Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009628.1 Hibiscus syriacus cultivar Beakdansim tig00117021_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: 2284295
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 5 of 10
Found at i:1040839 original size:20 final size:21
Alignment explanation
Indices: 1040810--1040867 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
1040800 GCAACGCGAA
1040810 TTGA-CTTTCGCGTTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
**
1040830 TTG-GCTTTCGTATTGCGATT
1 TTGAGCTTTCGCGTTGCGATT
*
1040850 TTGAG-TTTAGCGTTGCGA
1 TTGAGCTTTCGCGTTGCGA
1040868 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.12, C:0.16, G:0.28, T:0.45
Consensus pattern (21 bp):
TTGAGCTTTCGCGTTGCGATT
Found at i:1042448 original size:42 final size:42
Alignment explanation
Indices: 1042389--1042482 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
1042379 GTGAATCAGG
* *
1042389 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACATGGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCAACGATGACAGGGGC
* ** *
1042431 CTCTTGAACGGTGGGAGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
1042473 CTCTTGAACG
1 CTCTTGAACG
1042483 ATGACAGGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 41 0.91
43 4 0.09
ACGTcount: A:0.20, C:0.19, G:0.37, T:0.23
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCAACGATGACAGGGGC
Found at i:1042455 original size:21 final size:20
Alignment explanation
Indices: 1042389--1042458 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
1042379 GTGAATCAGG
*
1042389 CTCTTGAATGGTGGGAGGGA
1 CTCTTGAACGGTGGGAGGGA
* * ** *
1042409 CCTCTTCAACGATGACATGGGC
1 -CTCTTGAACGGTGGGA-GGGA
1042431 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGA-GGGA
1042452 CTCTTGA
1 CTCTTGA
1042459 GGGATGATAG
Statistics
Matches: 36, Mismatches: 12, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
21 33 0.92
22 3 0.08
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (20 bp):
CTCTTGAACGGTGGGAGGGA
Found at i:1042485 original size:21 final size:21
Alignment explanation
Indices: 1042404--1042490 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
1042394 GAATGGTGGG
* *
1042404 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
1042425 ATGGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
1042446 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
1042467 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
1042488 AGG
1 AGG
1042491 TGAGACGGGC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:1042962 original size:20 final size:20
Alignment explanation
Indices: 1042937--1042980 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1042927 AATAGTTTCT
1042937 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1042957 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1042977 GAAA
1 GAAA
1042981 ATGACTATCG
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:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1042990 original size:20 final size:20
Alignment explanation
Indices: 1042967--1043014 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1042957 GAAACTTAAA
1042967 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1042987 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
1043007 ATCGCAAC
1 ATCGCAAC
1043015 AAGACAATCA
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:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1043163 original size:20 final size:20
Alignment explanation
Indices: 1043131--1043198 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1043121 CGATTATTCT
* *
1043131 GTTGTGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
*
1043151 GTTGCGATGGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
* *
1043171 GTTGCGATAGTCATTTTCAC
1 GTTGCGATAGTCAATTTCGC
1043191 GTTGCGAT
1 GTTGCGAT
1043199 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:1045135 original size:20 final size:20
Alignment explanation
Indices: 1045110--1045153 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
1045100 AATAGTTTCT
1045110 GAAACTTAAAATCGCAACAC
1 GAAACTTAAAATCGCAACAC
*
1045130 GAAACTTAAAATCGCAACGC
1 GAAACTTAAAATCGCAACAC
1045150 GAAA
1 GAAA
1045154 ATGACTATCG
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:0.50, C:0.23, G:0.14, T:0.14
Consensus pattern (20 bp):
GAAACTTAAAATCGCAACAC
Found at i:1045163 original size:20 final size:20
Alignment explanation
Indices: 1045140--1045187 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1045130 GAAACTTAAA
1045140 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
1045160 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACT
1045180 ATCGCAAC
1 ATCGCAAC
1045188 AAGACAATCA
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:0.38, C:0.27, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1045336 original size:20 final size:20
Alignment explanation
Indices: 1045304--1045371 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
1045294 CGATTATTCT
* *
1045304 GTTGTGATAGTCAAATTCGC
1 GTTGCGATAGTCAATTTCGC
*
1045324 GTTGCGATGGTC-ATTTCCGC
1 GTTGCGATAGTCAATTT-CGC
* *
1045344 GTTGCGATAGTCATTTTCAC
1 GTTGCGATAGTCAATTTCGC
1045364 GTTGCGAT
1 GTTGCGAT
1045372 TTTAAGTTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.37
Consensus pattern (20 bp):
GTTGCGATAGTCAATTTCGC
Found at i:1047345 original size:20 final size:20
Alignment explanation
Indices: 1047290--1047395 Score: 108
Period size: 20 Copynumber: 5.4 Consensus size: 20
1047280 TCTGAAACTT
* *
1047290 AAAATCGCAACACAAAAATG
1 AAAATCGCAACGCGAAAATG
*
1047310 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
1047330 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
1047350 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
1047369 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
1047388 AAAATCGC
1 AAAATCGC
1047396 GTTGAGATTT
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
19 23 0.31
20 51 0.69
ACGTcount: A:0.46, C:0.24, G:0.16, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:1047815 original size:22 final size:22
Alignment explanation
Indices: 1047785--1047842 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
1047775 GATGGAGATA
1047785 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
1047807 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1047829 GACGGATGTCGCCG
1 GACGGATTTCGCCG
1047843 TAGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.45, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1048047 original size:41 final size:41
Alignment explanation
Indices: 1048002--1048083 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
1047992 ATTTTGTATT
* *
1048002 ATCGCAACACGATAGTCAGAATCGCGTTGCGAATTTGGAAA
1 ATCGCAACACGATAGTCAAAATCGCGTTGCGAATCTGGAAA
*** *
1048043 ATCGCAATGTGATAGTCAAAATCGCGTTGTGAATCTGGAAA
1 ATCGCAACACGATAGTCAAAATCGCGTTGCGAATCTGGAAA
1048084 CTGATTTGCG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.24
Consensus pattern (41 bp):
ATCGCAACACGATAGTCAAAATCGCGTTGCGAATCTGGAAA
Found at i:1052616 original size:2 final size:2
Alignment explanation
Indices: 1052611--1052645 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
1052601 TTATAAATAA
*
1052611 AT AT AT AT AT AT AT AT AT AT AT AG AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1052646 TGTATACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1059587 original size:21 final size:20
Alignment explanation
Indices: 1059539--1059587 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
1059529 AATTACTAAA
* * *
1059539 AATTTCAAATTATTTGAGTT
1 AATTTTAAATTATTCGAATT
1059559 AATATTTAAATTATTCGAATT
1 AAT-TTTAAATTATTCGAATT
1059580 ATATTTTA
1 A-ATTTTA
1059588 TATTTGGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 19 0.79
22 2 0.08
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (20 bp):
AATTTTAAATTATTCGAATT
Found at i:1062859 original size:25 final size:24
Alignment explanation
Indices: 1062808--1062882 Score: 93
Period size: 21 Copynumber: 3.1 Consensus size: 24
1062798 GAAAATAAAA
*
1062808 ATAAAATATTTTTAAATTAAGTTAAT
1 ATAAAATATATTT-AA-TAAGTTAAT
1062834 AGTAAAATATATTTAATAAGTTAAT
1 A-TAAAATATATTTAATAAGTTAAT
1062859 ATAAAA-ATATTT--TAAGTTAAT
1 ATAAAATATATTTAATAAGTTAAT
1062880 ATA
1 ATA
1062883 TATATAGTTT
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
21 12 0.26
23 6 0.13
24 5 0.11
25 10 0.21
26 3 0.06
27 11 0.23
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (24 bp):
ATAAAATATATTTAATAAGTTAAT
Found at i:1063171 original size:39 final size:39
Alignment explanation
Indices: 1063128--1063238 Score: 127
Period size: 39 Copynumber: 2.8 Consensus size: 39
1063118 TTTAAAAAAT
*
1063128 AATTTAAAATGTTAATGTGAAATAATTTAAGAAATTAAA
1 AATTTAAAATATTAATGTGAAATAATTTAAGAAATTAAA
* * *
1063167 AATTTAGAATATT-ATAGTGTCAA-AATTTAAAAAATTAAA
1 AATTTAAAATATTAAT-GTG-AAATAATTTAAGAAATTAAA
* *
1063206 ATTTTAAAATATTAAAGTGAAATAATTTGAAGA
1 AATTTAAAATATTAATGTGAAATAATTT-AAGA
1063239 TTGTGAATAA
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
38 4 0.07
39 48 0.83
40 6 0.10
ACGTcount: A:0.53, C:0.01, G:0.10, T:0.36
Consensus pattern (39 bp):
AATTTAAAATATTAATGTGAAATAATTTAAGAAATTAAA
Found at i:1063208 original size:15 final size:16
Alignment explanation
Indices: 1063188--1063221 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1063178 TTATAGTGTC
1063188 AAAA-TTTAAAAAATT
1 AAAATTTTAAAAAATT
*
1063203 AAAATTTTAAAATATT
1 AAAATTTTAAAAAATT
1063219 AAA
1 AAA
1063222 GTGAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATTTTAAAAAATT
Found at i:1066431 original size:17 final size:17
Alignment explanation
Indices: 1066409--1066476 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
1066399 AATTAAGAGT
1066409 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* **
1066426 TAGTTTGATTTATGAAC
1 TAGTTTAATAAATGAAC
*
1066443 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* *
1066460 TAACTTTATTAAATGAA
1 T-AGTTTAATAAATGAA
1066477 ATAGATGCTT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:1066489 original size:18 final size:17
Alignment explanation
Indices: 1066468--1066527 Score: 70
Period size: 16 Copynumber: 3.5 Consensus size: 17
1066458 ACTAACTTTA
1066468 TTAAATGAAATAG-ATGC
1 TTAAATGAAAT-GCATGC
*
1066485 TTTAAATGCAATGCATGC
1 -TTAAATGAAATGCATGC
*
1066503 TTAAATGAACT-CATGC
1 TTAAATGAAATGCATGC
1066519 TTAAATGAA
1 TTAAATGAA
1066528 GTAGTATGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
16 14 0.37
17 10 0.26
18 14 0.37
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (17 bp):
TTAAATGAAATGCATGC
Found at i:1066884 original size:18 final size:17
Alignment explanation
Indices: 1066856--1066890 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1066846 TTTATATTTT
*
1066856 TTATTATAATACATTAA
1 TTATTATAATAAATTAA
1066873 TTATTAATAATAAATTAA
1 TTATT-ATAATAAATTAA
1066891 GATAATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TTATTATAATAAATTAA
Found at i:1067287 original size:2 final size:2
Alignment explanation
Indices: 1067280--1067306 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1067270 CATCATGAAA
1067280 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 A
1067307 AAAACGATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1068938 original size:2 final size:2
Alignment explanation
Indices: 1068931--1068956 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1068921 AGATGAAAGT
1068931 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
1068957 TATATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1076793 original size:37 final size:38
Alignment explanation
Indices: 1076728--1076804 Score: 138
Period size: 37 Copynumber: 2.1 Consensus size: 38
1076718 TTAATTGGCT
1076728 AAGTAATTATTACTCCAATCGAAATAAAGAAATATTAC
1 AAGTAATTATTACTCCAATCGAAATAAAGAAATATTAC
*
1076766 AAGTAATTCTTACT-CAATCGAAATAAAGAAATATTAC
1 AAGTAATTATTACTCCAATCGAAATAAAGAAATATTAC
1076803 AA
1 AA
1076805 TTCCATCAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 25 0.66
38 13 0.34
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.29
Consensus pattern (38 bp):
AAGTAATTATTACTCCAATCGAAATAAAGAAATATTAC
Found at i:1104570 original size:21 final size:20
Alignment explanation
Indices: 1104531--1104576 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1104521 AATGACCAAC
* *
1104531 AATAACAAAATGGTAGAAAA
1 AATAACAAAACGATAGAAAA
*
1104551 AATAACAAAACCGATAGAAAT
1 AATAACAAAA-CGATAGAAAA
1104572 AATAA
1 AATAA
1104577 TGTTTCCGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (20 bp):
AATAACAAAACGATAGAAAA
Found at i:1104884 original size:20 final size:20
Alignment explanation
Indices: 1104823--1104887 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1104813 ACACATGTCT
1104823 TTTTCGCAACGCGAATTTGTA
1 TTTTCGCAACGCGAATTT-TA
* * **
1104844 -ATTCGCAAAGCG-CGTTTA
1 TTTTCGCAACGCGAATTTTA
1104862 TTTTCGCAACGCGAATTTTA
1 TTTTCGCAACGCGAATTTTA
1104882 TTTTCG
1 TTTTCG
1104888 AATTCGAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
18 2 0.06
19 12 0.35
20 20 0.59
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTTCGCAACGCGAATTTTA
Found at i:1104902 original size:26 final size:26
Alignment explanation
Indices: 1104864--1104913 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
1104854 CGCGTTTATT
* * * *
1104864 TTCGCAACGCGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
1104890 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
1104914 CAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:1105444 original size:20 final size:20
Alignment explanation
Indices: 1105419--1105456 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1105409 ATCGTGTTAG
1105419 TTTTCGCGTTGCGAATTTCA
1 TTTTCGCGTTGCGAATTTCA
*
1105439 TTTTCGTGTTGCGAATTT
1 TTTTCGCGTTGCGAATTT
1105457 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
TTTTCGCGTTGCGAATTTCA
Found at i:1105463 original size:20 final size:20
Alignment explanation
Indices: 1105420--1105463 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1105410 TCGTGTTAGT
* *
1105420 TTTCGCGTTGCGAATTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
1105440 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
1105460 TTTC
1 TTTC
1105464 AAAAACTACT
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:0.16, C:0.16, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:1107148 original size:21 final size:21
Alignment explanation
Indices: 1107117--1107166 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1107107 GTTAGGGGAG
* *
1107117 TTACGTAATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
* *
1107138 TTGCGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
1107159 TTACGTGA
1 TTACGTGA
1107167 CGACAATAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:1107271 original size:60 final size:61
Alignment explanation
Indices: 1107158--1107273 Score: 137
Period size: 60 Copynumber: 1.9 Consensus size: 61
1107148 AGGTCGGTAC
* * *
1107158 TTTACGTGACGACAATAGTGTATTGTGATGAGGTACGATCTTTATGTGGTGAGGTATCTGT
1 TTTACGTGACGACAATAGTGTATTGTGATGAGGTACGATCGTTACGTGATGAGGTATCTGT
* * * * *
1107219 TTTACGTGATGATAATGGTGT-TTGTGGTGAGGTATCTA-CGTTACGTGATGAGGTA
1 TTTACGTGACGACAATAGTGTATTGTGATGAGGTA-CGATCGTTACGTGATGAGGTA
1107274 GCCGCTCTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
60 26 0.57
61 20 0.43
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (61 bp):
TTTACGTGACGACAATAGTGTATTGTGATGAGGTACGATCGTTACGTGATGAGGTATCTGT
Found at i:1109543 original size:18 final size:18
Alignment explanation
Indices: 1109520--1109555 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1109510 AAGCCGGTTG
*
1109520 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1109538 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1109556 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1112006 original size:12 final size:12
Alignment explanation
Indices: 1111985--1112018 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1111975 GGTTGTGGGT
*
1111985 TTTGAGATTGTG
1 TTTGATATTGTG
1111997 TTTGATATTGTG
1 TTTGATATTGTG
*
1112009 TTTGGTATTG
1 TTTGATATTG
1112019 GAAATATGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1112823 original size:17 final size:17
Alignment explanation
Indices: 1112801--1112833 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1112791 TGCGTATTTG
1112801 TGTTGCGAAAA-TAAAAC
1 TGTTGC-AAAATTAAAAC
1112818 TGTTGCAAAATTAAAA
1 TGTTGCAAAATTAAAA
1112834 TTCGTGTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.27
Consensus pattern (17 bp):
TGTTGCAAAATTAAAAC
Found at i:1112843 original size:20 final size:21
Alignment explanation
Indices: 1112800--1112986 Score: 95
Period size: 20 Copynumber: 9.5 Consensus size: 21
1112790 CTGCGTATTT
1112800 GTGTTGCGAAAA-TAAAA--C
1 GTGTTGCGAAAATTAAAATTC
1112818 -TGTTGC-AAAATTAAAATTC
1 GTGTTGCGAAAATTAAAATTC
1112837 GTGTTGCG--AATTCGAAAA-TC
1 GTGTTGCGAAAATT--AAAATTC
* *
1112857 GAGTTGCGAAAA-CAAAATTC
1 GTGTTGCGAAAATTAAAATTC
*
1112877 GTGTTGCG--AATTAGAAAATC
1 GTGTTGCGAAAATTA-AAATTC
* * *
1112897 TTGTTGCGAAAATGAAACTT-
1 GTGTTGCGAAAATTAAAATTC
*
1112917 GTGTTGCGAAAA--GAAATTC
1 GTGTTGCGAAAATTAAAATTC
*
1112936 GCGTTGCG--AATTCAGAAATT-
1 GTGTTGCGAAAATT-A-AAATTC
* * *
1112956 GAGTTGCG-AATTTGAAATTCC
1 GTGTTGCGAAAATTAAAATT-C
1112977 GTGTTGCGAA
1 GTGTTGCGAA
1112987 TTTGGAAACT
Statistics
Matches: 128, Mismatches: 18, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
16 4 0.03
17 13 0.10
18 6 0.05
19 22 0.17
20 54 0.42
21 22 0.17
22 7 0.05
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.29
Consensus pattern (21 bp):
GTGTTGCGAAAATTAAAATTC
Found at i:1112874 original size:40 final size:41
Alignment explanation
Indices: 1112819--1112986 Score: 150
Period size: 40 Copynumber: 4.2 Consensus size: 41
1112809 AAATAAAACT
* *
1112819 GTTGC-AAAATTAAAATTCGTGTTGCGAATTCGAAAATCGA
1 GTTGCGAAAATCAAAATTCGTGTTGCGAATTAGAAAATCGA
**
1112859 GTTGCGAAAA-CAAAATTCGTGTTGCGAATTAGAAAATCTT
1 GTTGCGAAAATCAAAATTCGTGTTGCGAATTAGAAAATCGA
* * * * *
1112899 GTTGCGAAAATGAAACTT-GTGTTGCGAA-AAGAAATTCGC
1 GTTGCGAAAATCAAAATTCGTGTTGCGAATTAGAAAATCGA
* * * * *
1112938 GTTGCG-AATTCAGAAATT-GAGTTGCGAATTTGAAATTCCGT
1 GTTGCGAAAATCA-AAATTCGTGTTGCGAATTAGAAAAT-CGA
1112979 GTTGCGAA
1 GTTGCGAA
1112987 TTTGGAAACT
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
38 4 0.04
39 26 0.25
40 57 0.54
41 17 0.16
42 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (41 bp):
GTTGCGAAAATCAAAATTCGTGTTGCGAATTAGAAAATCGA
Found at i:1112922 original size:80 final size:80
Alignment explanation
Indices: 1112818--1113007 Score: 190
Period size: 80 Copynumber: 2.4 Consensus size: 80
1112808 AAAATAAAAC
* * ** *
1112818 TGTTGC-AAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAGTTGCGAAAACA-AAATTCGTGT
1 TGTTGCGAAAATGAAACTT-GTGTTGCGAA-AAGAAAATCGAGTTGCGAAAACAGAAATT-GAGT
*
1112881 TGCGAATTAGAAAAT-CT
63 TGCGAATTAGAAAATCCG
* * **
1112898 TGTTGCGAAAATGAAACTTGTGTTGCGAAAAGAAATTCGCGTTGCGAATTCAGAAATTGAGTTGC
1 TGTTGCGAAAATGAAACTTGTGTTGCGAAAAGAAAATCGAGTTGCGAAAACAGAAATTGAGTTGC
* *
1112963 GAATTTGAAATTCCG
66 GAATTAGAAAATCCG
**
1112978 TGTTGCGAATTTGGAAAC-TGTGTTGCGAAA
1 TGTTGCGAAAAT-GAAACTTGTGTTGCGAAA
1113008 TTGAAGTTCG
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
79 33 0.36
80 44 0.48
81 15 0.16
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.31
Consensus pattern (80 bp):
TGTTGCGAAAATGAAACTTGTGTTGCGAAAAGAAAATCGAGTTGCGAAAACAGAAATTGAGTTGC
GAATTAGAAAATCCG
Found at i:1112947 original size:99 final size:100
Alignment explanation
Indices: 1112799--1113012 Score: 244
Period size: 99 Copynumber: 2.2 Consensus size: 100
1112789 GCTGCGTATT
* * *
1112799 TGTGTTGCGAAAATAAAAC---TGTTGC-AAAATTAAAATTCGTGTTGCGAATTC-GAAAATCGA
1 TGTGTTGCGAAAATGAAACTTGTGTTGCGAAAA--GAAATTCGCGTTGCGAATTCAG-AAATCGA
1112859 GTTGCGAAAACAAAATT-CGTGTTGCGAATTAGAAAATC
63 GTTGCGAAAACAAAATTCCGTGTTGCGAATTAGAAAA-C
*
1112897 T-TGTTGCGAAAATGAAACTTGTGTTGCGAAAAGAAATTCGCGTTGCGAATTCAGAAATTGAGTT
1 TGTGTTGCGAAAATGAAACTTGTGTTGCGAAAAGAAATTCGCGTTGCGAATTCAGAAATCGAGTT
**** * *
1112961 GCGAATTTGAAATTCCGTGTTGCGAATTTGGAAAC
66 GCGAAAACAAAATTCCGTGTTGCGAATTAGAAAAC
*
1112996 TGTGTTGCGAAATTGAA
1 TGTGTTGCGAAAATGAA
1113013 GTTCGCGTTG
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
97 16 0.16
98 1 0.01
99 39 0.40
100 38 0.39
101 4 0.04
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (100 bp):
TGTGTTGCGAAAATGAAACTTGTGTTGCGAAAAGAAATTCGCGTTGCGAATTCAGAAATCGAGTT
GCGAAAACAAAATTCCGTGTTGCGAATTAGAAAAC
Found at i:1112981 original size:60 final size:60
Alignment explanation
Indices: 1112839--1112986 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 60
1112829 TAAAATTCGT
* * * * *
1112839 GTTGCGAATTCGAAAATCGAGTTGCGAAAACAAAATTCGTGTTGCGAATTAGAAAATCTT
1 GTTGCGAATTTGAAATTCGTGTTGCGAAAACAAAATTCGCGTTGCGAATTAGAAAATCTA
** *
1112899 GTTGCGAAAATGAAACTT-GTGTTGCGAAAA-GAAATTCGCGTTGCGAATTCAG-AAAT-TGA
1 GTTGCGAATTTGAAA-TTCGTGTTGCGAAAACAAAATTCGCGTTGCGAATT-AGAAAATCT-A
1112958 GTTGCGAATTTGAAATTCCGTGTTGCGAA
1 GTTGCGAATTTGAAATT-CGTGTTGCGAA
1112987 TTTGGAAACT
Statistics
Matches: 73, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
58 3 0.04
59 34 0.47
60 35 0.48
61 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (60 bp):
GTTGCGAATTTGAAATTCGTGTTGCGAAAACAAAATTCGCGTTGCGAATTAGAAAATCTA
Found at i:1112986 original size:41 final size:40
Alignment explanation
Indices: 1112910--1113028 Score: 132
Period size: 41 Copynumber: 3.0 Consensus size: 40
1112900 TTGCGAAAAT
* *
1112910 GAAACTTGTGTTGCGAAA-AGAAATTCGCGTTGCGAATTCA
1 GAAAC-TGAGTTGCGAAATTGAAATTCGCGTTGCGAATTCA
* * * **
1112950 GAAATTGAGTTGCGAATTTGAAATTCCGTGTTGCGAATTTG
1 GAAACTGAGTTGCGAAATTGAAATT-CGCGTTGCGAATTCA
* *
1112991 GAAACTGTGTTGCGAAATTGAAGTTCGCGTTGCGAATT
1 GAAACTGAGTTGCGAAATTGAAATTCGCGTTGCGAATT
1113029 TGTTGGTTAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
39 10 0.15
40 22 0.34
41 33 0.51
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.32
Consensus pattern (40 bp):
GAAACTGAGTTGCGAAATTGAAATTCGCGTTGCGAATTCA
Found at i:1113002 original size:20 final size:19
Alignment explanation
Indices: 1112877--1113012 Score: 78
Period size: 20 Copynumber: 6.8 Consensus size: 19
1112867 AACAAAATTC
*
1112877 GTGTTGCGAATTAGAAAATCT
1 GTGTTGCGAATTTG-AAA-CT
**
1112898 -TGTTGCGAAAATGAAACTT
1 GTGTTGCGAATTTGAAAC-T
** *
1112917 GTGTTGCGAA-AAGAAATT
1 GTGTTGCGAATTTGAAACT
* * *
1112935 CGCGTTGCGAATTCAGAAATT
1 -GTGTTGCGAATT-TGAAACT
* *
1112956 GAGTTGCGAATTTGAAATTCC
1 GTGTTGCGAATTTGAAA--CT
1112977 GTGTTGCGAATTTGGAAACT
1 GTGTTGCGAATTT-GAAACT
*
1112997 GTGTTGCGAAATTGAA
1 GTGTTGCGAATTTGAA
1113013 GTTCGCGTTG
Statistics
Matches: 93, Mismatches: 14, Indels: 18
0.74 0.11 0.14
Matches are distributed among these distances:
18 2 0.02
19 25 0.27
20 43 0.46
21 19 0.20
22 4 0.04
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
GTGTTGCGAATTTGAAACT
Found at i:1116471 original size:16 final size:16
Alignment explanation
Indices: 1116428--1116471 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
1116418 GAAAGGAATT
* *
1116428 GAAAGTAACCTGAACC
1 GAAAATAACCCGAACC
1116444 GAAAATTAACCCGAACC
1 GAAAA-TAACCCGAACC
1116461 GAAAATAACCC
1 GAAAATAACCC
1116472 AAACTGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.48, C:0.27, G:0.14, T:0.11
Consensus pattern (16 bp):
GAAAATAACCCGAACC
Found at i:1116480 original size:16 final size:16
Alignment explanation
Indices: 1116440--1116490 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1116430 AAGTAACCTG
*
1116440 AACCGAAAATTAACCCG
1 AACCGAAAA-TAACCCA
1116457 AACCGAAAATAACCCA
1 AACCGAAAATAACCCA
* **
1116473 AACTGAAAGCAACCCA
1 AACCGAAAATAACCCA
1116489 AA
1 AA
1116491 TTTAATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 21 0.70
17 9 0.30
ACGTcount: A:0.53, C:0.29, G:0.10, T:0.08
Consensus pattern (16 bp):
AACCGAAAATAACCCA
Found at i:1117002 original size:46 final size:46
Alignment explanation
Indices: 1116929--1117063 Score: 114
Period size: 46 Copynumber: 2.9 Consensus size: 46
1116919 GAAACAATCT
* * * *
1116929 GAATTAACTCGAAAATCTAAAAGTTGATCTGAA-CCAAAGTCAACCC
1 GAATTGACCCGAAAATCTAAAAGTTGATCCGAATCCAAA-CCAACCC
* * *
1116975 GAATTGACCCGAAAATCTGAATA-TTGATCCGAATCGAAACCTACCC
1 GAATTGACCCGAAAATCT-AAAAGTTGATCCGAATCCAAACCAACCC
* * * * *
1117021 GAATTGTCCCAAAAATCT-AAAGCTTGACCCGACTCGAAACCAA
1 GAATTGACCCGAAAATCTAAAAG-TTGATCCGAATCCAAACCAA
1117064 TCGACCCGAT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
44 2 0.03
46 63 0.88
47 7 0.10
ACGTcount: A:0.40, C:0.25, G:0.14, T:0.21
Consensus pattern (46 bp):
GAATTGACCCGAAAATCTAAAAGTTGATCCGAATCCAAACCAACCC
Found at i:1121790 original size:10 final size:10
Alignment explanation
Indices: 1121769--1121802 Score: 52
Period size: 11 Copynumber: 3.4 Consensus size: 10
1121759 AATATGAATA
1121769 TTTTGA-TTT
1 TTTTGATTTT
1121778 TTTTGATTTT
1 TTTTGATTTT
1121788 TTTTGAATTTT
1 TTTTG-ATTTT
1121799 TTTT
1 TTTT
1121803 TAAAAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.26
10 8 0.35
11 9 0.39
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (10 bp):
TTTTGATTTT
Found at i:1122171 original size:13 final size:13
Alignment explanation
Indices: 1122139--1122171 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
1122129 AATACAACAC
*
1122139 CCAAACACAACCT
1 CCAAACCCAACCT
1122152 CCAAACCCAACCT
1 CCAAACCCAACCT
1122165 CCAAACC
1 CCAAACC
1122172 ACACTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.42, C:0.52, G:0.00, T:0.06
Consensus pattern (13 bp):
CCAAACCCAACCT
Found at i:1122462 original size:21 final size:21
Alignment explanation
Indices: 1122436--1122479 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1122426 TTTATTTATT
*
1122436 TATTTT-TTTAGTATTAATTTA
1 TATTTTATTT-GTATAAATTTA
1122457 TATTTTAATTTGTATAAATTTA
1 TATTTT-ATTTGTATAAATTTA
1122479 T
1 T
1122480 TAAATTAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 11 0.55
23 3 0.15
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (21 bp):
TATTTTATTTGTATAAATTTA
Found at i:1124359 original size:3 final size:3
Alignment explanation
Indices: 1124345--1124375 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1124335 ATCTTTCATA
*
1124345 ATG ATA ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1124376 GAGTGAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:1124621 original size:18 final size:19
Alignment explanation
Indices: 1124598--1124634 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1124588 GTTCGAATTG
1124598 TTTTTATTATTT-AGTTGT
1 TTTTTATTATTTGAGTTGT
*
1124616 TTTTTATTGTTTGAGTTGT
1 TTTTTATTATTTGAGTTGT
1124635 ATCGTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.14, C:0.00, G:0.16, T:0.70
Consensus pattern (19 bp):
TTTTTATTATTTGAGTTGT
Found at i:1126112 original size:25 final size:24
Alignment explanation
Indices: 1126058--1126107 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1126048 CTACTAGGGG
*
1126058 CTATGAAATTTATCCCGAATGACCA
1 CTATGAAA-TTATCCCGAAGGACCA
*
1126083 CTATGAAA-TATCCCGAAGGATCA
1 CTATGAAATTATCCCGAAGGACCA
1126106 CT
1 CT
1126108 GTATGTCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (24 bp):
CTATGAAATTATCCCGAAGGACCA
Found at i:1179954 original size:2 final size:2
Alignment explanation
Indices: 1179947--1179972 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1179937 AGAAAATTTG
1179947 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1179973 AACAAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1180642 original size:49 final size:49
Alignment explanation
Indices: 1180571--1180673 Score: 179
Period size: 49 Copynumber: 2.1 Consensus size: 49
1180561 TTGACTTTAT
** *
1180571 TATATATTATTTTTTTTCTTTTGAATAATATAGGGTGTTTATAAAGTAA
1 TATATATTATTTTTTTTCTTTTGAATAATATAGGACGCTTATAAAGTAA
1180620 TATATATTATTTTTTTTCTTTTGAATAATATAGGACGCTTATAAAGTAA
1 TATATATTATTTTTTTTCTTTTGAATAATATAGGACGCTTATAAAGTAA
1180669 TATAT
1 TATAT
1180674 GTTTAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.51
Consensus pattern (49 bp):
TATATATTATTTTTTTTCTTTTGAATAATATAGGACGCTTATAAAGTAA
Found at i:1182424 original size:39 final size:38
Alignment explanation
Indices: 1182316--1182430 Score: 126
Period size: 39 Copynumber: 3.0 Consensus size: 38
1182306 TTAAATGTTT
* * * *
1182316 ATTTATAATTT-TCAAATTATTTCACTCTAACATTCTTA
1 ATTTTTAATTTCTTAAATTATTTTACT-TAACATTCTAA
* *
1182354 ATTTTTAATTTCTTAAATT-TTGCTTCCTTAACCTTCTAA
1 ATTTTTAATTTCTTAAATTATT--TTACTTAACATTCTAA
1182393 ATTTTTAATTTCTTAAATTATTTTACATTAACATTCTA
1 ATTTTTAATTTCTTAAATTATTTTAC-TTAACATTCTA
1182431 CTTTTTTTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
38 15 0.23
39 44 0.69
40 5 0.08
ACGTcount: A:0.31, C:0.15, G:0.01, T:0.53
Consensus pattern (38 bp):
ATTTTTAATTTCTTAAATTATTTTACTTAACATTCTAA
Found at i:1187280 original size:22 final size:21
Alignment explanation
Indices: 1187236--1187289 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 21
1187226 AAAATAGCTC
*
1187236 AGTAACGATACTCTTACTGGG
1 AGTATCGATACTCTTACTGGG
1187257 AGTATCGATACTC-TACCCTGGG
1 AGTATCGATACTCTTA--CTGGG
1187279 AGTATCGATAC
1 AGTATCGATAC
1187290 CAAAATTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 2 0.07
21 12 0.40
22 16 0.53
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (21 bp):
AGTATCGATACTCTTACTGGG
Found at i:1188463 original size:184 final size:183
Alignment explanation
Indices: 1188148--1188525 Score: 602
Period size: 184 Copynumber: 2.1 Consensus size: 183
1188138 ATTAAATTTT
*
1188148 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAAACATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGACTCAACCCAAAACATTTAAAACCCAATTAATAA
1188213 TTTAAGATCCAATAACTTTTAAACCTAAAGCAATATTAATTAATTAAAAAATATATATATAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAAGCAATATTAATTAATTAAAAAATATATATATAATTT
*
1188278 TTATTTTATAATTACATATTATATAAATTAATTGTAAA-TTGTTGTTTTAATTAA
131 TTATTTTATAATTACATATTATATAAATTAATTATAAACTT-TT-TTTTAATTAA
* *
1188332 AAATATTATATATATTATATATAACATATGGACT-AAGCCCAAACCATTTAAAACCCAATTAATA
1 AAATATTAAATATATTATATATAACATATGGACTCAA-CCCAAAACATTTAAAACCCAATTAATA
* *
1188396 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATT-AAAAATAT-TATCTGAAA
65 ATTTAAGATCCAATAACTTTTAAACCTAAAGCAATATTAATTAATTAAAAAATATATATAT--AA
* *
1188459 TTTTTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTAATTAA
128 TTTTTATTTTATAATTACATATTATATAAATTAATTATAAACTTTTTTTTAATTAA
*
1188515 AAACATTAAAT
1 AAATATTAAAT
1188526 TTGTATATAA
Statistics
Matches: 180, Mismatches: 10, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
182 4 0.02
183 29 0.16
184 145 0.81
185 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGACTCAACCCAAAACATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAAGCAATATTAATTAATTAAAAAATATATATATAATTT
TTATTTTATAATTACATATTATATAAATTAATTATAAACTTTTTTTTAATTAA
Found at i:1189529 original size:27 final size:27
Alignment explanation
Indices: 1189473--1189529 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
1189463 ACTCTAATTT
* *
1189473 ATTTTATTAATATATTATGTGATATGA
1 ATTTTATTAATATATTATGTAATATCA
* *
1189500 ATTTTATTATTATTTTAT-TAATATACA
1 ATTTTATTAATATATTATGTAATAT-CA
1189527 ATT
1 ATT
1189530 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (27 bp):
ATTTTATTAATATATTATGTAATATCA
Found at i:1189948 original size:17 final size:18
Alignment explanation
Indices: 1189916--1189951 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1189906 AATGTATAAT
1189916 TTAAAAAAAAATTAAATA
1 TTAAAAAAAAATTAAATA
*
1189934 TTAAAATAAAA-TAAATA
1 TTAAAAAAAAATTAAATA
1189951 T
1 T
1189952 GATAACTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAAAAATTAAATA
Found at i:1191278 original size:50 final size:50
Alignment explanation
Indices: 1191161--1191284 Score: 176
Period size: 50 Copynumber: 2.5 Consensus size: 50
1191151 AACAGTAAAA
1191161 CGCGCCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAG
1 CGCGCCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAG
* ** * * * *
1191211 CGCGCGCCCTGCCCCGCGATATACGGTGATTTTGCGCCACGTGGGTATAG
1 CGCGCCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAG
*
1191261 CGCGCCCCCTGATCCGCGCTATAC
1 CGCGCCCCCTGAACCGCGCTATAC
1191285 CTGGGTATCT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 63 1.00
ACGTcount: A:0.15, C:0.36, G:0.28, T:0.20
Consensus pattern (50 bp):
CGCGCCCCCTGAACCGCGCTATACGCTGATTTGGCACCACGTGGGTATAG
Found at i:1191430 original size:18 final size:18
Alignment explanation
Indices: 1191407--1191443 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1191397 TATCACACCA
*
1191407 AATTCTCTCAAATTCTCT
1 AATTCTCTCAAATACTCT
*
1191425 AATTCTCTTAAATACTCT
1 AATTCTCTCAAATACTCT
1191443 A
1 A
1191444 TCTTTTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTCTCTCAAATACTCT
Found at i:1191752 original size:111 final size:111
Alignment explanation
Indices: 1191558--1191890 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
1191548 TGAAAATCAT
* *
1191558 ATATCTCTACACTTTGCTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1191623 TATTTAGTTGATTTATTTAATACATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* * *
1191669 ATATCTCGACACTTTACTAATACAGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1191734 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1191780 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1191845 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1191891 TTTTTGTAAT
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1193481 original size:18 final size:18
Alignment explanation
Indices: 1193458--1193500 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1193448 CCTGCTCAGA
* *
1193458 ACGACGATGATGATGGTG
1 ACGACGACGATGATGATG
1193476 ACGACGACGATGATGATG
1 ACGACGACGATGATGATG
*
1193494 ACAACGA
1 ACGACGA
1193501 GGAGTAAGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (18 bp):
ACGACGACGATGATGATG
Found at i:1193500 original size:21 final size:21
Alignment explanation
Indices: 1193458--1193500 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1193448 CCTGCTCAGA
***
1193458 ACGACGATGATGATGGTGACG
1 ACGACGATGATGATGACAACG
1193479 ACGACGATGATGATGACAACG
1 ACGACGATGATGATGACAACG
1193500 A
1 A
1193501 GGAGTAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (21 bp):
ACGACGATGATGATGACAACG
Found at i:1193747 original size:35 final size:33
Alignment explanation
Indices: 1193708--1193792 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
1193698 ATATTTCAGT
1193708 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
1193743 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
1193778 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
1193793 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:1199570 original size:60 final size:60
Alignment explanation
Indices: 1199470--1199582 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 60
1199460 TTTTATAACC
* *
1199470 TTTAATAGTCGAGGGACTTAACAAAGTAACATTCTATAGTCGAAGGACCATTTTGTAGCT
1 TTTAATAGTCGAGGGACTTAACAAAGTAACATCCCATAGTCGAAGGACCATTTTGTAGCT
* * * * **
1199530 TTTAATAGTCTAGGGACTTGATAAAGTAACATCCCGTAGTCGGGGGACCATTT
1 TTTAATAGTCGAGGGACTTAACAAAGTAACATCCCATAGTCGAAGGACCATTT
1199583 GTATACTTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (60 bp):
TTTAATAGTCGAGGGACTTAACAAAGTAACATCCCATAGTCGAAGGACCATTTTGTAGCT
Found at i:1208963 original size:23 final size:23
Alignment explanation
Indices: 1208937--1208981 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1208927 TGATAGATTG
*
1208937 TTCATCTTTCAACCTTATGTTAA
1 TTCATCATTCAACCTTATGTTAA
*
1208960 TTCATCATTCAATCTTATGTTA
1 TTCATCATTCAACCTTATGTTA
1208982 CTCCTTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.04, T:0.49
Consensus pattern (23 bp):
TTCATCATTCAACCTTATGTTAA
Found at i:1227863 original size:20 final size:21
Alignment explanation
Indices: 1227838--1227930 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1227828 TTTTCCCAAT
*
1227838 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1227858 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1227879 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1227899 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1227920 TCGCAATGCGA
1 TCGCAATGCGA
1227931 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1227944 original size:20 final size:20
Alignment explanation
Indices: 1227919--1228020 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
1227909 AATTGGGAAA
*
1227919 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1227939 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1227960 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
1227980 TTCGCAACACGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1228000 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
1228020 A
1 A
1228021 AATGACCAAC
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.03
20 49 0.74
21 13 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1227945 original size:41 final size:41
Alignment explanation
Indices: 1227838--1227930 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1227828 TTTTCCCAAT
1227838 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1227879 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1227920 TCGCAATGCGA
1 TCGCAATGCGA
1227931 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1227993 original size:41 final size:41
Alignment explanation
Indices: 1227916--1227993 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
1227906 GCGAATTGGG
* * **
1227916 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAC
* *
1227957 AAAATCGCAACGAGATACTTACTTTCGCAACACGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACACGATA
1227994 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACACGATAATAC
Found at i:1228183 original size:20 final size:20
Alignment explanation
Indices: 1228158--1228231 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
1228148 TTTTCCCAAT
*
1228158 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
1228178 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
1228199 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
1228219 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1228232 TGGGAAAATC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:1228201 original size:21 final size:21
Alignment explanation
Indices: 1228175--1228245 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
1228165 GCGAATAAGT
1228175 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
1228196 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
1228216 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
1228237 AAATCGCAA
1 AAATCGCAA
1228246 ATGCGATACT
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.39
21 25 0.61
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.15
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:1228203 original size:41 final size:41
Alignment explanation
Indices: 1228158--1228251 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
1228148 TTTTCCCAAT
1228158 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1228199 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1228240 TCGCAAATGCGA
1 TCGC-AATGCGA
1228252 TACTGACTCG
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 45 0.87
42 7 0.13
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1228304 original size:19 final size:20
Alignment explanation
Indices: 1228288--1228342 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1228278 AATCGCAAGA
*
1228288 GATACTTACTTTCGCAACAC
1 GATACTGACTTTCGCAACAC
*
1228308 GATACTGACTTTCGCAACGC
1 GATACTGACTTTCGCAACAC
*
1228328 GAT-TTGACTTTCGCA
1 GATACTGACTTTCGCA
1228343 CGCGATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.31
Consensus pattern (20 bp):
GATACTGACTTTCGCAACAC
Found at i:1228347 original size:18 final size:19
Alignment explanation
Indices: 1228295--1228348 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1228285 AGAGATACTT
* *
1228295 ACTTTCGCAACACGATACTG
1 ACTTTCGCAACGCGAT-TTG
1228315 ACTTTCGCAACGCGATTTG
1 ACTTTCGCAACGCGATTTG
1228334 ACTTTCGC-ACGCGAT
1 ACTTTCGCAACGCGAT
1228349 AATACATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.22
19 10 0.31
20 15 0.47
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (19 bp):
ACTTTCGCAACGCGATTTG
Found at i:1228565 original size:22 final size:22
Alignment explanation
Indices: 1228537--1228580 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1228527 TCACTTCTCA
1228537 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1228559 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1228581 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1228839 original size:20 final size:20
Alignment explanation
Indices: 1228814--1228866 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1228804 CGATTTTAGT
1228814 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
* **
1228834 TTCGCGTTGTGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
1228854 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
1228867 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:1230195 original size:18 final size:18
Alignment explanation
Indices: 1230174--1230218 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1230164 TCCACTTCGG
*
1230174 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1230192 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1230210 GAGCCATCA
1 GAGCCATCA
1230219 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1230742 original size:19 final size:20
Alignment explanation
Indices: 1230688--1230754 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1230678 ATAGTTTACT
* *
1230688 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1230708 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1230728 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1230747 TCGCAACG
1 TCGCAACG
1230755 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1230762 original size:14 final size:14
Alignment explanation
Indices: 1230743--1230800 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1230733 ATGCGAAATG
1230743 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1230757 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
1230773 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1230789 AAAATCGCAACG
1 AAAATCGCAACG
1230801 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1230785 original size:32 final size:33
Alignment explanation
Indices: 1230727--1230805 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1230717 GGAAATGGCT
1230727 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1230760 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
1230792 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1230806 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:1232382 original size:142 final size:140
Alignment explanation
Indices: 1232129--1232410 Score: 482
Period size: 142 Copynumber: 2.0 Consensus size: 140
1232119 CACCGATAGA
1232129 GATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATGGCTAGAGCATATATCGAGACGCTGCCTA
1 GATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATGGCTAGAGCATATATCGAGACGCTGCCTA
1232194 CCTGCATCCGCGTTTGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGC-AGTTTTGTTAAC-AT
66 CCTGCATCCGCGTTTGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACTAT
1232257 ATACTCCTTTT
131 ATAC-CCTTTT
1232268 GATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATATGGCTAGAGCATATATTCGAGACGCTGC
1 GATAGAGCTGCAGTAGGCTTGTGGTTTCGGCA-T-TATGGCTAGAGCATATA-TCGAGACGCTGC
1232333 CTACCTGCATCCGCGTTATG-AAGTTGTCCATTGTT-ATTGGTAAGTCAAATGCAAGTTTTGTTA
63 CTACCTGCATCCGCGTT-TGAAAG-TGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTA
1232396 ACTATATACCCTTTT
126 ACTATATACCCTTTT
1232411 TGGTTTGAAA
Statistics
Matches: 136, Mismatches: 0, Indels: 10
0.93 0.00 0.07
Matches are distributed among these distances:
139 32 0.24
140 1 0.01
141 17 0.12
142 49 0.36
143 31 0.23
144 6 0.04
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.34
Consensus pattern (140 bp):
GATAGAGCTGCAGTAGGCTTGTGGTTTCGGCATTATGGCTAGAGCATATATCGAGACGCTGCCTA
CCTGCATCCGCGTTTGAAAGTGTCCATTGTTAATTGGTAAGTCAAATGCAAGTTTTGTTAACTAT
ATACCCTTTT
Found at i:1232796 original size:18 final size:16
Alignment explanation
Indices: 1232772--1232818 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 16
1232762 GCGCAACGAG
1232772 AAAATCGCAATGCGAA
1 AAAATCGCAATGCGAA
*
1232788 ATGAAATCGCAA--CGAG
1 A--AAATCGCAATGCGAA
1232804 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
1232819 TTTTCATTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 9 0.35
16 8 0.31
18 9 0.35
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (16 bp):
AAAATCGCAATGCGAA
Found at i:1233935 original size:24 final size:24
Alignment explanation
Indices: 1233908--1233961 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1233898 GTATTCGAAA
* *
1233908 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1233932 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1233956 TTTGAT
1 TTTGAT
1233962 GATGTTTTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1236458 original size:19 final size:19
Alignment explanation
Indices: 1236436--1236566 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
1236426 GGAAATTACT
1236436 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1236455 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
1236469 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1236488 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
1236502 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1236521 ATCGCAAT--G--A-GGGA
1 ATCGCAATGCGAAATGAAA
1236535 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1236554 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1236567 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 28 0.34
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 40 0.49
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1236478 original size:33 final size:33
Alignment explanation
Indices: 1236436--1236562 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1236426 GGAAATTACT
1236436 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
1236469 ATCGCAATGCAAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1236501 TTTCGCAATGCGAAATGAAAATCGCAATGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1236535 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1236563 CGAATTTAAT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
32 1 0.01
33 79 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1236543 original size:66 final size:66
Alignment explanation
Indices: 1236437--1236569 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1236427 GAAATTACTA
*
1236437 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
1236502 T
66 T
* * *
1236503 TCGCAATGCGAAATGAAAATCGCAATGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
1236568 T
66 T
1236569 T
1 T
1236570 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCAAAATGAAAATCGCAACGCGAAT
T
Found at i:1236584 original size:19 final size:19
Alignment explanation
Indices: 1236562--1236636 Score: 70
Period size: 19 Copynumber: 4.2 Consensus size: 19
1236552 AAATCGCAAC
*
1236562 GCGAATTTAATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
*
1236581 GCG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
1236595 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
1236614 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
1236633 GCGA
1 GCGA
1236637 TAGTACTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
14 9 0.20
16 3 0.07
17 2 0.04
18 1 0.02
19 31 0.67
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:1236637 original size:19 final size:19
Alignment explanation
Indices: 1236593--1236637 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1236583 GATTCTCTCG
*
1236593 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1236612 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1236631 TTGCGAT
1 TTGCGAT
1236638 AGTACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1236763 original size:14 final size:14
Alignment explanation
Indices: 1236744--1236780 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1236734 CATCAATTAA
1236744 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1236758 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1236772 ACAAATCAA
1 ACAAATCAA
1236781 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1238110 original size:21 final size:21
Alignment explanation
Indices: 1238044--1238110 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1238034 GTGAATCGGG
*
1238044 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1238064 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1238086 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1238107 CTCT
1 CTCT
1238111 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1238129 original size:42 final size:41
Alignment explanation
Indices: 1238044--1238166 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
1238034 GTGAATCGGG
* * * *
1238044 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1238086 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * * *
1238128 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGGCAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1238167 CGAGTCGGGC
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
41 4 0.06
42 56 0.85
43 6 0.09
ACGTcount: A:0.22, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1240206 original size:20 final size:20
Alignment explanation
Indices: 1240161--1240224 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
1240151 TCTTTTGGTT
1240161 GAAATGAAAATCGCAAC-AA
1 GAAATGAAAATCGCAACGAA
* **
1240180 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACGAA
**
1240201 GAAATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAACGA-A
1240222 GAA
1 GAA
1240225 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.80
21 5 0.14
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.12
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGAA
Found at i:1240278 original size:19 final size:19
Alignment explanation
Indices: 1240256--1240306 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1240246 GCGACGAGAG
1240256 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
* *
1240275 AATCGCAACGCAAAATGAA
1 AATCGCAACGCGAAATAAA
*
1240294 AATCGCAATGCGA
1 AATCGCAACGCGA
1240307 TTTTTGTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:1240280 original size:33 final size:33
Alignment explanation
Indices: 1240186--1240271 Score: 154
Period size: 33 Copynumber: 2.6 Consensus size: 33
1240176 ACAAGATAAT
1240186 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1240220 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1240253 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
1240272 AAAAATCGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 37 0.73
34 14 0.27
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1240904 original size:20 final size:20
Alignment explanation
Indices: 1240879--1240931 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1240869 GCGCTATGTA
1240879 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1240899 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1240919 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1240932 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1240965 original size:20 final size:20
Alignment explanation
Indices: 1240940--1240993 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1240930 GATTTTGTAT
1240940 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
1240960 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1240980 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1240994 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1240978 original size:61 final size:61
Alignment explanation
Indices: 1240880--1240996 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
1240870 CGCTATGTAA
* * * * *
1240880 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1240941 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1240997 TCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1241012 original size:61 final size:61
Alignment explanation
Indices: 1240875--1241014 Score: 160
Period size: 61 Copynumber: 2.3 Consensus size: 61
1240865 AATGGCGCTA
* * * * *
1240875 TGTAA-ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
1240935 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
1240996 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
1241015 CTACTTATTC
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
60 5 0.08
61 59 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:1252964 original size:17 final size:18
Alignment explanation
Indices: 1252931--1252964 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1252921 TATTTCAAAG
1252931 TTTAATAATTGTTTATAT
1 TTTAATAATTGTTTATAT
*
1252949 TTTAAT-ATTTTTTATA
1 TTTAATAATTGTTTATA
1252965 AATAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
TTTAATAATTGTTTATAT
Found at i:1261906 original size:40 final size:42
Alignment explanation
Indices: 1261861--1261957 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 42
1261851 CGTTTTTATT
1261861 AAACGCCGCATTTTT-AGTATTTTAGCGGC-TTTTTAACTAC
1 AAACGCCGCATTTTTCAGTATTTTAGCGGCATTTTTAACTAC
* * *
1261901 AAACGCCGTATTTTTCAGTATTTTAGTGGCATTTTTAATTAC
1 AAACGCCGCATTTTTCAGTATTTTAGCGGCATTTTTAACTAC
1261943 -AACGCCGCAATTTTT
1 AAACGCCGC-ATTTTT
1261958 GTGTCTTTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
40 14 0.28
41 20 0.40
42 16 0.32
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (42 bp):
AAACGCCGCATTTTTCAGTATTTTAGCGGCATTTTTAACTAC
Found at i:1267677 original size:2 final size:2
Alignment explanation
Indices: 1267670--1267712 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1267660 TGGAAGCCTA
1267670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1267712 A
1 A
1267713 AACTTCTGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1273439 original size:14 final size:15
Alignment explanation
Indices: 1273428--1273462 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
1273418 TAAAATTATA
1273428 AAATTTAAATTACAG
1 AAATTTAAATTACAG
* *
1273443 AAATTTAGATTACTG
1 AAATTTAAATTACAG
1273458 AAATT
1 AAATT
1273463 AAAAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.37
Consensus pattern (15 bp):
AAATTTAAATTACAG
Found at i:1276467 original size:6 final size:6
Alignment explanation
Indices: 1276458--1276523 Score: 105
Period size: 6 Copynumber: 11.0 Consensus size: 6
1276448 CTAAAGTTTT
1276458 AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG
1 AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG AGTTAG
* * *
1276506 GGTTAG GGTTAG GGTTAG
1 AGTTAG AGTTAG AGTTAG
1276524 GGTTTAGGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.29, C:0.00, G:0.38, T:0.33
Consensus pattern (6 bp):
AGTTAG
Found at i:1276524 original size:6 final size:6
Alignment explanation
Indices: 1276459--1276611 Score: 126
Period size: 7 Copynumber: 23.5 Consensus size: 6
1276449 TAAAGTTTTA
* * * * * * *
1276459 GTTAGA GTTAGA GTTAGA GTTAGA GTTAGA GTTAGA GTTAGA GTTAGG
1 GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG GTTAGG
1276507 GTTAGG GTTAGG GTTAGG GTTTAGG GTTTAGG GTTTAGG GTTTAGG GTTTAGG
1 GTTAGG GTTAGG GTTAGG G-TTAGG G-TTAGG G-TTAGG G-TTAGG G-TTAGG
*
1276560 GTTTAGG GTTTAGG GTTTAGG ATTTAGG GTTTAGG GTTTAGG GTTTAGG
1 G-TTAGG G-TTAGG G-TTAGG -GTTAGG G-TTAGG G-TTAGG G-TTAGG
1276609 GTT
1 GTT
1276612 TAAGATTTAA
Statistics
Matches: 141, Mismatches: 3, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
6 62 0.44
7 79 0.56
ACGTcount: A:0.20, C:0.00, G:0.41, T:0.39
Consensus pattern (6 bp):
GTTAGG
Found at i:1276532 original size:7 final size:7
Alignment explanation
Indices: 1276502--1276613 Score: 194
Period size: 7 Copynumber: 16.4 Consensus size: 7
1276492 AGAGTTAGAG
1276502 TTAGGG-
1 TTAGGGT
1276508 TTAGGG-
1 TTAGGGT
1276514 TTAGGG-
1 TTAGGGT
1276520 TTAGGGT
1 TTAGGGT
1276527 TTAGGGT
1 TTAGGGT
1276534 TTAGGGT
1 TTAGGGT
1276541 TTAGGGT
1 TTAGGGT
1276548 TTAGGGT
1 TTAGGGT
1276555 TTAGGGT
1 TTAGGGT
1276562 TTAGGGT
1 TTAGGGT
1276569 TTAGGGT
1 TTAGGGT
*
1276576 TTAGGAT
1 TTAGGGT
1276583 TTAGGGT
1 TTAGGGT
1276590 TTAGGGT
1 TTAGGGT
1276597 TTAGGGT
1 TTAGGGT
1276604 TTAGGGT
1 TTAGGGT
1276611 TTA
1 TTA
1276614 AGATTTAAGA
Statistics
Matches: 103, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
6 18 0.17
7 85 0.83
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:1282616 original size:32 final size:33
Alignment explanation
Indices: 1282580--1282657 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
1282570 TTTAAATAGT
* *
1282580 TATTATTTTTTA-TATTAAT-ATATTTATGTAAA
1 TATTATTTTTTATTA-AAATAATATTTATATAAA
*
1282612 TATTATTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATTAAAATAATATTTATATAAA
1282645 TATTATTTATTTA
1 TATTATTT-TTTA
1282658 GAATTATTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 15 0.38
33 21 0.52
34 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATTAAAATAATATTTATATAAA
Found at i:1289243 original size:13 final size:13
Alignment explanation
Indices: 1289225--1289250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1289215 GTTGTGAACC
1289225 AACAAAAAGAAAA
1 AACAAAAAGAAAA
1289238 AACAAAAAGAAAA
1 AACAAAAAGAAAA
1289251 CAAAGAAGGA
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:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
AACAAAAAGAAAA
Found at i:1289578 original size:22 final size:23
Alignment explanation
Indices: 1289552--1289602 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
1289542 ATTATTTAAC
*
1289552 TTTTTTATTTAAAATT-AAATATA
1 TTTTTAATTT-AAATTCAAATATA
*
1289575 TTTTTGAATTTAAATTCATATATA
1 TTTTT-AATTTAAATTCAAATATA
1289599 TTTT
1 TTTT
1289603 AACAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTTTAATTTAAATTCAAATATA
Found at i:1292422 original size:14 final size:14
Alignment explanation
Indices: 1292403--1292432 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1292393 AGATTTATAT
1292403 ATTAAGAATTAAAG
1 ATTAAGAATTAAAG
*
1292417 ATTAAGAATTATAG
1 ATTAAGAATTAAAG
1292431 AT
1 AT
1292433 AAAGGTTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (14 bp):
ATTAAGAATTAAAG
Found at i:1295648 original size:10 final size:10
Alignment explanation
Indices: 1295627--1295656 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
1295617 AACTTACAAA
1295627 GAAATGGAATT
1 GAAAT-GAATT
1295638 GAAATGAATT
1 GAAATGAATT
1295648 GAAATGAAT
1 GAAATGAAT
1295657 GGATTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (10 bp):
GAAATGAATT
Found at i:1296228 original size:27 final size:27
Alignment explanation
Indices: 1296196--1296259 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
1296186 CTTAAAATAT
1296196 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
* ** *
1296223 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
*
1296250 ATATATTTAA
1 ATATTTTTAA
1296260 TAAGTTTAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATGAAAATAAAAATAAA
Found at i:1296283 original size:27 final size:27
Alignment explanation
Indices: 1296217--1296308 Score: 97
Period size: 27 Copynumber: 3.5 Consensus size: 27
1296207 TGAAAATAAA
1296217 AATAAAATATT-TTTAAATTAAGTTAAT
1 AATAAAATATTATTT-AATTAAGTTAAT
1296244 AATAAAATA-TATTTAA-TAAGTTTAAT
1 AATAAAATATTATTTAATTAAG-TTAAT
*
1296270 -ATAAAAATATTATTTAAGTTAA-TAAAT
1 AAT-AAAATATTATTTAA-TTAAGTTAAT
1296297 -ATAAAATATTAT
1 AATAAAATATTAT
1296309 GAATTTAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 13
0.81 0.01 0.18
Matches are distributed among these distances:
25 6 0.10
26 24 0.41
27 25 0.43
29 3 0.05
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.42
Consensus pattern (27 bp):
AATAAAATATTATTTAATTAAGTTAAT
Found at i:1296302 original size:26 final size:26
Alignment explanation
Indices: 1296213--1296308 Score: 92
Period size: 26 Copynumber: 3.7 Consensus size: 26
1296203 TAAATGAAAA
*
1296213 TAAAAATAAAATATT-TTTAAATTAAG
1 TAAATATAAAATATTATTT-AATTAAG
*
1296239 TTAATAATAAAATA-TATTTAA-TAAG
1 TAAAT-ATAAAATATTATTTAATTAAG
*
1296264 TTTAATATAAAAATATTATTTAAGTTAA-
1 -TAAATAT-AAAATATTATTTAA-TTAAG
1296292 TAAATATAAAATATTAT
1 TAAATATAAAATATTAT
1296309 GAATTTAAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
25 6 0.10
26 27 0.45
27 24 0.40
29 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (26 bp):
TAAATATAAAATATTATTTAATTAAG
Found at i:1296319 original size:26 final size:27
Alignment explanation
Indices: 1296267--1296316 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
1296257 TAATAAGTTT
*
1296267 AATATAAAAATATTATTTAAGTTAATA
1 AATATAAAAATATTATTGAAGTTAATA
*
1296294 AATAT-AAAATATTA-TGAATTTAA
1 AATATAAAAATATTATTGAAGTTAA
1296317 ATATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 9 0.43
27 5 0.24
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (27 bp):
AATATAAAAATATTATTGAAGTTAATA
Found at i:1314038 original size:35 final size:37
Alignment explanation
Indices: 1313971--1314039 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
1313961 TATTGCCAAT
1313971 TTAAACTGAAGTAAAATAAATTAGGGTTTGTTGAAAG
1 TTAAACTGAAGTAAAATAAATTAGGGTTTGTTGAAAG
1314008 TTAAACTGAAGTAAAA-AAA-TAGGGTTTGTTGA
1 TTAAACTGAAGTAAAATAAATTAGGGTTTGTTGA
1314040 GTTGATAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 13 0.41
36 3 0.09
37 16 0.50
ACGTcount: A:0.43, C:0.03, G:0.22, T:0.32
Consensus pattern (37 bp):
TTAAACTGAAGTAAAATAAATTAGGGTTTGTTGAAAG
Found at i:1316612 original size:15 final size:16
Alignment explanation
Indices: 1316591--1316635 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
1316581 ACGATGATTC
1316591 AGATGATGATGAAGAA
1 AGATGATGATGAAGAA
*
1316607 AG-TGATGATGACG-A
1 AGATGATGATGAAGAA
1316621 AGATGATGATGAAGA
1 AGATGATGATGAAGA
1316636 TGACGAAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 3 0.12
15 20 0.80
16 2 0.08
ACGTcount: A:0.44, C:0.02, G:0.33, T:0.20
Consensus pattern (16 bp):
AGATGATGATGAAGAA
Found at i:1316625 original size:12 final size:12
Alignment explanation
Indices: 1316610--1316710 Score: 84
Period size: 12 Copynumber: 8.7 Consensus size: 12
1316600 TGAAGAAAGT
1316610 GATGATGACGAA
1 GATGATGACGAA
*
1316622 GATGATGATG-A
1 GATGATGACGAA
1316633 -A-GATGACGAA
1 GATGATGACGAA
1316643 GATGATGACGAA
1 GATGATGACGAA
* *
1316655 GATGACGACGAT
1 GATGATGACGAA
* * *
1316667 GAGGATGAAGAC
1 GATGATGACGAA
1316679 GATGATGAC-AA
1 GATGATGACGAA
* *
1316690 CGACGACGACGAA
1 -GATGATGACGAA
*
1316703 GACGATGA
1 GATGATGA
1316711 TGACGACTAA
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
9 6 0.09
10 2 0.03
11 3 0.04
12 57 0.81
13 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.34, T:0.14
Consensus pattern (12 bp):
GATGATGACGAA
Found at i:1316630 original size:18 final size:18
Alignment explanation
Indices: 1316592--1316650 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 18
1316582 CGATGATTCA
*
1316592 GATGATGATGAAGAA-A-
1 GATGATGATGACGAAGAT
1316608 G-TGATGATGACGAAGAT
1 GATGATGATGACGAAGAT
1316625 GATGATGAAGATGACGAAGAT
1 GATGAT---GATGACGAAGAT
1316646 GATGA
1 GATGA
1316651 CGAAGATGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 12 0.33
16 2 0.06
17 1 0.03
18 4 0.11
21 17 0.47
ACGTcount: A:0.42, C:0.03, G:0.34, T:0.20
Consensus pattern (18 bp):
GATGATGATGACGAAGAT
Found at i:1316637 original size:9 final size:9
Alignment explanation
Indices: 1316625--1316716 Score: 76
Period size: 9 Copynumber: 10.2 Consensus size: 9
1316615 TGACGAAGAT
*
1316625 GATGATGAA
1 GATGATGAC
* *
1316634 GATGACGAA
1 GATGATGAC
1316643 GATGATGAC
1 GATGATGAC
*
1316652 GAAGATGAC
1 GATGATGAC
* *
1316661 GACGATGAG
1 GATGATGAC
*
1316670 GATGAAGAC
1 GATGATGAC
1316679 GATGATGAC
1 GATGATGAC
* * *
1316688 AACGACGAC
1 GATGATGAC
* *
1316697 GACGAAGAC
1 GATGATGAC
1316706 GATGATGAC
1 GATGATGAC
1316715 GA
1 GA
1316717 CTAAGACGAA
Statistics
Matches: 66, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.40, C:0.13, G:0.34, T:0.13
Consensus pattern (9 bp):
GATGATGAC
Found at i:1316637 original size:21 final size:21
Alignment explanation
Indices: 1316613--1316677 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
1316603 AGAAAGTGAT
1316613 GATGACGAAGATGATGATGAA
1 GATGACGAAGATGATGATGAA
*
1316634 GATGACGAAGATGATGACGAA
1 GATGACGAAGATGATGATGAA
* *
1316655 GATGACGACGATGAGGATGAA
1 GATGACGAAGATGATGATGAA
1316676 GA
1 GA
1316678 CGATGATGAC
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:0.42, C:0.08, G:0.35, T:0.15
Consensus pattern (21 bp):
GATGACGAAGATGATGATGAA
Done.