Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008955.1 Hibiscus syriacus cultivar Beakdansim tig00112285_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: 4658001
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 23
Found at i:1275327 original size:21 final size:21
Alignment explanation
Indices: 1275301--1275373 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1275291 CACATGTCAT
1275301 CGTTCAAGAGGCCCCTCCTAC
1 CGTTCAAGAGGCCCCTCCTAC
* * *
1275322 CGTTCAAGAGGCCTCT-GTCAT
1 CGTTCAAGAGGCCCCTCCT-AC
* * *
1275343 CGTTTAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTCCTAC
1275364 CGTTCAAGAG
1 CGTTCAAGAG
1275374 CCTAATTCAA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.23
Consensus pattern (21 bp):
CGTTCAAGAGGCCCCTCCTAC
Found at i:1279429 original size:24 final size:24
Alignment explanation
Indices: 1279390--1279457 Score: 109
Period size: 24 Copynumber: 2.8 Consensus size: 24
1279380 CTGAAATATC
*
1279390 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
*
1279414 ATTAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
*
1279438 ATCAAAGTCCGGGTATTGAC
1 ATCAAAGTCCGAGTATTGAC
1279458 TAGTACTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAGTATTGACCAAG
Found at i:1280439 original size:20 final size:20
Alignment explanation
Indices: 1280416--1280526 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
1280406 TCGTGTTGTA
1280416 AATTCGAAAATCGAGTTGCG
1 AATTCGAAAATCGAGTTGCG
1280436 AATTC-AGAAATCGAGTTGCG
1 AATTCGA-AAATCGAGTTGCG
* *
1280456 AATT-TAAAATTCAGTGTTGCG
1 AATTCGAAAA-TC-GAGTTGCG
* ** *
1280477 AATTTG-ACTTCTATGTTGCG
1 AATTCGAAAATCGA-GTTGCG
* *
1280497 AATTAC-AAATTCGCGTTGCG
1 AATT-CGAAAATCGAGTTGCG
1280517 AATTCGAAAA
1 AATTCGAAAA
1280527 CTGTGTTGTG
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
19 5 0.07
20 50 0.70
21 16 0.23
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (20 bp):
AATTCGAAAATCGAGTTGCG
Found at i:1280534 original size:40 final size:39
Alignment explanation
Indices: 1280422--1280560 Score: 111
Period size: 40 Copynumber: 3.5 Consensus size: 39
1280412 TGTAAATTCG
* *
1280422 AAAA-TCGAGTTGCGAATTCAGAAATC-GAGTTGCGAATTT
1 AAAATTCGCGTTGCGAATTC-GAAATCTGTGTTGCGAA-TT
* * ** *
1280461 AAAATTCAGTGTTGCGAATTTGACTTCTATGTTGCGAATT
1 AAAATTC-GCGTTGCGAATTCGAAATCTGTGTTGCGAATT
* *
1280501 ACAAATTCGCGTTGCGAATTCGAAAACTGTGTTGTGAAATT
1 A-AAATTCGCGTTGCGAATTCGAAATCTGTGTTGCG-AATT
** *
1280542 GGAGTTCGCGTTGCGAATT
1 AAAATTCGCGTTGCGAATT
1280561 TGTTTGTCAT
Statistics
Matches: 79, Mismatches: 16, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
39 4 0.05
40 46 0.58
41 29 0.37
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (39 bp):
AAAATTCGCGTTGCGAATTCGAAATCTGTGTTGCGAATT
Found at i:1280838 original size:63 final size:62
Alignment explanation
Indices: 1280763--1280915 Score: 153
Period size: 63 Copynumber: 2.4 Consensus size: 62
1280753 TCTCACGTAG
* * *
1280763 AGCAGCTACCTCATCACGTAAAGCACCATTGTCATCATGTAAAACAGCTACCTCACCAAGTAA
1 AGCA-CTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAACACCGACCTCACCAAGTAA
* *** ** * * * * *
1280826 AGACCCTACCTCATCACACCATTCACCATTTTCGTCACGTAAAGCACCGACCTCATCACGTAA
1 AG-CACTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAACACCGACCTCACCAAGTAA
1280889 AGCACTGACCTCATCACGTAAAGCACC
1 AGCACT-ACCTCATCACGTAAAGCACC
1280916 TAACTCATCC
Statistics
Matches: 68, Mismatches: 20, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
62 3 0.04
63 64 0.94
64 1 0.01
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (62 bp):
AGCACTACCTCATCACGTAAAGCACCATTGTCATCACGTAAAACACCGACCTCACCAAGTAA
Found at i:1280884 original size:21 final size:21
Alignment explanation
Indices: 1280860--1280924 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1280850 ACCATTTTCG
1280860 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
1280881 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
1280902 TCACGTAAAGCACCTAACTCA
1 TCACGTAAAGCACCGACCTCA
1280923 TC
1 TC
1280925 CCGTGGAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:1281062 original size:42 final size:42
Alignment explanation
Indices: 1281003--1281201 Score: 263
Period size: 42 Copynumber: 4.7 Consensus size: 42
1280993 GTGGAGAAAA
* * * *
1281003 GGCTCGATGATGTGATGGCTCTCGGTGTCGATGTGTAGAATT
1 GGCTCGATCAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATC
1281045 GGCTCGATCAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATC
1 GGCTCGATCAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATC
*
1281087 GGCTCGATCAGGTGATGGCTCTCAGTGTCGAGGTGTAGAATC
1 GGCTCGATCAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATC
* * * **
1281129 GGCTCGATCAGGTGATGGATCTCGGTGTCGAAGTGGAGAAGA
1 GGCTCGATCAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATC
* * * * *
1281171 GGCTCGATGAGGTAATAGATATCGGTGTCGA
1 GGCTCGATCAGGTGATGGCTCTCGGTGTCGA
1281202 AGTAGGAGGT
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.20, C:0.16, G:0.37, T:0.27
Consensus pattern (42 bp):
GGCTCGATCAGGTGATGGCTCTCGGTGTCGAGGTGTAGAATC
Found at i:1281078 original size:21 final size:21
Alignment explanation
Indices: 1281054--1281121 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1281044 TGGCTCGATC
1281054 AGGTGATGGCTCTCGGTGTCG
1 AGGTGATGGCTCTCGGTGTCG
* **
1281075 AGGTG-TAG-AATCGGCTCGATC-
1 AGGTGATGGCTCTCGG-T-G-TCG
*
1281096 AGGTGATGGCTCTCAGTGTCG
1 AGGTGATGGCTCTCGGTGTCG
1281117 AGGTG
1 AGGTG
1281122 TAGAATCGGC
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 17 0.50
22 5 0.15
23 3 0.09
ACGTcount: A:0.16, C:0.18, G:0.40, T:0.26
Consensus pattern (21 bp):
AGGTGATGGCTCTCGGTGTCG
Found at i:1282735 original size:20 final size:20
Alignment explanation
Indices: 1282712--1282751 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1282702 AATTCGCAAC
*
1282712 ATGAAAATCGCAACTCGAAA
1 ATGAAAATCGCAACACGAAA
*
1282732 ATGAAATTCGCAACACGAAA
1 ATGAAAATCGCAACACGAAA
1282752 TTCGCAACGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.20, G:0.15, T:0.15
Consensus pattern (20 bp):
ATGAAAATCGCAACACGAAA
Found at i:1283174 original size:22 final size:22
Alignment explanation
Indices: 1283149--1283199 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1283139 ATGGAGGGGG
*
1283149 GTCGCCGGATATGAGGACGGAT
1 GTCGCCGGAGATGAGGACGGAT
1283171 GTCGCCGGAGATGAGGACGGAT
1 GTCGCCGGAGATGAGGACGGAT
1283193 GTCGCCG
1 GTCGCCG
1283200 TAGAGAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.43, T:0.16
Consensus pattern (22 bp):
GTCGCCGGAGATGAGGACGGAT
Found at i:1283334 original size:19 final size:20
Alignment explanation
Indices: 1283312--1283349 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1283302 ATATTTGTGT
1283312 TTCGAATT-CGAAAATAAAA
1 TTCGAATTACGAAAATAAAA
**
1283331 TTCGCGTTACGAAAATAAA
1 TTCGAATTACGAAAATAAA
1283350 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGAATTACGAAAATAAAA
Found at i:1283531 original size:19 final size:19
Alignment explanation
Indices: 1283415--1283564 Score: 75
Period size: 19 Copynumber: 7.6 Consensus size: 19
1283405 AGAAATTCGA
* * *
1283415 GTTGCAAATTTCAAAACTGA
1 GTTGCGAATTT-AAAATTGC
*
1283435 GTTGCGAATTTGGGAAATTCGC
1 GTTGCGAATTT--AAAATT-GC
* * *
1283457 GTTGCTAATTTAGAAACTGT
1 GTTGCGAATTTA-AAATTGC
* * * *
1283477 GTTGCGAAATTAGAGTTCGT
1 GTTGCGAATTTAAAATT-GC
**
1283497 GTTGCGAATTCGAAATTGC
1 GTTGCGAATTTAAAATTGC
**
1283516 GTTGCGAATTTAAAATCAC
1 GTTGCGAATTTAAAATTGC
* **
1283535 ATTGCGAATTTAAAATCAC
1 GTTGCGAATTTAAAATTGC
*
1283554 ATTGCGAATTT
1 GTTGCGAATTT
1283565 GTTGGTTATT
Statistics
Matches: 101, Mismatches: 25, Indels: 9
0.75 0.19 0.07
Matches are distributed among these distances:
19 47 0.47
20 35 0.35
21 8 0.08
22 11 0.11
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (19 bp):
GTTGCGAATTTAAAATTGC
Found at i:1287666 original size:60 final size:60
Alignment explanation
Indices: 1287589--1287760 Score: 174
Period size: 62 Copynumber: 2.8 Consensus size: 60
1287579 CCCTTATTTC
**
1287589 AAATTAGTCCCTAAACTTTTGAACATTTTAATTTTATCCTTAAACTATGAT-T-ATCATTCT
1 AAATTAGTCCCTAAACTTTTGAA-ATTTTAATTTTATCCCCAAACTAT-ATATCATCATTCT
* * *
1287649 AAATTAGT-CCTCAAACTTTTG-AATATATCATTTTCATCCCCAAACTATATAATCTTCATTCT
1 AAATTAGTCCCT-AAACTTTTGAAAT-TTTAATTTT-ATCCCCAAACTATAT-ATCATCATTCT
* *
1287711 AAATTAGTCCCTAAACTTTTTAAATATTTCAATTTTAT-CCCAAATTATAT
1 AAATTAGTCCCTAAACTTTTGAAAT-TTT-AATTTTATCCCCAAACTATAT
1287761 GTATATACTA
Statistics
Matches: 94, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
58 2 0.02
59 13 0.14
60 28 0.30
61 1 0.01
62 34 0.36
63 11 0.12
64 5 0.05
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (60 bp):
AAATTAGTCCCTAAACTTTTGAAATTTTAATTTTATCCCCAAACTATATATCATCATTCT
Found at i:1287727 original size:62 final size:58
Alignment explanation
Indices: 1287589--1287760 Score: 177
Period size: 60 Copynumber: 2.8 Consensus size: 58
1287579 CCCTTATTTC
* * **
1287589 AAATTAGTCCCTAAACTTTTGAACATTTTAATTTTATCCTTAAACTATGATTATCATTCT
1 AAATTAGTCCCTAAACTTTTGAATA-TTTCATTTTATCCCCAAACTAT-ATTATCATTCT
* *
1287649 AAATTAGT-CCTCAAACTTTTGAATATATCATTTTCATCCCCAAACTATATAATCTTCATTCT
1 AAATTAGTCCCT-AAACTTTTGAATATTTCATTTT-ATCCCCAAACTATAT--T-ATCATTCT
* *
1287711 AAATTAGTCCCTAAACTTTTTAAATATTTCAATTTTAT-CCCAAATTATAT
1 AAATTAGTCCCTAAAC-TTTTGAATATTTC-ATTTTATCCCCAAACTATAT
1287761 GTATATACTA
Statistics
Matches: 95, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
59 12 0.13
60 31 0.33
61 1 0.01
62 30 0.32
63 16 0.17
64 5 0.05
ACGTcount: A:0.35, C:0.19, G:0.03, T:0.43
Consensus pattern (58 bp):
AAATTAGTCCCTAAACTTTTGAATATTTCATTTTATCCCCAAACTATATTATCATTCT
Found at i:1289378 original size:23 final size:23
Alignment explanation
Indices: 1289312--1289380 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
1289302 CACCACATCT
* *
1289312 CGTATAATTGCACCGAAGTGACA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1289335 CATAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1289358 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1289381 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1290053 original size:21 final size:21
Alignment explanation
Indices: 1290029--1290071 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1290019 TCATATTCGT
* *
1290029 TTGAGGGGGAATCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
* *
1290050 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
1290071 T
1 T
1290072 AGCCCAAAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (21 bp):
TTGAAGGGGAACCGATTCCCC
Found at i:1294495 original size:22 final size:23
Alignment explanation
Indices: 1294470--1294518 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
1294460 AATTGTGTTT
*
1294470 CAATCTTAAAAAAGT-TTTGGAA
1 CAATCTTAAAAAAGTATTTCGAA
* * *
1294492 CAATTTTTACAAAGTATTTCGAA
1 CAATCTTAAAAAAGTATTTCGAA
1294515 CAAT
1 CAAT
1294519 AATCAAGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (23 bp):
CAATCTTAAAAAAGTATTTCGAA
Found at i:1295993 original size:20 final size:21
Alignment explanation
Indices: 1295970--1296020 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
1295960 AAAAAAACTA
1295970 AAAATAA-AAATTAAAT-TATT
1 AAAATAATAAA-TAAATATATT
*
1295990 AAAA-AATAAATAAATATTTT
1 AAAATAATAAATAAATATATT
*
1296010 AAAATACTAAA
1 AAAATAATAAA
1296021 ACTAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATAAATAAATATATT
Found at i:1296040 original size:20 final size:19
Alignment explanation
Indices: 1295982--1296042 Score: 52
Period size: 20 Copynumber: 3.2 Consensus size: 19
1295972 AATAAAAATT
*
1295982 AAAT-TATTAAAAAATAAA
1 AAATATATTAAAAAATTAA
* * *
1296000 TAAATATTTTAAAATACTAA
1 -AAATATATTAAAAAATTAA
*
1296020 AACTAATATTAAAAAATTAA
1 AAAT-ATATTAAAAAATTAA
1296040 AAA
1 AAA
1296043 AAACTAAATT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
19 7 0.23
20 24 0.77
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATATATTAAAAAATTAA
Found at i:1296589 original size:23 final size:22
Alignment explanation
Indices: 1296511--1296610 Score: 71
Period size: 23 Copynumber: 4.3 Consensus size: 22
1296501 AAATACTTTG
*
1296511 ATTTTTAAATAATTTTTTTTAT
1 ATTTTTAAATAATATTTTTTAT
* *
1296533 CATTTTATAACTTATGATATTTTTTAAA
1 -ATTTT-TAA---ATAATATTTTTT-AT
*
1296561 AATTTTAAATAATATTTTTTAGT
1 ATTTTTAAATAATATTTTTTA-T
1296584 ATTTTT-AA-AATATATTTTTA-
1 ATTTTTAAATAATAT-TTTTTAT
1296604 ATTTTTA
1 ATTTTTA
1296611 GTAATTTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
20 6 0.10
21 5 0.08
22 9 0.15
23 21 0.34
24 3 0.05
26 3 0.05
27 14 0.23
28 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
ATTTTTAAATAATATTTTTTAT
Found at i:1296625 original size:21 final size:22
Alignment explanation
Indices: 1296601--1296652 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1296591 AAATATATTT
1296601 TTAATTTTTAGTA-ATTTAATA
1 TTAATTTTTAGTATATTTAATA
* * *
1296622 TTAATTTTTAGTATTTTTATTT
1 TTAATTTTTAGTATATTTAATA
1296644 TTAATTTTT
1 TTAATTTTT
1296653 TTAATATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (22 bp):
TTAATTTTTAGTATATTTAATA
Found at i:1296662 original size:22 final size:22
Alignment explanation
Indices: 1296576--1296662 Score: 54
Period size: 22 Copynumber: 4.0 Consensus size: 22
1296566 TAAATAATAT
* * * *
1296576 TTTTTAGTATTTTTAAAATATA
1 TTTTTAATTTTTTTAATATTTA
*
1296598 TTTTTAA--TTTTTAGTAATTTA
1 TTTTTAATTTTTTTAAT-ATTTA
* * * *
1296619 ATATTAATTTTTAGT-ATTTTTA
1 TTTTTAATTTTT-TTAATATTTA
1296641 TTTTTAATTTTTTTAATATTTA
1 TTTTTAATTTTTTTAATATTTA
1296663 AATATTTCAT
Statistics
Matches: 47, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
20 6 0.13
21 10 0.21
22 26 0.55
23 4 0.09
24 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (22 bp):
TTTTTAATTTTTTTAATATTTA
Found at i:1297245 original size:22 final size:23
Alignment explanation
Indices: 1297220--1297264 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1297210 GAATAAAGAT
1297220 TAAATTGA-TAAA-ATTTTAAATA
1 TAAA-TGATTAAATATTTTAAATA
1297242 TAAATGATTAAATTATTTTAAAT
1 TAAATGATTAAA-TATTTTAAAT
1297265 TAGTTTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.15
22 8 0.40
24 9 0.45
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATGATTAAATATTTTAAATA
Found at i:1301117 original size:18 final size:18
Alignment explanation
Indices: 1301094--1301128 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1301084 AATAAAAAAT
*
1301094 TTTTATTTCTTTTCTTTA
1 TTTTATCTCTTTTCTTTA
1301112 TTTTATCTCTTTTCTTT
1 TTTTATCTCTTTTCTTT
1301129 GTTGCTTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTATCTCTTTTCTTTA
Found at i:1304355 original size:56 final size:57
Alignment explanation
Indices: 1304147--1304362 Score: 192
Period size: 58 Copynumber: 3.8 Consensus size: 57
1304137 TCTAACTTTG
* * * * * **
1304147 AAAAGGAATTAAATCGTTAAATTTATTTTCAT-ATGAATCTTCTATGATTATGTTCGGT
1 AAAAGAAAATAAATCGTCAAATTTATTTTCTTGA-GAATCTTGTATGATTATGTT-TAT
* * *
1304205 AAAAGAAAATAAAACGTCAAATTTATTTTCTTG-GAAATCTT-AATCGATTTCAT-CTTAT
1 AAAAGAAAATAAATCGTCAAATTTATTTTCTTGAG-AATCTTGTAT-GA-TT-ATGTTTAT
* * * *
1304263 AGAAGAAAATAAATAGTTAAATTTATTTTCAT-AGAATCTTGTATGATTATGTTTAT
1 AAAAGAAAATAAATCGTCAAATTTATTTTCTTGAGAATCTTGTATGATTATGTTTAT
* *
1304319 AAAAGAAAATAAATCGTCAGATTTA-TTTCTTGAGAATCATGTAT
1 AAAAGAAAATAAATCGTCAAATTTATTTTCTTGAGAATCTTGTAT
1304363 AATTCTATCT
Statistics
Matches: 127, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
55 7 0.06
56 38 0.30
57 11 0.09
58 66 0.52
59 3 0.02
60 2 0.02
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (57 bp):
AAAAGAAAATAAATCGTCAAATTTATTTTCTTGAGAATCTTGTATGATTATGTTTAT
Found at i:1310268 original size:29 final size:29
Alignment explanation
Indices: 1310223--1310296 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
1310213 TTTCATATGT
*
1310223 TCATGTA-CTCATATCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1310251 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
1310280 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
1310297 CTTCATATCA
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 7 0.16
29 37 0.84
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:1310329 original size:12 final size:12
Alignment explanation
Indices: 1310312--1310347 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
1310302 TATCATGTTC
1310312 TCATATCACATG
1 TCATATCACATG
*
1310324 TCATATCACATA
1 TCATATCACATG
1310336 TCATATCACATG
1 TCATATCACATG
1310348 AACATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (12 bp):
TCATATCACATG
Found at i:1310767 original size:64 final size:64
Alignment explanation
Indices: 1310655--1310879 Score: 197
Period size: 64 Copynumber: 3.5 Consensus size: 64
1310645 TAATGAAGGT
* * * ** ** * * **
1310655 ATGCATCGATGCACTACTGATTCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
* * *
1310719 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTTGATGTTTCACTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTGCATTCGATGTGTCACTATTAATGGG
* * * **
1310783 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGT-GTCACTATTAATGGG
**
1310846 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
1310880 ATTCAAACAA
Statistics
Matches: 134, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
63 5 0.04
64 126 0.94
65 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTGTCACTATTAATGGG
Found at i:1312182 original size:21 final size:20
Alignment explanation
Indices: 1312158--1312205 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
1312148 TCCTTTTTAA
1312158 ATCAGCATACGATTTCTGTCT
1 ATCAGCATA-GATTTCTGTCT
**
1312179 ATCAGTTGTAGATTTCTGTCT
1 ATCAG-CATAGATTTCTGTCT
1312200 ATCAGC
1 ATCAGC
1312206 TGCAGCTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
ATCAGCATAGATTTCTGTCT
Found at i:1312215 original size:21 final size:21
Alignment explanation
Indices: 1312168--1312215 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1312158 ATCAGCATAC
* *
1312168 GATTTCTGTCTATCAGTTGTA
1 GATTTCTGTCTATCAGCTGCA
1312189 GATTTCTGTCTATCAGCTGCA
1 GATTTCTGTCTATCAGCTGCA
*
1312210 GCTTTC
1 GATTTC
1312216 AGATTATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (21 bp):
GATTTCTGTCTATCAGCTGCA
Found at i:1317100 original size:15 final size:15
Alignment explanation
Indices: 1317077--1317109 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1317067 CGTAGGACTC
1317077 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
1317092 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
1317107 CTA
1 CTA
1317110 TTATACCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:1317271 original size:12 final size:12
Alignment explanation
Indices: 1317254--1317283 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1317244 TATCATGTTC
*
1317254 TCATATCACATG
1 TCATATCACATA
1317266 TCATATCACATA
1 TCATATCACATA
1317278 TCATAT
1 TCATAT
1317284 ATATGTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (12 bp):
TCATATCACATA
Found at i:1317776 original size:64 final size:63
Alignment explanation
Indices: 1317642--1317803 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
1317632 TTATTGCTGG
* * * *
1317642 GATGCATCGATGCACTCCTTATGCATCGATGCACCGATTGTATTCAATGTTTCACTATTAATGG
1 GATGCATCGATGCACTACTTATGCATCGATGCA-CGATTGCATTCAATGTTTCACTATTAAAGA
* * *
1317706 GATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTCTTTA-TTTTAAA-A
1 GATGCATCGATGCACTACTTATGCATCGATGCACG-ATTGCATTCAATGT-TTCACTATTAAAGA
** *
1317769 GAGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 GA-TGCATCGATGCACTACTTATGCATCGATGCAC
1317804 ATTCAAACAA
Statistics
Matches: 85, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 4 0.05
64 78 0.92
65 3 0.04
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (63 bp):
GATGCATCGATGCACTACTTATGCATCGATGCACGATTGCATTCAATGTTTCACTATTAAAGA
Found at i:1323077 original size:25 final size:25
Alignment explanation
Indices: 1323049--1323137 Score: 160
Period size: 25 Copynumber: 3.6 Consensus size: 25
1323039 AATTACATCT
* *
1323049 CATGGACCAATTATATCTATTCATG
1 CATGAACCAATTATATCCATTCATG
1323074 CATGAACCAATTATATCCATTCATG
1 CATGAACCAATTATATCCATTCATG
1323099 CATGAACCAATTATATCCATTCATG
1 CATGAACCAATTATATCCATTCATG
1323124 CATGAACCAATTAT
1 CATGAACCAATTAT
1323138 CAATGGGTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 62 1.00
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (25 bp):
CATGAACCAATTATATCCATTCATG
Found at i:1323376 original size:26 final size:26
Alignment explanation
Indices: 1323335--1323396 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
1323325 GAAGGTAAAT
*
1323335 ATTTGAAAACGGCTTACCGGGTTCGA
1 ATTTGAAAACGACTTACCGGGTTCGA
*
1323361 ATTTGAAAATGACTTACCGGGTTCGA
1 ATTTGAAAACGACTTACCGGGTTCGA
1323387 ATTTGAAAAC
1 ATTTGAAAAC
1323397 ACGGACTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (26 bp):
ATTTGAAAACGACTTACCGGGTTCGA
Found at i:1323534 original size:18 final size:18
Alignment explanation
Indices: 1323511--1323548 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1323501 ACTCTGACCA
1323511 AAGTCAATA-GCTCGAGTC
1 AAGTCAA-AGGCTCGAGTC
*
1323529 AAGTCAAAGGGTCGAGTC
1 AAGTCAAAGGCTCGAGTC
1323547 AA
1 AA
1323549 AGAAGTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.18
Consensus pattern (18 bp):
AAGTCAAAGGCTCGAGTC
Found at i:1325565 original size:21 final size:21
Alignment explanation
Indices: 1325536--1325592 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
1325526 GGGTCTACGC
*
1325536 GGTCCTTCGGGACAATATAGT
1 GGTCCTTCGGGACAATATAAT
*
1325557 GGTCATTCGGGACAATATAAT
1 GGTCCTTCGGGACAATATAAT
*
1325578 AGTCCTTCGGGACAA
1 GGTCCTTCGGGACAA
1325593 ATTTCATATG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (21 bp):
GGTCCTTCGGGACAATATAAT
Found at i:1326332 original size:23 final size:23
Alignment explanation
Indices: 1326288--1326330 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1326278 AACAGTACTG
* *
1326288 TAGCAGGGGGTATTGGTTCCCTA
1 TAGCAGGGGGAATCGGTTCCCTA
1326311 TAGCA-GGGGAATCGGTTCCC
1 TAGCAGGGGGAATCGGTTCCC
1326331 CTCTGACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.19, C:0.21, G:0.35, T:0.26
Consensus pattern (23 bp):
TAGCAGGGGGAATCGGTTCCCTA
Found at i:1326413 original size:20 final size:22
Alignment explanation
Indices: 1326368--1326420 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
1326358 TTAGGTATTG
*
1326368 TTCACGGTACTATTTATTATTA
1 TTCACGGTACTATTTATTACTA
*
1326390 TTCACAGTACT-TTT-TTACTA
1 TTCACGGTACTATTTATTACTA
1326410 TTCACGGTACT
1 TTCACGGTACT
1326421 GTTCATACCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 15 0.54
21 3 0.11
22 10 0.36
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (22 bp):
TTCACGGTACTATTTATTACTA
Found at i:1330388 original size:13 final size:13
Alignment explanation
Indices: 1330370--1330395 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1330360 GTAAAACTTG
1330370 GTAAGTGTAGTGT
1 GTAAGTGTAGTGT
1330383 GTAAGTGTAGTGT
1 GTAAGTGTAGTGT
1330396 AAATTATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (13 bp):
GTAAGTGTAGTGT
Found at i:1330707 original size:114 final size:111
Alignment explanation
Indices: 1330178--1330802 Score: 344
Period size: 114 Copynumber: 5.6 Consensus size: 111
1330168 TTCTTATTTA
* * * * *
1330178 TTTTTTATTTGAAATATAAATTAATTAGATTATTTATTTTGAATTTACAGATTAAACTGTA-TTG
1 TTTTTTATTTTAAATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTG
* * *
1330242 AGTGGCTTGGTAAGTTTAATTTAAATTTTCGTGTAATTTTTAGTGTAAT
65 AGTAGCTTGGTAAG-TTAATTTAAATTTTAGTGTAATTTTTA-TCTAAT
* * * * *
1330291 TTTTGTTTTTAACTTAAAT-TATAATTATTAAACTATTTATTTTAATTTTACATATTAAGTAGTA
1 TTTT-TTATT---TTAAATATA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTA
* * * * * * *
1330355 TTTGCGTAAAACTTGGTAAGTGTAGTGTGT-AAGTGTAGTGTAAATTATTA-CATTAT
61 TTTGAGT--AGCTTGGTAAGT-TAAT-T-TAAATTTTAGTGT-AATTTTTATC-TAAT
* ** * * * **
1330411 TTTTTTA-TTGAGTAATATAAATTACCAGACTAATTATTTTTATTTTATATATTAAATCATATTT
1 TTTTTTATTTTA--AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTT
* * * * * *
1330475 GAGTACCTTAGTAAGTTTAGTTTAAAATTTATTGT--TTTATT-T-T-GT
64 GAGTAGCTTGGTAAG-TTAATTTAAATTTTAGTGTAATTT-TTATCTAAT
* * ** * * * * *
1330520 TTTTTTATTGTAAAAATAAATTAATTATTCTATTTATTTTGATTTTATAGATTAAACTATATTCG
1 TTTTTTATTTTAAATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTG
* * *
1330585 AGTGGTTTGGTAAGTTAATTTTAAATTTTCGTGTAATTTTTAGTCTAAT
65 AGTAGCTTGGTAAGTTAA-TTTAAATTTTAGTGTAATTTTTA-TCTAAT
*
1330634 TTTTTTAATTTTAAAT-TATAATTATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTT
1 TTTTTT-ATTTTAAATATA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTT
* * *
1330698 GAGTAGTTTGATCAGTTTAATTTAAA--TTA---T-A--TTT-T-T-A-
64 GAGTAGCTTGGTAAG-TTAATTTAAATTTTAGTGTAATTTTTATCTAAT
** * * *
1330735 TTTTTTATTGAATAATATAAATTATT-GAAGTATTTATCTTGATTTTACATATTAAATCGTATTT
1 TTTTTTATTTTA-AATATAAATTATTAG-ACTATTTATTTTGATTTTACATATTAAATTGTATTT
1330799 GAGT
64 GAGT
1330803 GGTTTTGTAA
Statistics
Matches: 396, Mismatches: 81, Indels: 82
0.71 0.14 0.15
Matches are distributed among these distances:
100 5 0.01
101 52 0.13
102 3 0.01
103 1 0.00
104 1 0.00
106 3 0.01
108 13 0.03
109 63 0.16
110 5 0.01
111 5 0.01
112 5 0.01
113 6 0.02
114 73 0.18
115 30 0.08
116 33 0.08
117 56 0.14
118 4 0.01
119 14 0.04
120 16 0.04
121 8 0.02
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.52
Consensus pattern (111 bp):
TTTTTTATTTTAAATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATTGTATTTGA
GTAGCTTGGTAAGTTAATTTAAATTTTAGTGTAATTTTTATCTAAT
Found at i:1330769 original size:101 final size:102
Alignment explanation
Indices: 1330653--1330889 Score: 288
Period size: 101 Copynumber: 2.3 Consensus size: 102
1330643 TTTAAATTAT
* * *
1330653 AATT-ATTAGACTATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAG-TTTGATCAGTTT
1 AATTAATTAGACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAGTTTTG-TAAGTTT
1330716 AATTTAAATTATATTT-TTAT-TTTTTATTGAATAATATA
65 AATTTAAATT-TATTTGTTATGTTTTTATTGAA-AATATA
* * *
1330754 AATT-ATT-GAAGTATTTATCTTGATTTTACATATTAAATCGTATTTGAGTGGTTTTGTAAGTTT
1 AATTAATTAG-ACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAGTTTTGTAAGTTT
** * * *
1330817 GGTTTAAATTTTTTTGTTTTGTTTTTATTGTAAATATA
65 AATTTAAATTTATTTGTTATGTTTTTATTGAAAATATA
*
1330855 AATTAATTAGACTATTTATTTTGATTTAACATATT
1 AATTAATTAGACTATTTATTTTGATTTTACATATT
1330890 TTTTGTTTAA
Statistics
Matches: 116, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
100 5 0.04
101 71 0.61
102 39 0.34
103 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.11, T:0.54
Consensus pattern (102 bp):
AATTAATTAGACTATTTATTTTGATTTTACATATTAAATCGTATTTGAGTAGTTTTGTAAGTTTA
ATTTAAATTTATTTGTTATGTTTTTATTGAAAATATA
Found at i:1333446 original size:27 final size:27
Alignment explanation
Indices: 1333380--1333579 Score: 148
Period size: 27 Copynumber: 7.0 Consensus size: 27
1333370 AATATCCATC
* ** *
1333380 ATTCAACTATTAATATCCATCATATTA
1 ATTCAACTATTGATATTAATCACATTA
* *
1333407 ATTCAAATGTTGATATTAATCACATTA
1 ATTCAACTATTGATATTAATCACATTA
* *
1333434 ATTCAACTATTGATGATATTATTCACATTC
1 ATTCAACTA-T--TGATATTAATCACATTA
* *
1333464 ATTCAACTATTGATATTAATCATATTC
1 ATTCAACTATTGATATTAATCACATTA
* * * *
1333491 ATTAAAATATAGTGTCAATAAATATCCATCATATTA
1 ATTCAACTAT--TG---AT--AT-T-AATCACATTA
*
1333527 ATTCAAATATTGATATTAATCACATTA
1 ATTCAACTATTGATATTAATCACATTA
*
1333554 ATTCAACTATTGATATTAACCACATT
1 ATTCAACTATTGATATTAATCACATT
1333580 CATTAAAATA
Statistics
Matches: 140, Mismatches: 21, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
27 83 0.59
28 2 0.01
29 5 0.04
30 24 0.17
31 2 0.01
32 2 0.01
34 4 0.03
35 1 0.01
36 17 0.12
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTCAACTATTGATATTAATCACATTA
Found at i:1333558 original size:90 final size:88
Alignment explanation
Indices: 1333447--1333621 Score: 269
Period size: 90 Copynumber: 2.0 Consensus size: 88
1333437 CAACTATTGA
* * * * **
1333447 TGATATTATTCACATTCATTCAACTATTGATATTAATCATATTCATTAAAATATAGTGTCAATAA
1 TGATATTAATCACATTAATTCAACTATTGATATTAACCACATTCATTAAAATATAGCAT-AA-AA
*
1333512 ATATCCATCATATTAATTCAAATAT
64 ACATCCATCATATTAATTCAAATAT
1333537 TGATATTAATCACATTAATTCAACTATTGATATTAACCACATTCATTAAAATATAGCATAAAAAC
1 TGATATTAATCACATTAATTCAACTATTGATATTAACCACATTCATTAAAATATAGCATAAAAAC
1333602 ATCCATCATATTAATTCAAA
66 ATCCATCATATTAATTCAAA
1333622 AAAATAGACA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
88 23 0.29
89 2 0.03
90 53 0.68
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (88 bp):
TGATATTAATCACATTAATTCAACTATTGATATTAACCACATTCATTAAAATATAGCATAAAAAC
ATCCATCATATTAATTCAAATAT
Found at i:1335837 original size:34 final size:34
Alignment explanation
Indices: 1335772--1335869 Score: 171
Period size: 34 Copynumber: 2.9 Consensus size: 34
1335762 AATTTTAAAA
* *
1335772 AAATGAAAATATATTAATAATA-TTTTTTATTAT
1 AAATGTAAATATATTAACAATATTTTTTTATTAT
1335805 AAATGTAAATATATTAACAATATTTTTTTATTAT
1 AAATGTAAATATATTAACAATATTTTTTTATTAT
1335839 AAATGTAAATATATTAACAATATTTTTTTAT
1 AAATGTAAATATATTAACAATATTTTTTTAT
1335870 AAAAATAATG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 20 0.32
34 42 0.68
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (34 bp):
AAATGTAAATATATTAACAATATTTTTTTATTAT
Found at i:1336106 original size:45 final size:45
Alignment explanation
Indices: 1335996--1336123 Score: 166
Period size: 45 Copynumber: 2.8 Consensus size: 45
1335986 TTTCCCGTTT
* ** * *
1335996 AACCACCAACCTACCCGGAATATTAATGGATAAATAATAACTACC
1 AACCACCAACCTACACGGGTTATTAATGGATAATTAATAACCACC
* *
1336041 AACCACCAACCTACCCGGGTTATTAATGAATAATTAATAACCACC
1 AACCACCAACCTACACGGGTTATTAATGGATAATTAATAACCACC
* * *
1336086 AACCATCAACCTACATGGGTTATTAACGGATAATTAAT
1 AACCACCAACCTACACGGGTTATTAATGGATAATTAAT
1336124 GGTGTCATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.23
Consensus pattern (45 bp):
AACCACCAACCTACACGGGTTATTAATGGATAATTAATAACCACC
Found at i:1336399 original size:45 final size:45
Alignment explanation
Indices: 1336310--1336399 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
1336300 TTTTTCGTTC
* * *
1336310 AACCACCAACCACCAACCTACTCGGGTTATTAGTGAATAGTTAAT
1 AACCACAAACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
*
1336355 AACCACAAACCACCAACCTACTCGGGTTATTAATGGATAATTAAT
1 AACCACAAACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
1336400 GGTATCATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.38, C:0.26, G:0.12, T:0.24
Consensus pattern (45 bp):
AACCACAAACCACCAACCTACTCGGGTTATTAATGAATAATTAAT
Found at i:1336437 original size:24 final size:25
Alignment explanation
Indices: 1336406--1336464 Score: 93
Period size: 25 Copynumber: 2.4 Consensus size: 25
1336396 TAATGGTATC
**
1336406 ATTATTTTTTGTCA-TATAATAAAT
1 ATTATTTTTCATCATTATAATAAAT
1336430 ATTATTTTTCATCATTATAATAAAT
1 ATTATTTTTCATCATTATAATAAAT
1336455 ATTATTTTTC
1 ATTATTTTTC
1336465 TACTACAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 12 0.38
25 20 0.62
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (25 bp):
ATTATTTTTCATCATTATAATAAAT
Found at i:1336914 original size:201 final size:203
Alignment explanation
Indices: 1336665--1337076 Score: 657
Period size: 201 Copynumber: 2.0 Consensus size: 203
1336655 ACTTGAGAGT
* *
1336665 TTCTTTCAACAAGTTGATGTTATAAAAAAAACCTTTTCGAATTTCTTACTCACTTCTTTTTTACC
1 TTCTTCCAACAAGTTGATGTTAT-AAAAAAACCTTTTCGAAATTCTTACTCACTTCTTTTTTACC
* * * * *
1336730 TGCAACAACATATTAAAAGTAATATTTTAATAACCGTTCTGAAATAGAGATATATTATTCGAATA
65 TGCAACAACATAGTAAAAATAATATTATAAAAACCGTTCTGAAATAAAGATATATTATTCGAATA
** *
1336795 CGAATAAAATTTTATTCAAATAATACTTACATGTTAAATATTAAAAGAAAATTTCGTTCAAAA-T
130 CGAATAAAATTTTATTCAAATAATACTTACAAATTAAAGATTAAAAGAAAATTTCGTTCAAAATT
1336859 TCTCTACTA
195 TCTCTACTA
1336868 TTCTTCCAACAAGTTGATGTTAT-AAAAAACCTTTTCGAAATTCTTACTCACTTCTTTTTTACCT
1 TTCTTCCAACAAGTTGATGTTATAAAAAAACCTTTTCGAAATTCTTACTCACTTCTTTTTTACCT
* *
1336932 GCAACAACATAGTAAAAATAATATTATAAAAACCTTTCTGAAATAAAGATATTTTATTCGAATAC
66 GCAACAACATAGTAAAAATAATATTATAAAAACCGTTCTGAAATAAAGATATATTATTCGAATAC
** *
1336997 GAATAAAATTTTATTCAAATAATACTTACAAATTTTAGATTAGAAGAAAATTTCGTTCAAAATTT
131 GAATAAAATTTTATTCAAATAATACTTACAAATTAAAGATTAAAAGAAAATTTCGTTCAAAA-TT
1337062 TCTCTACTA
195 TCTCTACTA
1337071 TTCTTC
1 TTCTTC
1337077 TCGGATACTT
Statistics
Matches: 192, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
201 154 0.80
203 38 0.20
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.39
Consensus pattern (203 bp):
TTCTTCCAACAAGTTGATGTTATAAAAAAACCTTTTCGAAATTCTTACTCACTTCTTTTTTACCT
GCAACAACATAGTAAAAATAATATTATAAAAACCGTTCTGAAATAAAGATATATTATTCGAATAC
GAATAAAATTTTATTCAAATAATACTTACAAATTAAAGATTAAAAGAAAATTTCGTTCAAAATTT
CTCTACTA
Found at i:1340044 original size:60 final size:60
Alignment explanation
Indices: 1339928--1340040 Score: 160
Period size: 58 Copynumber: 1.9 Consensus size: 60
1339918 CCTCTTTTTG
*
1339928 GCAAACCATTGCAGTCAAAAGAGAATCATAAGAAGCAAGCTGAATGGGCTATAAAGCCCA
1 GCAAACCATTGCAGTCAAAAGAGAATCATAAGAAGCAAGCTGAATGGCCTATAAAGCCCA
** *
1339988 GCAAACCATTGCAGT-TGAA-AGAATCATAAGGAGCAAGCTGAA-GAGCCTATAAA
1 GCAAACCATTGCAGTCAAAAGAGAATCATAAGAAGCAAGCTGAATG-GCCTATAAA
1340041 AAGCTGGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 1 0.02
58 30 0.62
59 2 0.04
60 15 0.31
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (60 bp):
GCAAACCATTGCAGTCAAAAGAGAATCATAAGAAGCAAGCTGAATGGCCTATAAAGCCCA
Found at i:1342690 original size:17 final size:16
Alignment explanation
Indices: 1342665--1342708 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1342655 CTTAAAATTA
*
1342665 AATATTATTTTA-AAT
1 AATAATATTTTACAAT
1342680 AATTACATATTTTACAAT
1 AA-TA-ATATTTTACAAT
1342698 AATAATATTTT
1 AATAATATTTT
1342709 TACCACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 9 0.36
18 5 0.20
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAATATTTTACAAT
Found at i:1342711 original size:17 final size:18
Alignment explanation
Indices: 1342670--1342708 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1342660 AATTAAATAT
1342670 TATTTTA-AATAATTACA
1 TATTTTACAATAATTACA
1342687 TATTTTACAATAA-TA-A
1 TATTTTACAATAATTACA
1342703 TATTTT
1 TATTTT
1342709 TACCACATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 9 0.43
18 5 0.24
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTACAATAATTACA
Found at i:1345160 original size:15 final size:15
Alignment explanation
Indices: 1345142--1345184 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1345132 ATCCGCCTTG
*
1345142 CATCTGTCCGCCCCA
1 CATCTGCCCGCCCCA
1345157 CATCTGCCCGCCCCA
1 CATCTGCCCGCCCCA
1345172 CATCTGCCCGCCC
1 CATCTGCCCGCCC
1345185 ATCTAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.58, G:0.14, T:0.16
Consensus pattern (15 bp):
CATCTGCCCGCCCCA
Found at i:1348069 original size:19 final size:19
Alignment explanation
Indices: 1348045--1348088 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1348035 AAATAAAAAA
*
1348045 ATATTAAAATTAATA-TATT
1 ATATTAAAA-TAAAAGTATT
1348064 ATATTAAAATAAAAGTATT
1 ATATTAAAATAAAAGTATT
1348083 ATATTA
1 ATATTA
1348089 TATTTTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
ATATTAAAATAAAAGTATT
Found at i:1348266 original size:23 final size:24
Alignment explanation
Indices: 1348235--1348295 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
1348225 TATTATTAAA
*
1348235 ATAAGAATATAATATTA-TATATT
1 ATAATAATATAATATTAGTATATT
*
1348258 ATAATAATATAAT-TGAGTATATT
1 ATAATAATATAATATTAGTATATT
*
1348281 AT--TATTATAATATTA
1 ATAATAATATAATATTA
1348296 AAAATACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
21 8 0.25
22 4 0.12
23 20 0.62
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (24 bp):
ATAATAATATAATATTAGTATATT
Found at i:1348310 original size:33 final size:35
Alignment explanation
Indices: 1348247--1348332 Score: 85
Period size: 33 Copynumber: 2.5 Consensus size: 35
1348237 AAGAATATAA
* *
1348247 TATTAT-ATATTATAATAATATAATTGAGTATATTAT
1 TATTATAATATTA-AA-AATACAATTGAGTATACTAT
1348283 TATTATAATATTAAAAATACAA-T-AGTATACTAT
1 TATTATAATATTAAAAATACAATTGAGTATACTAT
1348316 TA--A-AATATTAATAAATA
1 TATTATAATATTAA-AAATA
1348333 TATTTTAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
30 8 0.17
31 6 0.13
33 11 0.24
34 1 0.02
35 6 0.13
36 8 0.17
37 6 0.13
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (35 bp):
TATTATAATATTAAAAATACAATTGAGTATACTAT
Found at i:1348328 original size:22 final size:22
Alignment explanation
Indices: 1348276--1348328 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1348266 ATAATTGAGT
* *
1348276 ATATTATTATTATAATATTAAA
1 ATATTAATAGTATAATATTAAA
* *
1348298 A-ATACAATAGTATACTATTAAA
1 ATAT-TAATAGTATAATATTAAA
1348320 ATATTAATA
1 ATATTAATA
1348329 AATATATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
21 2 0.08
22 20 0.83
23 2 0.08
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
ATATTAATAGTATAATATTAAA
Found at i:1348349 original size:23 final size:23
Alignment explanation
Indices: 1348315--1348369 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1348305 TAGTATACTA
1348315 TTAAAATATTAATAAAT-ATATT
1 TTAAAATATTAATAAATAATATT
* *
1348337 TTAAATATTTTAATAATTAATATTT
1 TTAAA-ATATTAATAAATAATA-TT
1348362 TTAAAATA
1 TTAAAATA
1348370 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 5 0.19
23 10 0.37
24 5 0.19
25 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAAAATATTAATAAATAATATT
Found at i:1352697 original size:50 final size:51
Alignment explanation
Indices: 1352609--1352803 Score: 263
Period size: 51 Copynumber: 3.9 Consensus size: 51
1352599 AATTCATACT
* *
1352609 ACAAAAAA-TGTAGCACTTAACATATACTTACACCGGTGTAAGTGAATAAA
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACTGGTGTAAGTGAATAAA
1352659 ACAAAAAAGTGTAGCA-TATAACACATAC-TACACTGGTGTAAGTGAATAAA
1 ACAAAAAAGTGTAGCACT-TAACACATACTTACACTGGTGTAAGTGAATAAA
* * *
1352709 ATAAAAAAGTGTAACACTTAACACATACTTACAAC-GGTGTAAGTAAATAAA
1 ACAAAAAAGTGTAGCACTTAACACATACTTAC-ACTGGTGTAAGTGAATAAA
* * * *
1352760 ATAAAAAAGTGTATCACTTAACAAATACTTACACTGATGTAAGT
1 ACAAAAAAGTGTAGCACTTAACACATACTTACACTGGTGTAAGT
1352804 ATATACATCT
Statistics
Matches: 131, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
50 56 0.43
51 73 0.56
52 2 0.02
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (51 bp):
ACAAAAAAGTGTAGCACTTAACACATACTTACACTGGTGTAAGTGAATAAA
Found at i:1352788 original size:101 final size:101
Alignment explanation
Indices: 1352611--1352803 Score: 282
Period size: 101 Copynumber: 1.9 Consensus size: 101
1352601 TTCATACTAC
* * * *
1352611 AAAAAATGTAGCACTTAACATATACTTACACCGGTGTAAGTGAATAAAACAAAAAAGTGTAGCAT
1 AAAAAATGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAACAAAAAAGTGTAGCAT
* *
1352676 ATAACACATAC-TACACTGGTGTAAGTGAATAAAAT
66 ATAACAAATACTTACACTGATGTAAGTGAATAAAAT
* *
1352711 AAAAAAGTGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAATAAAAAAGTGTATCA
1 AAAAAA-TGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAACAAAAAAGTGTAGCA
1352776 CT-TAACAAATACTTACACTGATGTAAGT
65 -TATAACAAATACTTACACTGATGTAAGT
1352804 ATATACATCT
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
100 6 0.07
101 61 0.74
102 15 0.18
ACGTcount: A:0.48, C:0.14, G:0.13, T:0.25
Consensus pattern (101 bp):
AAAAAATGTAACACTTAACACATACTTACAACGGTGTAAGTAAATAAAACAAAAAAGTGTAGCAT
ATAACAAATACTTACACTGATGTAAGTGAATAAAAT
Found at i:1355071 original size:43 final size:43
Alignment explanation
Indices: 1355010--1355103 Score: 152
Period size: 43 Copynumber: 2.2 Consensus size: 43
1355000 AGTAATTCAT
**
1355010 TCTGACCTCGTATGTAGAATTAACAGGCAACAAGTCAAAATAA
1 TCTGACCTCGTAAATAGAATTAACAGGCAACAAGTCAAAATAA
*
1355053 TCTGACCTCGTAAATAGAATTAACATGCAACAAGTCAAAATAA
1 TCTGACCTCGTAAATAGAATTAACAGGCAACAAGTCAAAATAA
*
1355096 TCTAACCT
1 TCTGACCT
1355104 TGTAGGTATA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (43 bp):
TCTGACCTCGTAAATAGAATTAACAGGCAACAAGTCAAAATAA
Found at i:1355450 original size:15 final size:17
Alignment explanation
Indices: 1355419--1355450 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1355409 ATGTATTTTT
1355419 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
1355436 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
1355451 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:1361967 original size:29 final size:32
Alignment explanation
Indices: 1361926--1362000 Score: 88
Period size: 32 Copynumber: 2.5 Consensus size: 32
1361916 ATAGTTATTA
1361926 TATTTTATATT-AAT-ATAATTATATAAATAT
1 TATTTTATATTAAATAATAATTATATAAATAT
* *
1361956 TATTTT-TATTAAAATAATATTTATATAATTAT
1 TATTTTATATT-AAATAATAATTATATAAATAT
1361988 TA-TTTAT-TTAAAT
1 TATTTTATATTAAAT
1362001 TTATTAATTA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
29 4 0.10
30 10 0.26
31 8 0.21
32 17 0.44
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (32 bp):
TATTTTATATTAAATAATAATTATATAAATAT
Found at i:1361991 original size:15 final size:15
Alignment explanation
Indices: 1361904--1362016 Score: 52
Period size: 15 Copynumber: 7.4 Consensus size: 15
1361894 TTTTTCAGTT
* *
1361904 ATTATTTTTTAAATA
1 ATTATTATTTATATA
* *
1361919 GTTATTATATTTTAT-
1 ATTATTAT-TTATATA
*
1361934 ATTAATATAATTATATA
1 ATT-AT-TATTTATATA
* *
1361951 AATATTATTTTTATTAA
1 ATTATTATTTATA-T-A
* *
1361968 AATAATATTTATATA
1 ATTATTATTTATATA
*
1361983 ATTATTATTTATTTA
1 ATTATTATTTATATA
* *
1361998 AAT-TTATTAAT-TA
1 ATTATTATTTATATA
1362011 ATTATT
1 ATTATT
1362017 TTTTGTGCTA
Statistics
Matches: 73, Mismatches: 18, Indels: 15
0.69 0.17 0.14
Matches are distributed among these distances:
13 4 0.05
14 9 0.12
15 29 0.40
16 15 0.21
17 16 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.58
Consensus pattern (15 bp):
ATTATTATTTATATA
Found at i:1363801 original size:42 final size:42
Alignment explanation
Indices: 1363725--1363824 Score: 110
Period size: 42 Copynumber: 2.4 Consensus size: 42
1363715 ATGCCACAAT
* * * *
1363725 GGTACATGCCCAGCCCTCCACTTCAGATGCCATCTCCTCAGG
1 GGTACATGCCAAGCCCACCAATTCAGATGCCATCTCCACAGG
* * *
1363767 GGTATATGCCAAGCCCACCAATTCATATGTCATCTCCACAGG
1 GGTACATGCCAAGCCCACCAATTCAGATGCCATCTCCACAGG
* * *
1363809 GTTACATTCCTAGCCC
1 GGTACATGCCAAGCCC
1363825 GCAGAGTTAC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (42 bp):
GGTACATGCCAAGCCCACCAATTCAGATGCCATCTCCACAGG
Found at i:1363835 original size:21 final size:21
Alignment explanation
Indices: 1363809--1363870 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1363799 TCTCCACAGG
1363809 GTTACATTCCTAGCCCGCAGA
1 GTTACATTCCTAGCCCGCAGA
*
1363830 GTTACATTCCTAGCCCGCCATA
1 GTTACATTCCTAGCCCG-CAGA
*
1363852 -TTACATACCTAGCCCGCAG
1 GTTACATTCCTAGCCCGCAG
1363871 GGTTTTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.05
21 32 0.86
22 3 0.08
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (21 bp):
GTTACATTCCTAGCCCGCAGA
Found at i:1364435 original size:34 final size:34
Alignment explanation
Indices: 1364397--1364503 Score: 160
Period size: 34 Copynumber: 3.1 Consensus size: 34
1364387 ATAAATATTT
1364397 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
1364431 TTAAAATACAAATAATATTATTCGAAATTTAAAT
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
* * *
1364465 TTAAAATATAAATTATAGTATTCAAAATTTAACA
1 TTAAAATACAAATTATAGTATTCGAAATTTAAAA
1364499 TTAAA
1 TTAAA
1364504 TTCAAGTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCGAAATTTAAAA
Found at i:1365152 original size:127 final size:127
Alignment explanation
Indices: 1364926--1365433 Score: 908
Period size: 127 Copynumber: 4.0 Consensus size: 127
1364916 GCGCTTTAAA
* * *
1364926 GTCCCCTAAGAAATAATAGGTATTGACATGAATAGATCCCGGGGGAGATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
1364991 CAATGATAACATATTCTCTAACAAAATAATGGAAGGCGCGCCCCTGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
1365053 GTCCCCTAAGGAATAATAGGTATTGACATAAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1365118 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
*
1365180 GTCCCCTAAGGAATAATATGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
* *
1365245 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCCCCCCCGGGAACGCGCCTTCACA
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
* *
1365307 GTCCCCTAAGGAATAATAGGTATTAACATGAATAGTTCCCGGGGGACATAAGTGATATAATAGGG
1 GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
*
1365372 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCACG
66 CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
1365434 TGAATAGTAC
Statistics
Matches: 365, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
127 365 1.00
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.21
Consensus pattern (127 bp):
GTCCCCTAAGGAATAATAGGTATTGACATGAATAGTTCCCGGGGGACATAAGTGACATAATAGGG
CAATGATAACATATTCTCTGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCACG
Found at i:1370016 original size:19 final size:19
Alignment explanation
Indices: 1369992--1370028 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1369982 ATGACCAACA
*
1369992 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
1370011 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
1370029 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:1370101 original size:21 final size:20
Alignment explanation
Indices: 1370073--1370171 Score: 92
Period size: 21 Copynumber: 4.8 Consensus size: 20
1370063 GATTTTGACC
*
1370073 ATCGCATTGTGATTTTCGAA
1 ATCGCATTGCGATTTTCGAA
*
1370093 ATCCGCATTGCGATTTTAGATA
1 AT-CGCATTGCGATTTTCGA-A
* * *
1370115 ATCGCAATGCGAATAT-GTAA
1 ATCGCATTGCGATTTTCG-AA
* *
1370135 ATTGCAATGCGATTTTCGAA
1 ATCGCATTGCGATTTTCGAA
1370155 ATCCGCATTGCGATTTT
1 AT-CGCATTGCGATTTT
1370172 AGATAATCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
20 21 0.33
21 40 0.62
22 3 0.05
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATTTTCGAA
Found at i:1370143 original size:20 final size:20
Alignment explanation
Indices: 1370114--1370228 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
1370104 GATTTTAGAT
1370114 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
* * *
1370134 AATTGCAATGCGATTTTCG-A
1 AATCGCAATGCGAATAT-GTA
* * *
1370154 AATCCGCATTGCGATTTTAG-A
1 AAT-CGCAATGCGAATAT-GTA
*
1370175 TAATCACAATGCGAATATGTA
1 -AATCGCAATGCGAATATGTA
1370196 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
* *
1370216 AATTGCAACGCGA
1 AATCGCAATGCGA
1370229 TGACACTTGA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
20 49 0.63
21 26 0.33
22 3 0.04
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:1370157 original size:62 final size:62
Alignment explanation
Indices: 1370073--1370208 Score: 236
Period size: 62 Copynumber: 2.2 Consensus size: 62
1370063 GATTTTGACC
* * *
1370073 ATCGCATTGTGATTTTCGAAATCCGCATTGCGATTTTAGATAATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATTTTCGAAATCCGCATTGCGATTTTAGATAATCACAATGCGAATATGTAA
*
1370135 ATTGCAATGCGATTTTCGAAATCCGCATTGCGATTTTAGATAATCACAATGCGAATATGTAA
1 ATCGCAATGCGATTTTCGAAATCCGCATTGCGATTTTAGATAATCACAATGCGAATATGTAA
1370197 ATCGCAATGCGA
1 ATCGCAATGCGA
1370209 ATATGTAAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 69 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (62 bp):
ATCGCAATGCGATTTTCGAAATCCGCATTGCGATTTTAGATAATCACAATGCGAATATGTAA
Found at i:1370187 original size:21 final size:21
Alignment explanation
Indices: 1370054--1370188 Score: 91
Period size: 21 Copynumber: 6.5 Consensus size: 21
1370044 GTTTCCAGAT
* **
1370054 TCGCAATACGATTTT-GACCA
1 TCGCAATGCGATTTTAGATAA
* * *
1370074 TCGCATTGTGATTTTCGA-AA
1 TCGCAATGCGATTTTAGATAA
*
1370094 TCCGCATTGCGATTTTAGATAA
1 T-CGCAATGCGATTTTAGATAA
* *
1370116 TCGCAATGCGAATAT-G-TAAA
1 TCGCAATGCGATTTTAGAT-AA
* *
1370136 TTGCAATGCGATTTTCGA-AA
1 TCGCAATGCGATTTTAGATAA
*
1370156 TCCGCATTGCGATTTTAGATAA
1 T-CGCAATGCGATTTTAGATAA
*
1370178 TCACAATGCGA
1 TCGCAATGCGA
1370189 ATATGTAAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.01
20 32 0.36
21 51 0.57
22 6 0.07
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTTAGATAA
Found at i:1370250 original size:82 final size:81
Alignment explanation
Indices: 1370114--1370269 Score: 181
Period size: 82 Copynumber: 1.9 Consensus size: 81
1370104 GATTTTAGAT
* *** **
1370114 AATCGCAATGCGAATATGTAAATTGCAATGCGATTTTCGAAATCCGCATTGCGATTTTAGA-TAA
1 AATCGCAATGCGAATATGTAAATTGCAACGCGATACACGAAATCCGCAACGCGATTTT-GACT-A
*
1370178 TCACAATGCGAATATGTA
64 TCACAACGCGAATATGTA
***
1370196 AATCGCAATGCGAATATGTAAATTGCAACGCGATGACACTTGAT-CGCAACGCGATTTTGACTAT
1 AATCGCAATGCGAATATGTAAATTGCAACGCGAT-ACACGAAATCCGCAACGCGATTTTGACTAT
1370260 CACAACGCGA
65 CACAACGCGA
1370270 TTCGGACTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
81 13 0.21
82 46 0.74
83 3 0.05
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (81 bp):
AATCGCAATGCGAATATGTAAATTGCAACGCGATACACGAAATCCGCAACGCGATTTTGACTATC
ACAACGCGAATATGTA
Found at i:1370267 original size:20 final size:20
Alignment explanation
Indices: 1370238--1370340 Score: 118
Period size: 20 Copynumber: 5.1 Consensus size: 20
1370228 ATGACACTTG
*
1370238 ATCGCAACGCGATTTTGACT
1 ATCGCAACGCGATTCTGACT
* *
1370258 ATCACAACGCGATTCGGACT
1 ATCGCAACGCGATTCTGACT
**
1370278 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
1370298 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
* *
1370319 ATCGCAACGAGATTCTAACT
1 ATCGCAACGCGATTCTGACT
1370339 AT
1 AT
1370341 TGCGTTGCGA
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.03
20 50 0.72
21 15 0.22
22 2 0.03
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1370355 original size:61 final size:61
Alignment explanation
Indices: 1370220--1370340 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 61
1370210 TATGTAAATT
* * * * * *
1370220 GCAACGCGATGACACTTGATCGCAACGCGATTTTGACTATCACAACGCGATTCGGACTATC
1 GCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTCGAACTATC
* *
1370281 GCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTAACTAT
1 GCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTCGAACTAT
1370341 TGCGTTGCGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 52 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (61 bp):
GCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCACAACGAGATTCGAACTATC
Found at i:1370538 original size:22 final size:22
Alignment explanation
Indices: 1370513--1370581 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
1370503 CTACGGTGAC
1370513 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
1370535 ATCCATCCCCATTTCTGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1370557 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
1370579 ATC
1 ATC
1370582 TGTCTATCTC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.25, C:0.42, G:0.12, T:0.22
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:1370975 original size:20 final size:19
Alignment explanation
Indices: 1370924--1370979 Score: 67
Period size: 20 Copynumber: 2.9 Consensus size: 19
1370914 CGCAACGACA
*
1370924 AAATTCACGTTGCGATAGC
1 AAATTCGCGTTGCGATAGC
* * *
1370943 CATTTCGCATTGCGATAGTC
1 AAATTCGCGTTGCGATAG-C
1370963 AAATTCGCGTTGCGATA
1 AAATTCGCGTTGCGATA
1370980 ATCATTTTCG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (19 bp):
AAATTCGCGTTGCGATAGC
Found at i:1370989 original size:20 final size:20
Alignment explanation
Indices: 1370931--1371018 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
1370921 ACAAAATTCA
*
1370931 CGTTGCGATAGCCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1370950 CATTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1370970 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
1370990 TGTTGTGATTTTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1371010 TGTTGCGAT
1 CGTTGCGAT
1371019 TTTAAGTTTC
Statistics
Matches: 56, Mismatches: 12, Indels: 1
0.81 0.17 0.01
Matches are distributed among these distances:
19 12 0.21
20 44 0.79
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1371028 original size:20 final size:20
Alignment explanation
Indices: 1370985--1371028 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1370975 CGATAATCAT
* * *
1370985 TTTCGTGTTGTGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1371005 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1371025 TTTC
1 TTTC
1371029 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1372904 original size:31 final size:31
Alignment explanation
Indices: 1372848--1372909 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1372838 TTGTCTTTGT
*
1372848 TTTGTCTTTTGGTTGAAGTTAGTAAATTCATA
1 TTTGTCTTTTGGTTG-ACTTAGTAAATTCATA
1372880 TTTGTCTTTTGGATTG-CTTAGTAAATTCAT
1 TTTGTCTTTTGG-TTGACTTAGTAAATTCAT
1372910 TCGATAGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 13 0.46
32 12 0.43
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.52
Consensus pattern (31 bp):
TTTGTCTTTTGGTTGACTTAGTAAATTCATA
Found at i:1373116 original size:20 final size:20
Alignment explanation
Indices: 1373022--1373131 Score: 72
Period size: 20 Copynumber: 5.8 Consensus size: 20
1373012 TGCAGAAGAA
* *
1373022 GAATAGTCGCAACACGAAAAT
1 GAATA-TCGCAACGCGGAAAT
* *
1373043 GATTATCGCAACGC-GAATT
1 GAATATCGCAACGCGGAAAT
*
1373062 TAACTATCGCAACG-GG--AT
1 GAA-TATCGCAACGCGGAAAT
* *
1373080 --A-ATCGCAATGCGAAAAT
1 GAATATCGCAACGCGGAAAT
* *
1373097 GACTATCGTAACGCGGAAAT
1 GAATATCGCAACGCGGAAAT
1373117 GAATATCGCAACGCG
1 GAATATCGCAACGCG
1373132 AATTTAGTTT
Statistics
Matches: 66, Mismatches: 15, Indels: 17
0.67 0.15 0.17
Matches are distributed among these distances:
14 8 0.12
15 1 0.02
16 1 0.02
17 2 0.03
18 1 0.02
19 4 0.06
20 45 0.68
21 4 0.06
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (20 bp):
GAATATCGCAACGCGGAAAT
Found at i:1373171 original size:19 final size:19
Alignment explanation
Indices: 1373138--1373174 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1373128 CGCGAATTTA
1373138 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
* *
1373157 GTTTTGCGTTTCGATTTT
1 GTTTCGCGTTGCGATTTT
1373175 CTCGTTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.05, C:0.14, G:0.27, T:0.54
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1373206 original size:20 final size:20
Alignment explanation
Indices: 1373177--1373222 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1373167 TCGATTTTCT
1373177 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1373197 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1373217 CGTTGC
1 CGTTGC
1373223 AATAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1373255 original size:20 final size:20
Alignment explanation
Indices: 1373232--1373275 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1373222 CAATAATCAT
*
1373232 TTTCGTGTTGTGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1373252 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1373272 TTTC
1 TTTC
1373276 AGAAACTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1373832 original size:21 final size:21
Alignment explanation
Indices: 1373738--1373839 Score: 73
Period size: 21 Copynumber: 4.9 Consensus size: 21
1373728 CTCGACTCAC
1373738 CTGTCATCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGGCCT
*
1373759 CT-TCTATCATTCAAGAGG-CT
1 CTGTC-ATCGTTCAAGAGGCCT
* ** ** *
1373779 CCTATCATCCCTCAAGAATCCC
1 -CTGTCATCGTTCAAGAGGCCT
** *
1373801 CTCCCACCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGGCCT
*
1373822 CTGTCATCGTTGAAGAGG
1 CTGTCATCGTTCAAGAGG
1373840 TCCCTCCCAA
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
20 4 0.07
21 52 0.88
22 3 0.05
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (21 bp):
CTGTCATCGTTCAAGAGGCCT
Found at i:1375300 original size:36 final size:30
Alignment explanation
Indices: 1375220--1375285 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1375210 ATAAGAGTTG
*
1375220 ATTTGTTTAATTGATGTGTAAATCATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
1375250 ATTTGTTTAATTGATGTGTAAATAATTCTT
1 ATTTGTTTAATTGATGTGTAAATAATTCTT
1375280 ATTTGT
1 ATTTGT
1375286 GCTTGTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.55
Consensus pattern (30 bp):
ATTTGTTTAATTGATGTGTAAATAATTCTT
Found at i:1375406 original size:20 final size:20
Alignment explanation
Indices: 1375381--1375551 Score: 192
Period size: 20 Copynumber: 8.8 Consensus size: 20
1375371 GCGATTTTCT
*
1375381 CGTTGCGATAGTCAAATTCC
1 CGTTGCGATAGTCAAATTCG
*
1375401 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1375421 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1375441 CGTTGTGATAGTTAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
1375461 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
* *
1375481 CATTGCGAT--T---A-TCC
1 CGTTGCGATAGTCAAATTCG
* *
1375495 CGTTGCGATAGTCAAGTTCA
1 CGTTGCGATAGTCAAATTCG
* *
1375515 CGTTGCGATAGTTATATTCG
1 CGTTGCGATAGTCAAATTCG
1375535 CGTTGCGATAGTCAAAT
1 CGTTGCGATAGTCAAAT
1375552 GAATGTGTAA
Statistics
Matches: 124, Mismatches: 21, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
20 112 0.90
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1375542 original size:114 final size:114
Alignment explanation
Indices: 1375342--1375551 Score: 305
Period size: 114 Copynumber: 1.8 Consensus size: 114
1375332 TCTGCATCAT
* * * *
1375342 ATTCGCGTTGCGATAGTCTAATACACTTTGCGATTTTCTCGTTGCGATAGTCAAATTCCCGTTGC
1 ATTCGCGTTGCGATAGTCTAATACACATTGCGATTATCCCGTTGCGATAGTCAAATTCACGTTGC
1375407 GATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATAGTTAA
66 GATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATAGTTAA
* * * *
1375456 ATTCGCGTTGCGATAGTC-ATTTTCGCATTGCGATTATCCCGTTGCGATAGTCAAGTTCACGTTG
1 ATTCGCGTTGCGATAGTCTA-ATACACATTGCGATTATCCCGTTGCGATAGTCAAATTCACGTTG
* * *
1375520 CGATAGTTATATTCGCGTTGCGATAGTCAAAT
65 CGATAATCAAATTCGCGTTGCGATAGTCAAAT
1375552 GAATGTGTAA
Statistics
Matches: 84, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
113 1 0.01
114 83 0.99
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (114 bp):
ATTCGCGTTGCGATAGTCTAATACACATTGCGATTATCCCGTTGCGATAGTCAAATTCACGTTGC
GATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATAGTTAA
Found at i:1375738 original size:18 final size:18
Alignment explanation
Indices: 1375715--1375749 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1375705 AAGCCGGTTG
*
1375715 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1375733 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1375750 GCCTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1377804 original size:14 final size:14
Alignment explanation
Indices: 1377785--1377821 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1377775 TCCCGTGGTA
1377785 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1377799 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1377813 TTCTTCTTC
1 TT-TTCTTC
1377822 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1378045 original size:24 final size:24
Alignment explanation
Indices: 1378011--1378064 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1378001 CTGAAACATC
1378011 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1378035 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1378059 ATCAAA
1 ATCAAA
1378065 TTTCAAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1378912 original size:20 final size:20
Alignment explanation
Indices: 1378884--1378945 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
1378874 AATTCAGTGA
*
1378884 TGCGTTAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1378904 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1378924 TGCGATAGTCAGAATCGCGT
1 TGCGATAGTCAGAATCGCGT
1378944 TG
1 TG
1378946 TGATCACGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (20 bp):
TGCGATAGTCAGAATCGCGT
Found at i:1378963 original size:21 final size:21
Alignment explanation
Indices: 1378937--1378991 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1378927 GATAGTCAGA
* *
1378937 ATCGCGTTGTGATCACGTATT
1 ATCGCGTTGCGATCAAGTATT
*
1378958 ATCGCGTTGCGATCAAGTGTT
1 ATCGCGTTGCGATCAAGTATT
*
1378979 ATCACGTTGCGAT
1 ATCGCGTTGCGAT
1378992 TTACATATTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (21 bp):
ATCGCGTTGCGATCAAGTATT
Found at i:1379010 original size:20 final size:20
Alignment explanation
Indices: 1378985--1379032 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1378975 TGTTATCACG
1378985 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
*
1379005 TTGCGATTTACATATTCGTA
1 TTGCGATTTACATATTCGCA
1379025 TTGCGATT
1 TTGCGATT
1379033 ATCTAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.17, G:0.17, T:0.44
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Found at i:1379130 original size:20 final size:19
Alignment explanation
Indices: 1379106--1379152 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1379096 TGGAAACTGA
*
1379106 ATTGCGATAATGGAGATCGC
1 ATTGCGAT-ATAGAGATCGC
* *
1379126 GTTGCGATTTAGAGATCGC
1 ATTGCGATATAGAGATCGC
1379145 ATTGCGAT
1 ATTGCGAT
1379153 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.30
Consensus pattern (19 bp):
ATTGCGATATAGAGATCGC
Found at i:1379142 original size:19 final size:19
Alignment explanation
Indices: 1379118--1379154 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1379108 TGCGATAATG
*
1379118 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
1379137 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1379155 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1383459 original size:16 final size:16
Alignment explanation
Indices: 1383433--1383480 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
1383423 ACTCATTAAT
*
1383433 AATACTTTTATAAATTA
1 AATA-TTTTATAAATAA
1383450 AATATTTTATTAAA-AA
1 AATATTTTA-TAAATAA
*
1383466 AATATATTATAAATA
1 AATATTTTATAAATA
1383481 CTTTCTAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 4 0.15
16 15 0.56
17 8 0.30
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
AATATTTTATAAATAA
Found at i:1384251 original size:11 final size:11
Alignment explanation
Indices: 1384231--1384287 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
1384221 TATTATATAG
1384231 ATTTTGAAAAT
1 ATTTTGAAAAT
*
1384242 ATTTTTAAAAT
1 ATTTTGAAAAT
*
1384253 A-TATGTAATATAT
1 ATTTTG-AA-A-AT
1384266 AGTTTTGAAAAT
1 A-TTTTGAAAAT
1384278 ATTTTGAAAA
1 ATTTTGAAAA
1384288 CGTTTATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
10 2 0.05
11 22 0.59
12 4 0.11
13 4 0.11
14 2 0.05
15 3 0.08
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (11 bp):
ATTTTGAAAAT
Found at i:1384279 original size:36 final size:36
Alignment explanation
Indices: 1384150--1384356 Score: 175
Period size: 36 Copynumber: 5.6 Consensus size: 36
1384140 TTTTTTTTAT
* *
1384150 TATAGTTTGTAAAAATATTTTTGACAA-A-ATATAATA
1 TATAGTTT-TGAAAATA-TTTTGAAAATATATATAATA
* * *
1384186 TATAATTTTCAGAAAATGATTTTCGAAAATTTATATATTA
1 TATAGTTTT--GAAAAT-ATTTT-GAAAATATATATAATA
* *
1384226 TATAGATTTTGAAAATATTTTTAAAATATATGTAATA
1 TATAG-TTTTGAAAATATTTTGAAAATATATATAATA
* *
1384263 TATAGTTTTGAAAATATTTTGAAAACGTTTATATATTA
1 TATAGTTTTGAAAATATTTTGAAAA--TATATATAATA
* * * * *
1384301 TATAGTTTTTAATACATTTTGAAAACATATATAGTA
1 TATAGTTTTGAAAATATTTTGAAAATATATATAATA
* *
1384337 TATAGTTTTAAAAACATTTT
1 TATAGTTTTGAAAATATTTT
1384357 TTTGAAAACT
Statistics
Matches: 140, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
35 1 0.01
36 52 0.37
37 26 0.19
38 40 0.29
39 6 0.04
40 11 0.08
41 4 0.03
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
TATAGTTTTGAAAATATTTTGAAAATATATATAATA
Found at i:1384561 original size:12 final size:12
Alignment explanation
Indices: 1384544--1384575 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1384534 TTTTCTTTCA
1384544 GGTCCAAAAACG
1 GGTCCAAAAACG
*
1384556 GGTCCAGAAACG
1 GGTCCAAAAACG
1384568 GGTCCAAA
1 GGTCCAAA
1384576 TCCAGTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.28, T:0.09
Consensus pattern (12 bp):
GGTCCAAAAACG
Found at i:1385987 original size:23 final size:23
Alignment explanation
Indices: 1385930--1385988 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
1385920 TCTTTTTATT
* *
1385930 TTATTTTATTATTCTATTGTTTTG
1 TTATTTT-TTATTCTAATGTTTTA
1385954 TTATTTATTTATT-TAATGTTTTA
1 TTATTT-TTTATTCTAATGTTTTA
1385977 TTATTATTTTAT
1 TTATT-TTTTAT
1385989 CATCTAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 18 0.58
24 12 0.39
25 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (23 bp):
TTATTTTTTATTCTAATGTTTTA
Found at i:1389630 original size:106 final size:106
Alignment explanation
Indices: 1389463--1390787 Score: 1962
Period size: 106 Copynumber: 12.6 Consensus size: 106
1389453 GGCGACTGTC
* * * *
1389463 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTTAACTTCATAGCGAAGGATACTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1389528 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1389569 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
1389634 AGACAACACATGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1389675 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTTAACTTCACAGCGAA--ATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* *
1389738 AGACAACGCATGTTCAACTTCACGACGAAGAGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1389779 TGGCAACAAACAACTTCTCAATTTCAGAGCCAATTTAAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1389844 AGACAACG-AATGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAA-GTTCAACTTCACGACGAAGGGACCGCTGGT
*
1389885 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTAAACTTCAC-ACGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1389949 AGACAACGCAAGTTCAACTT--CGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * *
1389988 TGTCAATAAACAACTTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1390053 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGATGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* *
1390094 TGTCAATAACCAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1390159 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1390200 TGTCAATAAACAACTTCTCAATTTTCAGAGCCAATTTC-ACTTCACAACGAAGGATATTGGACTC
1 TGTCAACAAACAACTTCTCAA-TTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1390264 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * *
1390306 TGTCAATAAACAACTTCCCAATTTCAGAGCCGATTTCAACTTCACAACAAAGGATATTGGACTCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
1390371 AGACAACGCATGTTCAACTTCACGACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
*
1390412 TGTCAACAAACAATTTCTCAATTTCAGAGCCAATTTCAACTTCACAAC-ATAGGATATTGGACTC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGA-AGGATATTGGACTC
* *
1390476 AAGACAACGCAAGTTCAACTTCACGACGAAGGGAACGCTGGT
65 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * * * *
1390518 TGTCAATAAACAACTTCCCAACTTCATAGCCAATTTTAACTTCTCAACGAAGGATCTTGGA-TCC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * *
1390582 AAGACAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGAT
66 -AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
* * * * *
1390624 TGTCAAC-AA-AA-TT-TC-A-TTCAGAGTCAATTCCAACTTCACAGCGAAAGATATTGGACTCA
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
1390683 AGACAACACAAGTTCAACTTCACAACGAAAGGA-CGACTGGT
66 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGT
* * * * * * ** *
1390724 TGTCAATAAACAATTTCCCGATTCCAGAGCCGATTTCAACTTCATGACGGAGGATATTGGACTC
1 TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1390788 GGAACAATGC
Statistics
Matches: 1119, Mismatches: 80, Indels: 40
0.90 0.06 0.03
Matches are distributed among these distances:
99 1 0.00
100 70 0.06
101 5 0.00
102 3 0.00
103 65 0.06
104 140 0.13
105 58 0.05
106 760 0.68
107 17 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
TGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
Found at i:1391131 original size:84 final size:84
Alignment explanation
Indices: 1391016--1391291 Score: 421
Period size: 83 Copynumber: 3.3 Consensus size: 84
1391006 GGGCTATCTG
** *
1391016 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1391081 CTAGAAGGGTTATCTGTCA
66 CTAGAAGGGTTATCTGTCA
* * *
1391100 CCAAAGACCTTCGAGTTCGACTACGA-TCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAG
1 CCAAAGACCTTCGAGTTCGACTAC-ACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAG
1391163 GCTAGAAGGGTTATCTGTCA
65 GCTAGAAGGGTTATCTGTCA
* * *
1391183 CCAAAGACCTTTGCGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
* *
1391248 CTAGAAGGGTTATCCGTCT
66 CTAGAAGGGTTATCTGTCA
1391267 CCAAAAGACCTTCGAGTTCGACTAC
1 CC-AAAGACCTTCGAGTTCGACTAC
1391292 GTTCAGCTCG
Statistics
Matches: 171, Mismatches: 17, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 75 0.44
84 75 0.44
85 20 0.12
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
CTAGAAGGGTTATCTGTCA
Found at i:1391164 original size:83 final size:84
Alignment explanation
Indices: 1391016--1391314 Score: 415
Period size: 84 Copynumber: 3.6 Consensus size: 84
1391006 GGGCTATCTG
** * *
1391016 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
1391081 CTAGAAGGGTTATCTGTCA
66 CTAGAAGGGTTATCTGTCA
* *
1391100 CCAAAGACCTTCGAGTTCGACTACGA-TCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAG
1 CCAAAGACCTTCGAGTTCGACTAC-ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAG
1391163 GCTAGAAGGGTTATCTGTCA
65 GCTAGAAGGGTTATCTGTCA
* * * *
1391183 CCAAAGACCTTTGCGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
* *
1391248 CTAGAAGGGTTATCCGTCT
66 CTAGAAGGGTTATCTGTCA
** * *
1391267 CCAAAAGACCTTCGAGTTCGACTACGTTCAGC-TCGATGACACATCATT
1 CC-AAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATT
1391315 CACACTACTT
Statistics
Matches: 189, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
82 1 0.01
83 75 0.40
84 88 0.47
85 25 0.13
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (84 bp):
CCAAAGACCTTCGAGTTCGACTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
CTAGAAGGGTTATCTGTCA
Found at i:1391891 original size:26 final size:26
Alignment explanation
Indices: 1391853--1391915 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
1391843 TTCAGAAAAT
* *
1391853 GATTTTCGAAAATTTATATATTATATA
1 GATTTT-GAAAATATATATAATATATA
*
1391880 GATTTTGAAAATATATGTAATATATA
1 GATTTTGAAAATATATATAATATATA
1391906 G-TTTTGAAAA
1 GATTTTGAAAA
1391916 CATTTTGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
25 9 0.27
26 18 0.55
27 6 0.18
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (26 bp):
GATTTTGAAAATATATATAATATATA
Found at i:1391902 original size:24 final size:23
Alignment explanation
Indices: 1391868--1391915 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
1391858 TCGAAAATTT
1391868 ATATATTATATAGA-TTTTGAAA
1 ATATATTATATAGAGTTTTGAAA
*
1391890 ATATATGTAATATATAGTTTTGAAA
1 ATATAT-T-ATATAGAGTTTTGAAA
1391915 A
1 A
1391916 CATTTTGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 6 0.27
23 1 0.05
24 6 0.27
25 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
ATATATTATATAGAGTTTTGAAA
Found at i:1391903 original size:64 final size:63
Alignment explanation
Indices: 1391831--1391956 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 63
1391821 TGATAAAATA
* *
1391831 TAATATATAATTTTCAGAAAATGATTTTCGAAA-ATTTATATATTATATAGATTTTGAAAATATA
1 TAATATATAGTTTT--GAAAA-CATTTTCGAAACATTTATATATTATATAG-TTTTGAAAATATA
1391895 TG
62 TG
* * *
1391897 TAATATATAGTTTTGAAAACATTTTGGAAACGTTTATATATTATATAGTTTTTAAAATAT
1 TAATATATAGTTTTGAAAACATTTTCGAAACATTTATATATTATATAGTTTTGAAAATAT
1391957 TTTGAAAACA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
63 20 0.37
64 21 0.39
66 13 0.24
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (63 bp):
TAATATATAGTTTTGAAAACATTTTCGAAACATTTATATATTATATAGTTTTGAAAATATATG
Found at i:1391922 original size:36 final size:36
Alignment explanation
Indices: 1391881--1392085 Score: 119
Period size: 38 Copynumber: 5.8 Consensus size: 36
1391871 TATTATATAG
*
1391881 ATTTTGAAAATATATGTAATATATAGTTTTGAAAAC
1 ATTTTGAAAATATATGTAATATATAGTTTTAAAAAC
* * * * * *
1391917 ATTTTGGAAACGTTTATATATTATATAGTTTTTAAAAT
1 ATTTT-GAAA-ATATATGTAATATATAGTTTTAAAAAC
* *
1391955 ATTTTGAAAACATATAG-AGTATATAGTTTTAAAAAC
1 ATTTTGAAAATATAT-GTAATATATAGTTTTAAAAAC
* * *
1391991 ATTTTTTGTGAAAT-TATAT-ATATATAG-TTTAAAAAT
1 A--TTTTG-AAAATATATGTAATATATAGTTTTAAAAAC
* *
1392027 TTTTTGAAAACT-TA--T-ATA-ATA-TTTTTAAAAC
1 ATTTTGAAAA-TATATGTAATATATAGTTTTAAAAAC
* *
1392058 GTTTTGAAAA-CTATGTAAT-TATAGTTTT
1 ATTTTGAAAATATATGTAATATATAGTTTT
1392086 GGAAACTTTT
Statistics
Matches: 131, Mismatches: 23, Indels: 32
0.70 0.12 0.17
Matches are distributed among these distances:
30 2 0.02
31 19 0.15
32 5 0.04
33 8 0.06
34 12 0.09
36 33 0.25
37 15 0.11
38 34 0.26
39 3 0.02
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (36 bp):
ATTTTGAAAATATATGTAATATATAGTTTTAAAAAC
Found at i:1391943 original size:38 final size:36
Alignment explanation
Indices: 1391881--1391995 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
1391871 TATTATATAG
* * *
1391881 ATTTTGAAAATATAT-GTAATATATAGTTTTGAAAAC
1 ATTTTGAAAACATATAG-AGTATATAGTTTTAAAAAC
* * * * * *
1391917 ATTTTGGAAACGTTTATATATTATATAGTTTTTAAAAT
1 ATTTTGAAAAC--ATATAGAGTATATAGTTTTAAAAAC
1391955 ATTTTGAAAACATATAGAGTATATAGTTTTAAAAAC
1 ATTTTGAAAACATATAGAGTATATAGTTTTAAAAAC
1391991 ATTTT
1 ATTTT
1391996 TTGTGAAATT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
36 34 0.54
38 29 0.46
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (36 bp):
ATTTTGAAAACATATAGAGTATATAGTTTTAAAAAC
Found at i:1391978 original size:74 final size:72
Alignment explanation
Indices: 1391881--1392048 Score: 193
Period size: 74 Copynumber: 2.3 Consensus size: 72
1391871 TATTATATAG
* *
1391881 ATTTTGAAAATATAT-GTAATATATAGTTTTGAAAACA-TTTTG-GAAACGTTTATATATTATAT
1 ATTTTGAAAACATATAGTAATATATAGTTTTAAAAACATTTTTGTGAAA---TTATATA-TATAT
*
1391943 AGTTTTTAAAAT
62 AG-TTTAAAAAT
*
1391955 ATTTTGAAAACATATAG-AGTATATAGTTTTAAAAACATTTTTTGTGAAATTATATATATATAGT
1 ATTTTGAAAACATATAGTAATATATAGTTTTAAAAACA-TTTTTGTGAAATTATATATATATAGT
1392019 TTAAAAAT
65 TTAAAAAT
* *
1392027 TTTTTGAAAACTTATA-TAATAT
1 ATTTTGAAAACATATAGTAATAT
1392049 TTTTAAAACG
Statistics
Matches: 82, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
72 26 0.32
73 7 0.09
74 39 0.48
75 1 0.01
76 5 0.06
77 4 0.05
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (72 bp):
ATTTTGAAAACATATAGTAATATATAGTTTTAAAAACATTTTTGTGAAATTATATATATATAGTT
TAAAAAT
Found at i:1392170 original size:5 final size:5
Alignment explanation
Indices: 1392162--1392187 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1392152 TATCATATTA
1392162 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
1392188 AATTTAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:1392235 original size:12 final size:12
Alignment explanation
Indices: 1392218--1392251 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1392208 TTTTTTCTTT
1392218 CAGGTCCAAAAA
1 CAGGTCCAAAAA
*
1392230 CAGGTCCAGAAA
1 CAGGTCCAAAAA
*
1392242 CGGGTCCAAA
1 CAGGTCCAAA
1392252 TCCAGTCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.24, T:0.09
Consensus pattern (12 bp):
CAGGTCCAAAAA
Found at i:1393057 original size:22 final size:22
Alignment explanation
Indices: 1393027--1393079 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
1393017 AAGGTAAAAA
1393027 GGCCGGAGCGACTGAGAGCGGC
1 GGCCGGAGCGACTGAGAGCGGC
*
1393049 GGCCAGAGCGACTGAGAGCGGC
1 GGCCGGAGCGACTGAGAGCGGC
*
1393071 AGCCGGAGC
1 GGCCGGAGC
1393080 TACACCGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.28, G:0.47, T:0.04
Consensus pattern (22 bp):
GGCCGGAGCGACTGAGAGCGGC
Found at i:1393530 original size:23 final size:24
Alignment explanation
Indices: 1393482--1393531 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1393472 ATTTCGTCTT
* *
1393482 TTTTTTTATTTTATTATTCTATTG
1 TTTTGTTATTTTATTATTCTAATG
1393506 TTTTGTTA-TTTATTTATT-TAATG
1 TTTTGTTATTTTA-TTATTCTAATG
1393529 TTT
1 TTT
1393532 AATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (24 bp):
TTTTGTTATTTTATTATTCTAATG
Found at i:1393638 original size:28 final size:28
Alignment explanation
Indices: 1393602--1393658 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1393592 AGGTAAACAA
1393602 TTCGAATCGGATAGTTTAAATTTTAATT
1 TTCGAATCGGATAGTTTAAATTTTAATT
1393630 TTCGAATCGGATAGTTTAAATTTTAATT
1 TTCGAATCGGATAGTTTAAATTTTAATT
1393658 T
1 T
1393659 AAATTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (28 bp):
TTCGAATCGGATAGTTTAAATTTTAATT
Found at i:1393985 original size:167 final size:167
Alignment explanation
Indices: 1393709--1394042 Score: 668
Period size: 167 Copynumber: 2.0 Consensus size: 167
1393699 TTGGTACCGA
1393709 AAGGGCGGTTCAAGGGTGCTAATCCTTCCTTGATCGTAACCGACTCCCGAACTTGACATGTTTCT
1 AAGGGCGGTTCAAGGGTGCTAATCCTTCCTTGATCGTAACCGACTCCCGAACTTGACATGTTTCT
1393774 GGTACAACGCAGATTAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAAAGTGGTCGGTGG
66 GGTACAACGCAGATTAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAAAGTGGTCGGTGG
1393839 CGACTCTAACCCAATCAATTCTAGTCGAAGCCCAATT
131 CGACTCTAACCCAATCAATTCTAGTCGAAGCCCAATT
1393876 AAGGGCGGTTCAAGGGTGCTAATCCTTCCTTGATCGTAACCGACTCCCGAACTTGACATGTTTCT
1 AAGGGCGGTTCAAGGGTGCTAATCCTTCCTTGATCGTAACCGACTCCCGAACTTGACATGTTTCT
1393941 GGTACAACGCAGATTAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAAAGTGGTCGGTGG
66 GGTACAACGCAGATTAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAAAGTGGTCGGTGG
1394006 CGACTCTAACCCAATCAATTCTAGTCGAAGCCCAATT
131 CGACTCTAACCCAATCAATTCTAGTCGAAGCCCAATT
1394043 CCGGGCCCAT
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
167 167 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.27
Consensus pattern (167 bp):
AAGGGCGGTTCAAGGGTGCTAATCCTTCCTTGATCGTAACCGACTCCCGAACTTGACATGTTTCT
GGTACAACGCAGATTAGGTAAGATGGTGTCCGACCCACCTAAATTCGTTTTAAAGTGGTCGGTGG
CGACTCTAACCCAATCAATTCTAGTCGAAGCCCAATT
Found at i:1400414 original size:30 final size:30
Alignment explanation
Indices: 1400379--1400451 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1400369 CCCGAAGGAC
*
1400379 CTATCCAGAGGTTATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1400409 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1400439 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1400452 CCGAAGAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1400475 original size:31 final size:31
Alignment explanation
Indices: 1400437--1400564 Score: 132
Period size: 31 Copynumber: 4.1 Consensus size: 31
1400427 GATCCTCGGT
* *
1400437 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* ** *
1400468 AACTGTCCATATGTTCCTTAGAACATAGATA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
* *
1400499 TACTGTCCATATGTCTCGAA-AGACATAGGTAA
1 AACTGTCCATATGTCCCGAAGA-ACATAGGT-A
* * *
1400531 AACTGTCCATATGTTCTGTAGAACATAGGTA
1 AACTGTCCATATGTCCCGAAGAACATAGGTA
1400562 AAC
1 AAC
1400565 CCTCGACTCT
Statistics
Matches: 77, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
30 1 0.01
31 51 0.66
32 24 0.31
33 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCGAAGAACATAGGTA
Found at i:1400553 original size:63 final size:62
Alignment explanation
Indices: 1400438--1400558 Score: 174
Period size: 62 Copynumber: 1.9 Consensus size: 62
1400428 ATCCTCGGTA
*
1400438 ACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGATAT
1 ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCTTAGAACATAGATAT
* *
1400500 ACTGTCCATATGTCTCGAA-AGACATAGGTAAAACTGTCCATATGTT-CTGTAGAACATAG
1 ACTGTCCATAGGTCCCGAAGA-ACATAGGT-AAACTGTCCATATGTTCCT-TAGAACATAG
1400559 GTAAACCCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
61 1 0.02
62 26 0.49
63 26 0.49
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (62 bp):
ACTGTCCATAGGTCCCGAAGAACATAGGTAAACTGTCCATATGTTCCTTAGAACATAGATAT
Done.