Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009580.1 Hibiscus syriacus cultivar Beakdansim tig00116954_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: 1633873
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 5 of 6
Found at i:1062607 original size:5 final size:5
Alignment explanation
Indices: 1062588--1062620 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
1062578 CACGTGAGGA
1062588 TTATT TTATT CTTATT TTA-T TTATT TTATT TTA
1 TTATT TTATT -TTATT TTATT TTATT TTATT TTA
1062621 CTGTCTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
TTATT
Found at i:1062618 original size:14 final size:15
Alignment explanation
Indices: 1062592--1062620 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1062582 TGAGGATTAT
1062592 TTTATTCTTATTTTA
1 TTTATTCTTATTTTA
1062607 TTTATT-TTATTTTA
1 TTTATTCTTATTTTA
1062621 CTGTCTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTATTCTTATTTTA
Found at i:1071423 original size:194 final size:194
Alignment explanation
Indices: 1071094--1071483 Score: 780
Period size: 194 Copynumber: 2.0 Consensus size: 194
1071084 CATTTCATCT
1071094 AGAGTGTGGGAGAGTAAGTGTGATGAGCTGACTCCCTTCGTAACAGCATAATAATAAAAAAAATC
1 AGAGTGTGGGAGAGTAAGTGTGATGAGCTGACTCCCTTCGTAACAGCATAATAATAAAAAAAATC
1071159 AAAGAAAATGGAGTAAAAATGTGCTTAATTATAAGTAAATGCCTTGACAAAAACTAGGGGACTTG
66 AAAGAAAATGGAGTAAAAATGTGCTTAATTATAAGTAAATGCCTTGACAAAAACTAGGGGACTTG
1071224 ATTAGAAATTGTCTAAATTCGCTAAGTATAGATTGGATACAATCACGCACACACACTACCACAA
131 ATTAGAAATTGTCTAAATTCGCTAAGTATAGATTGGATACAATCACGCACACACACTACCACAA
1071288 AGAGTGTGGGAGAGTAAGTGTGATGAGCTGACTCCCTTCGTAACAGCATAATAATAAAAAAAATC
1 AGAGTGTGGGAGAGTAAGTGTGATGAGCTGACTCCCTTCGTAACAGCATAATAATAAAAAAAATC
1071353 AAAGAAAATGGAGTAAAAATGTGCTTAATTATAAGTAAATGCCTTGACAAAAACTAGGGGACTTG
66 AAAGAAAATGGAGTAAAAATGTGCTTAATTATAAGTAAATGCCTTGACAAAAACTAGGGGACTTG
1071418 ATTAGAAATTGTCTAAATTCGCTAAGTATAGATTGGATACAATCACGCACACACACTACCACAA
131 ATTAGAAATTGTCTAAATTCGCTAAGTATAGATTGGATACAATCACGCACACACACTACCACAA
1071482 AG
1 AG
1071484 GATTTTGACC
Statistics
Matches: 196, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
194 196 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.24
Consensus pattern (194 bp):
AGAGTGTGGGAGAGTAAGTGTGATGAGCTGACTCCCTTCGTAACAGCATAATAATAAAAAAAATC
AAAGAAAATGGAGTAAAAATGTGCTTAATTATAAGTAAATGCCTTGACAAAAACTAGGGGACTTG
ATTAGAAATTGTCTAAATTCGCTAAGTATAGATTGGATACAATCACGCACACACACTACCACAA
Found at i:1072317 original size:23 final size:23
Alignment explanation
Indices: 1072291--1072335 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1072281 CACCACAGCT
*
1072291 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
1072314 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
1072336 ATATAATAAT
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:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:1072575 original size:148 final size:148
Alignment explanation
Indices: 1072303--1072615 Score: 594
Period size: 148 Copynumber: 2.1 Consensus size: 148
1072293 TATAATTGCA
1072303 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1072367 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
1072432 CCAAAGAATATACATATGTC
130 CCAAAGAATATAC-TATGTC
1072452 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATT-T
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1072516 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
1072581 CAAAGAATATACTATGTC
131 CAAAGAATATACTATGTC
1072599 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
1072616 CCCTCGACTC
Statistics
Matches: 163, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
147 23 0.14
148 79 0.48
149 61 0.37
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACTATGTC
Found at i:1073949 original size:21 final size:21
Alignment explanation
Indices: 1073919--1073963 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1073909 ATTCTGTCGT
* *
1073919 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1073940 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1073961 TTG
1 TTG
1073964 CCCATAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1076557 original size:21 final size:21
Alignment explanation
Indices: 1076531--1076575 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
1076521 TTTAAAAACT
* *
1076531 TTGAATGGGTATCGGTTCCCC
1 TTGAATGGGTACCGATTCCCC
1076552 TTGAATGGGTACCGATTCCCC
1 TTGAATGGGTACCGATTCCCC
1076573 TTG
1 TTG
1076576 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (21 bp):
TTGAATGGGTACCGATTCCCC
Found at i:1079608 original size:24 final size:24
Alignment explanation
Indices: 1079581--1079630 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1079571 TCGAAATTTT
1079581 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
1079605 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
1079629 AT
1 AT
1079631 GATGTGATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:1079785 original size:73 final size:74
Alignment explanation
Indices: 1079705--1079852 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
1079695 TTGATGATGA
1079705 AACAACCGCAGCCGAGGAAGATGTTG-TGATGATAATGAGGAGGAAGTTACGACTGTGAATGAAC
1 AACAACCGCAGCCGAGGAAGATGTTGTTGATGATAATGAGGAGGAAGTTACGACTGTGAATGAAC
1079769 ATGTTGAAC
66 ATGTTGAAC
1079778 AACAACCGCAGCCGAGGAAGATGTTGTTGATGATAATGAGGAGGAAGTTACGACTGTGAATGAAC
1 AACAACCGCAGCCGAGGAAGATGTTGTTGATGATAATGAGGAGGAAGTTACGACTGTGAATGAAC
1079843 ATGTTGAAC
66 ATGTTGAAC
1079852 A
1 A
1079853 TTCATTCTGT
Statistics
Matches: 74, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
73 26 0.35
74 48 0.65
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.21
Consensus pattern (74 bp):
AACAACCGCAGCCGAGGAAGATGTTGTTGATGATAATGAGGAGGAAGTTACGACTGTGAATGAAC
ATGTTGAAC
Found at i:1082429 original size:25 final size:25
Alignment explanation
Indices: 1082397--1082445 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
1082387 AAATCAATTA
*
1082397 AACATTGTTGTGGGTACATTATTTT
1 AACATTGTTATGGGTACATTATTTT
1082422 AACATTGTTATGGGTACATTATTT
1 AACATTGTTATGGGTACATTATTT
1082446 GGAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (25 bp):
AACATTGTTATGGGTACATTATTTT
Found at i:1082490 original size:66 final size:66
Alignment explanation
Indices: 1082408--1082540 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
1082398 ACATTGTTGT
1082408 GGGTACATTATTTTAACATTGTTATGGGTACATTATTTGGAAAATAATATTCCAGACTTCGTTAG
1 GGGTACATTATTTTAACATTGTTATGGGTACATTATTTGGAAAATAATATTCCAGACTTCGTTAG
1082473 A
66 A
1082474 GGGTACATTATTTTAACATTGTTATGGGTACATTATTTGGAAAATAATATTCCAGACTTCGTTAG
1 GGGTACATTATTTTAACATTGTTATGGGTACATTATTTGGAAAATAATATTCCAGACTTCGTTAG
1082539 A
66 A
1082540 G
1 G
1082541 ATAACCCTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (66 bp):
GGGTACATTATTTTAACATTGTTATGGGTACATTATTTGGAAAATAATATTCCAGACTTCGTTAG
A
Found at i:1082910 original size:18 final size:18
Alignment explanation
Indices: 1082889--1082925 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1082879 GTAATTGGAG
1082889 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
1082907 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
1082925 T
1 T
1082926 ATAAATTTCG
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:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:1082932 original size:24 final size:24
Alignment explanation
Indices: 1082881--1082933 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1082871 TTTCATATGT
* * *
1082881 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
1082905 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1082929 AATTT
1 AATTT
1082934 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1084387 original size:34 final size:33
Alignment explanation
Indices: 1084285--1084389 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 33
1084275 TTAAAACAAC
1084285 AAATCAACTTTTACAAATTAATTAAACAAGCAAAA
1 AAATCAACTTTTACAAA-TAATTAAACAAGC-AAA
* **
1084320 AAAT-AATTCTTATTTACACATAA--AATTAA--AAA
1 AAATCAA--C-T-TTTACAAATAATTAAACAAGCAAA
1084352 AAATCAACTTTTACAAATCAATTAAACAAGCAAA
1 AAATCAACTTTTACAAAT-AATTAAACAAGCAAA
1084386 AAAT
1 AAAT
1084390 AATTCTTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 21
0.67 0.07 0.26
Matches are distributed among these distances:
29 8 0.15
30 3 0.06
31 1 0.02
32 11 0.20
33 2 0.04
34 9 0.17
35 8 0.15
36 1 0.02
37 4 0.07
38 7 0.13
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (33 bp):
AAATCAACTTTTACAAATAATTAAACAAGCAAA
Found at i:1085697 original size:21 final size:20
Alignment explanation
Indices: 1085673--1085750 Score: 115
Period size: 21 Copynumber: 3.9 Consensus size: 20
1085663 GCCGGCGGGA
1085673 CCTCTTGAACGATGACAGGGG
1 CCTCTTGAACGATGA-AGGGG
*
1085694 CCTCTTGAACGGTGGAAGGGG
1 CCTCTTGAACGAT-GAAGGGG
1085715 CCTCTTG-ACGA-GAAGGGG
1 CCTCTTGAACGATGAAGGGG
1085733 CCTCTTGAACGATGAAGG
1 CCTCTTGAACGATGAAGG
1085751 TGCATCGGGC
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
18 14 0.27
19 4 0.08
20 8 0.15
21 24 0.46
22 2 0.04
ACGTcount: A:0.23, C:0.22, G:0.36, T:0.19
Consensus pattern (20 bp):
CCTCTTGAACGATGAAGGGG
Found at i:1087811 original size:19 final size:19
Alignment explanation
Indices: 1087760--1087813 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
1087750 AATAGTTTTT
*
1087760 GAAACTTAAATTCGCAATAC
1 GAAAC-TAAAATCGCAATAC
*
1087780 GAAAATGAAAATCGCAA-AGC
1 GAAACT-AAAATCGCAATA-C
1087800 GAAACTAAAATCGC
1 GAAACTAAAATCGC
1087814 GTTACGATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.50, C:0.19, G:0.15, T:0.17
Consensus pattern (19 bp):
GAAACTAAAATCGCAATAC
Found at i:1088240 original size:20 final size:21
Alignment explanation
Indices: 1088215--1088263 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1088205 TCTGAGAGAT
1088215 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
1088235 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
*
1088257 GAAGATG
1 GGAGATG
1088264 GGGACAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 1 0.04
22 17 0.71
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:1088249 original size:22 final size:22
Alignment explanation
Indices: 1088222--1088279 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
1088212 GATGGAGATA
*
1088222 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGAAGATGGG
*
1088244 GACGGATTTCGTCGAAGATGGG
1 GACGGATTTCGCCGAAGATGGG
* *
1088266 GACAGATATCGCCG
1 GACGGATTTCGCCG
1088280 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:0.22, C:0.19, G:0.40, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGAAGATGGG
Found at i:1088406 original size:20 final size:20
Alignment explanation
Indices: 1088381--1088439 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
1088371 TAATATTGTG
1088381 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
1088401 TTTCGCGTTGCGAATTTGAC
1 TTTCGCGTTGCGAATTTGAC
* *
1088421 TTTTGTGTTGCGAATTTGA
1 TTTCGCGTTGCGAATTTGA
1088440 AATTAGTGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.15, C:0.15, G:0.25, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTGAC
Found at i:1088448 original size:20 final size:20
Alignment explanation
Indices: 1088387--1088462 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1088377 TGTGTTTCGC
* *
1088387 GTTGCGAATTTGACTTTCGC
1 GTTGCGAATTTGACTTTAGT
*
1088407 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTAGT
**
1088427 GTTGCGAATTTGAAATTAGT
1 GTTGCGAATTTGACTTTAGT
* *
1088447 GTTGTGAATTTAACTT
1 GTTGCGAATTTGACTT
1088463 CTGTGTTGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.45
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTAGT
Found at i:1088456 original size:40 final size:40
Alignment explanation
Indices: 1088387--1088493 Score: 108
Period size: 40 Copynumber: 2.7 Consensus size: 40
1088377 TGTGTTTCGC
** * * *
1088387 GTTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTAGCGTTGCGAATTTAACTTCTGT
* *
1088427 GTTGCGAATTTGAAATTAGTGTTGTGAATTTAACTTCTGT
1 GTTGCGAATTTGAAATTAGCGTTGCGAATTTAACTTCTGT
* * *
1088467 GTTGAG-ATTTACAAATTCGCGTTGCGA
1 GTTGCGAATTT-GAAATTAGCGTTGCGA
1088494 TATTGGAAAC
Statistics
Matches: 54, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
39 4 0.07
40 50 0.93
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTAGCGTTGCGAATTTAACTTCTGT
Found at i:1090535 original size:14 final size:14
Alignment explanation
Indices: 1090516--1090542 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1090506 TGTGTCTGTG
1090516 TATGTATATATATA
1 TATGTATATATATA
1090530 TATGTATATATAT
1 TATGTATATATAT
1090543 TACCAAACCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TATGTATATATATA
Found at i:1092051 original size:169 final size:170
Alignment explanation
Indices: 1091772--1092110 Score: 662
Period size: 169 Copynumber: 2.0 Consensus size: 170
1091762 GAGGAATTAC
1091772 TTACTGTTATTGTCGGTAGATCATTTGTTTTGGTATTGAATTCTCAAGCTTGGGCGGTGGCATGC
1 TTACTGTTATTGTCGGTAGATCATTTGTTTTGGTATTGAATTCTCAAGCTTGGGCGGTGGCATGC
1091837 ATTTTCTACCGTTAAAATAAAATAAATGAAAGAGTGATGAGAGGAAAGGCAGAGCCAGCTAAGG-
66 ATTTTCTACCGTTAAAATAAAATAAATGAAAGAGTGATGAGAGGAAAGGCAGAGCCAGCTAAGGC
1091901 AGTGAGTGGAATGATGGAAAATCTTGGAACCTTGTCATGA
131 AGTGAGTGGAATGATGGAAAATCTTGGAACCTTGTCATGA
*
1091941 TTACTGTTATTGTCGGTAGATCATTTGTTTTGTTATTGAATTCTCAAGCTTGGGCGGTGGCATGC
1 TTACTGTTATTGTCGGTAGATCATTTGTTTTGGTATTGAATTCTCAAGCTTGGGCGGTGGCATGC
1092006 ATTTTCTACCGTTAAAATAAAATAAATGAAAGAGTGATGAGAGGAAAGGCAGAGCCAGCTAAGGC
66 ATTTTCTACCGTTAAAATAAAATAAATGAAAGAGTGATGAGAGGAAAGGCAGAGCCAGCTAAGGC
1092071 AGTGAGTGGAATGATGGAAAATCTTGGAACCTTGTCATGA
131 AGTGAGTGGAATGATGGAAAATCTTGGAACCTTGTCATGA
1092111 ATTTATCAAA
Statistics
Matches: 168, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
169 128 0.76
170 40 0.24
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (170 bp):
TTACTGTTATTGTCGGTAGATCATTTGTTTTGGTATTGAATTCTCAAGCTTGGGCGGTGGCATGC
ATTTTCTACCGTTAAAATAAAATAAATGAAAGAGTGATGAGAGGAAAGGCAGAGCCAGCTAAGGC
AGTGAGTGGAATGATGGAAAATCTTGGAACCTTGTCATGA
Found at i:1093663 original size:28 final size:28
Alignment explanation
Indices: 1093631--1093690 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
1093621 ATGAAAAATG
* *
1093631 TGTATGTATAAATGGTCAAACCATTTCA
1 TGTATGAACAAATGGTCAAACCATTTCA
1093659 TGTATGAACAAATGGTCAAACCATTTCA
1 TGTATGAACAAATGGTCAAACCATTTCA
1093687 TGTA
1 TGTA
1093691 CTTTACACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (28 bp):
TGTATGAACAAATGGTCAAACCATTTCA
Found at i:1098474 original size:98 final size:98
Alignment explanation
Indices: 1098305--1098501 Score: 394
Period size: 98 Copynumber: 2.0 Consensus size: 98
1098295 AATTCATCGT
1098305 CGGAAGGCAGCTTAGAGGCTGAAGAAATCCGCGTCAAAGACTCGACCAAAAATTTAGTCGATTCA
1 CGGAAGGCAGCTTAGAGGCTGAAGAAATCCGCGTCAAAGACTCGACCAAAAATTTAGTCGATTCA
1098370 ATGGAAGGAGAAACTAGTGCAGCCCCTGAAGTA
66 ATGGAAGGAGAAACTAGTGCAGCCCCTGAAGTA
1098403 CGGAAGGCAGCTTAGAGGCTGAAGAAATCCGCGTCAAAGACTCGACCAAAAATTTAGTCGATTCA
1 CGGAAGGCAGCTTAGAGGCTGAAGAAATCCGCGTCAAAGACTCGACCAAAAATTTAGTCGATTCA
1098468 ATGGAAGGAGAAACTAGTGCAGCCCCTGAAGTA
66 ATGGAAGGAGAAACTAGTGCAGCCCCTGAAGTA
1098501 C
1 C
1098502 CAACAAGAAC
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 99 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (98 bp):
CGGAAGGCAGCTTAGAGGCTGAAGAAATCCGCGTCAAAGACTCGACCAAAAATTTAGTCGATTCA
ATGGAAGGAGAAACTAGTGCAGCCCCTGAAGTA
Found at i:1103334 original size:21 final size:21
Alignment explanation
Indices: 1103286--1103334 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1103276 GTTCAGTGGT
*
1103286 GGCAATGGCCCCCGCTTTACC
1 GGCAGTGGCCCCCGCTTTACC
1103307 GGCAGTGGCCCCCGCTTTACC
1 GGCAGTGGCCCCCGCTTTACC
*
1103328 GGTAGTG
1 GGCAGTG
1103335 TCACCTGCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.12, C:0.37, G:0.31, T:0.20
Consensus pattern (21 bp):
GGCAGTGGCCCCCGCTTTACC
Found at i:1103344 original size:21 final size:21
Alignment explanation
Indices: 1103286--1103345 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
1103276 GTTCAGTGGT
* *
1103286 GGCAATGGCCCCCGCTTTACC
1 GGCAGTGGCACCCGCTTTACC
*
1103307 GGCAGTGGCCCCCGCTTTACC
1 GGCAGTGGCACCCGCTTTACC
* * *
1103328 GGTAGTGTCACCTGCTTT
1 GGCAGTGGCACCCGCTTT
1103346 GGCACCCAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.25
Consensus pattern (21 bp):
GGCAGTGGCACCCGCTTTACC
Found at i:1113904 original size:99 final size:99
Alignment explanation
Indices: 1113779--1114010 Score: 419
Period size: 99 Copynumber: 2.3 Consensus size: 99
1113769 CCTACGCTGG
*
1113779 GAGCTCCAATCGTAAAAGTCTTGCTCCTCATTACGGTTAGAGCTCCAATCATAAAACTCTTGTTC
1 GAGCTCCAATCGTAAAAGTCTTGCTCCTCGTTACGGTTAGAGCTCCAATCATAAAACTCTTGTTC
1113844 CTCATTACTTGCTCGTAATTTGTTACCACGTTCA
66 CTCATTACTTGCTCGTAATTTGTTACCACGTTCA
*
1113878 GAGCTCCAATCGTAAAAGTCTTGCTCCTCGTTACGTTTAGAGCTCCAATCATAAAACTCTTGTTC
1 GAGCTCCAATCGTAAAAGTCTTGCTCCTCGTTACGGTTAGAGCTCCAATCATAAAACTCTTGTTC
* *
1113943 CTCATTACTTGCTCGTAATTTGTTACTATGTTCA
66 CTCATTACTTGCTCGTAATTTGTTACCACGTTCA
*
1113977 GAGCTCCAGTCGTAAAAGTCTTGCTCCTCGTTAC
1 GAGCTCCAATCGTAAAAGTCTTGCTCCTCGTTAC
1114011 TTTCTGATGG
Statistics
Matches: 128, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
99 128 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (99 bp):
GAGCTCCAATCGTAAAAGTCTTGCTCCTCGTTACGGTTAGAGCTCCAATCATAAAACTCTTGTTC
CTCATTACTTGCTCGTAATTTGTTACCACGTTCA
Found at i:1113922 original size:39 final size:39
Alignment explanation
Indices: 1113871--1113950 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
1113861 ATTTGTTACC
* * *
1113871 ACGTTCAGAGCTCCAATCGTAAAAGTCTTGCTCCTCGTT
1 ACGTTCAGAGCTCCAATCATAAAACTCTTGCTCCTCATT
* *
1113910 ACGTTTAGAGCTCCAATCATAAAACTCTTGTTCCTCATT
1 ACGTTCAGAGCTCCAATCATAAAACTCTTGCTCCTCATT
1113949 AC
1 AC
1113951 TTGCTCGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.33
Consensus pattern (39 bp):
ACGTTCAGAGCTCCAATCATAAAACTCTTGCTCCTCATT
Found at i:1114011 original size:60 final size:60
Alignment explanation
Indices: 1113916--1114050 Score: 173
Period size: 60 Copynumber: 2.2 Consensus size: 60
1113906 CGTTACGTTT
*
1113916 AGAGCTCCAATCATAAAACTCTTGTTCCTCATTACTTGCTCG-TAATTTGTTACTATGTTC
1 AGAGCTCCAATCATAAAACTCTTGCTCCTCATTACTTGCT-GATAATTTGTTACTATGTTC
* * * * * **
1113976 AGAGCTCCAGTCGTAAAAGTCTTGCTCCTCGTTACTTTCTGATGGTTTGTTACTATGTTC
1 AGAGCTCCAATCATAAAACTCTTGCTCCTCATTACTTGCTGATAATTTGTTACTATGTTC
*
1114036 AGAGCTCCAAACATA
1 AGAGCTCCAATCATA
1114051 GAATGCATCC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 62 0.98
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (60 bp):
AGAGCTCCAATCATAAAACTCTTGCTCCTCATTACTTGCTGATAATTTGTTACTATGTTC
Found at i:1115319 original size:31 final size:31
Alignment explanation
Indices: 1115281--1115350 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
1115271 CTTTTAAAAC
*
1115281 TTGCAATACAATCCCCCAATATTTAGTCCGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
***
1115312 TTGCAATATGGTCCCCCAACATTTAGTCCGT
1 TTGCAATACAATCCCCCAACATTTAGTCCGT
1115343 TTGCAATA
1 TTGCAATA
1115351 TGGTCACTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (31 bp):
TTGCAATACAATCCCCCAACATTTAGTCCGT
Found at i:1115351 original size:31 final size:31
Alignment explanation
Indices: 1115292--1115355 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
1115282 TGCAATACAA
*
1115292 TCCCCCAATATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1115323 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1115354 TC
1 TC
1115356 ACTGACGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.28, G:0.16, T:0.34
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:1120853 original size:23 final size:21
Alignment explanation
Indices: 1120825--1120876 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 21
1120815 TGTTTTTATA
1120825 AATTTAACTTTAAATATATAAT
1 AATTTAACTTTAAA-ATATAAT
* *
1120847 ATATTTATATTTTTAAATATAAT
1 A-ATTTA-ACTTTAAAATATAAT
1120870 AATTTAA
1 AATTTAA
1120877 TATCTTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 6 0.23
23 13 0.50
24 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTTAACTTTAAAATATAAT
Found at i:1123996 original size:41 final size:41
Alignment explanation
Indices: 1123951--1124077 Score: 96
Period size: 41 Copynumber: 3.1 Consensus size: 41
1123941 GGTTATGTTT
* *
1123951 TTTAGCCGCCTTTTATATAAAAGCCGCTAAAGGTAATGATA
1 TTTAGCCGCCTTTTATACAAAAGCCGCTAAAGGTAATAATA
** ** * * *
1123992 TTTAGTGGTTTTTTTTACAAATGCCGCTAAAGGTTATAATA
1 TTTAGCCGCCTTTTATACAAAAGCCGCTAAAGGTAATAATA
*** * * * *
1124033 TTTAG--TATTTTTTTACAAATGCCGTTAAAGGTTATAATA
1 TTTAGCCGCCTTTTATACAAAAGCCGCTAAAGGTAATAATA
1124072 TTTAGC
1 TTTAGC
1124078 GTCGTTTTTC
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 36 0.49
41 37 0.51
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (41 bp):
TTTAGCCGCCTTTTATACAAAAGCCGCTAAAGGTAATAATA
Found at i:1124055 original size:39 final size:40
Alignment explanation
Indices: 1123973--1124076 Score: 156
Period size: 39 Copynumber: 2.6 Consensus size: 40
1123963 TTATATAAAA
* * *
1123973 GCCGCTAAAGGTAATGATATTTAGTGGTTTTTTTTACAAAT
1 GCCGCTAAAGGTTATAATATTTAGT-GATTTTTTTACAAAT
1124014 GCCGCTAAAGGTTATAATATTTAGT-ATTTTTTTACAAAT
1 GCCGCTAAAGGTTATAATATTTAGTGATTTTTTTACAAAT
*
1124053 GCCGTTAAAGGTTATAATATTTAG
1 GCCGCTAAAGGTTATAATATTTAG
1124077 CGTCGTTTTT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 36 0.61
41 23 0.39
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (40 bp):
GCCGCTAAAGGTTATAATATTTAGTGATTTTTTTACAAAT
Found at i:1130065 original size:2 final size:2
Alignment explanation
Indices: 1130058--1130109 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1130048 TCAGAATCCT
1130058 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1130100 TC TC TC TC TC
1 TC TC TC TC TC
1130110 CACCTCTTGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1135483 original size:15 final size:15
Alignment explanation
Indices: 1135465--1135493 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1135455 TTTTGCGTGA
1135465 GTAAAATTTGAATAT
1 GTAAAATTTGAATAT
1135480 GTAAAATTTGAATA
1 GTAAAATTTGAATA
1135494 ATCAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (15 bp):
GTAAAATTTGAATAT
Found at i:1139807 original size:68 final size:68
Alignment explanation
Indices: 1139688--1139841 Score: 247
Period size: 68 Copynumber: 2.3 Consensus size: 68
1139678 TTTTAGAAAA
* * **
1139688 CACAATCCATGTGAATTGGATTGCAACCATTGATAAAGAAATGGATCTTTCGATCTCAGTCATTC
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAATGGATATTTCGATCTCAACCATTC
1139753 ATT
66 ATT
*
1139756 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAA-GGAATATTTCGATCTCAACCGTT
1 CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAATGG-ATATTTCGATCTCAACCATT
1139820 CATT
65 CATT
1139824 CACAATCCATGTGAATTG
1 CACAATCCATGTGAATTG
1139842 TGCTTGCAAG
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 2 0.03
68 78 0.98
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (68 bp):
CACAATCCATGTGAATTGGATTACAACCATTGATAAAGAAATGGATATTTCGATCTCAACCATTC
ATT
Found at i:1139929 original size:100 final size:100
Alignment explanation
Indices: 1139782--1139995 Score: 374
Period size: 100 Copynumber: 2.1 Consensus size: 100
1139772 TGGATTACAA
1139782 CCATTGATAAAGAAAGGAATATTTCGATCTCAACCGTTCATTCACAATCCATGTGAATTGTGCTT
1 CCATTGATAAAGAAAGGAATATTTCGATCTCAACCGTTCATTCACAATCCATGTGAATTGTGCTT
1139847 GCAAGAAAACACAATCCATGTGAAAACAATTCTAC
66 GCAAGAAAACACAATCCATGTGAAAACAATTCTAC
* * *
1139882 CCATTGATAAAGAAATGAATCTTTCGATCTCAGCCGTTCATTCACAATCCATGTGAATTGTGCTT
1 CCATTGATAAAGAAAGGAATATTTCGATCTCAACCGTTCATTCACAATCCATGTGAATTGTGCTT
* *
1139947 GCAAGAAAATACAATCCTTGTGAAAACAATTCTAC
66 GCAAGAAAACACAATCCATGTGAAAACAATTCTAC
*
1139982 CCATTGATTAAGAA
1 CCATTGATAAAGAA
1139996 TTGACTCAAA
Statistics
Matches: 108, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 108 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.29
Consensus pattern (100 bp):
CCATTGATAAAGAAAGGAATATTTCGATCTCAACCGTTCATTCACAATCCATGTGAATTGTGCTT
GCAAGAAAACACAATCCATGTGAAAACAATTCTAC
Found at i:1144553 original size:149 final size:148
Alignment explanation
Indices: 1144279--1144584 Score: 486
Period size: 149 Copynumber: 2.1 Consensus size: 148
1144269 GAGTCAAGGG
* * * * * *
1144279 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
1144344 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTATGGGCATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTATGGACATTATTAT
*
1144409 ATGGCACTACGGTGCAAT
131 AAGGCACTACGGTGCAAT
* *
1144427 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
*
1144492 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTATGGACATTATTA
1144557 TAAGGCACTACGGTGCAAT
130 TAAGGCACTACGGTGCAAT
1144576 TCTACGCGG
1 TCTACGCGG
1144585 CACTACGGTG
Statistics
Matches: 144, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
148 48 0.33
149 96 0.67
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTAGTCCTTATGGACATTATTAT
AAGGCACTACGGTGCAAT
Found at i:1144626 original size:22 final size:23
Alignment explanation
Indices: 1144560--1144620 Score: 97
Period size: 23 Copynumber: 2.7 Consensus size: 23
1144550 ATTATTATAA
1144560 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
1144583 GGCACTACGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* *
1144605 TGCACTTCGGTGCAAT
1 GGCACTACGGTGCAAT
1144621 GATACGAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
22 14 0.39
23 22 0.61
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1145763 original size:21 final size:20
Alignment explanation
Indices: 1145739--1145780 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1145729 GTCATACAAC
*
1145739 TAATAATAGTTGTATAATGCA
1 TAATAATAGTT-CATAATGCA
*
1145760 TAATAATGGTTCATAATGCA
1 TAATAATAGTTCATAATGCA
1145780 T
1 T
1145781 TGTAAGTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.38
Consensus pattern (20 bp):
TAATAATAGTTCATAATGCA
Found at i:1147748 original size:18 final size:18
Alignment explanation
Indices: 1147721--1147765 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
1147711 AGGCATATCC
*
1147721 ATCAGGCCCGAGAGCCTT
1 ATCAGACCCGAGAGCCTT
1147739 ATCAGACCCGAGAGCCTT
1 ATCAGACCCGAGAGCCTT
1147757 ATCAGACCC
1 ATCAGACCC
1147766 TTGCTTAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.27, C:0.36, G:0.22, T:0.16
Consensus pattern (18 bp):
ATCAGACCCGAGAGCCTT
Found at i:1148090 original size:11 final size:10
Alignment explanation
Indices: 1148075--1148113 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
1148065 TTACAAATAT
1148075 AAAAAAAATC
1 AAAAAAAATC
*
1148085 AGAAAAAATAC
1 AAAAAAAAT-C
1148096 AAAAAAAAATC
1 -AAAAAAAATC
1148107 AAAAAAA
1 AAAAAAA
1148114 TAGTATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 15 0.60
11 2 0.08
12 8 0.32
ACGTcount: A:0.82, C:0.08, G:0.03, T:0.08
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:1148103 original size:22 final size:21
Alignment explanation
Indices: 1148075--1148115 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
1148065 TTACAAATAT
1148075 AAAAAAAATCAGAAAAAATACA
1 AAAAAAAATCA-AAAAAATACA
1148097 AAAAAAAATCAAAAAAATA
1 AAAAAAAATCAAAAAAATA
1148116 GTATGATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.10
Consensus pattern (21 bp):
AAAAAAAATCAAAAAAATACA
Found at i:1148171 original size:15 final size:16
Alignment explanation
Indices: 1148146--1148178 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1148136 TCAATGTATT
1148146 TTTATATATATTATAA
1 TTTATATATATTATAA
*
1148162 TTTA-ATATATTTTAA
1 TTTATATATATTATAA
1148177 TT
1 TT
1148179 AAAAAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTATATATATTATAA
Found at i:1149157 original size:60 final size:59
Alignment explanation
Indices: 1149063--1149191 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 59
1149053 AATAATACTA
* * *
1149063 ATAATTTAAATATTGATATAAAATATTTTAAAATTTTAATGATTAA-TATAAAATCAAAAAT
1 ATAATTTAAATAATAATATAAAATATTTTAAAA-TTTAAAGATTAACT-TAAAAT-AAAAAT
* *
1149124 ATAATTTAAA-AATAATATGAAATATTTTAAAATTTAAAGATTAACTTAAAATAAAATT
1 ATAATTTAAATAATAATATAAAATATTTTAAAATTTAAAGATTAACTTAAAATAAAAAT
1149182 ATAATTTAAA
1 ATAATTTAAA
1149192 GACATCTTGT
Statistics
Matches: 62, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
58 15 0.24
59 17 0.27
60 20 0.32
61 10 0.16
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (59 bp):
ATAATTTAAATAATAATATAAAATATTTTAAAATTTAAAGATTAACTTAAAATAAAAAT
Found at i:1149338 original size:12 final size:12
Alignment explanation
Indices: 1149321--1149346 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1149311 AGAACGTTTA
1149321 TAATAATTTTTT
1 TAATAATTTTTT
1149333 TAATAATTTTTT
1 TAATAATTTTTT
1149345 TA
1 TA
1149347 TTTTTTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TAATAATTTTTT
Found at i:1160738 original size:10 final size:10
Alignment explanation
Indices: 1160688--1160739 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
1160678 TATATTTATT
1160688 ATAATA-TTA
1 ATAATATTTA
*
1160697 AAAACTATTTA
1 ATAA-TATTTA
1160708 ATAATAATTTA
1 ATAAT-ATTTA
*
1160719 ATACTATTTA
1 ATAATATTTA
*
1160729 ATAATTTTTA
1 ATAATATTTA
1160739 A
1 A
1160740 AATTCAAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 3 0.09
10 17 0.49
11 15 0.43
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (10 bp):
ATAATATTTA
Found at i:1161254 original size:20 final size:19
Alignment explanation
Indices: 1161231--1161277 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
1161221 CGATATACTA
1161231 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
1161251 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1161271 GGTAAAA
1 GGTAAAA
1161278 CGTTACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1161354 original size:181 final size:183
Alignment explanation
Indices: 1161019--1161492 Score: 720
Period size: 182 Copynumber: 2.6 Consensus size: 183
1161009 GATCCAAATT
* * * ** *
1161019 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGACATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
1161084 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
* *
1161149 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAATGTCGATACTTT-TA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAATGTCGATACTTTAAA
1161201 AAAAATGTATCGATCCAAAACGATAT-ACTAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAAC-AGGTAAAAATATGATAAAACCGGTATCAAAATGAT
*
1161265 AAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGGTACTTT-ATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
* ** **
1161329 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAAA
130 CGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAATGTCGATACTTTAAA
* * *
1161383 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
1161448 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGGTACTTT
1161493 CGTAAGTACG
Statistics
Matches: 267, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
181 65 0.24
182 200 0.75
183 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (183 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAATGTCGATACTTTAAA
Found at i:1161436 original size:20 final size:19
Alignment explanation
Indices: 1161413--1161459 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
1161403 CGATATAACA
1161413 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
1161433 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
1161453 GGTAAAA
1 GGTAAAA
1161460 CGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1163705 original size:21 final size:21
Alignment explanation
Indices: 1163679--1163743 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
1163669 AAGACAATCA
*
1163679 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
1163700 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* * *
1163721 AGAGTCAAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
1163742 AG
1 AG
1163744 GCATAAGGGG
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:0.43, C:0.11, G:0.29, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:1163819 original size:33 final size:33
Alignment explanation
Indices: 1163777--1163842 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1163767 AAATAGATGG
*
1163777 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
1163810 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
1163843 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:1165654 original size:19 final size:19
Alignment explanation
Indices: 1165630--1165678 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1165620 AATGTAGGAT
1165630 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
1165649 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
1165668 TAATTTTGTAT
1 TAATTTTGTAT
1165679 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1166243 original size:200 final size:200
Alignment explanation
Indices: 1165900--1166407 Score: 962
Period size: 200 Copynumber: 2.5 Consensus size: 200
1165890 AAGTAAAAGG
* *
1165900 CATATATAAAAAATGTCGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
1 CATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
* * *
1165965 TCAATCTAACTGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACT
66 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAAAAATATATCGACACT
1166030 TTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGT
131 TTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGT
1166095 CGATC
196 CGATC
1166100 CATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
1 CATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
*
1166165 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAAAAATATGTCGACACT
66 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAAAAATATATCGACACT
1166230 TTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGT
131 TTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGT
1166295 CGATC
196 CGATC
1166300 CATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
1 CATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
1166365 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAG
66 TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAG
1166408 TAGTTTGTGT
Statistics
Matches: 302, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
200 302 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (200 bp):
CATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTT
TCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAAAAATATATCGACACT
TTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGT
CGATC
Found at i:1166442 original size:174 final size:174
Alignment explanation
Indices: 1166233--1166579 Score: 622
Period size: 174 Copynumber: 2.0 Consensus size: 174
1166223 CGACACTTTT
1166233 GTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGA
1 GTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGA
*
1166298 TCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATT
66 TCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATT
1166363 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
131 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
* *
1166407 GTAGTTTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGA
1 GTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGA
*
1166472 TCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTATTAGGTAATT
66 TCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATT
* * * *
1166537 TTTTAATCTAATCGGTATAAGTATACCGGTTTTATGGGAGAAT
131 TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAAT
1166580 TGGTATATAA
Statistics
Matches: 165, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 165 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (174 bp):
GTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGA
TCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATT
TTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATA
Found at i:1168109 original size:6 final size:6
Alignment explanation
Indices: 1168098--1168198 Score: 114
Period size: 6 Copynumber: 16.8 Consensus size: 6
1168088 CAAGCGGTCA
* * * * * * *
1168098 ATGAAG ATGAAG ATGACG ATGAAG ATGACG ATGAAT- ATGACG ACGATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATG-ATG ATGATG ATGATG
*
1168146 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATAATG
1 ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG ATGATG
1168194 ATGAT
1 ATGAT
1168199 CCAAACAAGT
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
5 1 0.01
6 81 0.98
7 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.31, T:0.27
Consensus pattern (6 bp):
ATGATG
Found at i:1169749 original size:183 final size:182
Alignment explanation
Indices: 1169402--1169972 Score: 991
Period size: 183 Copynumber: 3.1 Consensus size: 182
1169392 CAAAGTTTTC
*
1169402 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
1169467 CAAAAAGTGTCG-ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAAT
66 CAAAAAGTGTCGAATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAAT
*
1169531 ATAACCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAACCTATATCG
128 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1169586 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1169651 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGA-ATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
1169716 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1169769 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
1169834 CAAAAAGTGTCCATATTTACACATCGGAACCCCGAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGA-ATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* **
1169899 AATCGGTATAAATATACTAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
130 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1169952 ACACTTTTTAATATTGTGTCG
1 ACACTTTTTAATATTGTGTCG
1169973 CTAATTTTAA
Statistics
Matches: 373, Mismatches: 12, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
183 294 0.79
184 76 0.20
186 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.33
Consensus pattern (182 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGAATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATA
ACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1173455 original size:23 final size:23
Alignment explanation
Indices: 1173405--1173449 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1173395 TACCTATTTT
* *
1173405 ATTATATAAGCGTTATCTATTAC
1 ATTATATAAGCATTATCTAATAC
1173428 ATTATATAAGCATTATCTAATA
1 ATTATATAAGCATTATCTAATA
1173450 TGTTATTGTA
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:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (23 bp):
ATTATATAAGCATTATCTAATAC
Found at i:1176821 original size:18 final size:17
Alignment explanation
Indices: 1176793--1176827 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
1176783 TCTTGCTGGT
1176793 GTCCCCCATAAGGACTG
1 GTCCCCCATAAGGACTG
1176810 GTCCCTCCATAAGGACTG
1 GTCCC-CCATAAGGACTG
1176828 TTTGAATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (17 bp):
GTCCCCCATAAGGACTG
Found at i:1178426 original size:205 final size:197
Alignment explanation
Indices: 1178067--1178436 Score: 494
Period size: 205 Copynumber: 1.8 Consensus size: 197
1178057 TATTTTTGTC
**
1178067 CCATGTTTTGAAAAATTATGGATATTTTTAAAAATTAAAAAATATTAAAAATTCTACAATATATA
1 CCATGTTTTGAAAAATTATGGATATTTAAAAAAATTAAAAAATATTAAAAATTCTACAATATATA
*
1178132 TATATATGTGAAAAAACACAAACACATAACTAATTTTATATTTTTATTAAAATTATTTTAAAATA
66 TATATATATGAAAAAACACAAACACATAACTAATTTTATATTTTTATTAAAA-TATTTTAAAATA
* * *
1178197 ATTTTTATGATCGTAAAGTATATCATAACAGATAATATTAAAAAAAACATTAAAAATGAGTTTTC
130 ATTTTTATGAACGGAAACTATATCATAACAGATAATATTAAAAAAAACATTAAAAATGAGTTTTC
1178262 GTT
195 GTT
* *
1178265 CCATGTTTTGAAAAATTATGGATATTTAAAAAAAAACATTAAAAATTCTT-AAAATTCTACGAGA
1 CCATGTTTTGAAAAATTATGGATATTT---AAAAAA-ATTAAAAAATATTAAAAATTCTAC-A-A
* *
1178329 TATATATATATGTATATGCAAAAACACAAATACATAACTAATTTTAT-TTTTTCATTAAAA-ATG
60 TATATATATA--TATATGAAAAAACACAAACACATAACTAATTTTATATTTTT-ATTAAAATAT-
* * *
1178392 TTTAGAATTATTTTTTATTAACGGAAACTATATCATAACAGATAA
121 TTTA-AAATAATTTTTATGAACGGAAACTATATCATAACAGATAA
1178437 CAAAAAATCT
Statistics
Matches: 148, Mismatches: 13, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
198 27 0.18
201 14 0.09
202 12 0.08
203 13 0.09
204 9 0.06
205 73 0.49
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (197 bp):
CCATGTTTTGAAAAATTATGGATATTTAAAAAAATTAAAAAATATTAAAAATTCTACAATATATA
TATATATATGAAAAAACACAAACACATAACTAATTTTATATTTTTATTAAAATATTTTAAAATAA
TTTTTATGAACGGAAACTATATCATAACAGATAATATTAAAAAAAACATTAAAAATGAGTTTTCG
TT
Found at i:1179065 original size:16 final size:16
Alignment explanation
Indices: 1179040--1179074 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1179030 AACAAACCTT
*
1179040 GCTGCCTTTATGATCA
1 GCTGCCTTTATAATCA
*
1179056 GCTGCTTTTATAATCA
1 GCTGCCTTTATAATCA
1179072 GCT
1 GCT
1179075 CTCCACTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (16 bp):
GCTGCCTTTATAATCA
Found at i:1179702 original size:10 final size:10
Alignment explanation
Indices: 1179683--1179770 Score: 59
Period size: 10 Copynumber: 8.1 Consensus size: 10
1179673 GCATAGCTCG
*
1179683 CTCGGTTGCC
1 CTCGGATGCC
1179693 CTCGGATGCC
1 CTCGGATGCC
*
1179703 CTCGCATAGCTC
1 CTCGGAT-GC-C
*
1179715 GTTCGGATGGCC
1 -CTCGGAT-GCC
*
1179727 TCGGTCGGATGGC
1 -C--TCGGATGCC
*
1179740 CTCGGATGCT
1 CTCGGATGCC
*
1179750 CTCGGATGGC
1 CTCGGATGCC
1179760 CTCGGATGCC
1 CTCGGATGCC
1179770 C
1 C
1179771 AGCGTGTTGG
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
10 40 0.67
11 2 0.03
12 3 0.05
13 9 0.15
14 6 0.10
ACGTcount: A:0.09, C:0.34, G:0.33, T:0.24
Consensus pattern (10 bp):
CTCGGATGCC
Found at i:1179705 original size:33 final size:33
Alignment explanation
Indices: 1179668--1179770 Score: 104
Period size: 33 Copynumber: 3.1 Consensus size: 33
1179658 TCGCTCGATT
*
1179668 CCCTCGCATAGCTCGCTCGGTTGCCCTCGGATG
1 CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
*
1179701 CCCTCGCATAGCTCGTTCGGATGGCCTCGGTCGGATG
1 CCCTCGCATAGCTCGCTCGGAT-GCC-C--TCGGATG
* * *
1179738 GCCTCGGAT-GCT--CTCGGATGGCCTCGGATG
1 CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
1179768 CCC
1 CCC
1179771 AGCGTGTTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
30 9 0.15
32 1 0.02
33 22 0.37
34 9 0.15
35 1 0.02
36 3 0.05
37 14 0.24
ACGTcount: A:0.10, C:0.36, G:0.31, T:0.23
Consensus pattern (33 bp):
CCCTCGCATAGCTCGCTCGGATGCCCTCGGATG
Found at i:1179734 original size:14 final size:14
Alignment explanation
Indices: 1179712--1179744 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1179702 CCTCGCATAG
*
1179712 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1179726 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1179740 CTCGG
1 CTCGG
1179745 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1179756 original size:20 final size:20
Alignment explanation
Indices: 1179731--1179768 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1179721 ATGGCCTCGG
1179731 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
1179751 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
1179769 CCAGCGTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.37, T:0.24
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:1187136 original size:16 final size:17
Alignment explanation
Indices: 1187099--1187133 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1187089 TTAGCAGTAT
**
1187099 TTGAAAAACAAAGGGCC
1 TTGAAAAACAAAGAACC
1187116 TTGAAAAACAAAGAACC
1 TTGAAAAACAAAGAACC
1187133 T
1 T
1187134 GAAGTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.14
Consensus pattern (17 bp):
TTGAAAAACAAAGAACC
Found at i:1188649 original size:37 final size:37
Alignment explanation
Indices: 1188577--1188651 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
1188567 GTTGGAAAAT
* *
1188577 ATTTATATATTTTCTTTAAAAAATTTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAATATATAAA
* *
1188614 ATTTATATAATTTTTTTTACAAAATTGAAA-ATATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAATATATAAA
1188651 A
1 A
1188652 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAATATATAAA
Found at i:1197644 original size:57 final size:57
Alignment explanation
Indices: 1197551--1197661 Score: 177
Period size: 57 Copynumber: 1.9 Consensus size: 57
1197541 ATAATGCAAC
* *
1197551 TCCAAGTGGAGCCTGAAAGTAACCAAGTAAACTCAGCATTAAATTGCCTTAAAATAT
1 TCCAAGTGGAGCCTGAAAGTAACCAAGTAAACTCAGCATCAAATAGCCTTAAAATAT
* * *
1197608 TCCAAGTGGGGCCTGAAAGTAACCACGTAAATTCAGCATCAAATAGCCTTAAAA
1 TCCAAGTGGAGCCTGAAAGTAACCAAGTAAACTCAGCATCAAATAGCCTTAAAA
1197662 AACTCATTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (57 bp):
TCCAAGTGGAGCCTGAAAGTAACCAAGTAAACTCAGCATCAAATAGCCTTAAAATAT
Found at i:1199837 original size:9 final size:10
Alignment explanation
Indices: 1199814--1199839 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1199804 CCCTTAAATG
1199814 TTTTTTAATA
1 TTTTTTAATA
1199824 TTTTTTAATA
1 TTTTTTAATA
1199834 TTTTTT
1 TTTTTT
1199840 CACCTCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:1200327 original size:15 final size:15
Alignment explanation
Indices: 1200309--1200338 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1200299 TTGTTGTGTT
1200309 CATGGAATGATTTTG
1 CATGGAATGATTTTG
1200324 CATGGAATGATTTTG
1 CATGGAATGATTTTG
1200339 TATTTTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.27, T:0.40
Consensus pattern (15 bp):
CATGGAATGATTTTG
Found at i:1206772 original size:2 final size:2
Alignment explanation
Indices: 1206765--1206793 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1206755 TTTATTTAAA
1206765 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
1206794 ATCGAATGAA
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:1207245 original size:41 final size:42
Alignment explanation
Indices: 1207183--1207266 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 42
1207173 AATAAGAGCC
* * * *
1207183 TAATCATATATAATTTGATACATCAACCGTATATGAT-TCTA
1 TAATAATATATAATTGGATACATCAACCATATATAATATCTA
1207224 TAATAATATATAATTGGATACATCAACCATATATAATATCTA
1 TAATAATATATAATTGGATACATCAACCATATATAATATCTA
1207266 T
1 T
1207267 TTTAAACTGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 33 0.87
42 5 0.13
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (42 bp):
TAATAATATATAATTGGATACATCAACCATATATAATATCTA
Found at i:1207259 original size:23 final size:23
Alignment explanation
Indices: 1207187--1207260 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
1207177 AGAGCCTAAT
*
1207187 CATATATAATTTGATACATCAAC
1 CATATATAATTCGATACATCAAC
* * *
1207210 CGTATATGATTCTATA-AT--A-
1 CATATATAATTCGATACATCAAC
*
1207229 -ATATATAATTGGATACATCAAC
1 CATATATAATTCGATACATCAAC
1207251 CATATATAAT
1 CATATATAAT
1207261 ATCTATTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
18 11 0.29
19 2 0.05
20 1 0.03
21 1 0.03
22 2 0.05
23 21 0.55
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (23 bp):
CATATATAATTCGATACATCAAC
Found at i:1214173 original size:21 final size:21
Alignment explanation
Indices: 1214144--1214196 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1214134 ATTCTGACTA
1214144 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
1214165 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1214186 TCGCAATGCGA
1 TCGCATTGCGA
1214197 ATACGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1214211 original size:20 final size:20
Alignment explanation
Indices: 1214186--1214298 Score: 208
Period size: 20 Copynumber: 5.7 Consensus size: 20
1214176 TTTTCCTAAT
1214186 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1214206 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1214226 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1214246 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1214266 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
*
1214286 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1214299 CTGACTATCG
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 91 1.00
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1214511 original size:22 final size:22
Alignment explanation
Indices: 1214486--1214561 Score: 107
Period size: 22 Copynumber: 3.5 Consensus size: 22
1214476 CACTCTCTAA
* *
1214486 GACGACATCCGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
1214508 GACGAAATCAGTCCCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
* *
1214530 GACGATATCAGTCTCCATCTCC
1 GACGAAATCAGTCCCCATCTCC
*
1214552 GGCGAAATCA
1 GACGAAATCA
1214562 TTCACGGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.25, C:0.39, G:0.16, T:0.20
Consensus pattern (22 bp):
GACGAAATCAGTCCCCATCTCC
Found at i:1214954 original size:20 final size:20
Alignment explanation
Indices: 1214929--1215071 Score: 93
Period size: 20 Copynumber: 7.5 Consensus size: 20
1214919 TGCGATTCTT
*
1214929 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAATTTC
* * *
1214949 GCGTTGCAATAGGCATTTTC
1 GCGTTGCGATAGTCAATTTC
* **
1214969 GTGTTGCGATTTTC-ATTTC
1 GCGTTGCGATAGTCAATTTC
*
1214988 GCGTTGCG--A-TC--CTT-
1 GCGTTGCGATAGTCAATTTC
*
1215002 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAATTTC
* *
1215022 GCGTTGCGAAAGTCATTTTC
1 GCGTTGCGATAGTCAATTTC
* ** *
1215042 GTGTTGCGATTTTCATTTTC
1 GCGTTGCGATAGTCAATTTC
*
1215062 GTGTTGCGAT
1 GCGTTGCGAT
1215072 TTTAAGTTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 12
0.74 0.16 0.09
Matches are distributed among these distances:
14 8 0.08
15 2 0.02
16 3 0.03
17 2 0.02
19 13 0.14
20 68 0.71
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATAGTCAATTTC
Found at i:1215017 original size:73 final size:73
Alignment explanation
Indices: 1214898--1215071 Score: 287
Period size: 73 Copynumber: 2.4 Consensus size: 73
1214888 CGATTCTGTC
* *
1214898 GTTGCTATTTTCATTTCGCGTTGCGATTCTTGCGTTGCGATAGTCAAATTCGCGTTGC-AATAGG
1 GTTGCGATTTTCATTTCGCGTTGCGATCCTTGCGTTGCGATAGTCAAATTCGCGTTGCGAA-AGG
1214962 CATTTTCGT
65 CATTTTCGT
*
1214971 GTTGCGATTTTCATTTCGCGTTGCGATCCTTGCGTTGCGATAGTCAAATTCGCGTTGCGAAAGTC
1 GTTGCGATTTTCATTTCGCGTTGCGATCCTTGCGTTGCGATAGTCAAATTCGCGTTGCGAAAGGC
1215036 ATTTTCGT
66 ATTTTCGT
*
1215044 GTTGCGATTTTCATTTTCGTGTTGCGAT
1 GTTGCGATTTTCA-TTTCGCGTTGCGAT
1215072 TTTAAGTTTC
Statistics
Matches: 95, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
73 80 0.84
74 15 0.16
ACGTcount: A:0.16, C:0.19, G:0.24, T:0.41
Consensus pattern (73 bp):
GTTGCGATTTTCATTTCGCGTTGCGATCCTTGCGTTGCGATAGTCAAATTCGCGTTGCGAAAGGC
ATTTTCGT
Found at i:1215081 original size:20 final size:20
Alignment explanation
Indices: 1215038--1215081 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1215028 CGAAAGTCAT
* *
1215038 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1215058 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1215078 TTTC
1 TTTC
1215082 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1216988 original size:20 final size:20
Alignment explanation
Indices: 1216963--1217141 Score: 143
Period size: 20 Copynumber: 9.6 Consensus size: 20
1216953 AGAATAGTTT
* *
1216963 ACTATCGCAATGCAAAAATG
1 ACTATCGCAACGCGAAAATG
1216983 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
1217003 ACTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
1217023 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAACGCGAAAATG
* *
1217039 A--ATCACAATGCG-AAATG
1 ACTATCGCAACGCGAAAATG
**
1217056 AAAATCGCAA--C-AACAA--
1 ACTATCGCAACGCGAA-AATG
*
1217072 A--ATCACAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
1217090 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
* **
1217110 ACTATCGCAATGCGAATTTG
1 ACTATCGCAACGCGAAAATG
1217130 ACTATCGCAACG
1 ACTATCGCAACG
1217142 AAAGAATCGC
Statistics
Matches: 133, Mismatches: 12, Indels: 28
0.77 0.07 0.16
Matches are distributed among these distances:
14 12 0.09
16 10 0.08
17 8 0.06
18 5 0.04
19 6 0.05
20 92 0.69
ACGTcount: A:0.42, C:0.23, G:0.18, T:0.17
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:1217021 original size:40 final size:38
Alignment explanation
Indices: 1216963--1217160 Score: 163
Period size: 40 Copynumber: 5.4 Consensus size: 38
1216953 AGAATAGTTT
*
1216963 ACTATCGCAATGCAAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAA-GCGAAAA-G
* *
1217003 ACTATCGCAACGCGAAAATGACTATCGCAA-CG-AGAG
1 ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAAG
* **
1217039 A--ATCACAATGCG-AAATGAAAATCGCAA-C-AACAA-
1 ACTATCGCAATGCGAAAATGACTATCGCAAGCGAA-AAG
* *
1217072 A--ATCACAACGCGAAAATGACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATGACTATCGCAA-GCGAAAA-G
**
1217110 ACTATCGCAATGCGAATTTGACTATCGCAA-CG-AAAG
1 ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAAG
1217146 A--ATCGCAATGCGAAA
1 ACTATCGCAATGCGAAA
1217161 TGAAAACCGC
Statistics
Matches: 132, Mismatches: 16, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
33 26 0.20
34 36 0.27
36 7 0.05
37 7 0.05
38 5 0.04
40 51 0.39
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.16
Consensus pattern (38 bp):
ACTATCGCAATGCGAAAATGACTATCGCAAGCGAAAAG
Found at i:1217163 original size:107 final size:107
Alignment explanation
Indices: 1216977--1217171 Score: 327
Period size: 107 Copynumber: 1.8 Consensus size: 107
1216967 TCGCAATGCA
*
1216977 AAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAAT
1 AAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAAT
*
1217042 CACAATGCGAAATGAAAATCGCAACAACAAAATCACAACGCG
66 CACAATGCGAAATGAAAACCGCAACAACAAAATCACAACGCG
* * **
1217084 AAAATGACTATCGCAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAAT
1 AAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAAT
*
1217149 CGCAATGCGAAATGAAAACCGCA
66 CACAATGCGAAATGAAAACCGCA
1217172 TTGCGATTCT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 81 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.15
Consensus pattern (107 bp):
AAAATGACTATCGCAACGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAAT
CACAATGCGAAATGAAAACCGCAACAACAAAATCACAACGCG
Found at i:1217214 original size:20 final size:20
Alignment explanation
Indices: 1217184--1217252 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1217174 GCGATTCTCT
* **
1217184 CGTTTCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1217204 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1217224 TGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
1217244 CGTTGCGAT
1 CGTTGCGAT
1217253 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1217827 original size:21 final size:21
Alignment explanation
Indices: 1217736--1217840 Score: 86
Period size: 21 Copynumber: 5.0 Consensus size: 21
1217726 GACTCACCTG
*
1217736 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
* *
1217758 T-ATCGTTTAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1217778 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1217799 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1217820 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1217841 CCAACATTCT
Statistics
Matches: 61, Mismatches: 21, Indels: 3
0.72 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 57 0.93
22 1 0.02
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1217833 original size:42 final size:42
Alignment explanation
Indices: 1217733--1217843 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 42
1217723 CCCGACTCAC
* * * * *
1217733 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTTAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1217775 CTATCATCCCTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1217817 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1217844 ACATTCTAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
41 2 0.04
42 51 0.93
43 2 0.04
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1219258 original size:19 final size:20
Alignment explanation
Indices: 1219229--1219266 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1219219 AGAAATTTGT
1219229 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
1219249 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
1219267 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:1219309 original size:63 final size:62
Alignment explanation
Indices: 1219234--1219392 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
1219224 TTTGTTGAAG
* * * *
1219234 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
1219297 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
*
1219360 GTGCTTCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
1219393 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:1220158 original size:147 final size:147
Alignment explanation
Indices: 1219848--1220147 Score: 591
Period size: 147 Copynumber: 2.0 Consensus size: 147
1219838 GGGTAGAGGG
1219848 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1219913 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
1219978 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
1219995 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
1 TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
*
1220060 TTGATCCCTTGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
1220125 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
1220142 TCTACG
1 TCTACG
1220148 TGGCACTTCG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
147 152 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.36
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
TGGCACTACGGTGCAAT
Found at i:1220159 original size:23 final size:23
Alignment explanation
Indices: 1220125--1220170 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1220115 CATTATTATA
*
1220125 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
1220148 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
1220171 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:1225900 original size:19 final size:20
Alignment explanation
Indices: 1225871--1225908 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1225861 AGAAATTTGT
1225871 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
1225891 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
1225909 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:1225951 original size:63 final size:62
Alignment explanation
Indices: 1225876--1226034 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
1225866 TTTGTTGAAG
* * * *
1225876 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
* ** **
1225939 GTGCATCGATGCATAAGGAGTGCATCAATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
1226002 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
1226035 GCCTCCATAA
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
63 78 0.94
64 5 0.06
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:1226799 original size:149 final size:147
Alignment explanation
Indices: 1226487--1226788 Score: 577
Period size: 149 Copynumber: 2.0 Consensus size: 147
1226477 AGGTAGAGGG
*
1226487 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAGTCTTGTAAGACACATA
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGCGGAACATGTGTGAGTCTTGTAAGACACATA
1226552 CTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
66 CTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
1226617 TGGCACTACGGTGCAAT
131 TGGCACTACGGTGCAAT
1226634 TCTACGCGGTCCTTCGGGATATATATATATTCTGCGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGCGGAACATGTGTG-AGTCTTGTAAGACACAT
1226699 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 AC-TGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
1226764 TATGGCACTACGGTGCAAT
129 TATGGCACTACGGTGCAAT
1226783 TCTACG
1 TCTACG
1226789 TGGCACTTCG
Statistics
Matches: 152, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 46 0.30
148 19 0.12
149 87 0.57
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGCGGAACATGTGTGAGTCTTGTAAGACACATA
CTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATA
TGGCACTACGGTGCAAT
Found at i:1226800 original size:23 final size:23
Alignment explanation
Indices: 1226766--1226811 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1226756 CATTATTATA
* *
1226766 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTACAATTATACG
*
1226789 TGGCACTTCGGTACAATTATACG
1 TGGCACTACGGTACAATTATACG
1226812 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTACAATTATACG
Found at i:1228347 original size:33 final size:34
Alignment explanation
Indices: 1228297--1228390 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
1228287 AAAACAGACT
* ** *
1228297 ATCGCAACGCGGAAATGACTATCGTAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1228331 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
**
1228364 ATCGCAATGCTAAAATGAAAATCGCAA
1 ATCGCAATGCGGAAATGAAAATCGCAA
1228391 TGCGAAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.56
34 24 0.44
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:1228431 original size:20 final size:20
Alignment explanation
Indices: 1228403--1228455 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1228393 CGAAATTATT
1228403 TTCGCGTTGCGATAGTCAT-
1 TTCGCGTTGCGATAGTCATA
*
1228422 TTCCGTGTTGCGATAGTCATA
1 TT-CGCGTTGCGATAGTCATA
1228443 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1228456 TTCCGTGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCATA
Found at i:1231816 original size:20 final size:20
Alignment explanation
Indices: 1231791--1231877 Score: 147
Period size: 20 Copynumber: 4.3 Consensus size: 20
1231781 AAATTCAGTA
1231791 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
1231811 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
*
1231831 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
1231851 TTGCGATAGTTAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
1231871 TTGCGAT
1 TTGCGAT
1231878 TTACATATTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1231887 original size:20 final size:20
Alignment explanation
Indices: 1231864--1231996 Score: 185
Period size: 20 Copynumber: 6.7 Consensus size: 20
1231854 CGATAGTTAG
* *
1231864 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
1231884 ATTCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
**
1231904 ATTCGCATTATGATTTACGT
1 ATTCGCATTGCGATTTACGT
1231924 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1231944 ATTCGTATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
1231964 ATTCGCATTACGATTTACTT
1 ATTCGCATTGCGATTTACGT
1231984 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1231997 ATTAGGAAAA
Statistics
Matches: 102, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 102 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1232017 original size:21 final size:21
Alignment explanation
Indices: 1231993--1232033 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1231983 TATTCGCATT
1231993 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1232014 GCGAATTTGTAAAATCGCAA
1 GCGAATTAGGAAAATCGCAA
1232034 TGTCATAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1232434 original size:30 final size:30
Alignment explanation
Indices: 1232398--1232461 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
1232388 TGAAATGCCA
* *
1232398 CTTCAACATTTTCCTGGAAACTTAAATCTG
1 CTTCAACATTTTCCTGGAAACTCAAATATG
*
1232428 CTTCAACATTTTCCTGGCAACTCAAATATG
1 CTTCAACATTTTCCTGGAAACTCAAATATG
1232458 CTTC
1 CTTC
1232462 TTATGACTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (30 bp):
CTTCAACATTTTCCTGGAAACTCAAATATG
Found at i:1233320 original size:50 final size:50
Alignment explanation
Indices: 1233245--1233346 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1233235 TTGATCTTTT
1233245 TAATAAATCAGAAATATACTTCTTCTGATTTAAGATCAAGCCTTCTGAAG
1 TAATAAATCAGAAATATACTTCTTCTGATTTAAGATCAAGCCTTCTGAAG
1233295 TAATAAATCAGAAATATACTTCTTCTGATTTAAGATCAAGCCTTCTGAAG
1 TAATAAATCAGAAATATACTTCTTCTGATTTAAGATCAAGCCTTCTGAAG
1233345 TA
1 TA
1233347 TGCTCAACTT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (50 bp):
TAATAAATCAGAAATATACTTCTTCTGATTTAAGATCAAGCCTTCTGAAG
Found at i:1235467 original size:18 final size:18
Alignment explanation
Indices: 1235447--1235676 Score: 228
Period size: 18 Copynumber: 12.8 Consensus size: 18
1235437 AAAAAGTTAT
* *
1235447 GAGCAGAATCATTAATAT
1 GAGCAGAATTATTAATAC
* *
1235465 GAGCAGAATTATTAACAG
1 GAGCAGAATTATTAATAC
1235483 GAGCAGAATTATTAATAC
1 GAGCAGAATTATTAATAC
* * *
1235501 AAGCAGAATTATTAACAA
1 GAGCAGAATTATTAATAC
* *
1235519 AATCAGAATTATTAATAC
1 GAGCAGAATTATTAATAC
* * *
1235537 AAGCAGAATCATCAATAC
1 GAGCAGAATTATTAATAC
* * *
1235555 AAGCAGAATCATCAATAC
1 GAGCAGAATTATTAATAC
*
1235573 GAGCAGAATTATTAATAG
1 GAGCAGAATTATTAATAC
* * *
1235591 GCGCAAAATTATTAACAC
1 GAGCAGAATTATTAATAC
*
1235609 GAGCAGAATTATTAATAG
1 GAGCAGAATTATTAATAC
* * *
1235627 GCA-CATAATTATTAACAG
1 G-AGCAGAATTATTAATAC
*
1235645 GAGCGGAATTATTAATAC
1 GAGCAGAATTATTAATAC
1235663 GAGCAGAATTATTA
1 GAGCAGAATTATTA
1235677 TTAATAGACG
Statistics
Matches: 177, Mismatches: 33, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
17 1 0.01
18 175 0.99
19 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (18 bp):
GAGCAGAATTATTAATAC
Found at i:1235497 original size:36 final size:36
Alignment explanation
Indices: 1235447--1235702 Score: 237
Period size: 36 Copynumber: 7.0 Consensus size: 36
1235437 AAAAAGTTAT
* * *
1235447 GAGCAGAATCATTAATATGAGCAGAATTATTAACAG
1 GAGCAGAATTATTAATACGAGCAGAATTATTAATAG
* * *
1235483 GAGCAGAATTATTAATACAAGCAGAATTATTAACAA
1 GAGCAGAATTATTAATACGAGCAGAATTATTAATAG
* * * * * *
1235519 AATCAGAATTATTAATACAAGCAGAATCATCAATAC
1 GAGCAGAATTATTAATACGAGCAGAATTATTAATAG
* * *
1235555 AAGCAGAATCATCAATACGAGCAGAATTATTAATAG
1 GAGCAGAATTATTAATACGAGCAGAATTATTAATAG
* * *
1235591 GCGCAAAATTATTAACACGAGCAGAATTATTAATAG
1 GAGCAGAATTATTAATACGAGCAGAATTATTAATAG
* * * * *
1235627 GCA-CATAATTATTAACAGGAGCGGAATTATTAATAC
1 G-AGCAGAATTATTAATACGAGCAGAATTATTAATAG
*
1235663 GAGCAGAATTATTATTAATA-GACGTAGAATTATTAATAG
1 GAGCAG-A--ATTATTAATACGA-GCAGAATTATTAATAG
1235702 G
1 G
1235703 CAAACAAGTG
Statistics
Matches: 181, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
35 1 0.01
36 154 0.85
37 1 0.01
38 2 0.01
39 23 0.13
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (36 bp):
GAGCAGAATTATTAATACGAGCAGAATTATTAATAG
Found at i:1235681 original size:21 final size:21
Alignment explanation
Indices: 1235652--1235697 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1235642 CAGGAGCGGA
1235652 ATTATTAATACGA-GCAGAATT
1 ATTATTAATA-GACGCAGAATT
*
1235673 ATTATTAATAGACGTAGAATT
1 ATTATTAATAGACGCAGAATT
1235694 ATTA
1 ATTA
1235698 ATAGGCAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (21 bp):
ATTATTAATAGACGCAGAATT
Found at i:1239515 original size:2 final size:2
Alignment explanation
Indices: 1239503--1239550 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
1239493 TTATTCTCAC
*
1239503 AT AT TT 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
1239545 AT AT AT
1 AT AT AT
1239551 TGGACATAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1244102 original size:29 final size:29
Alignment explanation
Indices: 1244060--1244124 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
1244050 GTTTCCCTAT
1244060 AAAACTCGAAATGATTCTCGAATTCCACC
1 AAAACTCGAAATGATTCTCGAATTCCACC
1244089 AAAACTCGAAATGATTCTCGAATTCCACC
1 AAAACTCGAAATGATTCTCGAATTCCACC
1244118 AAAACTC
1 AAAACTC
1244125 AGGTTCATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.40, C:0.28, G:0.09, T:0.23
Consensus pattern (29 bp):
AAAACTCGAAATGATTCTCGAATTCCACC
Found at i:1257559 original size:29 final size:28
Alignment explanation
Indices: 1257502--1257568 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
1257492 TAAAACATTT
1257502 ACTTGTATAAAATAGTGAGTAATTTAAAA
1 ACTTGTAT-AAATAGTGAGTAATTTAAAA
1257531 ACTTGTATAAATAGTGAGTAATTTAAAA
1 ACTTGTATAAATAGTGAGTAATTTAAAA
*
1257559 ACTTTTATAA
1 ACTTGTATAA
1257569 CATATAACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
28 29 0.78
29 8 0.22
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.37
Consensus pattern (28 bp):
ACTTGTATAAATAGTGAGTAATTTAAAA
Found at i:1258394 original size:30 final size:30
Alignment explanation
Indices: 1258275--1258377 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
1258265 CCCGAAGGAC
* *
1258275 CTATCCAGAGGTCATAGAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1258305 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1258335 CTATCCAGGGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1258365 CTATCCATAGGTC
1 CTATCCAGAGGTC
1258378 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1258394 original size:60 final size:60
Alignment explanation
Indices: 1258275--1258394 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
1258265 CCCGAAGGAC
* * * * *
1258275 CTATCCAGAGGTCATAGAGATCCTTGGTAACTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
* * * *
1258335 CTATCCAGGGGTCATAAAGATCCTCGGTAACTATCCATAGGTCCCGAAGAACCTAGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
1258395 ACTGTCCATA
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (60 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAA
Found at i:1259131 original size:20 final size:22
Alignment explanation
Indices: 1259106--1259163 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1259096 TTCCCCTTGA
1259106 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
1259126 AGTGCATCAATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1259149 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1259164 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1259225 original size:65 final size:63
Alignment explanation
Indices: 1259151--1259292 Score: 171
Period size: 65 Copynumber: 2.2 Consensus size: 63
1259141 TCTTTAACAT
* *
1259151 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTTGATGTTTTCATT-TTTAAAG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATG-TTTC-TTCTTTAAAG
*
1259214 G
63 A
* * *
1259215 GATGCATCGATGCACTCCTTATGCATCGATTCACCAATTACATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
*
1259279 GTGCATTGATGCAC
1 GTGCATCGATGCAC
1259293 ATTGAATATG
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
63 14 0.21
64 15 0.22
65 39 0.57
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:1262386 original size:30 final size:30
Alignment explanation
Indices: 1262314--1262375 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1262304 CCCGAATTAC
* *
1262314 CTATCCAGAGGTCATAGAGATCCTTGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1262344 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1262374 CT
1 CT
1262376 GTCTATAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1262393 original size:30 final size:30
Alignment explanation
Indices: 1262314--1262393 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 30
1262304 CCCGAATTAC
* * *
1262314 CTATCCAGAGGTCATAGAGATCCTTGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
*
1262344 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCACAAAGATCCTCGGTAA
* * * *
1262374 CTGTCTATAGGTCCCAAAGA
1 CTATCCAGAGGTCACAAAGA
1262394 ACCTAGATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGATCCTCGGTAA
Found at i:1263154 original size:20 final size:22
Alignment explanation
Indices: 1263126--1263183 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1263116 TTCCCCTTGA
*
1263126 AGTGTATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1263146 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1263169 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1263184 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1263242 original size:65 final size:63
Alignment explanation
Indices: 1263171--1263312 Score: 162
Period size: 65 Copynumber: 2.2 Consensus size: 63
1263161 TCTTTAACAT
* *
1263171 GTGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCATT-TTTAAAG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGAT-ATTT-ATTCTTTAAAG
*
1263234 G
63 A
* * * *
1263235 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATATTTATTCTTTAAAGA
1 G-TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATATTTATTCTTTAAAGA
*
1263299 GTGCATCGGTGCAC
1 GTGCATCGATGCAC
1263313 ATTGAATGTG
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
63 15 0.22
64 14 0.21
65 38 0.57
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATATTTATTCTTTAAAGA
Found at i:1271039 original size:206 final size:207
Alignment explanation
Indices: 1270685--1271098 Score: 821
Period size: 206 Copynumber: 2.0 Consensus size: 207
1270675 CTAAGTTTCA
1270685 TGGCACCAAGAATAGAAAGAAAACACCAAACGGTAAGAAAAAAAAGATGACACTGCTAATTAAAC
1 TGGCACCAAGAATAGAAAGAAAACACCAAACGGTAAGAAAAAAAAGATGACACTGCTAATTAAAC
1270750 CCCGGGCTTGGGAACAGAAAACAGAGCAAACAAGCTGGTCCATGAAATAATGCAAACAATGAACA
66 CCCGGGCTTGGGAACAGAAAACAGAGCAAACAAGCTGGTCCATGAAATAATGCAAACAATGAACA
1270815 GATGACCGACCGTGAGACCCGAAAAACATAGATGTCTATTGAGAAA-TGAAATCTTTGCAAACTT
131 GATGACCGACCGTGAGACCCGAAAAACATAGATGTCTATTGAGAAATTGAAATCTTTGCAAACTT
1270879 ATCTGCTCTTTT
196 ATCTGCTCTTTT
1270891 TGGCACCAAGAATAGAAAGAAAACACCAAACGGTAAGAAAAAAAAGATGACACTGCTAATTAAAC
1 TGGCACCAAGAATAGAAAGAAAACACCAAACGGTAAGAAAAAAAAGATGACACTGCTAATTAAAC
1270956 CCCGGGCTTGGGAACAGAAAACAGAGCAAACAAGCTGGTCCATGAAATAATGCAAACAATGAACA
66 CCCGGGCTTGGGAACAGAAAACAGAGCAAACAAGCTGGTCCATGAAATAATGCAAACAATGAACA
1271021 GATGACCGACCGTGAGACCCGAAAAACATAGATGTCTATTGAGAAATTGAAATCTTTGCAAACTT
131 GATGACCGACCGTGAGACCCGAAAAACATAGATGTCTATTGAGAAATTGAAATCTTTGCAAACTT
1271086 ATCTGCTCTTTT
196 ATCTGCTCTTTT
1271098 T
1 T
1271099 TTTCCCTTTC
Statistics
Matches: 207, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
206 176 0.85
207 31 0.15
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (207 bp):
TGGCACCAAGAATAGAAAGAAAACACCAAACGGTAAGAAAAAAAAGATGACACTGCTAATTAAAC
CCCGGGCTTGGGAACAGAAAACAGAGCAAACAAGCTGGTCCATGAAATAATGCAAACAATGAACA
GATGACCGACCGTGAGACCCGAAAAACATAGATGTCTATTGAGAAATTGAAATCTTTGCAAACTT
ATCTGCTCTTTT
Found at i:1271112 original size:2 final size:2
Alignment explanation
Indices: 1271107--1271133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1271097 TTTTTCCCTT
1271107 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1271134 TTTTGGATCT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1277377 original size:164 final size:164
Alignment explanation
Indices: 1277199--1277527 Score: 658
Period size: 164 Copynumber: 2.0 Consensus size: 164
1277189 TTTGAGATAT
1277199 AATCTATCAACATAAACTACAAACATACCAACCAAACTAACACTCGATTATTAATTATATAAAAT
1 AATCTATCAACATAAACTACAAACATACCAACCAAACTAACACTCGATTATTAATTATATAAAAT
1277264 TAATTTAGTTAAGATATGGGTTTCTACAATTAATTAACACAATTTTCTTATTAAAAAGAAAATTT
66 TAATTTAGTTAAGATATGGGTTTCTACAATTAATTAACACAATTTTCTTATTAAAAAGAAAATTT
1277329 GACAAATAATAATATGATTGTTGAGTGCAACAAA
131 GACAAATAATAATATGATTGTTGAGTGCAACAAA
1277363 AATCTATCAACATAAACTACAAACATACCAACCAAACTAACACTCGATTATTAATTATATAAAAT
1 AATCTATCAACATAAACTACAAACATACCAACCAAACTAACACTCGATTATTAATTATATAAAAT
1277428 TAATTTAGTTAAGATATGGGTTTCTACAATTAATTAACACAATTTTCTTATTAAAAAGAAAATTT
66 TAATTTAGTTAAGATATGGGTTTCTACAATTAATTAACACAATTTTCTTATTAAAAAGAAAATTT
1277493 GACAAATAATAATATGATTGTTGAGTGCAACAAA
131 GACAAATAATAATATGATTGTTGAGTGCAACAAA
1277527 A
1 A
1277528 CGACACGACC
Statistics
Matches: 165, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
164 165 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (164 bp):
AATCTATCAACATAAACTACAAACATACCAACCAAACTAACACTCGATTATTAATTATATAAAAT
TAATTTAGTTAAGATATGGGTTTCTACAATTAATTAACACAATTTTCTTATTAAAAAGAAAATTT
GACAAATAATAATATGATTGTTGAGTGCAACAAA
Found at i:1286174 original size:21 final size:22
Alignment explanation
Indices: 1286150--1286199 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1286140 ATTTATGTAC
*
1286150 AGATTTTTTT-TAAATATAGTA
1 AGATTTTTTTAAAAATATAGTA
1286171 AGATTTTTTTAAAAATATAGTA
1 AGATTTTTTTAAAAATATAGTA
1286193 AGATTTT
1 AGATTTT
1286200 CATGTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
AGATTTTTTTAAAAATATAGTA
Done.