Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007822.1 Hibiscus syriacus cultivar Beakdansim tig00110159_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: 1828853
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 10
Found at i:1273979 original size:21 final size:21
Alignment explanation
Indices: 1273917--1274006 Score: 119
Period size: 21 Copynumber: 4.3 Consensus size: 21
1273907 CCATCTCCGT
*
1273917 AGGGTTACATTCCGAGCCCGT
1 AGGGTTACATTCCGAGCCCGC
1273938 AGGGTTACATTCCGAGCCCGC
1 AGGGTTACATTCCGAGCCCGC
*
1273959 AGGGTTACATTCCTAGCCCGCC
1 AGGGTTACATTCCGAGCCCG-C
* * *
1273981 A-GGTTACATGCCTAGCACGC
1 AGGGTTACATTCCGAGCCCGC
1274001 AGGGTT
1 AGGGTT
1274007 TTATACCATA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.22
Consensus pattern (21 bp):
AGGGTTACATTCCGAGCCCGC
Found at i:1274558 original size:28 final size:28
Alignment explanation
Indices: 1274526--1274620 Score: 118
Period size: 28 Copynumber: 3.2 Consensus size: 28
1274516 GATAAATGTT
* *
1274526 TTTAAAATACAAATTATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
1274554 TTTAAAATAAAAATAATATTATTCGAAA
1 TTTAAAATAAAAATAATATTATTCGAAA
1274582 TTTAAAATTAAAATATAAATTATAGTATTCGAAA
1 TTTAAAA-TAAAA-AT-AA-TAT--TATTCGAAA
1274616 TTTAA
1 TTTAA
1274621 CATTAAATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
28 33 0.56
29 5 0.08
30 2 0.03
31 2 0.03
32 3 0.05
34 14 0.24
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
TTTAAAATAAAAATAATATTATTCGAAA
Found at i:1274593 original size:34 final size:34
Alignment explanation
Indices: 1274555--1274627 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
1274545 TATTCGAAAT
*
1274555 TTAAAATAAAAATAATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATAATAGTATTCGAAATTTAAAA
* * *
1274589 TTAAAATATAAATTATAGTATTCGAAATTTAACA
1 TTAAAATAAAAATAATAGTATTCGAAATTTAAAA
1274623 TTAAA
1 TTAAA
1274628 TTTCAACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
TTAAAATAAAAATAATAGTATTCGAAATTTAAAA
Found at i:1275251 original size:128 final size:128
Alignment explanation
Indices: 1275023--1275629 Score: 1124
Period size: 128 Copynumber: 4.7 Consensus size: 128
1275013 ACAATCCATC
1275023 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1275088 GGAAGGTGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
* * *
1275151 TAGTGTCCTCGAGGGACATGAGTGACATAATAGGGCAATGATAACATGTTCTTTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* *
1275216 GGAAGGGGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
1275279 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1275344 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCTTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
*
1275407 TAGTGTCCCCGAGGGACATGACTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1275472 GGAAGGCGCGTCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
1275535 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
*
1275600 GGAAGGCGCCCCCCCGGGAACGCGCCTTCA
66 GGAAGGCGCGCCCCCGGGAACGCGCCTTCA
1275630 TGTGAATAGT
Statistics
Matches: 462, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 462 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.21
Consensus pattern (128 bp):
TAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
GGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGGTACTGATATGAA
Found at i:1275723 original size:8 final size:8
Alignment explanation
Indices: 1275710--1275750 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1275700 TCACAAGCTT
1275710 TCAAATTC
1 TCAAATTC
1275718 TCAAATTC
1 TCAAATTC
* *
1275726 CCAAACTC
1 TCAAATTC
1275734 T-AAATTC
1 TCAAATTC
1275741 TCAAATTC
1 TCAAATTC
1275749 TC
1 TC
1275751 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1280292 original size:28 final size:29
Alignment explanation
Indices: 1280211--1280314 Score: 149
Period size: 29 Copynumber: 3.6 Consensus size: 29
1280201 ATTAAATTTG
*
1280211 TTATAAATTGCAATAAAGTACAAAACTAT
1 TTATAAATTACAATAAAGTACAAAACTAT
* *
1280240 TTATAAATTATAATAAAGTACAAAACAAT
1 TTATAAATTACAATAAAGTACAAAACTAT
*
1280269 TTA-AAATTACAATGAAA-TAAAAAACTAT
1 TTATAAATTACAAT-AAAGTACAAAACTAT
1280297 TTATAAATTACAATAAAG
1 TTATAAATTACAATAAAG
1280315 GATAAGACGG
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
28 24 0.36
29 42 0.64
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.31
Consensus pattern (29 bp):
TTATAAATTACAATAAAGTACAAAACTAT
Found at i:1281890 original size:2 final size:2
Alignment explanation
Indices: 1281883--1281911 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1281873 AGTTGCCATA
1281883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1281912 AGTATTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1286085 original size:14 final size:14
Alignment explanation
Indices: 1286062--1286095 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1286052 TGAACAGTAA
*
1286062 AATACGGTATGAAC
1 AATACCGTATGAAC
1286076 AATACCGTATGAAC
1 AATACCGTATGAAC
*
1286090 AGTACC
1 AATACC
1286096 CAAATGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (14 bp):
AATACCGTATGAAC
Found at i:1286752 original size:31 final size:30
Alignment explanation
Indices: 1286726--1286838 Score: 163
Period size: 31 Copynumber: 3.7 Consensus size: 30
1286716 GTCCATAGAT
* *
1286726 TCCGAAGAACCTAGGTAATCAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
*
1286756 TCCCAAAGAACATAGGTAAACAGTCCATATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATG
*
1286787 TCTCGAAGAACTTAGGTAAACAGTCCATATG
1 TC-CGAAGAACATAGGTAAACAGTCCATATG
1286818 TCCTGAAGAACATAGGTAAAC
1 TCC-GAAGAACATAGGTAAAC
1286839 CCTCGACCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
30 3 0.04
31 71 0.96
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (30 bp):
TCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:1287454 original size:35 final size:37
Alignment explanation
Indices: 1287406--1287477 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1287396 TTTCATTTAG
*
1287406 GGGGAATCGATACC-CCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCAATACCTCCCCAGGGGGGAATCTGTTCCC
1287441 GGGGAATCAATACCTCCCCAGGGGGGAATCTGTTCCC
1 GGGGAATCAATACCTCCCCAGGGGGGAATCTGTTCCC
1287478 CCTGCACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 13 0.38
36 5 0.15
37 16 0.47
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (37 bp):
GGGGAATCAATACCTCCCCAGGGGGGAATCTGTTCCC
Found at i:1291103 original size:31 final size:31
Alignment explanation
Indices: 1291065--1291220 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
1291055 CCCGAAGGAC
* * *
1291065 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1291096 CAGTCCATATGTCCCGAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1291127 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1291158 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
** *
1291189 TTGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1291220 C
1 C
1291221 CCTCGGCCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1295277 original size:25 final size:25
Alignment explanation
Indices: 1295219--1295280 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1295209 ATAAGTCTAG
* *
1295219 ATTCAATATTTTGATACATGATCAC
1 ATTCAATATTATGATACATGATCAA
*
1295244 ATTCTATATTATGATACATGA-CATGA
1 ATTCAATATTATGATACATGATCA--A
1295270 ATTC-ATATTAT
1 ATTCAATATTAT
1295281 ATGTATTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.06
25 26 0.81
26 4 0.12
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCAATATTATGATACATGATCAA
Found at i:1295358 original size:31 final size:28
Alignment explanation
Indices: 1295322--1295384 Score: 99
Period size: 31 Copynumber: 2.1 Consensus size: 28
1295312 GTTATATGAG
1295322 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTAT-GAAAAT-A-ATGT
1295353 CTATGTGATAAAGGTATGAAAATAATGT
1 CTATGTGATAAAGGTATGAAAATAATGT
1295381 CTAT
1 CTAT
1295385 TAAATACACT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
28 8 0.25
29 1 0.03
30 6 0.19
31 17 0.53
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.33
Consensus pattern (28 bp):
CTATGTGATAAAGGTATGAAAATAATGT
Found at i:1295496 original size:23 final size:23
Alignment explanation
Indices: 1295466--1295509 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1295456 GAGTAGAGGG
1295466 TCTACGTGGTCCTTCGGGACAAT
1 TCTACGTGGTCCTTCGGGACAAT
*
1295489 TCTACGTGGTCTTTCGGGACA
1 TCTACGTGGTCCTTCGGGACA
1295510 TATATGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (23 bp):
TCTACGTGGTCCTTCGGGACAAT
Found at i:1295607 original size:22 final size:22
Alignment explanation
Indices: 1295573--1295624 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
1295563 TTGGTATATG
* *
1295573 TATATGATTCTTAAGG-AATTT
1 TATATGGTCCTTAAGGAAATTT
*
1295594 CTATATGGTCCTTATGGACAATTT
1 -TATATGGTCCTTAAGGA-AATTT
1295618 TATATGG
1 TATATGG
1295625 AACTACGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 13 0.52
23 7 0.28
24 5 0.20
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (22 bp):
TATATGGTCCTTAAGGAAATTT
Found at i:1295701 original size:24 final size:24
Alignment explanation
Indices: 1295636--1295707 Score: 60
Period size: 24 Copynumber: 3.0 Consensus size: 24
1295626 ACTACGGTGC
* *
1295636 AATTCTACGTAGCACTTCTGTG-C-
1 AATTCTACGTGGCACTTC-GGGACA
* *
1295659 ATTTCTACGCGGTCA-TTCGGGACA
1 AATTCTACGTGG-CACTTCGGGACA
*
1295683 AATTCTACGTGGCACTTCGGTACA
1 AATTCTACGTGGCACTTCGGGACA
1295707 A
1 A
1295708 TTTATACAAG
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
22 2 0.05
23 15 0.39
24 21 0.55
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGGACA
Found at i:1296290 original size:21 final size:21
Alignment explanation
Indices: 1296264--1296305 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1296254 CGGTGTTTTT
1296264 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
*
1296285 GTGCATTGGTACACTGTAGCA
1 GTGCATCGGTACACTGTAGCA
1296306 TTGTTCATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
GTGCATCGGTACACTGTAGCA
Found at i:1299666 original size:49 final size:49
Alignment explanation
Indices: 1299612--1299773 Score: 173
Period size: 49 Copynumber: 3.3 Consensus size: 49
1299602 CATACTCCAA
*
1299612 TTTGCCTTTTCATCGGGACTATGAGGGTTGGTTAGAGTCATTTATCGAG
1 TTTGCCTTTTCATCGAGACTATGAGGGTTGGTTAGAGTCATTTATCGAG
* * * * * * *
1299661 TTTGCCTTTTCATTGAGACTATGAGGGTTTGATATGACACTTATCTATCTA-
1 TTTGCCTTTTCATCGAGACTATGAGGG-TTGGT-T-AGAGTCATTTATCGAG
* * * *
1299712 TTTGTCTTTTCATCGCGACTAGGAGGGTTGGTGAGAGTCATTTATCGAG
1 TTTGCCTTTTCATCGAGACTATGAGGGTTGGTTAGAGTCATTTATCGAG
*
1299761 TTTGTCTTTTCAT
1 TTTGCCTTTTCAT
1299774 TACGACTATG
Statistics
Matches: 90, Mismatches: 19, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
48 10 0.11
49 38 0.42
50 8 0.09
51 24 0.27
52 10 0.11
ACGTcount: A:0.19, C:0.15, G:0.24, T:0.42
Consensus pattern (49 bp):
TTTGCCTTTTCATCGAGACTATGAGGGTTGGTTAGAGTCATTTATCGAG
Found at i:1299732 original size:51 final size:51
Alignment explanation
Indices: 1299661--1299814 Score: 143
Period size: 51 Copynumber: 3.1 Consensus size: 51
1299651 ATTTATCGAG
* *
1299661 TTTGCCTTTTCATTGAGACTATGAGGGTTTGATATGACACTTATCTATCTA
1 TTTGTCTTTTCATTGCGACTATGAGGGTTTGATATGACACTTATCTATCTA
* * * * * * * *
1299712 TTTGTCTTTTCATCGCGACTAGGAGGG-TTG--GTGAGAGTCATTTATCGA
1 TTTGTCTTTTCATTGCGACTATGAGGGTTTGATATGACACTTATCTATCTA
* * * * *
1299760 GTTTGTCTTTTCATTACGACTATGAAGGTTTGATATGACATTTATCCATATA
1 -TTTGTCTTTTCATTGCGACTATGAGGGTTTGATATGACACTTATCTATCTA
1299812 TTT
1 TTT
1299815 TCCATAAATC
Statistics
Matches: 77, Mismatches: 22, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
48 12 0.16
49 23 0.30
50 6 0.08
51 26 0.34
52 10 0.13
ACGTcount: A:0.23, C:0.14, G:0.20, T:0.43
Consensus pattern (51 bp):
TTTGTCTTTTCATTGCGACTATGAGGGTTTGATATGACACTTATCTATCTA
Found at i:1299784 original size:100 final size:100
Alignment explanation
Indices: 1299611--1299814 Score: 311
Period size: 100 Copynumber: 2.0 Consensus size: 100
1299601 TCATACTCCA
* * *
1299611 ATTTGCCTTTTCATCGGGACTATGAGGGTTGGTTAGAGTCATTTATCGAGTTTGCCTTTTCATTG
1 ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTGAGAGTCATTTATCGAGTTTGCCTTTTCATTG
* * *
1299676 AGACTATGAGGGTTTGATATGACACTTATCTATCT
66 AGACTATGAAGGTTTGATATGACACTTATCCATAT
* *
1299711 ATTTGTCTTTTCATCGCGACTAGGAGGGTTGGTGAGAGTCATTTATCGAGTTTGTCTTTTCATT-
1 ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTGAGAGTCATTTATCGAGTTTGCCTTTTCATTG
*
1299775 ACGACTATGAAGGTTTGATATGACATTTATCCATAT
66 A-GACTATGAAGGTTTGATATGACACTTATCCATAT
1299811 ATTT
1 ATTT
1299815 TCCATAAATC
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
99 1 0.01
100 93 0.99
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (100 bp):
ATTTGCCTTTTCATCGCGACTAGGAGGGTTGGTGAGAGTCATTTATCGAGTTTGCCTTTTCATTG
AGACTATGAAGGTTTGATATGACACTTATCCATAT
Found at i:1299848 original size:19 final size:19
Alignment explanation
Indices: 1299803--1299848 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1299793 TATGACATTT
*
1299803 ATCCATATATTTTCCATAA
1 ATCCATCTATTTTCCATAA
1299822 ATCCATCTATTTTCCATAA
1 ATCCATCTATTTTCCATAA
*
1299841 ATCTATCT
1 ATCCATCT
1299849 GCACCATCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (19 bp):
ATCCATCTATTTTCCATAA
Found at i:1304559 original size:18 final size:18
Alignment explanation
Indices: 1304536--1304573 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1304526 GAGGAGGTCC
1304536 TCCAAGCCTTCTCCCAAA
1 TCCAAGCCTTCTCCCAAA
1304554 TCCAAGCCTTCTCCCAAA
1 TCCAAGCCTTCTCCCAAA
1304572 TC
1 TC
1304574 AACCCGAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.45, G:0.05, T:0.24
Consensus pattern (18 bp):
TCCAAGCCTTCTCCCAAA
Found at i:1314534 original size:39 final size:39
Alignment explanation
Indices: 1314430--1314535 Score: 119
Period size: 39 Copynumber: 2.7 Consensus size: 39
1314420 TATAGTTATG
* *
1314430 AAATTATTTTAC-TCTAACCTTCTAAATTCTTAATTTCTT
1 AAATTATTTCACAT-TAACATTCTAAATTCTTAATTTCTT
* *
1314469 AAATT-TTGCTACCA-TAATATTCTAAATTCTTAATTTCTT
1 AAATTATTTC-A-CATTAACATTCTAAATTCTTAATTTCTT
*
1314508 AAATTATTTCACATTAACATTTTAAATT
1 AAATTATTTCACATTAACATTCTAAATT
1314536 ATTTTTTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
38 4 0.07
39 47 0.85
40 4 0.07
ACGTcount: A:0.35, C:0.15, G:0.01, T:0.49
Consensus pattern (39 bp):
AAATTATTTCACATTAACATTCTAAATTCTTAATTTCTT
Found at i:1314557 original size:14 final size:14
Alignment explanation
Indices: 1314526--1314559 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1314516 TCACATTAAC
*
1314526 ATTTTAAATTATTT
1 ATTTTAAAATATTT
1314540 -TTTTAAAATATTT
1 ATTTTAAAATATTT
1314553 ATTTTAA
1 ATTTTAA
1314560 CTTTCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTAAAATATTT
Found at i:1315358 original size:23 final size:23
Alignment explanation
Indices: 1315332--1315402 Score: 67
Period size: 23 Copynumber: 3.0 Consensus size: 23
1315322 TTAATATTCA
1315332 AATTATAATTTATAT-TATATTAT
1 AATTATAATTTATATATATA-TAT
*
1315355 AATTA-ATTATTATATATATATAT
1 AATTATAAT-TTATATATATATAT
*
1315378 AA-TATAATTAATGATAATATATAT
1 AATTATAATTTAT-AT-ATATATAT
1315402 A
1 A
1315403 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.17
23 20 0.50
24 13 0.32
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (23 bp):
AATTATAATTTATATATATATAT
Found at i:1315372 original size:2 final size:2
Alignment explanation
Indices: 1315365--1315417 Score: 55
Period size: 2 Copynumber: 29.0 Consensus size: 2
1315355 AATTAATTAT
1315365 TA TA TA TA TA TA TA -A TA TA -A T- TA -A TGA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA
1315403 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
1315418 GTTAATATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
1 6 0.14
2 36 0.82
3 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1315386 original size:28 final size:27
Alignment explanation
Indices: 1315332--1315415 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 27
1315322 TTAATATTCA
* *
1315332 AATTATAATTTATAT-TATATTATAATT
1 AATTATAATATATATATATAATAT-ATT
*
1315359 AATTATTATATATATATATAATATAATT
1 AATTATAATATATATATATAATAT-ATT
*
1315387 AATGATAATATATATATATATATATATT
1 AATTATAATATATATATATA-ATATATT
1315415 A
1 A
1315416 TAGTTAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
27 13 0.26
28 33 0.66
29 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (27 bp):
AATTATAATATATATATATAATATATT
Found at i:1315423 original size:28 final size:27
Alignment explanation
Indices: 1315342--1315425 Score: 86
Period size: 28 Copynumber: 3.1 Consensus size: 27
1315332 AATTATAATT
*
1315342 TATAT-TATAT-TATA-ATTAA-TTAT
1 TATATATATATATATATATTAAGTTAA
*
1315365 TATATATATATATAATATAATTAATGATAA
1 TATATATATATAT-ATAT-ATTAA-GTTAA
1315395 TATATATATATATATATATTATAGTTAA
1 TATATATATATATATATATTA-AGTTAA
1315423 TAT
1 TAT
1315426 TCAAATTATA
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 5 0.10
24 5 0.10
25 1 0.02
26 3 0.06
28 16 0.32
29 5 0.10
30 15 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TATATATATATATATATATTAAGTTAA
Found at i:1318615 original size:2 final size:2
Alignment explanation
Indices: 1318608--1318638 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1318598 GGTTGAGAAC
1318608 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1318639 CATTGAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1320273 original size:20 final size:20
Alignment explanation
Indices: 1320250--1320298 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1320240 ATATGAACAT
*
1320250 TACCGATACTGTTCATGTGG
1 TACCGATACTGTTCATGTGA
*
1320270 TACCGATATTGTTCATGTGA
1 TACCGATACTGTTCATGTGA
*
1320290 TATCGATAC
1 TACCGATAC
1320299 CCCAAGTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.37
Consensus pattern (20 bp):
TACCGATACTGTTCATGTGA
Found at i:1323228 original size:21 final size:21
Alignment explanation
Indices: 1323202--1323247 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1323192 AGGACTGAAG
*
1323202 GATGGACTTGAAGGGGAATAA
1 GATGGACATGAAGGGGAATAA
* * *
1323223 GATGGAGATGCAGGTGAATAA
1 GATGGACATGAAGGGGAATAA
1323244 GATG
1 GATG
1323248 CTGATGTCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.39, T:0.20
Consensus pattern (21 bp):
GATGGACATGAAGGGGAATAA
Found at i:1323582 original size:21 final size:21
Alignment explanation
Indices: 1323540--1323601 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
1323530 TTGTGGATTG
* *
1323540 TAACTTGGAGAGGTAGGG-CTA
1 TAACTAGGTGAGGT-GGGACTA
*
1323561 TAACTAGGTGATGTGGGACTA
1 TAACTAGGTGAGGTGGGACTA
* *
1323582 TAACTTGGTGAGGTTGGACT
1 TAACTAGGTGAGGTGGGACT
1323602 GTACCCTGGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 3 0.09
21 31 0.91
ACGTcount: A:0.26, C:0.10, G:0.35, T:0.29
Consensus pattern (21 bp):
TAACTAGGTGAGGTGGGACTA
Found at i:1323663 original size:21 final size:21
Alignment explanation
Indices: 1323639--1323790 Score: 169
Period size: 21 Copynumber: 7.2 Consensus size: 21
1323629 CGGTGAAGTT
1323639 GGGCTGTAGGAAGGAGATGTC
1 GGGCTGTAGGAAGGAGATGTC
1323660 GGGCTGTAGGAAGGAGATGTC
1 GGGCTGTAGGAAGGAGATGTC
* * * * *
1323681 GGACTGTAGGAGGGTGAGGTT
1 GGGCTGTAGGAAGGAGATGTC
*
1323702 GGGCTGTAGGAAGGAGATGCC
1 GGGCTGTAGGAAGGAGATGTC
* * * *
1323723 GGGCTGTAGGAGGGTGAGGTT
1 GGGCTGTAGGAAGGAGATGTC
*
1323744 GGGCTGTAGGAAGGAGATGTT
1 GGGCTGTAGGAAGGAGATGTC
* * * *
1323765 GGGCTGTATGATGGAGAAGTG
1 GGGCTGTAGGAAGGAGATGTC
1323786 GGGCT
1 GGGCT
1323791 ATATGCAGGT
Statistics
Matches: 108, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 108 1.00
ACGTcount: A:0.21, C:0.08, G:0.50, T:0.21
Consensus pattern (21 bp):
GGGCTGTAGGAAGGAGATGTC
Found at i:1323667 original size:63 final size:63
Alignment explanation
Indices: 1323600--1323730 Score: 145
Period size: 63 Copynumber: 2.1 Consensus size: 63
1323590 TGAGGTTGGA
** * * * *
1323600 CTGTACCCTGGAGAAGTGGGGCTATAAGCCGGTGAAGTTGGGCTGTAGGAAGGAGATGTCGGG
1 CTGTACCAAGGAGAAGTCGGACTATAAGACGGTGAAGTTGGGCTGTAGGAAGGAGATGCCGGG
** * * * * *
1323663 CTGTAGGAAGGAGATGTCGGACTGTAGGAGGGTGAGGTTGGGCTGTAGGAAGGAGATGCCGGG
1 CTGTACCAAGGAGAAGTCGGACTATAAGACGGTGAAGTTGGGCTGTAGGAAGGAGATGCCGGG
1323726 CTGTA
1 CTGTA
1323731 GGAGGGTGAG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
63 55 1.00
ACGTcount: A:0.22, C:0.12, G:0.45, T:0.21
Consensus pattern (63 bp):
CTGTACCAAGGAGAAGTCGGACTATAAGACGGTGAAGTTGGGCTGTAGGAAGGAGATGCCGGG
Found at i:1323688 original size:42 final size:42
Alignment explanation
Indices: 1323639--1323790 Score: 196
Period size: 42 Copynumber: 3.6 Consensus size: 42
1323629 CGGTGAAGTT
* * *
1323639 GGGCTGTAGGAAGGAGATGTCGGGCTGTAGGAAGGAGATGTC
1 GGGCTGTAGGAGGGAGAGGTTGGGCTGTAGGAAGGAGATGTC
* * *
1323681 GGACTGTAGGAGGGTGAGGTTGGGCTGTAGGAAGGAGATGCC
1 GGGCTGTAGGAGGGAGAGGTTGGGCTGTAGGAAGGAGATGTC
* *
1323723 GGGCTGTAGGAGGGTGAGGTTGGGCTGTAGGAAGGAGATGTT
1 GGGCTGTAGGAGGGAGAGGTTGGGCTGTAGGAAGGAGATGTC
* * * *
1323765 GGGCTGTATGATGGAGAAGTGGGGCT
1 GGGCTGTAGGAGGGAGAGGTTGGGCT
1323791 ATATGCAGGT
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 96 1.00
ACGTcount: A:0.21, C:0.08, G:0.50, T:0.21
Consensus pattern (42 bp):
GGGCTGTAGGAGGGAGAGGTTGGGCTGTAGGAAGGAGATGTC
Found at i:1323731 original size:63 final size:63
Alignment explanation
Indices: 1323630--1323781 Score: 196
Period size: 63 Copynumber: 2.4 Consensus size: 63
1323620 GCTATAAGCC
* * *
1323630 GGTGAAGTTGGGCTGTAGGAAGGAGATGTCGGGCTGTAGGAAGGAGATGTCGGACTGTAGGAG
1 GGTGAAGTTGGGCTGTAGGAAGGAGATGCCGGGCTGTAGGAAGGAGAGGTCGGACTGTAGGAA
* * * * *
1323693 GGTGAGGTTGGGCTGTAGGAAGGAGATGCCGGGCTGTAGGAGGGTGAGGTTGGGCTGTAGGAA
1 GGTGAAGTTGGGCTGTAGGAAGGAGATGCCGGGCTGTAGGAAGGAGAGGTCGGACTGTAGGAA
* * * *
1323756 GGAGATGTTGGGCTGTATGATGGAGA
1 GGTGAAGTTGGGCTGTAGGAAGGAGA
1323782 AGTGGGGCTA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 77 1.00
ACGTcount: A:0.22, C:0.07, G:0.49, T:0.22
Consensus pattern (63 bp):
GGTGAAGTTGGGCTGTAGGAAGGAGATGCCGGGCTGTAGGAAGGAGAGGTCGGACTGTAGGAA
Found at i:1323795 original size:21 final size:21
Alignment explanation
Indices: 1323756--1323832 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
1323746 GCTGTAGGAA
* * *
1323756 GGAGATGTTGGGCTGTATGAT
1 GGAGAAGTAGGGCTATATGAT
*
1323777 GGAGAAGTGGGGCTATATGCA-
1 GGAGAAGTAGGGCTATATG-AT
* *
1323798 GGTGAAGTAGGGCTATATGCT
1 GGAGAAGTAGGGCTATATGAT
*
1323819 GGTGAAGTAGGGCT
1 GGAGAAGTAGGGCT
1323833 GTAGCTAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
21 47 0.98
22 1 0.02
ACGTcount: A:0.23, C:0.08, G:0.43, T:0.26
Consensus pattern (21 bp):
GGAGAAGTAGGGCTATATGAT
Found at i:1323811 original size:42 final size:42
Alignment explanation
Indices: 1323765--1323898 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 42
1323755 AGGAGATGTT
*
1323765 GGGCTGTATGATGGAGAAGTGGGGCTATATGC-AGGTGAAGTA
1 GGGCTGTATGATGGAGAAGTAGGGCTATA-GCTAGGTGAAGTA
* * * *
1323807 GGGCTATATGCTGGTGAAGTAGGGCTGTAGCTAGGTGAAGTA
1 GGGCTGTATGATGGAGAAGTAGGGCTATAGCTAGGTGAAGTA
* * * * * * *
1323849 GGGCTGTA-GCTAGGGGAGGTAGGGCTGTAGCTTGGGGAGGTA
1 GGGCTGTATGAT-GGAGAAGTAGGGCTATAGCTAGGTGAAGTA
1323891 GGGCTGTA
1 GGGCTGTA
1323899 GCTCGGGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
41 5 0.06
42 74 0.94
ACGTcount: A:0.22, C:0.09, G:0.46, T:0.24
Consensus pattern (42 bp):
GGGCTGTATGATGGAGAAGTAGGGCTATAGCTAGGTGAAGTA
Found at i:1323843 original size:21 final size:21
Alignment explanation
Indices: 1323780--1323901 Score: 140
Period size: 21 Copynumber: 5.8 Consensus size: 21
1323770 GTATGATGGA
* *
1323780 GAAGTGGGGCTATATGC-AGGT
1 GAAGTAGGGCTGTA-GCTAGGT
*
1323801 GAAGTAGGGCTATATGCT-GGT
1 GAAGTAGGGCTGTA-GCTAGGT
1323822 GAAGTAGGGCTGTAGCTAGGT
1 GAAGTAGGGCTGTAGCTAGGT
*
1323843 GAAGTAGGGCTGTAGCTAGGG
1 GAAGTAGGGCTGTAGCTAGGT
* * *
1323864 GAGGTAGGGCTGTAGCTTGGG
1 GAAGTAGGGCTGTAGCTAGGT
*
1323885 GAGGTAGGGCTGTAGCT
1 GAAGTAGGGCTGTAGCT
1323902 CGGGGAGGTT
Statistics
Matches: 94, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
20 3 0.03
21 91 0.97
ACGTcount: A:0.21, C:0.10, G:0.45, T:0.24
Consensus pattern (21 bp):
GAAGTAGGGCTGTAGCTAGGT
Found at i:1323906 original size:21 final size:21
Alignment explanation
Indices: 1323825--1323910 Score: 136
Period size: 21 Copynumber: 4.1 Consensus size: 21
1323815 TGCTGGTGAA
* *
1323825 GTAGGGCTGTAGCTAGGTGAA
1 GTAGGGCTGTAGCTAGGGGAG
1323846 GTAGGGCTGTAGCTAGGGGAG
1 GTAGGGCTGTAGCTAGGGGAG
*
1323867 GTAGGGCTGTAGCTTGGGGAG
1 GTAGGGCTGTAGCTAGGGGAG
*
1323888 GTAGGGCTGTAGCTCGGGGAG
1 GTAGGGCTGTAGCTAGGGGAG
1323909 GT
1 GT
1323911 TGGAGAATAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.17, C:0.10, G:0.50, T:0.22
Consensus pattern (21 bp):
GTAGGGCTGTAGCTAGGGGAG
Found at i:1324010 original size:21 final size:21
Alignment explanation
Indices: 1323986--1324077 Score: 112
Period size: 21 Copynumber: 4.4 Consensus size: 21
1323976 GACTGTAGGT
*
1323986 AGGTGATGTGGGGCTGTACCC
1 AGGTGATGTTGGGCTGTACCC
*
1324007 AGGTGAGGTTGGGCTGTACCC
1 AGGTGATGTTGGGCTGTACCC
* * * *
1324028 GGGGGATGTAGGGCTGTAACC
1 AGGTGATGTTGGGCTGTACCC
*
1324049 AGGTGAGGTTGGGCTGTACCC
1 AGGTGATGTTGGGCTGTACCC
*
1324070 AGGAGATG
1 AGGTGATG
1324078 ATGGACTTCC
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.17, C:0.16, G:0.45, T:0.22
Consensus pattern (21 bp):
AGGTGATGTTGGGCTGTACCC
Found at i:1324024 original size:42 final size:42
Alignment explanation
Indices: 1323990--1324077 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
1323980 GTAGGTAGGT
* * *
1323990 GATGTGGGGCTGTACCCAGGTGAGGTTGGGCTGTACCCGGGG
1 GATGTAGGGCTGTAACCAGGTGAGGTTGGGCTGTACCCAGGG
*
1324032 GATGTAGGGCTGTAACCAGGTGAGGTTGGGCTGTACCCAGGA
1 GATGTAGGGCTGTAACCAGGTGAGGTTGGGCTGTACCCAGGG
1324074 GATG
1 GATG
1324078 ATGGACTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.22
Consensus pattern (42 bp):
GATGTAGGGCTGTAACCAGGTGAGGTTGGGCTGTACCCAGGG
Found at i:1330930 original size:18 final size:18
Alignment explanation
Indices: 1330888--1330931 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1330878 TTGAAGATAA
* *
1330888 ATAATTTATTTTTTTTAT
1 ATAAATTATTTTTATTAT
1330906 -TATAATTATTTTTATTAT
1 ATA-AATTATTTTTATTAT
1330924 ATAAATTA
1 ATAAATTA
1330932 GAATAATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 18 0.82
19 2 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
ATAAATTATTTTTATTAT
Found at i:1331240 original size:40 final size:41
Alignment explanation
Indices: 1331196--1331327 Score: 175
Period size: 40 Copynumber: 3.2 Consensus size: 41
1331186 TAACAAATGT
1331196 CGCAATAG-TGGTAAATTAGCGGCGTTTATACCACAAACGC
1 CGCAATAGATGGTAAATTAGCGGCGTTTATACCACAAACGC
*
1331236 CGCAATAGAT--TAACATATAGTGGCGTTT-TAGCCA-AAACGC
1 CGCAATAGATGGTAA-AT-TAGCGGCGTTTATA-CCACAAACGC
*
1331276 CGCAATAGATCGGTAAATTAGCGGTGTTTATACCACAAACGC
1 CGCAATAGAT-GGTAAATTAGCGGCGTTTATACCACAAACGC
1331318 CGCAATAGAT
1 CGCAATAGAT
1331328 TACACATATA
Statistics
Matches: 80, Mismatches: 3, Indels: 16
0.81 0.03 0.16
Matches are distributed among these distances:
39 3 0.04
40 28 0.35
41 26 0.32
42 20 0.25
43 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.23
Consensus pattern (41 bp):
CGCAATAGATGGTAAATTAGCGGCGTTTATACCACAAACGC
Found at i:1331348 original size:42 final size:41
Alignment explanation
Indices: 1331216--1331348 Score: 166
Period size: 42 Copynumber: 3.2 Consensus size: 41
1331206 GTAAATTAGC
1331216 GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
1 GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
*
1331257 GGCGTTT-TAGCCA-AAACGCCGCAATAGATCGGTAA-AT-TAGC
1 GGCGTTTATA-CCACAAACGCCGCAATAGAT---TAACATATAGT
*
1331298 GGTGTTTATACCACAAACGCCGCAATAGATTACACATATAGT
1 GGCGTTTATACCACAAACGCCGCAATAGATTA-ACATATAGT
*
1331340 GGCATTTAT
1 GGCGTTTAT
1331349 TCTTAAAATG
Statistics
Matches: 78, Mismatches: 5, Indels: 17
0.78 0.05 0.17
Matches are distributed among these distances:
39 2 0.03
40 19 0.24
41 24 0.31
42 30 0.38
43 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
GGCGTTTATACCACAAACGCCGCAATAGATTAACATATAGT
Found at i:1331473 original size:41 final size:43
Alignment explanation
Indices: 1331363--1331490 Score: 147
Period size: 41 Copynumber: 3.0 Consensus size: 43
1331353 AAAATGCCGT
* **
1331363 AATAGTGATAATAAATAGTGGCG--TTTTTAGACAAACGCCGT
1 AATAGTGATAATCAATAGTGGCGTTTTTTTAGACAAACGCCAC
* * *
1331404 AATAATGTTAATCGATAGTGGCGTTTTTTTA-ACAAACGCCAC
1 AATAGTGATAATCAATAGTGGCGTTTTTTTAGACAAACGCCAC
* *
1331446 AATAGTG-TAATCAATAGTGGCGTTTTTTTTGTATAAACGCCAC
1 AATAGTGATAATCAATAGTGGCGTTTTTTTAG-ACAAACGCCAC
1331489 AA
1 AA
1331491 AATGTTAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
41 40 0.55
42 15 0.21
43 18 0.25
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (43 bp):
AATAGTGATAATCAATAGTGGCGTTTTTTTAGACAAACGCCAC
Found at i:1332817 original size:43 final size:44
Alignment explanation
Indices: 1332723--1332820 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 44
1332713 TAAAAGGTAA
* * * * *
1332723 TTAGCGGCGTTTGTATCCAGAAATGCCGCTATAGATCTGACATT
1 TTAGTGGCGTTTGTATCCAAAAATGCCGCTAAAGATCTAACACT
* *
1332767 TTA-TGGCGTTTGTATCCAAAAATGCCGCTAAAGA-GTAATACT
1 TTAGTGGCGTTTGTATCCAAAAATGCCGCTAAAGATCTAACACT
1332809 TTAGTGGCGTTT
1 TTAGTGGCGTTT
1332821 TTGAAACAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
42 7 0.15
43 36 0.78
44 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (44 bp):
TTAGTGGCGTTTGTATCCAAAAATGCCGCTAAAGATCTAACACT
Found at i:1332927 original size:41 final size:41
Alignment explanation
Indices: 1332879--1333138 Score: 196
Period size: 41 Copynumber: 6.3 Consensus size: 41
1332869 TTTTTCCAAT
*
1332879 AAACGCCGCTATAGGTACGTACTTTAGTGGCATTTT-TATAC
1 AAACGCCGCTATA-GTACGTACTTTAGTGGCATTTTGAATAC
*
1332920 AAACGCCGCTATA-TACTAGTACTTTAGTGGCGTTTCT--ATAC
1 AAACGCCGCTATAGTAC--GTACTTTAGTGGCATTT-TGAATAC
*** * *
1332961 AAATATCGCTATA-TACTAGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGTAC--GTACTTTAGTGGCATTTTGAATAC
* * * * *
1333003 AAACGCCGCTAAAG-ACCCGTACTTTAATAGCATTTT-TATAT
1 AAACGCCGCTATAGTA--CGTACTTTAGTGGCATTTTGAATAC
* * *
1333044 AAACGTCGCTATAG-ACTCGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGTA--CGTACTTTAGTGGCATTTTGAATAC
*
1333086 AAACGCTGCTATAG-ACTCGTACTTTAGTGGCATTTTGAATAC
1 AAACGCCGCTATAGTA--CGTACTTTAGTGGCATTTTGAATAC
*
1333128 AAGCGCCGCTA
1 AAACGCCGCTA
1333139 ATGACTCATA
Statistics
Matches: 180, Mismatches: 30, Indels: 17
0.79 0.13 0.07
Matches are distributed among these distances:
39 3 0.02
40 1 0.01
41 97 0.54
42 78 0.43
44 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATAGTACGTACTTTAGTGGCATTTTGAATAC
Found at i:1333026 original size:42 final size:42
Alignment explanation
Indices: 1332879--1333179 Score: 283
Period size: 42 Copynumber: 7.2 Consensus size: 42
1332869 TTTTTCCAAT
* * *
1332879 AAACGCCGCTATAG-GTACGTACTTTAGTGGCATTTT-TATAC
1 AAACGCCGCTATAGACT-CGTACTTTAGTGGCGTTTTGAATAC
* *
1332920 AAACGCCGCTATATACTAGTACTTTAGTGGCGTTTCT--ATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTT-TGAATAC
*** * * *
1332961 AAATATCGCTATATACTAGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * * * * * *
1333003 AAACGCCGCTAAAGACCCGTACTTTAATAGCATTTT-TATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* *
1333044 AAACGTCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATGC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* *
1333086 AAACGCTGCTATAGACTCGTACTTTAGTGGCATTTTGAATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
* * *
1333128 AAGCGCCGCTA-ATGACTCATACTTTAGTGGCGTTTAT-ATTTAC
1 AAACGCCGCTATA-GACTCGTACTTTAGTGGCGTTT-TGA-ATAC
1333171 AAACGCCGC
1 AAACGCCGC
1333180 AATTTTACAG
Statistics
Matches: 212, Mismatches: 40, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
40 1 0.00
41 98 0.46
42 101 0.48
43 12 0.06
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (42 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTGAATAC
Found at i:1333028 original size:83 final size:83
Alignment explanation
Indices: 1332897--1333162 Score: 288
Period size: 83 Copynumber: 3.2 Consensus size: 83
1332887 CTATAGGTAC
* * * * * *
1332897 GTACTTTAGTGGCATTTT-TATACAAACGCCGCTATATACTAGTACTTTAGTGGCGTTTCTATAC
1 GTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTCTATAC
* *
1332961 AAATATCGCTATATACTA
66 AAACATCGCTATAGACTA
* * * * * *
1332979 GTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTAAAGACCCGTACTTTAATAGCATTTTTATAT
1 GTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTCTATAC
* *
1333044 AAACGTCGCTATAGACTC
66 AAACATCGCTATAGACTA
*
1333062 GTACTTTAGTGGCGTTTTGAATGCAAACGCTGCTATAGACTCGTACTTTAGTGGCATTT-TGAAT
1 GTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTCT--AT
* **
1333126 ACAAGCGCCGCTA-ATGACTCA
64 ACAAACATCGCTATA-GACT-A
1333147 -TACTTTAGTGGCGTTT
1 GTACTTTAGTGGCGTTT
1333163 ATATTTACAA
Statistics
Matches: 154, Mismatches: 25, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
82 18 0.12
83 104 0.68
84 32 0.21
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (83 bp):
GTACTTTAGTGGCGTTTTGAATGCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTCTATAC
AAACATCGCTATAGACTA
Found at i:1336767 original size:128 final size:129
Alignment explanation
Indices: 1336541--1336825 Score: 396
Period size: 128 Copynumber: 2.2 Consensus size: 129
1336531 GGCGTTTACA
* *
1336541 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCTATAGATC
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCAATAGATC
* * *
1336606 TAATCTTTTACGTCGTTTGTTCCAATACACGCCGCTATAGATCT-GACCTTTTGCGACGTTTGT
66 TAACCTTTTACGGCGTTTGTTCCAATACACGCCGCTATAGATCTCGACCTTCTGCGACGTTTGT
* * *
1336669 TCCAAAAACGTCGCTATAGATCTCGACCTTTTGTGGCGTTTGTTCCAAAAACGCCGCAATAGATC
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCAATAGATC
* ** * *
1336734 TCGACCTTTTGTGGCGTTTGTTCCAA-A-ATCGCCGCTATAGATCTCGACCTTCTGTGGCGTTTG
66 T-AACCTTTTACGGCGTTTGTTCCAATACA-CGCCGCTATAGATCTCGACCTTCTGCGACGTTTG
1336797 T
129 T
* *
1336798 TTCAAAAACGCCGCTATAGATCTTGACC
1 TCCAAAAACGCCGCTATAGATCTCGACC
1336826 AAAGGCGGCG
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
127 1 0.01
128 77 0.56
129 60 0.43
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (129 bp):
TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGTTCAAAAAACGCCGCAATAGATC
TAACCTTTTACGGCGTTTGTTCCAATACACGCCGCTATAGATCTCGACCTTCTGCGACGTTTGT
Found at i:1336838 original size:43 final size:43
Alignment explanation
Indices: 1336541--1336825 Score: 394
Period size: 43 Copynumber: 6.7 Consensus size: 43
1336531 GGCGTTTACA
*
1336541 TCCAAAAACGCCGCTATAGATCTCAACCTTTTGCGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
* * * * *
1336584 TCAAAAAACGCCGCTATAGATCT-AATCTTTTACGTCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
* *
1336626 TCCAATACACGCCGCTATAGATCT-GACCTTTTGCGACGTTTGT
1 TCCAA-AAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
* *
1336669 TCCAAAAACGTCGCTATAGATCTCGACCTTTTGTGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
* *
1336712 TCCAAAAACGCCGCAATAGATCTCGACCTTTTGTGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
* * *
1336755 TCCAAAATCGCCGCTATAGATCTCGACCTTCTGTGGCGTTTGT
1 TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
* *
1336798 TTCAAAAACGCCGCTATAGATCTTGACC
1 TCCAAAAACGCCGCTATAGATCTCGACC
1336826 AAAGGCGGCG
Statistics
Matches: 218, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
42 36 0.17
43 182 0.83
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (43 bp):
TCCAAAAACGCCGCTATAGATCTCGACCTTTTGCGGCGTTTGT
Found at i:1337545 original size:3 final size:3
Alignment explanation
Indices: 1337537--1337623 Score: 174
Period size: 3 Copynumber: 29.0 Consensus size: 3
1337527 ACACGCGCGT
1337537 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1337585 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1337624 AAACCTGTAA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1339542 original size:19 final size:20
Alignment explanation
Indices: 1339518--1339561 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1339508 TTCACGTATA
1339518 AGTAAGAAGCAAGAGT-AGG
1 AGTAAGAAGCAAGAGTAAGG
* * *
1339537 AGTAAGGAGTAGGAGTAAGG
1 AGTAAGAAGCAAGAGTAAGG
1339557 AGTAA
1 AGTAA
1339562 TGAGAAACAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.39, T:0.14
Consensus pattern (20 bp):
AGTAAGAAGCAAGAGTAAGG
Found at i:1339544 original size:7 final size:7
Alignment explanation
Indices: 1339530--1339561 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
1339520 TAAGAAGCAA
1339530 GAGT-AG
1 GAGTAAG
1339536 GAGTAAG
1 GAGTAAG
1339543 GAGT-AG
1 GAGTAAG
1339549 GAGTAAG
1 GAGTAAG
1339556 GAGTAA
1 GAGTAA
1339562 TGAGAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 10 0.42
7 14 0.58
ACGTcount: A:0.41, C:0.00, G:0.44, T:0.16
Consensus pattern (7 bp):
GAGTAAG
Found at i:1339546 original size:13 final size:13
Alignment explanation
Indices: 1339530--1339560 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1339520 TAAGAAGCAA
1339530 GAGTAGGAGTAAG
1 GAGTAGGAGTAAG
1339543 GAGTAGGAGTAAG
1 GAGTAGGAGTAAG
1339556 GAGTA
1 GAGTA
1339561 ATGAGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.45, T:0.16
Consensus pattern (13 bp):
GAGTAGGAGTAAG
Found at i:1341707 original size:3 final size:3
Alignment explanation
Indices: 1341699--1341821 Score: 138
Period size: 3 Copynumber: 41.0 Consensus size: 3
1341689 CCATATTGAT
* * * * * * *
1341699 TTA TTA TTA TAA TAA TAA TTA TTA TTA TTA TAA TTA CTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1341747 TTA TTA TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1341795 TAA ATA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1341822 AATATATATA
Statistics
Matches: 100, Mismatches: 20, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1341828 original size:27 final size:28
Alignment explanation
Indices: 1341699--1341828 Score: 178
Period size: 27 Copynumber: 4.7 Consensus size: 28
1341689 CCATATTGAT
*
1341699 TTATTATTATAATAATA-ATTATTATTA
1 TTATTATTATTATAATATATTATTATTA
* *
1341726 TTATAATTACTATAA-ATATTATTATTA
1 TTATTATTATTATAATATATTATTATTA
*
1341753 TTATTATTACTATAAATATTATTATTATTA
1 TTATTATTATTAT-AATA-TATTATTATTA
1341783 TTATTATTATTATAA-ATATTATTATTA
1 TTATTATTATTATAATATATTATTATTA
1341810 TTATTATTATTA-AATATAT
1 TTATTATTATTATAATATAT
1341829 ATATATACAT
Statistics
Matches: 93, Mismatches: 5, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
26 3 0.03
27 61 0.66
28 3 0.03
29 3 0.03
30 23 0.25
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATTATTATTATAATATATTATTATTA
Found at i:1341951 original size:16 final size:16
Alignment explanation
Indices: 1341932--1341972 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
1341922 CTCTAACCCT
1341932 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
1341948 AGCCGCCTCTGCCTCC
1 AGCCGCCTCTGCCTCC
*
1341964 AACCGCCTC
1 AGCCGCCTC
1341973 AGCCAACGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.56, G:0.17, T:0.17
Consensus pattern (16 bp):
AGCCGCCTCTGCCTCC
Found at i:1354505 original size:7 final size:7
Alignment explanation
Indices: 1354493--1354573 Score: 121
Period size: 7 Copynumber: 11.4 Consensus size: 7
1354483 ATTATGCTTG
1354493 AAGAAAA
1 AAGAAAA
1354500 AAGAAAAA
1 AAG-AAAA
1354508 AAGAAAA
1 AAGAAAA
1354515 AA-AAAA
1 AAGAAAA
1354521 AAGAAAA
1 AAGAAAA
1354528 AAGAAAA
1 AAGAAAA
1354535 AAGAAAA
1 AAGAAAA
1354542 AA-AAAA
1 AAGAAAA
1354548 AAGAAAAA
1 AAG-AAAA
1354556 AAGAGAAA
1 AAGA-AAA
1354564 AAGAAAA
1 AAGAAAA
1354571 AAG
1 AAG
1354574 GGGGGTCAAG
Statistics
Matches: 69, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
6 12 0.17
7 36 0.52
8 21 0.30
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:1354507 original size:1 final size:1
Alignment explanation
Indices: 1354496--1354572 Score: 73
Period size: 1 Copynumber: 77.0 Consensus size: 1
1354486 ATGCTTGAAG
* * * * * * * *
1354496 AAAAAAGAAAAAAAGAAAAAAAAAAAAGAAAAAAGAAAAAAGAAAAAAAAAAAAGAAAAAAAGAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1354561 AAAAAGAAAAAA
1 AAAAAAAAAAAA
1354573 GGGGGGTCAA
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:1354509 original size:8 final size:8
Alignment explanation
Indices: 1354496--1354572 Score: 89
Period size: 8 Copynumber: 10.6 Consensus size: 8
1354486 ATGCTTGAAG
1354496 AAAAAAGA
1 AAAAAAGA
1354504 AAAAAAG-
1 AAAAAAGA
1354511 -AAAAA-A
1 AAAAAAGA
1354517 AAAAAAG-
1 AAAAAAGA
1354524 AAAAAAG-
1 AAAAAAGA
1354531 AAAAAAG-
1 AAAAAAGA
1354538 -AAAAA-A
1 AAAAAAGA
1354544 AAAAAAGA
1 AAAAAAGA
1354552 AAAAAAGA
1 AAAAAAGA
*
1354560 GAAAAAGA
1 AAAAAAGA
1354568 AAAAA
1 AAAAA
1354573 GGGGGGTCAA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
6 10 0.16
7 24 0.39
8 27 0.44
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:1354521 original size:20 final size:19
Alignment explanation
Indices: 1354496--1354571 Score: 98
Period size: 20 Copynumber: 3.7 Consensus size: 19
1354486 ATGCTTGAAG
*
1354496 AAAAAAGAAAAAAAGAAAA
1 AAAAAAAAAAAAAAGAAAA
1354515 AAAAAAAAGAAAAAAGAAAA
1 AAAAAAAA-AAAAAAGAAAA
1354535 AAGAAAAAAAAAAAAGAAAA
1 AA-AAAAAAAAAAAAGAAAA
1354555 AAAGAGAAAAAGAAAAA
1 AAA-A-AAAAA-AAAAA
1354572 AGGGGGGTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
19 8 0.16
20 27 0.53
21 11 0.22
22 5 0.10
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAGAAAA
Found at i:1354533 original size:28 final size:28
Alignment explanation
Indices: 1354493--1354572 Score: 135
Period size: 27 Copynumber: 2.9 Consensus size: 28
1354483 ATTATGCTTG
1354493 AAGAAAAAAGAAAAAAAGAAAAAAAAAA
1 AAGAAAAAAGAAAAAAAGAAAAAAAAAA
1354521 AAGAAAAAAG-AAAAAAGAAAAAAAAAA
1 AAGAAAAAAGAAAAAAAGAAAAAAAAAA
*
1354548 AAGAAAAAAAGAGAAAAAGAAAAAA
1 AAG-AAAAAAGAAAAAAAGAAAAAA
1354573 GGGGGGTCAA
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
27 20 0.41
28 17 0.35
29 12 0.24
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (28 bp):
AAGAAAAAAGAAAAAAAGAAAAAAAAAA
Found at i:1354533 original size:35 final size:36
Alignment explanation
Indices: 1354493--1354573 Score: 139
Period size: 35 Copynumber: 2.3 Consensus size: 36
1354483 ATTATGCTTG
1354493 AAGAAAAAAGAAAAAAAGAAAAA-AAAAAAAGA-AAA
1 AAGAAAAAAGAAAAAAA-AAAAAGAAAAAAAGAGAAA
1354528 AAGAAAAAAGAAAAAAAAAAAAGAAAAAAAGAGAAA
1 AAGAAAAAAGAAAAAAAAAAAAGAAAAAAAGAGAAA
1354564 AAGAAAAAAG
1 AAGAAAAAAG
1354574 GGGGGTCAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 5 0.11
35 26 0.59
36 13 0.30
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (36 bp):
AAGAAAAAAGAAAAAAAAAAAAGAAAAAAAGAGAAA
Found at i:1355847 original size:83 final size:83
Alignment explanation
Indices: 1355705--1355970 Score: 478
Period size: 83 Copynumber: 3.2 Consensus size: 83
1355695 AAACATTAAA
* * *
1355705 TGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGGGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
*
1355770 TGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
1355788 TGAAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
1 TGGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
1355853 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
*
1355871 TGGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGC
1 TGGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
1355936 AGAACCAATCATTGAATT
66 AGAACCAATCATTGAATT
1355954 TGGAAGATGAATTTGCT
1 TGGAAGATGAATTTGCT
1355971 CATAGTAGAA
Statistics
Matches: 176, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 176 1.00
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (83 bp):
TGGAAGATGAATTTGCTAATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGC
AGAACCAATCATTGAATT
Found at i:1356978 original size:113 final size:112
Alignment explanation
Indices: 1356791--1357283 Score: 695
Period size: 113 Copynumber: 4.4 Consensus size: 112
1356781 TAGATTGACA
1356791 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1356856 AGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAGCT
66 AGAATTTGTTCAACCTTTTG-CTGAATTCATCACTTGATGGATCAGCT
*
1356904 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
1356969 AGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
66 AGAATTTGTTCAACCTTTT-GCTGAATTCATCACTTGATGGATCAGCT
*
1357017 TTTCCAGAAAAAGTTCATAATGA-AATGAACTCATCTGAAGAAGGATG-AGAAGTTCATAATGAG
1 TTTCCAGAAAAAGTTCATAATGAGAA-GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
* * * *
1357080 AAGAATTTGTTCAACCTTTTGCTCAAATCTATCACTTGATAGATTAGCT
65 AAGAATTTGTTCAACCTTTTGCTGAATTC-ATCACTTGATGGATCAGCT
**** * * * *
1357129 TTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTAAAGAATGATGAAGAAGTTCATAATGAGA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * *
1357194 AGAATTTGTTCAGA-TTTTTGCTCAAATCCATCACTTGATGGATCAACT
66 AGAATTTGTTCA-ACCTTTTGCT-GAATTCATCACTTGATGGATCAGCT
* *
1357242 TTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1 TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAA
1357284 AGAACTTGTT
Statistics
Matches: 337, Mismatches: 36, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
111 6 0.02
112 89 0.26
113 238 0.71
114 4 0.01
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (112 bp):
TTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTGCTGAATTCATCACTTGATGGATCAGCT
Found at i:1357183 original size:225 final size:226
Alignment explanation
Indices: 1356764--1357283 Score: 708
Period size: 225 Copynumber: 2.3 Consensus size: 226
1356754 TAGCAAAGAT
* * * ** *
1356764 TCAAATCTATCATTTGATAGATTGACATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAATTGATGGATCAACCTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* *
1356829 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCATCACTTGA
* * *
1356894 TGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
131 TAGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTT
1356959 CATAATGAGAAGAACTTGTTCA-ACCTTTTACC
196 CATAATGAGAAGAACTTGTTCAGA--TTTTACC
* * *
1356991 T-GAATTCATCAATTGATGGATCAGCCTTTCCAGAAAAAGTTCATAATGA-AATGAACTCATCTG
1 TCAAATCCATCAATTGATGGATCAACCTTTCCAGAAAAAGTTCATAATGAGAA-GAACTCATCTG
*
1357054 AAGAAGGATG-AGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-CTCAAATCTATCACTT
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATC-ATCACTT
* **** * *
1357117 GATAGATTAGCTTTTCCAGTTCGAGTTCATAATAAGAAGAACTCATCTAAAGAATGATGAAGAAG
129 GATAGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAG
* **
1357182 TTCATAATGAGAAGAATTTGTTCAGATTTTTGC
194 TTCATAATGAGAAGAACTTGTTCAGATTTTACC
* * * *
1357215 TCAAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAATTGATGGATCAACCTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1357280 AGAA
66 AGAA
1357284 AGAACTTGTT
Statistics
Matches: 256, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
224 12 0.05
225 181 0.71
226 62 0.24
227 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (226 bp):
TCAAATCCATCAATTGATGGATCAACCTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTCAAATCATCACTTGA
TAGATCAGCTTTTCCAGAGAAAGTTCATAATAAGAAGAACTCATCTAAAGAAGGAAGAAGAAGTT
CATAATGAGAAGAACTTGTTCAGATTTTACC
Found at i:1357635 original size:3 final size:3
Alignment explanation
Indices: 1357627--1357740 Score: 129
Period size: 3 Copynumber: 38.0 Consensus size: 3
1357617 CCATATTGAT
* * * * * *
1357627 TTA TTA TTA TAA TTA TAA TTA TTA TTA TAA TTA CTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
1357675 TTA TTA TTA TTA CTA TAA ATA TTA TTA TTA TTA TTA TTA TAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1357723 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
1357741 AAATATATAT
Statistics
Matches: 89, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1357664 original size:27 final size:27
Alignment explanation
Indices: 1357627--1357746 Score: 167
Period size: 27 Copynumber: 4.6 Consensus size: 27
1357617 CCATATTGAT
* * *
1357627 TTATTATTATAATTATAATTATTATTA
1 TTATTACTATAAATATTATTATTATTA
*
1357654 TAATTACTATAAATATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTA
1357681 TTATTACTATAAATATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTA
1357708 TTA-T--TATAAATATTATTATTATTA
1 TTATTACTATAAATATTATTATTATTA
*
1357732 TTATTATTA-AAATAT
1 TTATTACTATAAATAT
1357747 ATATATATAT
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
24 23 0.27
25 1 0.01
26 7 0.08
27 54 0.64
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
TTATTACTATAAATATTATTATTATTA
Found at i:1357872 original size:16 final size:16
Alignment explanation
Indices: 1357853--1357885 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1357843 CTCTAACCCT
1357853 AGCCACCTCTGCCTCC
1 AGCCACCTCTGCCTCC
*
1357869 AGCCGCCTCTGCCTCC
1 AGCCACCTCTGCCTCC
1357885 A
1 A
1357886 ACCGCCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.55, G:0.15, T:0.18
Consensus pattern (16 bp):
AGCCACCTCTGCCTCC
Found at i:1357890 original size:16 final size:16
Alignment explanation
Indices: 1357858--1357893 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1357848 ACCCTAGCCA
*
1357858 CCTCTGCCTCCAGCCG
1 CCTCTGCCTCCAACCG
1357874 CCTCTGCCTCCAACCG
1 CCTCTGCCTCCAACCG
1357890 CCTC
1 CCTC
1357894 AGCCAACGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.08, C:0.58, G:0.14, T:0.19
Consensus pattern (16 bp):
CCTCTGCCTCCAACCG
Found at i:1359118 original size:13 final size:13
Alignment explanation
Indices: 1359102--1359141 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
1359092 ATATAATAAA
1359102 TAAATATTTATTT
1 TAAATATTTATTT
*
1359115 TAAATAAATTATTT
1 TAAAT-ATTTATTT
1359129 T-AATATTTATTT
1 TAAATATTTATTT
1359141 T
1 T
1359142 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:1362238 original size:19 final size:19
Alignment explanation
Indices: 1362216--1362257 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
1362206 ACTTACAAAC
1362216 AGCTAATTAAACTACAATT
1 AGCTAATTAAACTACAATT
1362235 AGCTAATTAAACTACAATT
1 AGCTAATTAAACTACAATT
1362254 AGCT
1 AGCT
1362258 TTCCACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (19 bp):
AGCTAATTAAACTACAATT
Found at i:1364940 original size:15 final size:16
Alignment explanation
Indices: 1364916--1364960 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1364906 GCAAATAGCA
*
1364916 TCTTCTTCTTCTTC-C
1 TCTTCCTCTTCTTCTC
1364931 TCTTCCTCTTC-TCTC
1 TCTTCCTCTTCTTCTC
*
1364946 TCTTGCTCTTCTTCT
1 TCTTCCTCTTCTTCT
1364961 GAGGACTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 2 0.08
15 21 0.81
16 3 0.12
ACGTcount: A:0.00, C:0.40, G:0.02, T:0.58
Consensus pattern (16 bp):
TCTTCCTCTTCTTCTC
Found at i:1366303 original size:20 final size:22
Alignment explanation
Indices: 1366278--1366317 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1366268 AAAGTTATCT
1366278 AAAATATT-ATTTT-TTATTAA
1 AAAATATTAATTTTATTATTAA
1366298 AAAATATTAATTTTATTATT
1 AAAATATTAATTTTATTATT
1366318 TAATTTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
AAAATATTAATTTTATTATTAA
Found at i:1371410 original size:24 final size:24
Alignment explanation
Indices: 1371376--1371435 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
1371366 TATCATGTTA
*
1371376 TATCTTAGCTAGTGTCAAGACACT
1 TATCTTTGCTAGTGTCAAGACACT
1371400 TATCTTTGCTAGTGTCAAGACACT
1 TATCTTTGCTAGTGTCAAGACACT
*
1371424 TATCTTTACTAG
1 TATCTTTGCTAG
1371436 CTAGACGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (24 bp):
TATCTTTGCTAGTGTCAAGACACT
Found at i:1378110 original size:22 final size:22
Alignment explanation
Indices: 1378080--1378127 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1378070 TCGAGGGTTT
* *
1378080 CATAGGTCCTTTAGGACATATA
1 CATAAGTCCTTCAGGACATATA
*
1378102 CATAAGTCCTTCGGGACATATA
1 CATAAGTCCTTCAGGACATATA
1378124 CATA
1 CATA
1378128 GATCATTCGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (22 bp):
CATAAGTCCTTCAGGACATATA
Found at i:1378136 original size:22 final size:22
Alignment explanation
Indices: 1378093--1378141 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1378083 AGGTCCTTTA
*
1378093 GGACATATACATAAGTCCTTCG
1 GGACATATACATAAGTCATTCG
1378115 GGACATATACAT-AGATCATTCG
1 GGACATATACATAAG-TCATTCG
1378137 GGACA
1 GGACA
1378142 AATTTCATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (22 bp):
GGACATATACATAAGTCATTCG
Found at i:1381148 original size:30 final size:31
Alignment explanation
Indices: 1381112--1381187 Score: 127
Period size: 30 Copynumber: 2.5 Consensus size: 31
1381102 GAAGAACCTA
*
1381112 TCCATATGTTCCGAAGAACATAGGT-AACTG
1 TCCATATGTCCCGAAGAACATAGGTAAACTG
1381142 TCCATATGTCCCGAAGAACATAGGTAAACTG
1 TCCATATGTCCCGAAGAACATAGGTAAACTG
*
1381173 TCCATATGTCTCGAA
1 TCCATATGTCCCGAA
1381188 AGATATAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 24 0.56
31 19 0.44
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (31 bp):
TCCATATGTCCCGAAGAACATAGGTAAACTG
Found at i:1381175 original size:31 final size:30
Alignment explanation
Indices: 1381112--1381200 Score: 126
Period size: 30 Copynumber: 2.9 Consensus size: 30
1381102 GAAGAACCTA
*
1381112 TCCATATGTTCCGAAGAACATAGGTAACTG
1 TCCATATGTCCCGAAGAACATAGGTAACTG
1381142 TCCATATGTCCCGAAGAACATAGGTAAACTG
1 TCCATATGTCCCGAAGAACATAGGT-AACTG
* *
1381173 TCCATATGTCTCGAA-AGATATAGGTAAC
1 TCCATATGTCCCGAAGA-ACATAGGTAAC
1381201 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
30 28 0.52
31 26 0.48
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (30 bp):
TCCATATGTCCCGAAGAACATAGGTAACTG
Found at i:1381319 original size:24 final size:25
Alignment explanation
Indices: 1381291--1381338 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1381281 ATTCATATAG
*
1381291 ACATATGA-TTCACTTTCACATATT
1 ACATATAATTTCACTTTCACATATT
* *
1381315 ACATATAATTTCTCTTTCATATAT
1 ACATATAATTTCACTTTCACATAT
1381339 CTCATGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.46
Consensus pattern (25 bp):
ACATATAATTTCACTTTCACATATT
Found at i:1382729 original size:21 final size:21
Alignment explanation
Indices: 1382703--1382758 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
1382693 TCTTATTGTT
1382703 TTAAGCTTATATAAGCTTTCC
1 TTAAGCTTATATAAGCTTTCC
1382724 TTAAGCTTATATAAGCTTTCC
1 TTAAGCTTATATAAGCTTTCC
1382745 TTAAGCTTATATAA
1 TTAAGCTTATATAA
1382759 CACCCAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (21 bp):
TTAAGCTTATATAAGCTTTCC
Found at i:1384392 original size:16 final size:16
Alignment explanation
Indices: 1384353--1384394 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1384343 TAAAATTTCA
*
1384353 TAAATAATTA-AATAT
1 TAAATAAATATAATAT
1384368 TAAATAAATATAATAT
1 TAAATAAATATAATAT
1384384 ATAAA-AAATAT
1 -TAAATAAATAT
1384395 TTTATCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 9 0.38
16 11 0.46
17 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAATAAATATAATAT
Found at i:1386783 original size:22 final size:23
Alignment explanation
Indices: 1386746--1386789 Score: 72
Period size: 22 Copynumber: 1.9 Consensus size: 23
1386736 GGCGTGGAGT
1386746 TTTTATTGCATAATAATGCATACG
1 TTTTATT-CATAATAATGCATACG
1386770 TTTTATT-ATAATAATGCATA
1 TTTTATTCATAATAATGCATA
1386790 ATAATGTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (23 bp):
TTTTATTCATAATAATGCATACG
Found at i:1387272 original size:23 final size:22
Alignment explanation
Indices: 1387241--1387285 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1387231 AGGTTGAACG
1387241 ATTTATTAAATAGCTATATAAAT
1 ATTTATT-AATAGCTATATAAAT
*
1387264 ATTTGTTAATAGCTATATAAAT
1 ATTTATTAATAGCTATATAAAT
1387286 GTTGGTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.44
Consensus pattern (22 bp):
ATTTATTAATAGCTATATAAAT
Found at i:1392837 original size:23 final size:23
Alignment explanation
Indices: 1392807--1392862 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
1392797 CCACCAGTGC
1392807 ACATGCAAAAGCTACCGTAGAAT
1 ACATGCAAAAGCTACCGTAGAAT
1392830 ACATGCAAAAGCTACCGTAGAAT
1 ACATGCAAAAGCTACCGTAGAAT
1392853 ACATGCAAAA
1 ACATGCAAAA
1392863 CATTTCATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.16, T:0.16
Consensus pattern (23 bp):
ACATGCAAAAGCTACCGTAGAAT
Found at i:1393428 original size:21 final size:20
Alignment explanation
Indices: 1393402--1393455 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
1393392 TTCTTTAAAA
1393402 TATAATATTATGAATATATTT
1 TATAATATTA-GAATATATTT
* * *
1393423 TATAATTTTAGATTGTATTT
1 TATAATATTAGAATATATTT
1393443 TAT-ATATTA-AATA
1 TATAATATTAGAATA
1393456 AAATTACAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
20 11 0.41
21 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
TATAATATTAGAATATATTT
Found at i:1397232 original size:18 final size:18
Alignment explanation
Indices: 1397209--1397246 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1397199 GGTAAATAAA
* *
1397209 TTACCTAAAATATTAATT
1 TTACCTAAAACATCAATT
1397227 TTACCTAAAACATCAATT
1 TTACCTAAAACATCAATT
1397245 TT
1 TT
1397247 TGAACATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (18 bp):
TTACCTAAAACATCAATT
Found at i:1398053 original size:23 final size:23
Alignment explanation
Indices: 1398026--1398073 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1398016 AAAATACATT
1398026 TATTA-ATATTTCTAATAATATAA
1 TATTATAT-TTTCTAATAATATAA
* *
1398049 TATTATATTTTTTAATATTATAA
1 TATTATATTTTCTAATAATATAA
1398072 TA
1 TA
1398074 AAATACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTATATTTTCTAATAATATAA
Found at i:1398191 original size:24 final size:26
Alignment explanation
Indices: 1398122--1398214 Score: 66
Period size: 27 Copynumber: 3.5 Consensus size: 26
1398112 TTTTTATTTT
*
1398122 AATAATATATAATAAATTATTAATAA-A
1 AATAATAT-TATTAAATTA-TAATAATA
* * * *
1398149 ATTTATATTATATTTAATT-TCATAA-A
1 AATAATA-T-TATTAAATTATAATAATA
*
1398175 AATAATATTATTAAATTACTAATAATG
1 AATAATATTATTAAATTA-TAATAATA
1398202 AATAATATTATTA
1 AATAATATTATTA
1398215 TTTTTTTGAT
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
24 8 0.15
25 1 0.02
26 16 0.31
27 18 0.35
28 9 0.17
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (26 bp):
AATAATATTATTAAATTATAATAATA
Found at i:1398810 original size:26 final size:27
Alignment explanation
Indices: 1398781--1398838 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 27
1398771 ATAAATAATT
* *
1398781 AATATAATTTAAT-ATATTTTTATTTC
1 AATAAAATGTAATAATATTTTTATTTC
*
1398807 AATAAAATGTATTAATATTTTTA-TT-
1 AATAAAATGTAATAATATTTTTATTTC
1398832 AATAAAA
1 AATAAAA
1398839 AAATAGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 7 0.25
26 12 0.43
27 9 0.32
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (27 bp):
AATAAAATGTAATAATATTTTTATTTC
Found at i:1398908 original size:30 final size:30
Alignment explanation
Indices: 1398848--1398909 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1398838 AAAATAGAAA
* ***
1398848 TAATATTTTAATAATAATAATAAGTTATTT
1 TAATATTTTAAAAATAATAATAACAAATTT
*
1398878 TAATATTTTAAAAATAATAATATCAAATTT
1 TAATATTTTAAAAATAATAATAACAAATTT
1398908 TA
1 TA
1398910 TAAATAATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (30 bp):
TAATATTTTAAAAATAATAATAACAAATTT
Found at i:1399978 original size:37 final size:36
Alignment explanation
Indices: 1399903--1399978 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1399893 TTTTTATATT
*
1399903 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1399939 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1399976 TTT
1 TTT
1399979 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1400160 original size:20 final size:20
Alignment explanation
Indices: 1400124--1400161 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1400114 ATCCTATTCC
**
1400124 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
1400144 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1400162 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:1401605 original size:20 final size:21
Alignment explanation
Indices: 1401582--1401630 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1401572 CGAATATGTG
1401582 AATT-GCATTGCGATTTTCTA
1 AATTCGCATTGCGATTTTCTA
*
1401602 AATTCGCGTTGCGATTTTCTA
1 AATTCGCATTGCGATTTTCTA
1401623 AATTCGCA
1 AATTCGCA
1401631 ACGCGAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.41
Consensus pattern (21 bp):
AATTCGCATTGCGATTTTCTA
Found at i:1401636 original size:21 final size:21
Alignment explanation
Indices: 1401555--1401636 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 21
1401545 CGTAACTCAG
* *
1401555 TTTCCAAATTCGCAACGCGAA
1 TTTCTAAATTCGCAACGCGAT
* * * **
1401576 TATGTGAATT-GCATTGCGAT
1 TTTCTAAATTCGCAACGCGAT
***
1401596 TTTCTAAATTCGCGTTGCGAT
1 TTTCTAAATTCGCAACGCGAT
1401617 TTTCTAAATTCGCAACGCGA
1 TTTCTAAATTCGCAACGCGA
1401637 ATATGTAAAT
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 14 0.30
21 32 0.70
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (21 bp):
TTTCTAAATTCGCAACGCGAT
Found at i:1401645 original size:21 final size:21
Alignment explanation
Indices: 1401560--1401652 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 21
1401550 CTCAGTTTCC
*
1401560 AAATTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATATCT
* ** * *
1401581 GAATT-GCATTGCGATTTTCT
1 AAATTCGCAACGCGAATATCT
*** * *
1401601 AAATTCGCGTTGCGATTTTCT
1 AAATTCGCAACGCGAATATCT
*
1401622 AAATTCGCAACGCGAATATGT
1 AAATTCGCAACGCGAATATCT
1401643 AAA-TCGCAAC
1 AAATTCGCAAC
1401653 ACAGAAGTCA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.37
21 36 0.63
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (21 bp):
AAATTCGCAACGCGAATATCT
Found at i:1401720 original size:20 final size:20
Alignment explanation
Indices: 1401617--1401730 Score: 103
Period size: 19 Copynumber: 5.7 Consensus size: 20
1401607 GCGTTGCGAT
*
1401617 TTTCTAAATTCGCAACGCGAA
1 TTTC-AAATTCGCAACACGAA
1401638 TATGT-AAA-TCGCAACACAGAA
1 T-T-TCAAATTCGCAACAC-GAA
* *
1401659 -GTCAAATTTGCAACACTGAA
1 TTTCAAATTCGCAACAC-GAA
*
1401679 TTTCAAATTCGCAA-ATGAA
1 TTTCAAATTCGCAACACGAA
1401698 TTTCAAATTCGCAACACGAA
1 TTTCAAATTCGCAACACGAA
*
1401718 TTT-AATTTCGCAA
1 TTTCAAATTCGCAA
1401731 TAGGTTTTAG
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.01
19 29 0.38
20 27 0.35
21 18 0.23
22 1 0.01
23 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.28
Consensus pattern (20 bp):
TTTCAAATTCGCAACACGAA
Found at i:1404716 original size:20 final size:20
Alignment explanation
Indices: 1404693--1404767 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
1404683 TCGCAACGCA
* *
1404693 AATTTAACTTTCGCGTTGCG
1 AATTTGACTTTCACGTTGCG
* *
1404713 AATTTTGACTTTAACGTTGCA
1 AA-TTTGACTTTCACGTTGCG
*
1404734 AATTTGACTTTCACGTTGTG
1 AATTTGACTTTCACGTTGCG
*
1404754 AATTTGACTATCAC
1 AATTTGACTTTCAC
1404768 AACAACAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.41
Consensus pattern (20 bp):
AATTTGACTTTCACGTTGCG
Found at i:1406302 original size:21 final size:21
Alignment explanation
Indices: 1406276--1406351 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
1406266 GGGCACGGGA
*
1406276 TCTTGAACGGTTG-GAGGGGCC
1 TCTTGAAC-GATGAGAGGGGCC
*
1406297 TCTTGAACGATGAGAGTGGCC
1 TCTTGAACGATGAGAGGGGCC
1406318 TCTTGAACGATGAGAGGGGCC
1 TCTTGAACGATGAGAGGGGCC
* *
1406339 TCTTAAATGATGA
1 TCTTGAACGATGA
1406352 CAGGTGCATC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (21 bp):
TCTTGAACGATGAGAGGGGCC
Found at i:1406527 original size:4 final size:4
Alignment explanation
Indices: 1406495--1406540 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
1406485 GGGCTGCTGA
* * * *
1406495 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1406541 TGCCAAAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1408537 original size:20 final size:20
Alignment explanation
Indices: 1408509--1408673 Score: 258
Period size: 20 Copynumber: 8.2 Consensus size: 20
1408499 ATTCACAATG
1408509 CGAAAATGAAAATCGCAACA
1 CGAAAATGAAAATCGCAACA
*
1408529 CGAACATGAAAATCGCAACA
1 CGAAAATGAAAATCGCAACA
* *
1408549 CGAACATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACA
1408569 CGAAAATGAAAATCGCAACA
1 CGAAAATGAAAATCGCAACA
*
1408589 CGAACATGAAAATCGCAACA
1 CGAAAATGAAAATCGCAACA
* *
1408609 CGAACATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACA
*
1408629 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACA
*
1408649 CGAAAATGAAAATCGCAACG
1 CGAAAATGAAAATCGCAACA
1408669 CGAAA
1 CGAAA
1408674 CTAAATTTGC
Statistics
Matches: 138, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 138 1.00
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
CGAAAATGAAAATCGCAACA
Found at i:1408581 original size:60 final size:60
Alignment explanation
Indices: 1408508--1408672 Score: 303
Period size: 60 Copynumber: 2.8 Consensus size: 60
1408498 AATTCACAAT
1408508 GCGAAAATGAAAATCGCAACACGAACATGAAAATCGCAACACGAACATGAAAATCGCAAC
1 GCGAAAATGAAAATCGCAACACGAACATGAAAATCGCAACACGAACATGAAAATCGCAAC
1408568 GCGAAAATGAAAATCGCAACACGAACATGAAAATCGCAACACGAACATGAAAATCGCAAC
1 GCGAAAATGAAAATCGCAACACGAACATGAAAATCGCAACACGAACATGAAAATCGCAAC
* * *
1408628 GCGAAAATGAAAATCGCAACGCGAAAATGAAAATCGCAACGCGAA
1 GCGAAAATGAAAATCGCAACACGAACATGAAAATCGCAACACGAA
1408673 ACTAAATTTG
Statistics
Matches: 102, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 102 1.00
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (60 bp):
GCGAAAATGAAAATCGCAACACGAACATGAAAATCGCAACACGAACATGAAAATCGCAAC
Found at i:1408735 original size:20 final size:20
Alignment explanation
Indices: 1408692--1408735 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1408682 GCGTTGCGAT
* * * *
1408692 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTAGCGAATTTAAG
1408712 TTTCGTGTAGCGAATTTAAG
1 TTTCGTGTAGCGAATTTAAG
1408732 TTTC
1 TTTC
1408736 AAAAAATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGTGTAGCGAATTTAAG
Found at i:1409257 original size:20 final size:20
Alignment explanation
Indices: 1409232--1409288 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1409222 AAACGCGCTG
1409232 TGACTTATGTGTTGCGAATT
1 TGACTTATGTGTTGCGAATT
1409252 TGACTTATGTGTTGCGAATT
1 TGACTTATGTGTTGCGAATT
* *
1409272 TGACTTCTATGTTGCGA
1 TGACTTATGTGTTGCGA
1409289 TTTACATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (20 bp):
TGACTTATGTGTTGCGAATT
Found at i:1409287 original size:40 final size:40
Alignment explanation
Indices: 1409232--1409313 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
1409222 AAACGCGCTG
* * *
1409232 TGACTTATGTGTTGCGAATTTGACTTA-T-GTGTTGCGAATT
1 TGACTTATATGTTGCG-ATTT-ACATATTCGCGTTGCGAATT
*
1409272 TGACTTCTATGTTGCGATTTACATATTCGCGTTGCGAATT
1 TGACTTATATGTTGCGATTTACATATTCGCGTTGCGAATT
1409312 TG
1 TG
1409314 GAAAATCACA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 4 0.11
39 5 0.14
40 27 0.75
ACGTcount: A:0.20, C:0.13, G:0.23, T:0.44
Consensus pattern (40 bp):
TGACTTATATGTTGCGATTTACATATTCGCGTTGCGAATT
Found at i:1411378 original size:2 final size:2
Alignment explanation
Indices: 1411360--1411398 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
1411350 ACTTGTGGTA
*
1411360 AT AT AA AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1411399 CAATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1411720 original size:7 final size:7
Alignment explanation
Indices: 1411704--1411762 Score: 68
Period size: 7 Copynumber: 8.6 Consensus size: 7
1411694 CCTTAACTTA
*
1411704 AAACCCT
1 AAACCTT
1411711 AAACCTT
1 AAACCTT
1411718 AAACCTT
1 AAACCTT
*
1411725 AAACCCT
1 AAACCTT
1411732 AAA-CTCT
1 AAACCT-T
1411739 AAACCTT
1 AAACCTT
*
1411746 AAACCCT
1 AAACCTT
1411753 AAACC-T
1 AAACCTT
1411759 AAAC
1 AAAC
1411763 ATAACCCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
6 6 0.13
7 38 0.83
8 2 0.04
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCTT
Found at i:1411721 original size:14 final size:14
Alignment explanation
Indices: 1411704--1411762 Score: 84
Period size: 14 Copynumber: 4.3 Consensus size: 14
1411694 CCTTAACTTA
1411704 AAACCCTAAACCTT
1 AAACCCTAAACCTT
* *
1411718 AAACCTTAAACCCT
1 AAACCCTAAACCTT
*
1411732 AAACTCTAAACCTT
1 AAACCCTAAACCTT
1411746 AAACCCTAAACC-T
1 AAACCCTAAACCTT
1411759 AAAC
1 AAAC
1411763 ATAACCCTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
13 5 0.13
14 34 0.87
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:1411730 original size:21 final size:21
Alignment explanation
Indices: 1411704--1411762 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
1411694 CCTTAACTTA
1411704 AAACCCTAAACCTTAAACCTT
1 AAACCCTAAACCTTAAACCTT
1411725 AAACCCTAAA-CTCTAAACCTT
1 AAACCCTAAACCT-TAAACCTT
1411746 AAACCCTAAACC-TAAAC
1 AAACCCTAAACCTTAAAC
1411763 ATAACCCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.19
21 28 0.78
22 1 0.03
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (21 bp):
AAACCCTAAACCTTAAACCTT
Found at i:1422446 original size:21 final size:23
Alignment explanation
Indices: 1422404--1422446 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1422394 AAGACAAAAC
1422404 CCTTGCTCACAGCCTGCAAAATAA
1 CCTTGCT-ACAGCCTGCAAAATAA
1422428 CCTTGCT-CAGCCT-CAAAAT
1 CCTTGCTACAGCCTGCAAAAT
1422447 GGAGCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
24 7 0.37
ACGTcount: A:0.30, C:0.35, G:0.12, T:0.23
Consensus pattern (23 bp):
CCTTGCTACAGCCTGCAAAATAA
Found at i:1425753 original size:23 final size:23
Alignment explanation
Indices: 1425699--1425764 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
1425689 CATTAGGGGA
*
1425699 TTAGGG-TTAAAACCTAATTTGTT
1 TTAGGGTTTGAAACCTAA-TTGTT
1425722 TTAGGGTTTGAAACCTTAATTG-T
1 TTAGGGTTTGAAACC-TAATTGTT
1425745 TTAGGGTTTGAAACCCTAAT
1 TTAGGGTTTGAAA-CCTAAT
1425765 CTGATGGGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 24 0.62
24 12 0.31
25 3 0.08
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.41
Consensus pattern (23 bp):
TTAGGGTTTGAAACCTAATTGTT
Found at i:1425888 original size:13 final size:14
Alignment explanation
Indices: 1425870--1425902 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1425860 AATATGTAAT
1425870 TAATAAACTAT-AA
1 TAATAAACTATAAA
*
1425883 TAATAAATTATAAA
1 TAATAAACTATAAA
1425897 TAATAA
1 TAATAA
1425903 TAATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATAAACTATAAA
Found at i:1425905 original size:10 final size:10
Alignment explanation
Indices: 1425879--1425925 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1425869 TTAATAAACT
1425879 ATAATAATAA
1 ATAATAATAA
1425889 AT--T-ATAA
1 ATAATAATAA
1425896 ATAATAAT-A
1 ATAATAATAA
1425905 AT-ATATATAA
1 ATAATA-ATAA
1425915 ATAATAATAA
1 ATAATAATAA
1425925 A
1 A
1425926 AAAAGACCCG
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
7 6 0.19
8 4 0.13
9 6 0.19
10 12 0.39
11 3 0.10
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (10 bp):
ATAATAATAA
Found at i:1425921 original size:7 final size:7
Alignment explanation
Indices: 1425881--1425921 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
1425871 AATAAACTAT
1425881 AATAATA
1 AATAATA
*
1425888 AATTATA
1 AATAATA
1425895 AATAAT-
1 AATAATA
1425901 AATAATA
1 AATAATA
*
1425908 TAT-ATA
1 AATAATA
1425914 AATAATA
1 AATAATA
1425921 A
1 A
1425922 TAAAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (7 bp):
AATAATA
Found at i:1429139 original size:311 final size:311
Alignment explanation
Indices: 1428428--1429353 Score: 1323
Period size: 311 Copynumber: 3.0 Consensus size: 311
1428418 ATAATTATAC
* * * * *
1428428 CAATTTTATTTAAGTGTCATATCGACACTTCTATTAAATA-TAACGACTG-GGGCTTAATTG---
1 CAATTTTA-TTAACTGTCACATCAACACTTCTATTAAATATTAACGAATGCTGGCTTAATTGAAT
* *
1428488 ATAATTAAATAGTTAAGTGGTCTGATTGAAAAAATTGAAAGATCGATGATAAAAGT-AAAAAATG
65 ATAATCAAATAGTTAAGTGGTCTGATTGACAAAATTGAAAGATCGATGATAAAAGTAAAAAAAT-
* * *
1428552 CTAAATAGTTGAGTGGTCAATGGTATAGTTTACCC-TAAATAATTTACCTTTAAATTTTAACTAA
129 CTAAATAGTTGAGTGGTTAATGATATAGTTTACCCTTAAATAATTTACATTTAAATTTTAACTAA
* * *
1428616 TTTATAA-T-TACGTTGAGT-TTTATAATTTTAATGTTTTATAAATTAATTTATCGGCGCTTATC
194 TTTATAATTATACATTGAGTACTTATAATTTTAATG-TTT-TAAATTAATTTATCGGCGCTCATC
* *
1428678 GTTAGTGGTACTCATCGCTG--CGTCGAGTGTGGAAGACTCATCATTTAAATAAG
257 GTTAGTGGTACTCATCGCTGCTCGTCGAGTGTGGAAGACTCGTCATTTAAATAAA
** *
1428731 CAAATTTTA-TAACTGTCACATCAGGA-TTTTATTAAATATTAAC-AACTGCTGGCTTAATTGAA
1 C-AATTTTATTAACTGTCACATCAACACTTCTATTAAATATTAACGAA-TGCTGGCTTAATTGAA
* * * *
1428793 TATAATCAAATACTTAAATGGTCTGATTGACAAAATTGAAAAATTGATGATAAAAGTAAAAAAAT
64 TATAATCAAATAGTTAAGTGGTCTGATTGACAAAATTGAAAGATCGATGATAAAAGTAAAAAAAT
*
1428858 CTAAATAGTTGAGTGGTTAATGATATAGTTTACCCTTAAAAAATTTACATTTAAATTTTTAACTA
129 CTAAATAGTTGAGTGGTTAATGATATAGTTTACCCTTAAATAATTTACATTTAAA-TTTTAACTA
1428923 ATTTATAATTATAC-TTGAGTACTTATAATTTTAATGTTTTAAATTAATTTATCGGCGCTCATCG
193 ATTTATAATTATACATTGAGTACTTATAATTTTAATGTTTTAAATTAATTTATCGGCGCTCATCG
* * *
1428987 TTAGTGGTACTCATCGTTGCTCGTCGAGTGTGGAAGGCCCGTCATTTAAATAAA
258 TTAGTGGTACTCATCGCTGCTCGTCGAGTGTGGAAGACTCGTCATTTAAATAAA
1429041 CAATTTTATTAACTGTCACATCAACACTTCTATTAAATATTAACGAATGCTGGCTTAATTGAATA
1 CAATTTTATTAACTGTCACATCAACACTTCTATTAAATATTAACGAATGCTGGCTTAATTGAATA
*
1429106 TAATCAAATAGTTAAGTGGTCTGATTGACAAAATTGAAAGATCGATGATAAAAGTAAAAAATTCT
66 TAATCAAATAGTTAAGTGGTCTGATTGACAAAATTGAAAGATCGATGATAAAAGTAAAAAAATCT
*
1429171 CAATAGTTGAGTGGTTAATGATATAGTTTACCCTTAAATAATTTACATTTAAAATTTTAACTAAT
131 AAATAGTTGAGTGGTTAATGATATAGTTTACCCTTAAATAATTTACATTT-AAATTTTAACTAAT
* * * *
1429236 TTGTAATTATACATTGAATACTTTATAATTTTAATGTTTT--A-TAAATTATCGACGCTCATCGT
195 TTATAATTATACATTGAGTAC-TTATAATTTTAATGTTTTAAATTAATTTATCGGCGCTCATCGT
* * *
1429298 TAGTGGTACTCATCGCTGCTCGTCGAGCGTGGAAGAATCGTCCTTTAAATAAA
259 TAGTGGTACTCATCGCTGCTCGTCGAGTGTGGAAGACTCGTCATTTAAATAAA
1429351 CAA
1 CAA
1429354 GAAACTTGTA
Statistics
Matches: 557, Mismatches: 45, Indels: 35
0.87 0.07 0.05
Matches are distributed among these distances:
301 12 0.02
302 18 0.03
303 11 0.02
304 7 0.01
306 83 0.15
307 24 0.04
308 59 0.11
309 17 0.03
310 131 0.24
311 165 0.30
312 12 0.02
313 18 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (311 bp):
CAATTTTATTAACTGTCACATCAACACTTCTATTAAATATTAACGAATGCTGGCTTAATTGAATA
TAATCAAATAGTTAAGTGGTCTGATTGACAAAATTGAAAGATCGATGATAAAAGTAAAAAAATCT
AAATAGTTGAGTGGTTAATGATATAGTTTACCCTTAAATAATTTACATTTAAATTTTAACTAATT
TATAATTATACATTGAGTACTTATAATTTTAATGTTTTAAATTAATTTATCGGCGCTCATCGTTA
GTGGTACTCATCGCTGCTCGTCGAGTGTGGAAGACTCGTCATTTAAATAAA
Found at i:1434840 original size:14 final size:15
Alignment explanation
Indices: 1434804--1434835 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1434794 GGCCAATGGT
1434804 ATAATTTACCCTTAA
1 ATAATTTACCCTTAA
*
1434819 ATAATTTACCTTTAA
1 ATAATTTACCCTTAA
1434834 AT
1 AT
1434836 TTTTAACTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATTTACCCTTAA
Found at i:1443548 original size:21 final size:21
Alignment explanation
Indices: 1443522--1443561 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1443512 CCCCCTTTGA
*
1443522 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
1443543 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
1443562 TGGGGTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:1447221 original size:21 final size:21
Alignment explanation
Indices: 1447197--1447241 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1447187 AGTAATGCAA
* *
1447197 ATTTTTAATTCATATAAAAAT
1 ATTTTCAAGTCATATAAAAAT
* *
1447218 ATTTTCAAGTCATTTTAAAAT
1 ATTTTCAAGTCATATAAAAAT
1447239 ATT
1 ATT
1447242 AAATTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (21 bp):
ATTTTCAAGTCATATAAAAAT
Done.