1486715 GAAATTCTCA
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
7 1 0.02
8 45 0.94
9 2 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (8 bp):
CTCTTAAA
Found at i:1486688 original size:16 final size:16
Alignment explanation
Indices: 1486638--1486726 Score: 81
Period size: 16 Copynumber: 5.6 Consensus size: 16
1486628 TAATTCCCCG
* *
1486638 ACTCTCAATCTCTTAA
1 ACTCTCAAACTCTGAA
* *
1486654 ACTCTTAAATTCTTG-A
1 ACTCTCAAACTC-TGAA
*
1486670 ACTCTCTAACTCTGAA
1 ACTCTCAAACTCTGAA
* *
1486686 ACTATCAAACTCTCAA
1 ACTCTCAAACTCTGAA
*
1486702 ACTTTCAAACTCTGAA
1 ACTCTCAAACTCTGAA
*
1486718 ATTCTCAAA
1 ACTCTCAAA
1486727 ATGGTTCATA
Statistics
Matches: 57, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
15 2 0.04
16 54 0.95
17 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (16 bp):
ACTCTCAAACTCTGAA
Found at i:1486711 original size:24 final size:24
Alignment explanation
Indices: 1486669--1486726 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
1486659 TAAATTCTTG
* *
1486669 AACTCTCTAACTCTGAAACTATCA
1 AACTCTCAAACTCTCAAACTATCA
* * *
1486693 AACTCTCAAACTTTCAAACTCTGA
1 AACTCTCAAACTCTCAAACTATCA
*
1486717 AATTCTCAAA
1 AACTCTCAAA
1486727 ATGGTTCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.03, T:0.29
Consensus pattern (24 bp):
AACTCTCAAACTCTCAAACTATCA
Found at i:1490819 original size:51 final size:50
Alignment explanation
Indices: 1490721--1490851 Score: 122
Period size: 51 Copynumber: 2.6 Consensus size: 50
1490711 ACCCTTTGCA
* * * * *
1490721 GTAAGACGCGCCCCCTGCAGCGCGCTTTACGCTGATCTGGTGCCACGTGGG
1 GTAAGGCGCGCCCCCTGCAGCGCACCTTACACTGATCTGGTGACACGT-GG
* *
1490772 GTAAGGCGCGCCCCCTGCAGCGCACCTTATACTGA-CATGGAT-ACACGTGT
1 GTAAGGCGCGCCCCCTGCAGCGCACCTTACACTGATC-TGG-TGACACGTGG
* * * *
1490822 TTAAAGCGCGGCCCCTGCTGCGCACCTTAC
1 GTAAGGCGCGCCCCCTGCAGCGCACCTTAC
1490852 CTTTAAATCT
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 27 0.41
51 38 0.58
52 1 0.02
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (50 bp):
GTAAGGCGCGCCCCCTGCAGCGCACCTTACACTGATCTGGTGACACGTGG
Found at i:1495378 original size:42 final size:44
Alignment explanation
Indices: 1495316--1495399 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 44
1495306 CTCATATCCA
* *
1495316 AAACTAACAATGATTTTG-AAAGTAAAA-TTAGTGATTTGCAAATC
1 AAACTAACAATGAGTTTGAAAAGAAAAATTTA--GATTTGCAAATC
1495360 AAACTAA-AA-GAGTTTGAAAAGAAAAATTTAGATTTGCAAA
1 AAACTAACAATGAGTTTGAAAAGAAAAATTTAGATTTGCAAA
1495400 ATTTACTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
42 16 0.44
43 10 0.28
44 10 0.28
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (44 bp):
AAACTAACAATGAGTTTGAAAAGAAAAATTTAGATTTGCAAATC
Found at i:1501992 original size:65 final size:63
Alignment explanation
Indices: 1501875--1502075 Score: 185
Period size: 65 Copynumber: 3.1 Consensus size: 63
1501865 TTTTCAGAGT
* **
1501875 GATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATTTCATGCA
1 GATGCA-CAA-CCATGCATCGATGCACTCA-GG-CTATTTTGAAACATCGAATGCATTTCATGCA
*
1501938 CC
62 TC
* * *
1501940 GATGCACATACTATGCATCGATGCACTCAGAG-T-TTTATGAAAACATCAAATGCATTTGATGCA
1 GATGCACA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTCATGCA
1502003 TC
62 TC
* * * * *
1502005 AATGCACCAGCCATGCGTCGATGCACTCAGGCTATTTTGAAACATCGAATGTATTTTATGCATC
1 GATGCA-CAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATC
1502069 GATGCAC
1 GATGCAC
1502076 TCTTAGTGCA
Statistics
Matches: 113, Mismatches: 14, Indels: 20
0.77 0.10 0.14
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 46 0.41
65 57 0.50
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (63 bp):
GATGCACAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATC
Found at i:1503162 original size:34 final size:33
Alignment explanation
Indices: 1503095--1503182 Score: 90
Period size: 33 Copynumber: 2.6 Consensus size: 33
1503085 TAATACTTAT
*
1503095 TTTATTTCGTT-AATTTGGTTGGATTTATTTTAA
1 TTTATTTTGTTAAATTT-GTTGGATTTATTTTAA
1503128 TTTATTTTGTTAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTGTTAAATTTGTTGGA-TTTATT-TTAA
** *
1503162 TGCATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAAATTTGTT
1503183 TATTACCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
33 18 0.38
34 18 0.38
35 11 0.23
ACGTcount: A:0.19, C:0.03, G:0.16, T:0.61
Consensus pattern (33 bp):
TTTATTTTGTTAAATTTGTTGGATTTATTTTAA
Found at i:1508535 original size:28 final size:30
Alignment explanation
Indices: 1508495--1508565 Score: 94
Period size: 28 Copynumber: 2.5 Consensus size: 30
1508485 CTCCCTAAAT
*
1508495 TTTTTTGGAATTTTTA-GGAATTT-AGGAG
1 TTTTTTGAAATTTTTATGGAATTTAAGGAG
**
1508523 TTTTTTGAAA-TTTTATGGAATTTAAGGTT
1 TTTTTTGAAATTTTTATGGAATTTAAGGAG
1508552 TTTTTTGAAATTTT
1 TTTTTTGAAATTTT
1508566 AATAATTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 5 0.14
28 16 0.43
29 13 0.35
30 3 0.08
ACGTcount: A:0.25, C:0.00, G:0.18, T:0.56
Consensus pattern (30 bp):
TTTTTTGAAATTTTTATGGAATTTAAGGAG
Found at i:1508555 original size:29 final size:27
Alignment explanation
Indices: 1508494--1508566 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 27
1508484 ACTCCCTAAA
* *
1508494 TTTTTTTGGAATTTTTAGGAATTTAGG
1 TTTTTTTTGAAATTTTAGGAATTTAGG
**
1508521 AGTTTTTTGAAATTTTATGGAATTTAAGG
1 TTTTTTTTGAAATTTTA-GGAATTT-AGG
1508550 TTTTTTTTGAAATTTTA
1 TTTTTTTTGAAATTTTA
1508567 ATAATTTCAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 13 0.34
28 7 0.18
29 18 0.47
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (27 bp):
TTTTTTTTGAAATTTTAGGAATTTAGG
Found at i:1508583 original size:29 final size:28
Alignment explanation
Indices: 1508494--1508585 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 28
1508484 ACTCCCTAAA
* *
1508494 TTTTTTTGGAATTTTTAGGAATTT-AGGAG
1 TTTTTTT-GAAATTTTATGAATTTAAGG-G
*
1508523 -TTTTTTGAAATTTTATGGAATTTAAGGT
1 TTTTTTTGAAATTTTAT-GAATTTAAGGG
*
1508551 TTTTTTTGAAATTTTAAT-AATTTCATGGG
1 TTTTTTTGAAATTTT-ATGAATTT-AAGGG
1508580 TTTTTT
1 TTTTTT
1508586 AAAAAACAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
27 8 0.15
28 17 0.32
29 26 0.49
30 2 0.04
ACGTcount: A:0.25, C:0.01, G:0.17, T:0.57
Consensus pattern (28 bp):
TTTTTTTGAAATTTTATGAATTTAAGGG
Found at i:1510934 original size:15 final size:15
Alignment explanation
Indices: 1510914--1510943 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1510904 GTCGACTAGC
1510914 GTAGTTCATAGTATT
1 GTAGTTCATAGTATT
1510929 GTAGTTCATAGTATT
1 GTAGTTCATAGTATT
1510944 TCTTTTGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
GTAGTTCATAGTATT
Found at i:1516114 original size:12 final size:12
Alignment explanation
Indices: 1516097--1516146 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
1516087 GTCTCTGTCT
*
1516097 TCCCTATATCGA
1 TCCCTATCTCGA
*
1516109 TCCCTATCTCTA
1 TCCCTATCTCGA
* *
1516121 TCTCTATCTCTA
1 TCCCTATCTCGA
1516133 TCCCTATCTCGA
1 TCCCTATCTCGA
1516145 TC
1 TC
1516147 ACGTTCCCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.18, C:0.38, G:0.04, T:0.40
Consensus pattern (12 bp):
TCCCTATCTCGA
Found at i:1516123 original size:6 final size:6
Alignment explanation
Indices: 1516112--1516142 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1516102 ATATCGATCC
*
1516112 CTATCT CTATCT CTATCT CTATCC CTATCT C
1 CTATCT CTATCT CTATCT CTATCT CTATCT C
1516143 GATCACGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.16, C:0.39, G:0.00, T:0.45
Consensus pattern (6 bp):
CTATCT
Found at i:1516154 original size:18 final size:18
Alignment explanation
Indices: 1516133--1516167 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1516123 TCTATCTCTA
*
1516133 TCCCTATCTCGATCACGT
1 TCCCTATCACGATCACGT
*
1516151 TCCCTGTCACGATCACG
1 TCCCTATCACGATCACG
1516168 ATTGCGGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.40, G:0.14, T:0.29
Consensus pattern (18 bp):
TCCCTATCACGATCACGT
Found at i:1524618 original size:107 final size:105
Alignment explanation
Indices: 1524471--1524853 Score: 339
Period size: 107 Copynumber: 3.7 Consensus size: 105
1524461 AGTCAATACT
* * ** * *
1524471 ATTATCAATAAAAAATACGATGAACTTGTTCGACACTGAAAATATATTTTGTGACAATCAATATT
1 ATTATCAATAGAAATTGTGATGAACTTGTTCGACACTGAAAATATATTTTGTGACCATCAAT-GT
1524536 TATCACACTAAGTATACATTTAATGACCAAATGTTTGACAAA
65 TATCACACTAAGTAT-CATTTAATGACCAAATGTTTGACAAA
* * * * *
1524578 ATTTTCAATGGAAATTGTGATGAA-TTCGTTCGACGCTGAAAATATATTTTCTAACCATCAATGT
1 ATTATCAATAGAAATTGTGATGAACTT-GTTCGACACTGAAAATATATTTTGTGACCATCAATGT
* * ** * * **
1524642 TGTCACACTAAATATTTTTTAGTGACCAAGTGTTTGACACT
65 TATCACACTAAGTATCATTTAATGACCAAATGTTTGACAAA
* * * *
1524683 ATTATCAATAGAAATTGTGATGAATTTTTTTC-A-ACTGATAATATATTTTGTGACCACCAATGT
1 ATTATCAATAGAAATTGTGATGAA-CTTGTTCGACACTGAAAATATATTTTGTGACCATCAATGT
* * * * * **
1524746 TACCACACTAAGTAT-TTTTAGTGACCAAATATTCGACACT
65 TATCACACTAAGTATCATTTAATGACCAAATGTTTGACAAA
* * ** * *
1524786 ATTATCCATTA-AAATTGT-ATGAA-TTTTTTAACACTAAAAATATATTTTATGACCATCAATGT
1 ATTAT-CAATAGAAATTGTGATGAACTTGTTCGACACTGAAAATATATTTTGTGACCATCAATGT
*
1524848 TGTCAC
65 TATCAC
1524854 TAAGTAAATT
Statistics
Matches: 229, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
100 5 0.02
101 1 0.00
102 35 0.15
103 34 0.15
104 41 0.18
105 43 0.19
106 19 0.08
107 51 0.22
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (105 bp):
ATTATCAATAGAAATTGTGATGAACTTGTTCGACACTGAAAATATATTTTGTGACCATCAATGTT
ATCACACTAAGTATCATTTAATGACCAAATGTTTGACAAA
Found at i:1524802 original size:103 final size:102
Alignment explanation
Indices: 1524503--1524965 Score: 429
Period size: 103 Copynumber: 4.5 Consensus size: 102
1524493 AACTTGTTCG
* * ** *
1524503 ACACTGAAAATATATTTTGTGACAATCAATATTTATCACACTAAGTATACATTTAATGACCAAAT
1 ACACTGAAAATATATTTTGTGACCATCAAT-GTTATCACACTAAGTAT-TTTTTAGTGACCAAAT
* * ** * ** **
1524568 GTTTGACAAAATTTTCAATGGAAATTGTGATGAATTCGTTC
64 ATTCGACACTATTATC-ATTAAAATTGT-ATGAATTTTTTC
* * * * * * *
1524609 GACGCTGAAAATATATTTTCTAACCATCAATGTTGTCACACTAAATATTTTTTAGTGACCAAGTG
1 -ACACTGAAAATATATTTTGTGACCATCAATGTTATCACACTAAGTATTTTTTAGTGACCAAATA
* *
1524674 TTTGACACTATTATCAATAGAAATTGTGATGAATTTTTTTC
65 TTCGACACTATTATCATTA-AAATTGT-ATGAA-TTTTTTC
* * *
1524715 A-ACTGATAATATATTTTGTGACCACCAATGTTACCACACTAAGTA-TTTTTAGTGACCAAATAT
1 ACACTGAAAATATATTTTGTGACCATCAATGTTATCACACTAAGTATTTTTTAGTGACCAAATAT
*
1524778 TCGACACTATTATCCATTAAAATTGTATGAATTTTTTA
66 TCGACACTATTAT-CATTAAAATTGTATGAATTTTTTC
* * *
1524816 ACACTAAAAATATATTTTATGACCATCAATGTTGT--CACTAAGTAAATTTTTTAGTGACCAAAT
1 ACACTGAAAATATATTTTGTGACCATCAATGTTATCACACTAAGT--ATTTTTTAGTGACCAAAT
* *
1524879 ATTCGACACTATTAT--TCAAAATTGTATGAATTTTTTA
64 ATTCGACACTATTATCATTAAAATTGTATGAATTTTTTC
* * * * * *
1524916 ACATTAAAAATATATTTTGTGACAATTAATATTGTCAC-C-AAGTATTTTTT
1 ACACTGAAAATATATTTTGTGACCATCAATGTTATCACACTAAGTATTTTTT
1524966 TTTTAGTGAC
Statistics
Matches: 303, Mismatches: 44, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
98 7 0.02
100 63 0.21
101 8 0.03
102 34 0.11
103 66 0.22
104 41 0.14
105 39 0.13
106 19 0.06
107 26 0.09
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (102 bp):
ACACTGAAAATATATTTTGTGACCATCAATGTTATCACACTAAGTATTTTTTAGTGACCAAATAT
TCGACACTATTATCATTAAAATTGTATGAATTTTTTC
Found at i:1524917 original size:100 final size:100
Alignment explanation
Indices: 1524616--1524980 Score: 366
Period size: 100 Copynumber: 3.6 Consensus size: 100
1524606 TTCGACGCTG
* * * * *
1524616 AAAATATATTTTCTAACCATCAATGTTGTCACACTAA--ATATTTTTTAGTGACCAAGTGTTTGA
1 AAAATATATTTTGTGACCATCAATGTTGT--CACTAAGTATATTTTTTAGTGACCAAATATTCGA
* *
1524679 CACTATTA-TCAATAGAAATTGTGATGAATTTTTT-TCAACTG
64 CACTATTATTC---A-AAATTGT-ATGAATTTTTTAAC-ACTA
* * **
1524720 ATAATATATTTTGTGACCACCAATGTTACCACACTAAG--TA-TTTTTAGTGACCAAATATTCGA
1 AAAATATATTTTGTGACCATCAATGTT--GTCACTAAGTATATTTTTTAGTGACCAAATATTCGA
*
1524782 CACTATTATCCATTAAAATTGTATGAATTTTTTAACACTA
64 CACTATTAT---TCAAAATTGTATGAATTTTTTAACACTA
* *
1524822 AAAATATATTTTATGACCATCAATGTTGTCACTAAGTAAATTTTTTAGTGACCAAATATTCGACA
1 AAAATATATTTTGTGACCATCAATGTTGTCACTAAGTATATTTTTTAGTGACCAAATATTCGACA
*
1524887 CTATTATTCAAAATTGTATGAATTTTTTAACATTA
66 CTATTATTCAAAATTGTATGAATTTTTTAACACTA
* * * * *
1524922 AAAATATATTTTGTGACAATTAATATTGTCACCAAGTATTTTTTTTTTAGTGACCAAAT
1 AAAATATATTTTGTGACCATCAATGTTGTCACTAAGTA--TATTTTTTAGTGACCAAAT
1524981 GTTAGACAGT
Statistics
Matches: 221, Mismatches: 27, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
100 66 0.30
102 56 0.25
103 66 0.30
104 32 0.14
107 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (100 bp):
AAAATATATTTTGTGACCATCAATGTTGTCACTAAGTATATTTTTTAGTGACCAAATATTCGACA
CTATTATTCAAAATTGTATGAATTTTTTAACACTA
Found at i:1533096 original size:16 final size:16
Alignment explanation
Indices: 1533077--1533114 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1533067 TAGGTCCTTA
1533077 TATTTTATGTT-TATTT
1 TATTTTATGTTGT-TTT
1533093 TATTTTATGTTGTTTT
1 TATTTTATGTTGTTTT
1533109 TATTTT
1 TATTTT
1533115 TTTATTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (16 bp):
TATTTTATGTTGTTTT
Found at i:1534549 original size:20 final size:20
Alignment explanation
Indices: 1534524--1534566 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
1534514 TTTCTTATTT
1534524 AAATTAAAATTAATTTTT-TA
1 AAATT-AAATTAATTTTTGTA
*
1534544 AAATTAAATTTATTTTTGTA
1 AAATTAAATTAATTTTTGTA
1534564 AAA
1 AAA
1534567 AATAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
AAATTAAATTAATTTTTGTA
Found at i:1541074 original size:22 final size:23
Alignment explanation
Indices: 1541043--1541089 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
1541033 TAATCGCGAG
1541043 TTTAGAAGATACGA-TTCTGGGC
1 TTTAGAAGATACGATTTCTGGGC
* * *
1541065 TTTAGCAGATATGATTTTTGGGC
1 TTTAGAAGATACGATTTCTGGGC
1541088 TT
1 TT
1541090 GTTTAGGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (23 bp):
TTTAGAAGATACGATTTCTGGGC
Found at i:1543635 original size:16 final size:15
Alignment explanation
Indices: 1543614--1543647 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1543604 ATGTTTTTAG
1543614 TTTTTTATTAAATATT
1 TTTTTTATTAAAT-TT
*
1543630 TTTTTTATTTAATTT
1 TTTTTTATTAAATTT
1543645 TTT
1 TTT
1543648 AAATAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTTATTAAATTT
Found at i:1546959 original size:3 final size:3
Alignment explanation
Indices: 1546951--1547003 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
1546941 ATTTATTTAT
* *
1546951 TTA TTA TTA TTA -TA ATA ATA TTA TTA TTA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1546995 TTA TTA TTA
1 TTA TTA TTA
1547004 ATAAAAAATA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
2 4 0.09
3 39 0.85
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:1548640 original size:140 final size:139
Alignment explanation
Indices: 1548367--1548641 Score: 301
Period size: 140 Copynumber: 2.0 Consensus size: 139
1548357 AATTTTATAA
* * * *
1548367 TAATGTTTATTTATTTTAATATCAAAGAAAATGGCAGTCTTAAAGCAACTAGATGTCTGTTTTCT
1 TAATATTTATTTATTTTAATATCAAAGAAAATGGCAGTCTTAAAACAACTAGAAGTCTCTTTTCT
* * * * * * **
1548432 GATATTTTTAAATAAATAAATATTTTACTTTTATAAATTGTATATATTAATCTATTTTTTTTAGA
66 GATATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAATTATAGTAGA
1548497 TAAATGTTT
131 TAAATGTTT
* * *
1548506 TAATATTTATTTATTTTTTAATATCAAAGGAAA-GAGCTGTCTTAAAACACCTAGAAG-CTCTTT
1 TAATATTTATTTA--TTTTAATATCAAAGAAAATG-GCAGTCTTAAAACAACTAGAAGTCTCTTT
*
1548569 TCTGATATTTCTAAATAAATAAATATCTTA-TTTATATAAATTAATAAAT-TTACT-TAAAATTA
63 TCTGATATTTCTAAATAAATAAATATCTTACTTT-TATAAATT-ATAAATATTAATCT--AATTA
1548631 TAGTA-ATAAAT
124 TAGTAGATAAAT
1548642 TTAAATTAAA
Statistics
Matches: 113, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
139 16 0.14
140 52 0.46
141 45 0.40
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.45
Consensus pattern (139 bp):
TAATATTTATTTATTTTAATATCAAAGAAAATGGCAGTCTTAAAACAACTAGAAGTCTCTTTTCT
GATATTTCTAAATAAATAAATATCTTACTTTTATAAATTATAAATATTAATCTAATTATAGTAGA
TAAATGTTT
Found at i:1549145 original size:25 final size:26
Alignment explanation
Indices: 1549098--1549159 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
1549088 AATTCTTTTC
* *
1549098 TTTTAAATT-TTTTATTACTTATTAT
1 TTTTATATTATTTTATTACATATTAT
*
1549123 TTTTATATTATTTTATTA-ATATTTT
1 TTTTATATTATTTTATTACATATTAT
*
1549148 TTTTATTTTATT
1 TTTTATATTATT
1549160 CAAGTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 24 0.75
26 8 0.25
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (26 bp):
TTTTATATTATTTTATTACATATTAT
Found at i:1549155 original size:20 final size:22
Alignment explanation
Indices: 1549120--1549159 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1549110 TATTACTTAT
1549120 TATTTTTATATTATTTTATTAA
1 TATTTTTATATTATTTTATTAA
1549142 TATTTTT-T-TTATTTTATT
1 TATTTTTATATTATTTTATT
1549160 CAAGTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (22 bp):
TATTTTTATATTATTTTATTAA
Found at i:1555032 original size:114 final size:114
Alignment explanation
Indices: 1554827--1555046 Score: 370
Period size: 114 Copynumber: 1.9 Consensus size: 114
1554817 CACATTCTCG
*
1554827 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* * *
1554892 GGTATGAACCCCTAAACCAATTATTGGATTTGAAAGATGAATTTGCTCA
66 GGTAGGAACCCCTAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
* *
1554941 TAGTAGAAATAAGGAGACCCAATAGCATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
1555006 GGTAGGAACCCC-AGAACCAATCATTGGAATTGAAAGATGAA
66 GGTAGGAACCCCTA-AACCAATCATTGGAATTGAAAGATGAA
1555047 CTGCATGATC
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
113 1 0.01
114 98 0.99
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCTAAACCAATCATTGGAATTGAAAGATGAATTTGCTCA
Found at i:1556232 original size:38 final size:38
Alignment explanation
Indices: 1556190--1556309 Score: 97
Period size: 38 Copynumber: 3.2 Consensus size: 38
1556180 TTTCAATCAG
1556190 AATCAGCAAAATGCTTGGGCATGCTGAAAGCCTTTTTC
1 AATCAGCAAAATGCTTGGGCATGCTGAAAGCCTTTTTC
* * * * * *
1556228 AATCAGAATCAGGAATG-TTGATGTATCCTGAATG--TTTAT-
1 AATCAG---CA-AAATGCTTG-GGCATGCTGAAAGCCTTTTTC
*
1556267 -ATCAGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTC
1 AATCAGCAAAATGCTTGGGCATGCTGAAAGCCTTTTTC
1556304 AATCAG
1 AATCAG
1556310 AATGAAGAAT
Statistics
Matches: 59, Mismatches: 13, Indels: 20
0.64 0.14 0.22
Matches are distributed among these distances:
34 13 0.22
35 4 0.07
36 4 0.07
38 16 0.27
40 4 0.07
41 5 0.08
42 13 0.22
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (38 bp):
AATCAGCAAAATGCTTGGGCATGCTGAAAGCCTTTTTC
Found at i:1556320 original size:76 final size:76
Alignment explanation
Indices: 1556191--1556368 Score: 259
Period size: 76 Copynumber: 2.4 Consensus size: 76
1556181 TTCAATCAGA
* *
1556191 ATCAGCAAAATGCTTGGGCATGCTGAAAGCCTTTTTCAATCAGAATCAGGAATGTTGATGTATCC
1 ATCAGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTCAATCAGAATCAAGAATGTTGATGTATCC
* *
1556256 TGAATGTTTAT
66 TGAACGTTCAT
* **
1556267 ATCAGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTCAATCAGAATGAAGAATGTTGATGTATTT
1 ATCAGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTCAATCAGAATCAAGAATGTTGATGTATCC
*
1556332 TGAACGTTCGT
66 TGAACGTTCAT
* *
1556343 ATCAGC-AATTGTTGGGGCATGCTGAA
1 ATCAGCAAAATGCTGGGGCATGCTGAA
1556369 GGTCCATATC
Statistics
Matches: 92, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 18 0.20
76 74 0.80
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (76 bp):
ATCAGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTCAATCAGAATCAAGAATGTTGATGTATCC
TGAACGTTCAT
Found at i:1557228 original size:22 final size:22
Alignment explanation
Indices: 1557196--1557254 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
1557186 ACATCTACAC
1557196 TCTTTTCAAAGATGATAGATTA
1 TCTTTTCAAAGATGATAGATTA
* *
1557218 TCTTTTTAAAGATGATAGATTC
1 TCTTTTCAAAGATGATAGATTA
*
1557240 TCTTTTCAAAAATGA
1 TCTTTTCAAAGATGA
1557255 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (22 bp):
TCTTTTCAAAGATGATAGATTA
Found at i:1558034 original size:113 final size:113
Alignment explanation
Indices: 1557765--1558406 Score: 819
Period size: 113 Copynumber: 5.7 Consensus size: 113
1557755 CCGCAAGAGT
* * *
1557765 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
* ** * ** * * *
1557830 TCAACCTTTTGCTCAAATCCATCACTTAATGGATCAGCTTTTTCCAGAG
66 TCAACTTTTTGCTTGAATTCATCACTCGATGGATCAGC-ATTGCCAGTG
* *
1557879 -GAAGTTCATAATGAGAAGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAACTTA
1 AG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * *
1557943 TTCAACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTT
65 TTCAACTTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGTG
*
1557992 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAATAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * *
1558057 TCAAATTTTTGTTTGAATTCATCATTTGATGGATCAACA-TCCCTAGTG
66 TCAACTTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCC-AGTG
*
1558105 AAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 --AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
1558170 GTTCAACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGG
64 GTTCAACTTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGTG
* *
1558220 CGAGTTCATAATGAGAAGAACTCATCT---GAAGAAAGAAGAAGTTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * * * *
1558282 TCAACTTTTTGCTCGAATTCATCACTCGATAGATCAACTTTTCCAGAG
66 TCAACTTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGTG
*
1558330 AGAGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAAGAAGAAGTTCATAATGAGAAGAGCTTG
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGA-AAGAAGAAGTTCATAATGAGAAGAACTTG
* *
1558394 TTCGACCTTTTGC
65 TTCAACTTTTTGC
1558407 ATGACTCTAT
Statistics
Matches: 463, Mismatches: 55, Indels: 21
0.86 0.10 0.04
Matches are distributed among these distances:
110 99 0.21
112 4 0.01
113 167 0.36
114 90 0.19
115 100 0.22
116 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACTTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAGTG
Found at i:1558193 original size:228 final size:227
Alignment explanation
Indices: 1557763--1558396 Score: 897
Period size: 228 Copynumber: 2.8 Consensus size: 227
1557753 ATCCGCAAGA
* *
1557763 GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTT
1 GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * *
1557828 GTTCAACCTTTTGCTCAAATCCATCACTTAATGGATCAGCTTTTTCCA-GAG-GAAGTTCATAAT
66 GTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAAC-TTTTCCAGGAGAG-AGTTCATAAT
* *
1557891 GAGAAGAACTCATCTGAAGAATA-AAGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTTG
129 GAGAAGAACTCATCTGAAGAA-AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCG
*
1557955 CTTAAATTCATCACCCGGTGGATCAGCAGTGCCAG
193 CTTAAATTCATCACCCGATGGATCAGCAGTGCCAG
* * *
1557990 TTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAATAACTT
1 GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTT
* * * * * * *
1558055 GTTCAAATTTTTGTTTGAATTCATCATTTGATGGATCAAC-ATCCCTAGTGAAAGAGTTCATAAT
66 GTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAACTTTTCC-AG-GAGAGAGTTCATAAT
*
1558119 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
129 GAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* ** *
1558184 TTGAATTCATCATTCGATGGATCAGCATTGCCAG
194 TTAAATTCATCACCCGATGGATCAGCAGTGCCAG
**
1558218 GGCGAGTTCATAATGAGAAGAACTCATCT---GAAGAAAGAAGAAGTTCATAATGAGAAGAATTT
1 GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTT
* *
1558280 GTTCAACTTTTTGCTCGAATTCATCACTCGATAGATCAACTTTTCCA-GAGAGAGTTCATAATGA
66 GTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAACTTTTCCAGGAGAGAGTTCATAATGA
*
1558344 GAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
131 GAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1558397 GACCTTTTGC
Statistics
Matches: 360, Mismatches: 41, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
223 67 0.19
225 69 0.19
226 4 0.01
227 91 0.25
228 128 0.36
229 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (227 bp):
GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAGAATTT
GTTCAACTTTTTGCTCGAATTCATCACTTGATGGATCAACTTTTCCAGGAGAGAGTTCATAATGA
GAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGCTT
AAATTCATCACCCGATGGATCAGCAGTGCCAG
Found at i:1558385 original size:338 final size:340
Alignment explanation
Indices: 1557765--1558396 Score: 952
Period size: 338 Copynumber: 1.9 Consensus size: 340
1557755 CCGCAAGAGT
*
1557765 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
* *
1557830 TCAACCTTTTGCTCAAATCCATCACTTAATGGATCAGCTTTTTCCAGAGGAAGTTCATAATGAGA
66 TCAACCTTTTGCTCAAATCCATCACTTAATGGATCAGCTATTGCCAGAGGAAGTTCATAATGAGA
*
1557895 AGAACTCATCTGAAGAATAAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTTGCTTAA
131 AGAACTCATCTGAAG-A-AAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTTGCTCAA
* * * **
1557960 ATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
194 ATTCATCACCCGATAGATCAACAGTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAA
*
1558025 GAAAGAAGAAGTTCATAATGAGAATAACTTGTTCAAATTTTTGTTTGAATTCATCATTTGATGGA
259 GAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGTTTGAATTCATCATTTGATGGA
1558090 TCAACATCCCTAGTGAA
324 TCAACATCCCTAGTGAA
*
1558107 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
** * * *
1558172 TCAA-CTTTTCGCTTGAATTCATCA-TTCGATGGATCAGC-ATTGCCAG-GGCGAGTTCATAATG
66 TCAACCTTTT-GCTCAAATCCATCACTT-AATGGATCAGCTATTGCCAGAGG-AAGTTCATAATG
* * *
1558233 AGAAGAACTCATCTGAAG-AAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTCG
128 AGAAGAACTCATCTGAAGAAAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTTGCTCA
* ** *
1558297 AATTCATCACTCGATAGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
193 AATTCATCACCCGATAGATCAACAGTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
1558362 A-AGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
258 AGA-AAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1558397 GACCTTTTGC
Statistics
Matches: 262, Mismatches: 24, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
337 1 0.00
338 129 0.49
340 2 0.01
341 42 0.16
342 88 0.34
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (340 bp):
AGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTCAAATCCATCACTTAATGGATCAGCTATTGCCAGAGGAAGTTCATAATGAGA
AGAACTCATCTGAAGAAAAGAAGAAGTTCATAATGAGAAGAACTTATTCAACTTTTTGCTCAAAT
TCATCACCCGATAGATCAACAGTGCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAATTTTTGTTTGAATTCATCATTTGATGGATC
AACATCCCTAGTGAA
Found at i:1558469 original size:124 final size:116
Alignment explanation
Indices: 1558321--1558546 Score: 296
Period size: 117 Copynumber: 1.9 Consensus size: 116
1558311 TAGATCAACT
* *
1558321 TTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCT-------GAAGAAGAAGTTCACAATGAGA
*
1558386 AGAGCTTGTTCGACCTTTTGC-ATGACT-CTATCACAGAAGGAGATATATCATCATCAGCA
59 AGAGCTTGTTCAACC-TTTGCTA-GACTAC-ATCACAGAAGGAGATATATCATCATCAGCA
1558445 TTTCCAGA-AGGAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGTTCACAATGAGAAGAGCT
1 TTTCCAGAGA-GAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGTTCACAATGAGAAGAGCT
*
1558509 TGTTCAACCTTTGCTAGATTACATCACAGAAGGAGATA
65 TGTTCAACCTTTGCTAGACTACATCACAGAAGGAGATA
1558547 AATTGTCATC
Statistics
Matches: 95, Mismatches: 4, Indels: 14
0.84 0.04 0.12
Matches are distributed among these distances:
116 24 0.25
117 37 0.39
123 1 0.01
124 33 0.35
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.24
Consensus pattern (116 bp):
TTTCCAGAGAGAGTTCACAATGAGAAGAACTCATCTGAAGAAGAAGTTCACAATGAGAAGAGCTT
GTTCAACCTTTGCTAGACTACATCACAGAAGGAGATATATCATCATCAGCA
Found at i:1558505 original size:17 final size:17
Alignment explanation
Indices: 1558450--1558505 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1558440 CAGCATTTCC
*
1558450 AGAAGGAGTTCACAATG
1 AGAAGAAGTTCACAATG
*
1558467 AGAAGAA-CTCATC--TG
1 AGAAGAAGTTCA-CAATG
1558482 AAGAAGAAGTTCACAATG
1 -AGAAGAAGTTCACAATG
1558500 AGAAGA
1 AGAAGA
1558506 GCTTGTTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
15 2 0.06
16 11 0.35
17 16 0.52
18 2 0.06
ACGTcount: A:0.46, C:0.12, G:0.25, T:0.16
Consensus pattern (17 bp):
AGAAGAAGTTCACAATG
Found at i:1558762 original size:3 final size:3
Alignment explanation
Indices: 1558754--1558804 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
1558744 TTTATTTAAT
* * *
1558754 TTA TTA TTA TTA TAA TAA TAA TTA TTA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
1558799 TTA TTA
1 TTA TTA
1558805 AAAAATAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.89
4 3 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:1558803 original size:18 final size:21
Alignment explanation
Indices: 1558754--1558815 Score: 87
Period size: 18 Copynumber: 3.1 Consensus size: 21
1558744 TTTATTTAAT
1558754 TTATTATTATTATAATAATAA
1 TTATTATTATTATAATAATAA
1558775 TTATTATTATTAT-AT-AT-A
1 TTATTATTATTATAATAATAA
*
1558793 TTATTATTATTA-AAAAATAA
1 TTATTATTATTATAATAATAA
1558813 TTA
1 TTA
1558816 CAGGCCCAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
18 14 0.38
19 4 0.11
20 6 0.16
21 13 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATTATTATTATAATAATAA
Found at i:1560117 original size:22 final size:21
Alignment explanation
Indices: 1560087--1560140 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
1560077 TATTTTATTG
1560087 TTATATATTTAAATTAATAATAA
1 TTAT-TATTTAAA-TAATAATAA
* * *
1560110 TTATTATTTTAATCATATTAA
1 TTATTATTTAAATAATAATAA
1560131 TATATTATTT
1 T-TATTATTT
1560141 GATTAATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 15 0.56
23 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
TTATTATTTAAATAATAATAA
Found at i:1561576 original size:27 final size:27
Alignment explanation
Indices: 1561546--1561649 Score: 75
Period size: 27 Copynumber: 3.7 Consensus size: 27
1561536 AAACGTTATG
*
1561546 AAAACATTTATATAATATATAATTTTTA
1 AAAACATTT-TAAAATATATAATTTTTA
** *
1561574 AAAACCATTTTGAAAATATATTTTTTTTTT
1 AAAA-CATTTT-AAAATATA-TAATTTTTA
* * * * *
1561604 GAAA-ATTATATAATATATAGTTTTTG
1 AAAACATTTTAAAATATATAATTTTTA
*
1561630 AAAACGTTTTAAAATATATA
1 AAAACATTTTAAAATATATA
1561650 TAATATATAC
Statistics
Matches: 58, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
26 9 0.16
27 19 0.33
28 9 0.16
29 12 0.21
30 9 0.16
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (27 bp):
AAAACATTTTAAAATATATAATTTTTA
Found at i:1561688 original size:38 final size:36
Alignment explanation
Indices: 1561605--1561694 Score: 112
Period size: 35 Copynumber: 2.5 Consensus size: 36
1561595 TTTTTTTTTG
* *
1561605 AAAA-TTATATAATATATAGTTTTTGAAAACGTTTT
1 AAAATTTATATAATATATAGCTTTTGAAAACGTTTA
*
1561640 AAAATATATATAATATATA-CTTTTGAAAACGTTATGA
1 AAAATTTATATAATATATAGCTTTTGAAAACGTT-T-A
1561677 AAACATTTATATAATATA
1 AAA-ATTTATATAATATA
1561695 ATTTTTAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 17 0.36
36 14 0.30
37 3 0.06
38 13 0.28
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (36 bp):
AAAATTTATATAATATATAGCTTTTGAAAACGTTTA
Found at i:1561688 original size:94 final size:94
Alignment explanation
Indices: 1561505--1561679 Score: 227
Period size: 94 Copynumber: 1.9 Consensus size: 94
1561495 TTTGAAAACG
* *
1561505 TTTTTAAAATATATATAATATATACTTTTGAAAACGTTATGAAAACATTTATATAATATATAATT
1 TTTTTAAAATATATATAATATATACTTTTGAAAACGTTATGAAAACATATATATAATATATAACT
*
1561570 TTTAAAAACCATTTTGAAAATATATTTTT
66 TTTAAAAACCATTATGAAAATATATTTTT
* *
1561599 TTTTTGAAAAT-TATATAATATATAGTTTTTGAAAACGTT-T-TAAA-ATATATATAATATAT-A
1 TTTTT-AAAATATATATAATATATA-CTTTTGAAAACGTTATGAAAACATATATATAATATATAA
* *
1561659 CTTTTGAAAA-CGTTATGAAAA
64 CTTTTAAAAACCATTATGAAAA
1561680 CATTTATATA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
90 9 0.12
91 9 0.12
92 14 0.19
93 3 0.04
94 19 0.26
95 18 0.25
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.45
Consensus pattern (94 bp):
TTTTTAAAATATATATAATATATACTTTTGAAAACGTTATGAAAACATATATATAATATATAACT
TTTAAAAACCATTATGAAAATATATTTTT
Found at i:1561716 original size:38 final size:37
Alignment explanation
Indices: 1561399--1561727 Score: 189
Period size: 38 Copynumber: 9.5 Consensus size: 37
1561389 TGCAAATTGT
* * *
1561399 TTTTG-AAAATACATAT-ATATATA-GTTT-AAAACA
1 TTTTGAAAAATATATATAATATATATTTTTGAAAACG
* * **
1561432 TTTTG-AAAATATGTATATTATATAGTTTTT-AAAATAT
1 TTTTGAAAAATATATATAATATATA-TTTTTGAAAA-CG
1561469 TTTTG-AAAAT-TATATAATATATAGTTTTTGAAAACG
1 TTTTGAAAAATATATATAATATATA-TTTTTGAAAACG
* *
1561505 TTTT-TAAAATATATATAATATATACTTTTGAAAACG
1 TTTTGAAAAATATATATAATATATATTTTTGAAAACG
* * * *
1561541 TTATGAAAACATTTATATAATATATAATTTTTAAAAACCA
1 TTTTGAAAA-ATATATATAATATAT-ATTTTTGAAAA-CG
1561581 TTTTG-AAAATATAT-T--T-T-T-TTTTTGAAAA--
1 TTTTGAAAAATATATATAATATATATTTTTGAAAACG
*
1561609 --TT-----ATATA-AT-ATATA-GTTTTTGAAAACG
1 TTTTGAAAAATATATATAATATATATTTTTGAAAACG
*
1561636 TTTT--AAAATATATATAATATATACTTTTGAAAACG
1 TTTTGAAAAATATATATAATATATATTTTTGAAAACG
* * * *
1561671 TTATGAAAACATTTATATAATATA-ATTTTTAAAAACCA
1 TTTTGAAAA-ATATATATAATATATATTTTTGAAAA-CG
1561709 TTTTGAAAATATATATATA
1 TTTTGAAAA-ATATATATA
1561728 GGTTTTTTTT
Statistics
Matches: 236, Mismatches: 30, Indels: 55
0.74 0.09 0.17
Matches are distributed among these distances:
22 6 0.03
23 1 0.00
24 1 0.00
25 10 0.04
26 2 0.01
29 2 0.01
31 9 0.04
32 5 0.02
33 17 0.07
34 12 0.05
35 15 0.06
36 47 0.20
37 43 0.18
38 49 0.21
39 12 0.05
40 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATATTTTTGAAAACG
Found at i:1561724 original size:130 final size:131
Alignment explanation
Indices: 1561468--1561722 Score: 489
Period size: 130 Copynumber: 2.0 Consensus size: 131
1561458 TTTTAAAATA
1561468 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
1561533 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATATTTT
66 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATATTTT
1561598 T
131 T
1561599 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
1561663 TGAAAACGTTATGAAAACATTTATAT-A-ATATAATTTTTAAAAACCATTTTGAAAATATAT
66 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATAT
1561723 ATATAGGTTT
Statistics
Matches: 124, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
128 33 0.27
129 1 0.01
130 53 0.43
131 37 0.30
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (131 bp):
TTTTTGAAAATTATATAATATATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCATTTTGAAAATATATTTT
T
Found at i:1561781 original size:24 final size:25
Alignment explanation
Indices: 1561750--1561796 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
1561740 AAAAAAAACA
1561750 TTTTAAAA-ATTTATAT-TATATGT
1 TTTTAAAACATTTATATATATATGT
*
1561773 TTTTGAAAACGTTTATATATATAT
1 TTTT-AAAACATTTATATATATAT
1561797 ATATTATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 7 0.35
26 5 0.25
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.53
Consensus pattern (25 bp):
TTTTAAAACATTTATATATATATGT
Found at i:1562283 original size:25 final size:28
Alignment explanation
Indices: 1562255--1562305 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
1562245 GAAAACCCAT
*
1562255 ATCATCA-AACC-CACAC-AAAAACAGA
1 ATCATCATAACCAAACACGAAAAACAGA
1562280 ATCATCATAACCAAACACGAAAAACA
1 ATCATCATAACCAAACACGAAAAACA
1562306 CAAGCCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 4 0.18
28 7 0.32
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.10
Consensus pattern (28 bp):
ATCATCATAACCAAACACGAAAAACAGA
Found at i:1562297 original size:27 final size:27
Alignment explanation
Indices: 1562236--1562307 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
1562226 CCACAGTAAG
*
1562236 CCAAACACAGAAAACCCATATCATCAAA
1 CCAAACACA-AAAACACATATCATCAAA
* *
1562264 CC-CACACAAAAACAGA-ATCATCATAA
1 CCAAACACAAAAACACATATCATCA-AA
1562290 CCAAACACGAAAAACACA
1 CCAAACAC-AAAAACACA
1562308 AGCCAACAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 10 0.28
27 9 0.25
28 10 0.28
ACGTcount: A:0.56, C:0.32, G:0.04, T:0.08
Consensus pattern (27 bp):
CCAAACACAAAAACACATATCATCAAA
Found at i:1563055 original size:13 final size:14
Alignment explanation
Indices: 1563039--1563068 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1563029 TTTTATCTAT
1563039 TTTTATTATT-TTA
1 TTTTATTATTGTTA
1563052 TTTTATTATTGTTA
1 TTTTATTATTGTTA
1563066 TTT
1 TTT
1563069 CTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTATTGTTA
Found at i:1563325 original size:29 final size:29
Alignment explanation
Indices: 1563276--1563334 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
1563266 TTTGATTTAT
*
1563276 ATTCATTTATTTATTTATTTTTTCTTCCTA
1 ATTCATTTACTTATTTATTTTTT-TTCCTA
*
1563306 ATTCA-TTACTTATTTGTTTTTTTTCCTA
1 ATTCATTTACTTATTTATTTTTTTTCCTA
1563334 A
1 A
1563335 CATCTTCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 15 0.56
30 5 0.19
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.64
Consensus pattern (29 bp):
ATTCATTTACTTATTTATTTTTTTTCCTA
Found at i:1568233 original size:165 final size:165
Alignment explanation
Indices: 1567961--1568678 Score: 1339
Period size: 165 Copynumber: 4.4 Consensus size: 165
1567951 TAAACAAACT
* *
1567961 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1568026 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
1568091 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
1568126 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTTCACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1568191 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
1568256 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
1568291 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
1568356 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTGACC-AAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
*
1568420 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACACC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
1568455 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1568520 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
*
1568585 TTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* * **
1568620 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCTAAAGACCTTCGAGTTCGATTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
1568679 TATTCAACTT
Statistics
Matches: 539, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
164 162 0.30
165 377 0.70
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (165 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1568560 original size:329 final size:330
Alignment explanation
Indices: 1567961--1568678 Score: 1339
Period size: 329 Copynumber: 2.2 Consensus size: 330
1567951 TAAACAAACT
* *
1567961 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
*
1568026 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTGACCAAAAGACC
*
1568091 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
*
1568156 TATCTGCCAAAGACCCCCGAGTTCGATTTCACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
196 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
1568221 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
261 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1568286 ACATC
326 ACATC
1568291 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1568356 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTGACC-AAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTGACCAAAAGACC
1568420 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
131 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
1568485 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
196 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
*
1568550 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGC
261 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1568615 ACATC
326 ACATC
* * **
1568620 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCTAAAGACCTTCGAGTTCGATTA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
1568679 TATTCAACTT
Statistics
Matches: 378, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
329 259 0.69
330 119 0.31
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (330 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTGACCAAAAGACC
TTCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
ACATC
Found at i:1568756 original size:329 final size:325
Alignment explanation
Indices: 1567961--1568759 Score: 1267
Period size: 329 Copynumber: 2.4 Consensus size: 325
1567951 TAAACAAACT
*
1567961 ATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCTGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCC-GAGTTCGATTACACTCA
* *
1568026 GCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
65 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGT---CAAAA-AAC
*
1568091 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
126 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
*
1568156 TATCTGCCAAAGACCCCCGAGTTCGATTTCACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
191 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAAC
1568221 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
256 TCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
1568286 ACATC
321 ACATC
1568291 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA-CCCCGAGTTCGATTACACTCA
* *
1568356 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTGACCAAAGACCT
65 GCTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGT---CAAAAAACT
1568421 TCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
127 TCGAGTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGCT
1568486 ATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
192 ATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACT
*
1568551 CAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCA
257 CAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCA
1568616 CATC
322 CATC
* * * * *
1568620 ATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCTAAAGACCTTCGAGTTCGATTATATTCA
1 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC-CCGAGTTCGATTACACTCA
* * * * * * * * *
1568685 ACTTAGA-GGCAAATCAAGCTTACAGAATAGCTCAATGCAAGAAGGGCTATCTGTCAATAAAACT
65 GCTTCGAGGGCACATC-A-TTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTCAA-AAAACT
1568749 GTCGAGTTCGA
127 -TCGAGTTCGA
1568760 TTCTAATCAG
Statistics
Matches: 441, Mismatches: 22, Indels: 13
0.93 0.05 0.03
Matches are distributed among these distances:
327 3 0.01
328 13 0.03
329 273 0.62
330 148 0.34
331 4 0.01
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (325 bp):
ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCGAGTTCGATTACACTCAG
CTTCGAGGGCACATCATTTACAGCATAACTCAAAGCTAGAAGGGTTATCTGTCAAAAAACTTCGA
GTTCGACTACGCTCAGCTCCAAGGCACACCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
GCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
GCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:1569535 original size:27 final size:25
Alignment explanation
Indices: 1569489--1569539 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
1569479 TATATATTTT
*
1569489 TTTTTGAAAATTATATAATATATAG
1 TTTTTGAAAATTATAAAATATATAG
*
1569514 TTTTTGAAAACGTTTTAAAATATATA
1 TTTTTGAAAA--TTATAAAATATATA
1569540 TAATATATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
27 12 0.55
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTTGAAAATTATAAAATATATAG
Found at i:1569616 original size:131 final size:131
Alignment explanation
Indices: 1569358--1569614 Score: 475
Period size: 131 Copynumber: 2.0 Consensus size: 131
1569348 TTTTAAAATA
1569358 TTTTTGAAAATTATATAATAATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTT
1 TTTTTGAAAATTATATAATAATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTT
1569423 GAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCAATTTGAAAATATATATTT
66 GAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCAATTTGAAAATATATATTT
1569488 T
131 T
1569489 TTTTTGAAAATTATATAATATATAGTTTTTGAAAACG-TTTTAAAATATATATAATATATACTTT
1 TTTTTGAAAATTATATAATA-ATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTT
*
1569553 TGAAAACGTTATGAAAACATTTATAT-A-ATATAATTTTTAAAAACCATTTTGAAAATATATAT
65 TGAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCAATTTGAAAATATATAT
1569615 ATATAGTTTT
Statistics
Matches: 124, Mismatches: 1, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
129 34 0.27
130 1 0.01
131 73 0.59
132 16 0.13
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (131 bp):
TTTTTGAAAATTATATAATAATAGTTTTTGAAAACGTTTTTAAAATATATATAATATATACTTTT
GAAAACGTTATGAAAACATTTATATAATATATAATTTTTAAAAACCAATTTGAAAATATATATTT
T
Found at i:1569626 original size:36 final size:35
Alignment explanation
Indices: 1569289--1569678 Score: 197
Period size: 35 Copynumber: 11.1 Consensus size: 35
1569279 TTTGCAAATT
* **
1569289 GTTTTGAAAATACATAT-ATATATAGTTT-AAAAC
1 GTTTTGAAAATATATATAATATATTTTTTGAAAAC
* * * * *
1569322 ATTTTTGAAAATATGTATTATATAGTTTTT-AAAATA
1 -GTTTTGAAAATATATATAATATATTTTTTGAAAA-C
* *
1569358 TTTTTGAAAAT-TATATAATAATAGTTTTTGAAAAC
1 GTTTTGAAAATATATATAAT-ATATTTTTTGAAAAC
* *
1569393 GTTTTTAAAATATATATAATATATACTTTTGAAAAC
1 GTTTTGAAAATATATATAATATAT-TTTTTGAAAAC
* * *
1569429 GTTATGAAAACATTTATATAATATATAATTTTTAAAAACC
1 GTTTTG-AAA-ATATATATAATATAT--TTTTTGAAAA-C
**
1569469 AATTTGAAAATATATAT--T-T-TTTTTTGAAAA-
1 GTTTTGAAAATATATATAATATATTTTTTGAAAAC
*
1569499 ---TT----ATATA-AT-ATATAGTTTTTGAAAAC
1 GTTTTGAAAATATATATAATATATTTTTTGAAAAC
*
1569525 GTTTT-AAAATATATATAATATATACTTTTGAAAAC
1 GTTTTGAAAATATATATAATATAT-TTTTTGAAAAC
* * * *
1569560 GTTATGAAAACATTTATATAATATAATTTTTAAAAACC
1 GTTTTG-AAA-ATATATATAATATATTTTTTGAAAA-C
* * *
1569598 ATTTTGAAAATATATATATATAGTTTTTTTTTAAAAAAAAC
1 GTTTTGAAAATATATATA-ATA--TATTTTTT---GAAAAC
* * * *
1569639 ATTTTAAAAATTTATATATTATATGTTTTTGAAAAC
1 GTTTTGAAAATATATATAATATAT-TTTTTGAAAAC
1569675 GTTT
1 GTTT
1569679 ATATATATAT
Statistics
Matches: 279, Mismatches: 43, Indels: 66
0.72 0.11 0.17
Matches are distributed among these distances:
22 2 0.01
23 6 0.02
24 1 0.00
25 10 0.04
27 2 0.01
29 2 0.01
32 14 0.05
33 2 0.01
34 26 0.09
35 59 0.21
36 43 0.15
37 20 0.07
38 41 0.15
39 23 0.08
40 6 0.02
41 17 0.06
42 5 0.02
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (35 bp):
GTTTTGAAAATATATATAATATATTTTTTGAAAAC
Found at i:1569668 original size:39 final size:38
Alignment explanation
Indices: 1569490--1569673 Score: 96
Period size: 36 Copynumber: 4.9 Consensus size: 38
1569480 ATATATTTTT
* * * *
1569490 TTTTGAAAA-TTATATAATATATAGTTTTT--GAAAACG
1 TTTTAAAAATTTATATATTATATA-TTTTTAAAAAAACA
* * * * *
1569526 TTTT-AAAATATATATAATATATACTTTT--GAAAACG
1 TTTTAAAAATTTATATATTATATATTTTTAAAAAAACA
* * *
1569561 TTATGAAAACATTTATATAATATA-ATTTTT-AAAAACCA
1 TT-TTAAAA-ATTTATATATTATATATTTTTAAAAAAACA
* * * *
1569599 TTTTGAAAATATATATATATAGTTTTTTTTTAAAAAAAACA
1 TTTTAAAAATTTATATAT-TA-TATATTTTT-AAAAAAACA
* *
1569640 TTTTAAAAATTTATATATTATATGTTTTTGAAAA
1 TTTTAAAAATTTATATATTATATATTTTTAAAAA
1569674 CGTTTATATA
Statistics
Matches: 118, Mismatches: 20, Indels: 18
0.76 0.13 0.12
Matches are distributed among these distances:
35 17 0.14
36 26 0.22
37 14 0.12
38 24 0.20
39 12 0.10
40 2 0.02
41 23 0.19
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
TTTTAAAAATTTATATATTATATATTTTTAAAAAAACA
Found at i:1570174 original size:25 final size:28
Alignment explanation
Indices: 1570146--1570196 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
1570136 GAAAACCCAT
*
1570146 ATCATCA-AACC-CACAC-AAAAACAGA
1 ATCATCATAACCAAACACGAAAAACAGA
1570171 ATCATCATAACCAAACACGAAAAACA
1 ATCATCATAACCAAACACGAAAAACA
1570197 CAAGCCAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 4 0.18
28 7 0.32
ACGTcount: A:0.57, C:0.29, G:0.04, T:0.10
Consensus pattern (28 bp):
ATCATCATAACCAAACACGAAAAACAGA
Found at i:1570188 original size:27 final size:27
Alignment explanation
Indices: 1570127--1570198 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 27
1570117 CCACAGTAAG
*
1570127 CCAAACACAGAAAACCCATATCATCAAA
1 CCAAACACA-AAAACACATATCATCAAA
* *
1570155 CC-CACACAAAAACAGA-ATCATCATAA
1 CCAAACACAAAAACACATATCATCA-AA
1570181 CCAAACACGAAAAACACA
1 CCAAACAC-AAAAACACA
1570199 AGCCAACAGC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
25 7 0.19
26 10 0.28
27 9 0.25
28 10 0.28
ACGTcount: A:0.56, C:0.32, G:0.04, T:0.08
Consensus pattern (27 bp):
CCAAACACAAAAACACATATCATCAAA
Found at i:1570948 original size:13 final size:14
Alignment explanation
Indices: 1570932--1570961 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1570922 TTTTATCTAT
1570932 TTTTATTATT-TTA
1 TTTTATTATTGTTA
1570945 TTTTATTATTGTTA
1 TTTTATTATTGTTA
1570959 TTT
1 TTT
1570962 CTTTCCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTATTGTTA
Found at i:1571322 original size:7 final size:6
Alignment explanation
Indices: 1571288--1571321 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
1571278 GCATCGAGTT
1571288 TTTAAA TTTAAA TTTAAA TTTAAA TTTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTT
1571322 TCGCAACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:1571929 original size:138 final size:137
Alignment explanation
Indices: 1571698--1572221 Score: 520
Period size: 138 Copynumber: 3.8 Consensus size: 137
1571688 TCCCTAAACT
* ** * * * *
1571698 TTTAATTTAGGACAA-TTTTAATTTGGTCATTATTTTTGTACCC-GGTGTTCCATTTTAATTATT
1 TTTAATTTAGGAGAATTTTTAATTTGGTCATCGTTTTTATGCCCAAG-GTTCCATATTAATTATT
* * * * * *
1571761 CAATCCAATAATTTGTTAAAATTGGTTAGGATTATTATTAGAGCCTACATTTTAGATTAATTTTA
65 CGATCCAATAATTTGTTAAAATT-GTTAGGATTAATATTAGAACCTTCATCTTAGATTAATTTCA
*
1571826 TTTTAGTCC
129 CTTTAGTCC
** * *
1571835 TTTAATTTAGGAGAGGTTTTGATTTGGTCATCGTTTTTATGCCCGAGGTTCCATATTAATTATTC
1 TTTAATTTAGGAGAATTTTTAATTTGGTCATCGTTTTTATGCCCAAGGTTCCATATTAATTATTC
* * * *
1571900 GATCCAATAATTTGTTAAAATTAGTTAGGATTAATATTAAAAACTTCACCTTAGATTAGTTTCAC
66 GATCCAATAATTTGTTAAAATT-GTTAGGATTAATATTAGAACCTTCATCTTAGATTAATTTCAC
* **
1571965 TTGAGTTA
130 TTTAGTCC
* * * *
1571973 TTTAATTTAGGAGAATTTTTTATTTGGTCCTCGCTTTTATGCCCAAGGCTT-CATATCAATTATT
1 TTTAATTTAGGAGAATTTTTAATTTGGTCATCGTTTTTATGCCCAAGG-TTCCATATTAATTATT
* * *
1572037 GGATCCAATCATTTGTTAAAATTGATTAGGATTAATATTAGAACCTTCATCTTAGGTTTAATTTC
65 CGATCCAATAATTTGTTAAAATTG-TTAGGATTAATATTAGAACCTTCATCTTA-GATTAATTTC
*
1572102 ACATTAGTCC
128 ACTTTAGTCC
* * * * *
1572112 TTTAATTTAAGG-GAATTTTTAATTTGATCAT--TACTTTATGCCAAAGGTTCTATTTTAATTAT
1 TTTAATTT-AGGAGAATTTTTAATTTGGTCATCGT-TTTTATGCCCAAGGTTCCATATTAATTAT
* ** ** *
1572174 TCGATCCAATAAATTGCAAAAAATCATTAGGTTTCAATATTAGAACCT
64 TCGATCCAATAATTTG-TTAAAATTGTTAGGATT-AATATTAGAACCT
1572222 ACCTTTTAGA
Statistics
Matches: 318, Mismatches: 59, Indels: 18
0.81 0.15 0.05
Matches are distributed among these distances:
137 16 0.05
138 240 0.75
139 59 0.19
140 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.44
Consensus pattern (137 bp):
TTTAATTTAGGAGAATTTTTAATTTGGTCATCGTTTTTATGCCCAAGGTTCCATATTAATTATTC
GATCCAATAATTTGTTAAAATTGTTAGGATTAATATTAGAACCTTCATCTTAGATTAATTTCACT
TTAGTCC
Found at i:1572700 original size:13 final size:13
Alignment explanation
Indices: 1572682--1572706 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1572672 TTTAATAAAA
1572682 TAAAATTATTTAT
1 TAAAATTATTTAT
1572695 TAAAATTATTTA
1 TAAAATTATTTA
1572707 ATTTTAAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAAATTATTTAT
Found at i:1574447 original size:3 final size:3
Alignment explanation
Indices: 1574439--1574540 Score: 204
Period size: 3 Copynumber: 34.0 Consensus size: 3
1574429 ACATGTCTAC
1574439 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1574487 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1574535 ATA ATA
1 ATA ATA
1574541 GGTTAATATT
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 99 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1575746 original size:72 final size:73
Alignment explanation
Indices: 1575665--1575829 Score: 269
Period size: 72 Copynumber: 2.3 Consensus size: 73
1575655 ATACCTAAGT
*
1575665 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGTCAAACGGGTACCG
1 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAACGGGTACCG
1575730 ATAC-CCC
66 ATACTCCC
* * *
1575737 CATAGGTACCGATACCCTTGTGTTAATTTTGGCTCCGAGAAAAACAGAATGCCCAATGGGTACCG
1 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAACGGGTACCG
1575802 ATACTCCC
66 ATACTCCC
* *
1575810 TAGAGGTACCGATACCCTTA
1 CATAGGTACCGATACCCTTA
1575830 GTCATTTAAC
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
72 65 0.76
73 20 0.24
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (73 bp):
CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAACGGGTACCG
ATACTCCC
Found at i:1577330 original size:9 final size:9
Alignment explanation
Indices: 1577316--1577346 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1577306 AAGTTAATAG
*
1577316 TGATTATGA
1 TGATTACGA
1577325 TGATTACGA
1 TGATTACGA
1577334 TGATTACGA
1 TGATTACGA
1577343 TGAT
1 TGAT
1577347 GATGAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.32, C:0.06, G:0.23, T:0.39
Consensus pattern (9 bp):
TGATTACGA
Found at i:1578509 original size:25 final size:24
Alignment explanation
Indices: 1578480--1578533 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1578470 TCTCTCTAGT
*
1578480 TTTTATAAA-AGTTTTCACTTTTTAC
1 TTTTATAAATACTTTTCA-TTTTT-C
*
1578505 TTTTA-AAATTCTTTTCATTTTTC
1 TTTTATAAATACTTTTCATTTTTC
1578528 TTTTAT
1 TTTTAT
1578534 TTTTCAAGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 6 0.24
24 8 0.32
25 11 0.44
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (24 bp):
TTTTATAAATACTTTTCATTTTTC
Found at i:1585671 original size:20 final size:19
Alignment explanation
Indices: 1585625--1585669 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1585615 AAGAGCTGTT
1585625 AAAAAAAA-GTAAAAAAGA
1 AAAAAAAACGTAAAAAAGA
* *
1585643 AAAAAAAACGTGAAAATGA
1 AAAAAAAACGTAAAAAAGA
1585662 AAAAAAAA
1 AAAAAAAA
1585670 ACAAAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.80, C:0.02, G:0.11, T:0.07
Consensus pattern (19 bp):
AAAAAAAACGTAAAAAAGA
Found at i:1591041 original size:20 final size:20
Alignment explanation
Indices: 1591016--1591071 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1591006 TTGTGCACCT
*
1591016 GGTATCGATACCCTTTTATA
1 GGTATCGATACCCTTTGATA
* *
1591036 GGTATCGATACCCCTTGCTA
1 GGTATCGATACCCTTTGATA
1591056 GGTATCGATACTCCTT
1 GGTATCGATAC-CCTT
1591072 AAACGTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 28 0.90
21 3 0.10
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
GGTATCGATACCCTTTGATA
Found at i:1591083 original size:21 final size:21
Alignment explanation
Indices: 1591057--1591110 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 21
1591047 CCCTTGCTAG
1591057 GTATCGATACTCCTTAAACGT
1 GTATCGATACTCCTTAAACGT
* * *
1591078 GTATCGATACCCTCTTTGAATGT
1 GTATCGATA--CTCCTTAAACGT
1591101 GTATCGATAC
1 GTATCGATAC
1591111 CCCTATAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 10 0.36
23 18 0.64
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (21 bp):
GTATCGATACTCCTTAAACGT
Found at i:1592820 original size:13 final size:14
Alignment explanation
Indices: 1592789--1592822 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1592779 AAGGTGAGTA
1592789 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
1592803 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
1592815 ATTTTCAA
1 ATTTTCAA
1592823 TAAGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 15 0.79
14 1 0.05
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:1593199 original size:73 final size:72
Alignment explanation
Indices: 1593114--1593278 Score: 231
Period size: 73 Copynumber: 2.3 Consensus size: 72
1593104 ATACCTAAGT
* * *
1593114 CATAGGTCCCGATACCCTTATGTTGATTTTGGCTCCGAGAAAAATAGAATGCCAAATGGGTACCG
1 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCG
1593179 ATAACCCC
66 AT-ACCCC
* * *
1593187 CATAGGTACCGATACCCTTGTGTTAATTTTGGCTCCGAGAAAAACAGAATGCCCAATGGGTGCCG
1 CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCG
*
1593252 ATACTCC
66 ATACCCC
* * *
1593259 TAGAGGTATCGATACCCTTA
1 CATAGGTACCGATACCCTTA
1593279 GTCATTTAAC
Statistics
Matches: 81, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
72 20 0.25
73 61 0.75
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (72 bp):
CATAGGTACCGATACCCTTATGTTAATTTTGGCTCCGAGAAAAACAGAATGCCAAATGGGTACCG
ATACCCC
Found at i:1598359 original size:30 final size:31
Alignment explanation
Indices: 1598291--1598373 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 31
1598281 TTAGTGATCG
*
1598291 AATTGATATTTTATTTAAAATTTAAGAAATA
1 AATTAATATTTTATTTAAAATTTAAGAAATA
* **
1598322 AATTAATATTTTATTTAAAGTTTAAG-GTTA
1 AATTAATATTTTATTTAAAATTTAAGAAATA
*
1598352 TATTAATATTTT-TTCTAAAATT
1 AATTAATATTTTATT-TAAAATT
1598374 CAGGGACCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.04
30 19 0.42
31 24 0.53
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (31 bp):
AATTAATATTTTATTTAAAATTTAAGAAATA
Found at i:1599020 original size:60 final size:60
Alignment explanation
Indices: 1598904--1599020 Score: 139
Period size: 60 Copynumber: 1.9 Consensus size: 60
1598894 AAGTATGATC
* * * * *
1598904 TCATTTTAAATTGGTCTCTAAACTTTTAAATGTTTTACTTTCATCCCTATAATATGATTA
1 TCATTCTAAATTGGTCTCTAAACTTTTAAATATTTCAATTTCATCCCCATAATATGATTA
* *
1598964 TCATTCTAAATTAGT-TCTCAAACTTTTGAATATTTCAATTTCATCCCCA-AACTATGA
1 TCATTCTAAATTGGTCTCT-AAACTTTTAAATATTTCAATTTCATCCCCATAA-TATGA
1599021 CCTTTATTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
59 5 0.10
60 43 0.90
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (60 bp):
TCATTCTAAATTGGTCTCTAAACTTTTAAATATTTCAATTTCATCCCCATAATATGATTA
Found at i:1599599 original size:20 final size:20
Alignment explanation
Indices: 1599505--1599873 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
1599495 GATTTTCCAT
* ** *
1599505 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1599525 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1599545 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1599565 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1599585 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1599605 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1599625 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1599645 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1599665 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
1599685 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1599705 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1599725 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1599745 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1599765 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1599785 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1599805 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1599825 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1599845 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1599865 AATCACAAC
1 AATCGCAAC
1599874 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1600596 original size:24 final size:24
Alignment explanation
Indices: 1600557--1600603 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1600547 AAATTTGGTC
1600557 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1600581 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1600604 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1600795 original size:12 final size:12
Alignment explanation
Indices: 1600778--1600802 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1600768 ATATAATCCT
1600778 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1600790 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1600802 G
1 G
1600803 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1603107 original size:19 final size:19
Alignment explanation
Indices: 1603085--1603358 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
1603075 CGGAAAATAC
*
1603085 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1603104 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1603118 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1603138 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1603152 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603171 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1603190 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1603204 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1603223 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603242 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603261 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603280 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603299 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1603313 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603332 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1603351 AATCGCAA
1 AATCGCAA
1603359 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1603236 original size:71 final size:74
Alignment explanation
Indices: 1603085--1603380 Score: 314
Period size: 71 Copynumber: 4.2 Consensus size: 74
1603075 CGGAAAATAC
* *
1603085 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-AAATCGCA
*
1603145 A--CG--A-GAG
63 ATGCGAAATGAA
*
1603152 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
*
1603214 CGAAATTAA
66 CGAAATGAA
1603223 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
1603288 TGCGAAATGAA
64 TGCGAAATGAA
1603299 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
*
1603359 --CG--A-GAT
64 TGCGAAATGAA
1603365 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
1603381 TATAAACGCA
Statistics
Matches: 203, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
66 18 0.09
67 26 0.13
68 8 0.04
69 6 0.03
70 2 0.01
71 93 0.46
72 13 0.06
73 5 0.02
74 6 0.03
76 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (74 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAA
Found at i:1603284 original size:109 final size:104
Alignment explanation
Indices: 1603113--1603380 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 104
1603103 AAATCCCAAC
*
1603113 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
1603178 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1603218 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
1603283 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
1603327 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
1603381 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.10
106 2 0.01
107 2 0.01
108 1 0.01
109 98 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:1603346 original size:161 final size:157
Alignment explanation
Indices: 1603085--1603396 Score: 502
Period size: 161 Copynumber: 2.0 Consensus size: 157
1603075 CGGAAAATAC
*
1603085 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
1603150 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
1603215 GAAATTA-AAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGAAATGAA
* *
1603242 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
1603306 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
1603371 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
1603397 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.17
159 1 0.01
161 98 0.69
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAAATGAA
Found at i:1603396 original size:52 final size:52
Alignment explanation
Indices: 1603113--1603380 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
1603103 AAATCCCAAC
1603113 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1603166 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
1603218 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1603275 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1603327 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1603379 AT
1 AT
1603381 TATAAACGCA
Statistics
Matches: 201, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 133 0.66
53 17 0.08
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1603496 original size:19 final size:19
Alignment explanation
Indices: 1603387--1603488 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1603377 AAATTATAAA
1603387 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1603406 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1603426 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1603442 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1603459 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1603478 CGCATTGCGAT
1 CGCATTGCGAT
1603489 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1603614 original size:14 final size:14
Alignment explanation
Indices: 1603595--1603631 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1603585 CATCAATTAC
1603595 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1603609 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1603623 ACAAATCAA
1 ACAAATCAA
1603632 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1605577 original size:19 final size:19
Alignment explanation
Indices: 1605533--1605667 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
1605523 TAGTTTACTT
* *
1605533 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
* **
1605553 TAGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1605572 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1605591 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
*
1605605 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1605624 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1605638 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1605657 TCGCAATGCGA
1 TCGCAACGCGA
1605668 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 18 0.19
15 1 0.01
16 8 0.08
17 8 0.08
18 1 0.01
19 48 0.51
20 11 0.12
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1605609 original size:33 final size:33
Alignment explanation
Indices: 1605567--1605662 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
1605557 AACGCGAAAC
1605567 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
*
1605600 CAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 CAAAATCGCAACGCGAAATGAAAATCGCAACGA
1605633 -AAGAATCGCAACGCGAAATGAAAATCGCAA
1 CAA-AATCGCAACGCGAAATGAAAATCGCAA
1605663 TGCGATTTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 2 0.03
33 58 0.97
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (33 bp):
CAAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:1605641 original size:14 final size:14
Alignment explanation
Indices: 1605589--1605645 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 14
1605579 GCGAAATGAA
1605589 AATCGCAACGACAA-
1 AATCGCAACGA-AAG
1605603 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1605620 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1605636 AATCGCAACG
1 AATCGCAACG
1605646 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 18 0.49
15 2 0.05
16 4 0.11
17 5 0.14
19 8 0.22
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1605685 original size:19 final size:19
Alignment explanation
Indices: 1605663--1605791 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1605653 AAAATCGCAA
1605663 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1605682 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1605696 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1605715 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1605729 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1605748 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1605767 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1605787 TGCGA
1 TGCGA
1605792 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1605705 original size:33 final size:33
Alignment explanation
Indices: 1605663--1605754 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1605653 AAAATCGCAA
1605663 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1605696 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1605729 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1605755 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1606006 original size:92 final size:93
Alignment explanation
Indices: 1605835--1606121 Score: 549
Period size: 93 Copynumber: 3.1 Consensus size: 93
1605825 TTGAATGGAT
1605835 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1605900 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1605928 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1605992 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1606020 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1606085 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1606113 AAATTTACT
1 AAATTTACT
1606122 AAGCAATCTA
Statistics
Matches: 190, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
92 91 0.48
93 99 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1607844 original size:14 final size:14
Alignment explanation
Indices: 1607825--1607881 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1607815 TTGAAATGAA
1607825 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1607839 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1607856 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
1607872 AATCGCAACG
1 AATCGCAACG
1607882 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1607862 original size:33 final size:33
Alignment explanation
Indices: 1607817--1607900 Score: 150
Period size: 33 Copynumber: 2.5 Consensus size: 33
1607807 TCTTTTGGTT
1607817 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1607850 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1607883 GAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
1607901 CGAAATGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1607863 original size:19 final size:19
Alignment explanation
Indices: 1607839--1607922 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1607829 GCAACGAGAG
* *
1607839 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
1607858 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1607872 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
1607891 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1607910 AATCGCAATGCGA
1 AATCGCAACGCGA
1607923 TTTTGGTTTC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 41 0.72
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1607953 original size:14 final size:14
Alignment explanation
Indices: 1607934--1607988 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1607924 TTTGGTTTCG
1607934 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1607948 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1607967 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1607981 CGTTGCGA
1 CGTTGCGA
1607989 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1607966 original size:33 final size:33
Alignment explanation
Indices: 1607918--1607988 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1607908 AAAATCGCAA
**
1607918 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1607951 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1607984 TGCGA
1 TGCGA
1607989 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1607996 original size:33 final size:33
Alignment explanation
Indices: 1607929--1608010 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1607919 GCGATTTTGG
***
1607929 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1607962 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1607995 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1608011 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1608015 original size:20 final size:20
Alignment explanation
Indices: 1607941--1608029 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1607931 TCGCGTTGCG
1607941 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1607961 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1607974 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1607994 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1608014 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1608030 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1608151 original size:33 final size:33
Alignment explanation
Indices: 1608109--1608179 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1608099 AATACTAACT
*
1608109 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1608142 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1608175 TGAAA
1 TGAAA
1608180 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1608413 original size:22 final size:22
Alignment explanation
Indices: 1608361--1608415 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1608351 TGGTTGTGAG
**
1608361 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1608383 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1608405 GGATTTCTTCG
1 GGATTTCTTCG
1608416 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1608586 original size:20 final size:20
Alignment explanation
Indices: 1608561--1608753 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1608551 CTTTAAATAT
1608561 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1608581 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1608603 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1608622 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1608642 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1608662 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1608682 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1608702 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1608722 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1608742 CGCGTTGCGATT
1 CGCGTTGCGATT
1608754 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1608748 original size:60 final size:60
Alignment explanation
Indices: 1608561--1608753 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1608551 CTTTAAATAT
**
1608561 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1608622 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1608682 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1608742 CGCGTTGCGATT
1 CGCGTTGCGATT
1608754 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1608834 original size:20 final size:20
Alignment explanation
Indices: 1608809--1608860 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1608799 AAGAATCGCG
*
1608809 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1608829 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1608849 TTGCGATTCTGG
1 TTGCGATTCTGG
1608861 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1610962 original size:37 final size:37
Alignment explanation
Indices: 1610905--1611010 Score: 131
Period size: 37 Copynumber: 2.9 Consensus size: 37
1610895 CATTTTCGTC
* *
1610905 CTACTATGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
1610942 TTGCTAGGATTCAAACTCCTAAAAATGGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
1610979 CTACTATGATTTAAACTCCTAAAGATAGGATA
1 CTACTAGGATTCAAACTCCTAAAAATAGGATA
1611011 CACAAGCACT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:1611566 original size:2 final size:2
Alignment explanation
Indices: 1611546--1611588 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
1611536 TTTTTAATAC
* *
1611546 TA TA TT TA T- TA TT 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
1611587 TA
1 TA
1611589 CTTTTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1611904 original size:25 final size:25
Alignment explanation
Indices: 1611842--1611905 Score: 60
Period size: 25 Copynumber: 2.6 Consensus size: 25
1611832 GTTATGATTA
*
1611842 TTATTT-TTCTATTTTACTCATTTAT
1 TTATTTATT-TATTTTAATCATTTAT
* * *
1611867 ATATATATATATTTTAAT-ATTTCAT
1 TTATTTATTTATTTTAATCATTT-AT
1611892 TTATTTATTTATTT
1 TTATTTATTTATTT
1611906 ATTTTTCCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
24 4 0.13
25 25 0.83
26 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (25 bp):
TTATTTATTTATTTTAATCATTTAT
Found at i:1611905 original size:12 final size:13
Alignment explanation
Indices: 1611884--1611962 Score: 51
Period size: 12 Copynumber: 6.4 Consensus size: 13
1611874 TATATTTTAA
1611884 TATTTCATTTATT
1 TATTTCATTTATT
1611897 TATTT-ATTTATT
1 TATTTCATTTATT
* *
1611909 T-TTCCTTTTATT
1 TATTTCATTTATT
* *
1611921 T-TTTTACTTATT
1 TATTTCATTTATT
* *
1611933 TTTATTC-TTCATT
1 TAT-TTCATTTATT
1611946 T-TTTCATTTATT
1 TATTTCATTTATT
*
1611958 CATTT
1 TATTT
1611963 TTTCCCTCTA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
11 5 0.10
12 29 0.58
13 14 0.28
14 2 0.04
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (13 bp):
TATTTCATTTATT
Found at i:1616406 original size:20 final size:21
Alignment explanation
Indices: 1616381--1616468 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 21
1616371 AATCAGAACA
1616381 AAAAGAAAAAAA-CAAAAAAG
1 AAAAGAAAAAAAGCAAAAAAG
1616401 AAAAGAAGCAAAAAAGCAAAAAAG
1 AAAAG-A--AAAAAAGCAAAAAAG
*
1616425 AAGAA-AACAAAAG-AAAAAAG
1 AA-AAGAAAAAAAGCAAAAAAG
*
1616445 -AAAGAACAAAAATC-AAAAAG
1 AAAAGAA-AAAAAGCAAAAAAG
1616465 AAAA
1 AAAA
1616469 AGGGACAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
18 2 0.04
19 3 0.05
20 22 0.39
21 10 0.18
23 7 0.12
24 10 0.18
25 2 0.04
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.01
Consensus pattern (21 bp):
AAAAGAAAAAAAGCAAAAAAG
Found at i:1616413 original size:24 final size:22
Alignment explanation
Indices: 1616386--1616456 Score: 83
Period size: 24 Copynumber: 3.2 Consensus size: 22
1616376 GAACAAAAAG
1616386 AAAAAAACAAAAAAGAAAAGAAGC
1 AAAAAAACAAAAAAG-AAAGAA-C
*
1616410 AAAAAAGCAAAAAAG-AAGAA-
1 AAAAAAACAAAAAAGAAAGAAC
* *
1616430 AACAAAAGAAAAAAGAAAGAAC
1 AAAAAAACAAAAAAGAAAGAAC
1616452 AAAAA
1 AAAAA
1616457 TCAAAAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.30
21 5 0.12
22 9 0.22
24 14 0.35
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAAGAAAGAAC
Done.