Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 24
Found at i:2980271 original size:14 final size:14
Alignment explanation
Indices: 2980252--2980288 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
2980242 CATCAATTAA
2980252 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
2980266 ACAAATCACCTTTT
1 ACAAATCAACTTTT
2980280 ACAAATCAA
1 ACAAATCAA
2980289 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:2981712 original size:21 final size:21
Alignment explanation
Indices: 2981646--2981712 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2981636 GTGAATCGGG
*
2981646 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2981666 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2981688 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2981709 CTCT
1 CTCT
2981713 CGAGGAATAA
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:2981731 original size:42 final size:42
Alignment explanation
Indices: 2981685--2981768 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
2981675 CGATGACAGT
* * *
2981685 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATAATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATAATAGG
* * * *
2981727 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATAATAGG
2981769 CGAGTCGAGC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.24, C:0.17, G:0.38, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATAATAGG
Found at i:2983851 original size:33 final size:33
Alignment explanation
Indices: 2983794--2983892 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
2983784 ACGAGATAAT
*
2983794 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
2983828 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
2983861 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
2983893 GCGAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 45 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.26, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:2983886 original size:19 final size:19
Alignment explanation
Indices: 2983769--2983972 Score: 212
Period size: 19 Copynumber: 11.1 Consensus size: 19
2983759 TCTTTTGGTT
*
2983769 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
2983788 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
2983808 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
2983826 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
2983842 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
2983860 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2983875 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
2983895 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2983914 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
2983933 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
2983952 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
2983971 GA
1 GA
2983973 TTTTGGTTTC
Statistics
Matches: 157, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
14 19 0.12
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 81 0.52
20 45 0.29
21 2 0.01
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:2984001 original size:19 final size:19
Alignment explanation
Indices: 2983968--2984030 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
2983958 AAAATCGCAA
**
2983968 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
2983987 TGCGATTTTTATTTCGCGT
1 TGCGATTTTCATTTCGCGT
**
2984006 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
2984026 TGCGA
1 TGCGA
2984031 CTCTCATTCT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 28 0.74
20 10 0.26
ACGTcount: A:0.11, C:0.19, G:0.27, T:0.43
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:2984037 original size:20 final size:18
Alignment explanation
Indices: 2983979--2984038 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
2983969 GCGATTTTGG
* *
2983979 TTTCGCGTTGCGATTTTTA
1 TTTCGCGTTGCGA-TCTCA
*
2983998 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-CTCA
2984017 TTTCCGCGTTGCGACTCTCA
1 TTT-CGCGTTGCGA-TCTCA
2984037 TT
1 TT
2984039 CTCGAAACTA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 18 0.51
20 15 0.43
21 1 0.03
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (18 bp):
TTTCGCGTTGCGATCTCA
Found at i:2984636 original size:20 final size:20
Alignment explanation
Indices: 2984551--2984644 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
2984541 CGCTAAGTAA
*
2984551 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
2984571 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
2984591 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
2984612 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
2984632 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
2984645 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:2984663 original size:41 final size:41
Alignment explanation
Indices: 2984633--2984728 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
2984623 ATAGTCAGTA
* * *
2984633 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
* *
2984674 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
2984715 TCGCATTGCGAATT
1 TCGCATTGCGAATT
2984729 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:2984677 original size:20 final size:20
Alignment explanation
Indices: 2984633--2984725 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
2984623 ATAGTCAGTA
* **
2984633 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
2984654 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* **
2984674 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTTAT
*
2984695 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
2984715 TCGCATTGCGA
1 TCGCATTGCGA
2984726 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:2986983 original size:15 final size:15
Alignment explanation
Indices: 2986965--2987040 Score: 79
Period size: 15 Copynumber: 5.3 Consensus size: 15
2986955 ATAAAATTCT
2986965 AATTATTTAAATAAA
1 AATTATTTAAATAAA
*
2986980 AATTATTTATATAAA
1 AATTATTTAAATAAA
*
2986995 AATTCA--TAGAT-AA
1 AATT-ATTTAAATAAA
*
2987008 TA-TATTTAAATAAA
1 AATTATTTAAATAAA
*
2987022 AATTATTTATATAAA
1 AATTATTTAAATAAA
2987037 AATT
1 AATT
2987041 TATCGATAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
11 1 0.02
12 1 0.02
13 7 0.14
14 7 0.14
15 33 0.66
16 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (15 bp):
AATTATTTAAATAAA
Found at i:2986997 original size:21 final size:21
Alignment explanation
Indices: 2986973--2987039 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
2986963 CTAATTATTT
2986973 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
* * * **
2986994 AAATTCATAGA-TA-ATATATTT
1 AAA-T-AAAAATTATTTATATAA
2987015 AAATAAAAATTATTTATATAA
1 AAATAAAAATTATTTATATAA
2987036 AAAT
1 AAAT
2987040 TTATCGATAA
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
19 3 0.09
20 3 0.09
21 20 0.62
22 3 0.09
23 3 0.09
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (21 bp):
AAATAAAAATTATTTATATAA
Found at i:2987015 original size:42 final size:42
Alignment explanation
Indices: 2986964--2987055 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
2986954 AATAAAATTC
2986964 TAAT-TATTTAAATAAAAATTATTTATATAAAAATTCATAGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATTCATAGA
* *
2987005 TAATATATTTAAATAAAAATTATTTATATAAAAATTTATCGA
1 TAATATATTTAAATAAAAATTATTTATATAAAAATTCATAGA
2987047 TAATATATT
1 TAATATATT
2987056 ATTTTATTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
TAATATATTTAAATAAAAATTATTTATATAAAAATTCATAGA
Found at i:2987363 original size:31 final size:32
Alignment explanation
Indices: 2987307--2987372 Score: 116
Period size: 31 Copynumber: 2.1 Consensus size: 32
2987297 ATTCCTCGAA
*
2987307 AGATGATTTCTACCGAGTCGGACTCTTGTTAC
1 AGATGATTTCTACCGAGCCGGACTCTTGTTAC
2987339 AGATGATTTCTA-CGAGCCGGACTCTTGTTAC
1 AGATGATTTCTACCGAGCCGGACTCTTGTTAC
2987370 AGA
1 AGA
2987373 CGTTATGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (32 bp):
AGATGATTTCTACCGAGCCGGACTCTTGTTAC
Found at i:2990888 original size:64 final size:64
Alignment explanation
Indices: 2990753--2990892 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 64
2990743 TTGTTCAGTT
* * *
2990753 TGTATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATAGAAACATCGAATACAATTAG
1 TGTATCGATGCAAAGGAAGAGCATCGATGCACCCATTAAAAATAGAAACATCGAAGACAATTAG
* * ***
2990817 TGCATCGATGCATAAGG-AGAGCATCGATGCACCCCCTT-AAAAT-GAAAACATCGAAGGTGATT
1 TGTATCGATGCA-AAGGAAGAGCATCGATGCA-CCCATTAAAAATAG-AAACATCGAAGACAATT
*
2990879 GG
63 AG
2990881 TGTATCGATGCA
1 TGTATCGATGCA
2990893 CTTCAAGGGA
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
63 1 0.02
64 54 0.86
65 8 0.13
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (64 bp):
TGTATCGATGCAAAGGAAGAGCATCGATGCACCCATTAAAAATAGAAACATCGAAGACAATTAG
Found at i:2992075 original size:2 final size:2
Alignment explanation
Indices: 2992068--2992107 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2992058 GAACATGTAA
2992068 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
2992108 GATAAGACAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2992535 original size:23 final size:23
Alignment explanation
Indices: 2992509--2992566 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
2992499 GGAACTTCGA
*
2992509 TGCATTTCTATGCGGCACTACGG
1 TGCATTTCTACGCGGCACTACGG
* * *
2992532 TGCAATTCTACGTGGCACTTCGG
1 TGCATTTCTACGCGGCACTACGG
*
2992555 TGCATTTATACG
1 TGCATTTCTACG
2992567 AGCTGTGGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TGCATTTCTACGCGGCACTACGG
Found at i:2993585 original size:25 final size:25
Alignment explanation
Indices: 2993551--2993604 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
2993541 TATTTTATAT
*
2993551 TTTTATATTAATTATATATATAATA
1 TTTTATATTAATTATATATAAAATA
*
2993576 TTTTATATTAATTTTATATAAAATA
1 TTTTATATTAATTATATATAAAATA
2993601 TTTT
1 TTTT
2993605 CGGGTTCAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTATATTAATTATATATAAAATA
Found at i:2993591 original size:11 final size:11
Alignment explanation
Indices: 2993551--2993594 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 11
2993541 TATTTTATAT
2993551 TTTTATATTAA
1 TTTTATATTAA
*
2993562 TTATATATATAATA
1 TT-T-TATATTA-A
2993576 TTTTATATTAA
1 TTTTATATTAA
2993587 TTTTATAT
1 TTTTATAT
2993595 AAAATATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 11 0.39
12 7 0.25
13 7 0.25
14 3 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTATATTAA
Found at i:3001826 original size:2 final size:2
Alignment explanation
Indices: 3001819--3001848 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3001809 TGACATCAAC
3001819 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
3001849 TTATCAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3002008 original size:7 final size:7
Alignment explanation
Indices: 3001996--3002020 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3001986 CTAAGCTTCT
3001996 ACTCCAC
1 ACTCCAC
3002003 ACTCCAC
1 ACTCCAC
3002010 ACTCCAC
1 ACTCCAC
3002017 ACTC
1 ACTC
3002021 TACCAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.56, G:0.00, T:0.16
Consensus pattern (7 bp):
ACTCCAC
Found at i:3005390 original size:6 final size:6
Alignment explanation
Indices: 3005381--3005585 Score: 410
Period size: 6 Copynumber: 34.2 Consensus size: 6
3005371 TACATATACA
3005381 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
3005429 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
3005477 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
3005525 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
1 TACACG TACACG TACACG TACACG TACACG TACACG TACACG TACACG
3005573 TACACG TACACG T
1 TACACG TACACG T
3005586 TGCGGTTTGA
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 199 1.00
ACGTcount: A:0.33, C:0.33, G:0.17, T:0.17
Consensus pattern (6 bp):
TACACG
Found at i:3009166 original size:10 final size:10
Alignment explanation
Indices: 3009151--3009175 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3009141 TAAAGGAATG
3009151 ATATCAAATC
1 ATATCAAATC
3009161 ATATCAAATC
1 ATATCAAATC
3009171 ATATC
1 ATATC
3009176 TTTATAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (10 bp):
ATATCAAATC
Found at i:3020201 original size:23 final size:23
Alignment explanation
Indices: 3020175--3020224 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3020165 ATCAAGCACA
3020175 ATAACAT-ATCAGGTAGCGCTTAT
1 ATAACATAAT-AGGTAGCGCTTAT
*
3020198 ATAACGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
3020221 ATAA
1 ATAA
3020225 TAAAATAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:3020231 original size:23 final size:23
Alignment explanation
Indices: 3020185--3020232 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3020175 ATAACATATC
**
3020185 AGGTAGCGCTTATATAACGTAAT
1 AGGTAGCGCTTATATAACAAAAT
*
3020208 AGGTAGCGCTTATATAATAAAAT
1 AGGTAGCGCTTATATAACAAAAT
3020231 AG
1 AG
3020233 ATTAATTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (23 bp):
AGGTAGCGCTTATATAACAAAAT
Found at i:3020388 original size:23 final size:23
Alignment explanation
Indices: 3020344--3020388 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3020334 AACATATTAG
**
3020344 GTAGCACTTATATAACGTAATAT
1 GTAGCACTTATATAACAAAATAT
* *
3020367 GTAGCGCTTATATAATAAAATA
1 GTAGCACTTATATAACAAAATA
3020389 GGTTAATTAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.33
Consensus pattern (23 bp):
GTAGCACTTATATAACAAAATAT
Found at i:3020437 original size:157 final size:157
Alignment explanation
Indices: 3020134--3020526 Score: 606
Period size: 157 Copynumber: 2.5 Consensus size: 157
3020124 AATATAGACA
* * *
3020134 ATAACATAATCGGTTAATTACTGTTAATATTATCAAGCACAATAACATATCAGGTAGCGCTTATA
1 ATAACATAATCGATT-ATTACTGTTAATATTATCAAGCACAATAACATATTAGGTAGCACTTATA
3020199 TAACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTTAATTTGTTATTACAACATAT
65 TAACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTTAATTTGTTATTACAACATAT
3020264 TAGGTAAACGCCTAAAATGTTACCAAGG
130 TAGGTAAACGCCTAAAATGTTACCAAGG
* *
3020292 ATACCATAATCGATTATTACCGTTAATATTATCAAGCACAATAACATATTAGGTAGCACTTATAT
1 ATAACATAATCGATTATTACTGTTAATATTATCAAGCACAATAACATATTAGGTAGCACTTATAT
* *
3020357 AACGTAATATGTAGCGCTTATATAATAAAATAGGTTAATTACTTAATTTGTTATTACAACATATT
66 AACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTTAATTTGTTATTACAACATATT
*
3020422 AGGTAAACGCTTAAAATGTTACCAAGG
131 AGGTAAACGCCTAAAATGTTACCAAGG
* * ** * * * * *
3020449 ATAACATAATTGTTTTATTACTGGAAACATTATCAAGCATAATAACATATTAGGTAGCGCTTGTG
1 ATAACATAATCG-ATTATTACTGTTAATATTATCAAGCACAATAACATATTAGGTAGCACTTATA
*
3020514 TAACATAATAGGT
65 TAACGTAATAGGT
3020527 TGCACATTAT
Statistics
Matches: 213, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
157 146 0.69
158 67 0.31
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (157 bp):
ATAACATAATCGATTATTACTGTTAATATTATCAAGCACAATAACATATTAGGTAGCACTTATAT
AACGTAATAGGTAGCGCTTATATAATAAAATAGATTAATTACTTAATTTGTTATTACAACATATT
AGGTAAACGCCTAAAATGTTACCAAGG
Found at i:3023468 original size:200 final size:200
Alignment explanation
Indices: 3022809--3023837 Score: 1488
Period size: 199 Copynumber: 5.2 Consensus size: 200
3022799 CGTAATTTTA
* * *
3022809 AAAAAATATCGATACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACC
* *
3022874 GATATATTTCTACCGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
66 GATATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
* * * * * *
3022939 TTTGGATCGATACAATTT--TAAATGTATTGACCCTTTATGCGTCCACCTCGTTGGGCATTCATT
131 TTAGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATT
3023002 CTGGAC
195 CTGGAC
** * * * * * *
3023008 AAAAAAAATCGACACAAATTTAAAAAGTGTCGATACAATATGTTTACCTATTCTCTCATAAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACC
* *
3023073 GATATATTTCTACCGGTTACATTGTAAATTTACGTACTATATTATAATTATCGGTTTCGATGTTT
66 GATATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
* *
3023138 TTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTC-TTTGGGCATTCAT
131 TTAGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGCATTCAT
3023200 TCTGGATC
194 TCTGGA-C
*
3023208 -AAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTGGACCTATTTTCTAATTAAACC
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACC
* **
3023272 GGTATATTTCTACATGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
66 GATATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
* * *
3023337 TTAGGATCGATACTTTTAATAAATATATCGACACTTTATGTGTGCACCTCGTTTGACATTCATTC
131 TTAGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTC
3023402 TGGAC
196 TGGAC
* *
3023407 AAAAAGTATAGACAC-AATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTATAATT-AAC
1 AAAAAGTATCGACACAAATTTAAAAA-GTATCGATACATTATGTTGACCTATTTTCTAATTAAAC
*
3023470 C-AGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
65 CGA-TATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGT
*
3023534 TTTTTGGAATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCA
129 TTTTAGG-ATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCA
3023599 TTCTGGAC
193 TTCTGGAC
* *
3023607 AAAAAGTATCAACAC-AATTTAAAAAAGTATCGATACATTATGTTGATCTATTTTCTAATT-AAC
1 AAAAAGTATCGACACAAATTT-AAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAAC
*
3023670 CGATATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCAGTTTCGATGTT
65 CGATATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTT
* ** * * * *
3023735 TTGA-GATCGATACTTACAATAAATGTATCGACACTTTATGTGTGCATCTTGTTTGGAATTCATT
130 TTTAGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATT
3023799 CTGGAC
195 CTGGAC
* *
3023805 CAAAAGTATCGAAACAAATTTAAAAAGTATCGA
1 AAAAAGTATCGACACAAATTTAAAAAGTATCGA
3023838 CATAAATTTT
Statistics
Matches: 755, Mismatches: 63, Indels: 25
0.90 0.07 0.03
Matches are distributed among these distances:
198 88 0.12
199 391 0.52
200 267 0.35
201 9 0.01
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (200 bp):
AAAAAGTATCGACACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACC
GATATATTTCTACCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTT
TTAGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGGCATTCATTC
TGGAC
Found at i:3023812 original size:398 final size:399
Alignment explanation
Indices: 3022822--3023995 Score: 1507
Period size: 398 Copynumber: 2.9 Consensus size: 399
3022812 AAATATCGAT
*
3022822 ACAAATTTAAAAAGTGTCGATACATTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTAC
1 ACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTAC
* *
3022887 CGGTTATATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTTG-GATCGATA
66 CGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATG--TTTTGAGATCGATA
* ** * * * * * * **
3022951 C-AATTTTAAATGTATTGACCCTTTATGCGTCCACCTCGTTGGGCATTCATTCTGGACAAAAAAA
129 CTTATAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGAATTCATTCTGGACAAAAAGT
* * *
3023015 ATCGACACAAATTTAAAAA-GTGTCGATACAATATGTTTACCTATTCTCTCATAA--AACCGATA
194 ATCGACACAAATTTAAAAAGGTATCGATACATTATGTTGACCTATT-T-T-ATAATTAACCG-TA
* * *
3023077 TATTTCTACCGGTTACATTGTAAATTTACGTACTATATTATAATTATCGGTTTCGATGTTTTTGG
255 TATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGG
*
3023142 GATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCTTTGGGCATTCATTCTGG
320 GATCGATACATTTTAATAAATGTATCGACACTTTATGCGTGCACCTCTTTGGGCATTCATTCTGG
*
3023205 ATCAAAAGTATCGAC
385 ATCAAAAGTATCAAC
* *
3023220 ACAAATTTAAAAAGTATCGATACATTATGTGGACCTATTTTCTAATTAAACCGGTATATTTCTAC
1 ACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTAC
** *
3023285 ATGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTTTTAGGATCGATAC
66 CGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTTTGA-GATCGATAC
* *
3023350 TTTTAATAAATATATCGACACTTTATGTGTGCACCTCGTTT-GACATTCATTCTGGACAAAAAGT
130 TTATAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGA-ATTCATTCTGGACAAAAAGT
*
3023414 ATAGACAC-AATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTATAATTAACCAGTATAT
194 ATCGACACAAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTATAATTAACC-GTATAT
*
3023478 TTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTTGGAA
258 TTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATG-TTTTTGGGA
3023543 TCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTT-GGCATTCATTCTGGA
322 TCGATACATTTTAATAAATGTATCGACACTTTATGCGTGCACCTC-TTTGGGCATTCATTCTGGA
3023606 -CAAAAAGTATCAAC
386 TC-AAAAGTATCAAC
*
3023620 AC-AATTTAAAAAAGTATCGATACATTATGTTGATCTATTTTCTAATT-AACCGATATATTTCTA
1 ACAAATTT-AAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTA
*
3023683 CCGGTTACATTGTAAATTTACCTATTATATTATAATTATCAGTTTCGATGTTTTGAGATCGATAC
65 CCGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTTTGAGATCGATAC
* * * *
3023748 TTACAATAAATGTATCGACACTTTATGTGTGCATCTTGTTTGGAATTCATTCTGGACCAAAAGTA
130 TTATAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGAATTCATTCTGGACAAAAAGTA
* *
3023813 TCGAAACAAATTTAAAAAGTATCGACATAAATTTTAAAAGTATCGATACATTGTGTTGACCTATT
195 TCGACACAAATTT-AAAA--A--G---------------GTATCGATACATTATGTTGACCTATT
* * *
3023878 TTCTAATTAAACCGGTATATTTCTACCGATTACATTGTAAATTTATCTATTACATTATAATTATC
240 TTATAATT-AACC-GTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATC
* * *
3023943 GGGTTCGATGTTTTTGGGATCGATACAATTTTAA-AAAT-TATCGATACATTATG
303 GGTTTCGATGTTTTTGGGATCGATAC-ATTTTAATAAATGTATCGACACTTTATG
3023996 TTTACTTATT
Statistics
Matches: 682, Mismatches: 55, Indels: 57
0.86 0.07 0.07
Matches are distributed among these distances:
396 8 0.01
397 1 0.00
398 262 0.38
399 174 0.26
400 100 0.15
401 3 0.00
402 1 0.00
404 1 0.00
419 60 0.09
420 66 0.10
421 6 0.01
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.39
Consensus pattern (399 bp):
ACAAATTTAAAAAGTATCGATACATTATGTTGACCTATTTTCTAATTAAACCGATATATTTCTAC
CGGTTACATTGTAAATTTACCTATTATATTATAATTATCGGTTTCGATGTTTTGAGATCGATACT
TATAATAAATGTATCGACACTTTATGTGTGCACCTCGTTTGGAATTCATTCTGGACAAAAAGTAT
CGACACAAATTTAAAAAGGTATCGATACATTATGTTGACCTATTTTATAATTAACCGTATATTTC
TACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGA
TACATTTTAATAAATGTATCGACACTTTATGCGTGCACCTCTTTGGGCATTCATTCTGGATCAAA
AGTATCAAC
Found at i:3023831 original size:21 final size:21
Alignment explanation
Indices: 3023806--3023858 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3023796 ATTCTGGACC
3023806 AAAAGTATCGAAACAAATTTA
1 AAAAGTATCGAAACAAATTTA
* * *
3023827 AAAAGTATCGACATAAATTTT
1 AAAAGTATCGAAACAAATTTA
3023848 AAAAGTATCGA
1 AAAAGTATCGA
3023859 TACATTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.26
Consensus pattern (21 bp):
AAAAGTATCGAAACAAATTTA
Found at i:3027734 original size:2 final size:2
Alignment explanation
Indices: 3027727--3027752 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3027717 GTATCCGGAG
3027727 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
3027753 TTCCCCATGA
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):
AT
Found at i:3029084 original size:199 final size:198
Alignment explanation
Indices: 3028406--3029171 Score: 1052
Period size: 199 Copynumber: 3.8 Consensus size: 198
3028396 CGCGTAATTT
* * * * *
3028406 AAAAAATATCGATATAATTTAAAAAGTGTCGATACAATATGTTTACCTATTCTCTCATAAAACCG
1 AAAAAGTATCGACACAATTTAAAAAGTGTCGATACAATATGTTGACCTATTCTCTCATAAAACTG
* *
3028471 GTATATTTTTACCAGTTACATTGTAAATTTACCTATTACATTATAATTATCAGTTTCGATGTTTT
66 GTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
*
3028536 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTA
131 TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTG
3028601 GAC
196 GAC
* * *
3028604 AAAAAGTATCGACAAAAATTTAAAAAGTGTCGATACAATATGTTTACCTATTTTCTCATAAAACT
1 AAAAAGTATCGAC-ACAATTTAAAAAGTGTCGATACAATATGTTGACCTATTCTCTCATAAAACT
* * *
3028669 GGTATATTTTTACTGGTTACATTGTAAATTTACATATTACATTATAATTATCGGTTTTGATGTTT
65 GGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
3028734 TTGGGATTGATAC-TTTTAATAAATGTATCGACACTTTATACGTGCACCTCGTTGGGAATTCATT
130 TTGGGATCGATACAATTT--TAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATT
*
3028798 CTGTAC
193 CTGGAC
* * * * * * *
3028804 AAAAAGTATCGACACAAATTTAAAAAGTGTCAATATATTACGTTGACCTATTTTCTAATTAAACT
1 AAAAAGTATCGACAC-AATTTAAAAAGTGTCGATACAATATGTTGACCTATTCTCTCATAAAACT
*
3028869 GGTATATTTCTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
65 GGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTT
* * * *
3028934 TCGGGATCGATACAATTTTAAATGTATCGACACTTTATGCTTGTACCTCGTTGGTCATTCATTCT
130 TTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
3028999 GGAC
195 GGAC
* * * * *
3029003 CAAACGTATCGACACAATTTAAAAAAGTATCGACACAATATGTTGACCTATTCTGTCATAAAA-T
1 AAAAAGTATCGACACAATTT-AAAAAGTGTCGATACAATATGTTGACCTATTCTCTCATAAAACT
* * * * * *
3029067 CGATATATTCTTACCGGTTACATTGTAAATTTATCGATTACTTTATAATTATTGGTTTCGATGTT
65 -GGTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTT
* *
3029132 TTTGGGATCGATACAATTTTAAAAT-TATCGATACATTATG
129 TTTGGGATCGATACAATTTT-AAATGTATCGACACTTTATG
3029172 TTTACCTATT
Statistics
Matches: 501, Mismatches: 59, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
198 20 0.04
199 300 0.60
200 178 0.36
201 3 0.01
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (198 bp):
AAAAAGTATCGACACAATTTAAAAAGTGTCGATACAATATGTTGACCTATTCTCTCATAAAACTG
GTATATTTTTACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
TGGGATCGATACAATTTTAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTG
GAC
Found at i:3036694 original size:183 final size:183
Alignment explanation
Indices: 3036331--3036978 Score: 1017
Period size: 183 Copynumber: 3.5 Consensus size: 183
3036321 TATTGACACA
* * * * * *
3036331 TTCAACATATATGGTAGCACTTTACTGGTTTTGTCATAATGAAACTGATTTTTTCATATTTTTAC
1 TTCAACATATCTAGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTAC
* * * * * *
3036396 CTGTTATATTGTTATGTATCGATACGTTTTTCTAAAAATATCGACACTTTATAGGTGCTATTACT
66 ATGTTATATTGTTATGGATCGATACATTTTTAT-AAAGTATCGACACTTTATAGGCGCTATTACT
* * * * *
3036461 GTTTTTATTTTAAATTCTAAAAGTGTCGATACTTATTTCAATGTAATCGATACT
130 GCTTATCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATCGATACT
* * *
3036515 TTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATAAAACCGGTTTTGTCATATTTTTAC
1 TTCAACATATCTAGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTAC
* *
3036580 CTGTTATTTTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTG
66 ATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTG
*
3036645 CTTCTCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATCGATACT
131 CTTATCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATCGATACT
** * *
3036698 TTCAACATATCTAGTAAAGCTTTACCGGTTTTGTCATAATGAAATCGGTTTTGTCATATTTTTAC
1 TTCAACATATCTAGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTAC
*
3036763 ATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGACGCTATTACTG
66 ATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTG
3036828 CTTATCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATCGATACT
131 CTTATCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATCGATACT
*
3036881 TTCAACATATCCAGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTAC
1 TTCAACATATCTAGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTAC
*
3036946 ATGTTATATTGTTATGGATCGATATATTTTTAT
66 ATGTTATATTGTTATGGATCGATACATTTTTAT
3036979 TTGTATCGAT
Statistics
Matches: 431, Mismatches: 33, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
183 344 0.80
184 87 0.20
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (183 bp):
TTCAACATATCTAGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTAC
ATGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTTTATAGGCGCTATTACTG
CTTATCTTTTAAATTCCAAAAGTGTCGATACTTATTTCAATGGAATCGATACT
Found at i:3041551 original size:45 final size:48
Alignment explanation
Indices: 3041493--3041594 Score: 138
Period size: 50 Copynumber: 2.1 Consensus size: 48
3041483 ATAATTAGTC
* * *
3041493 TATATTATTAATGTATG-A-TTTTTTT-AGATCGATATAATTAATTTA
1 TATATTATTAATGTATGAATTTTTTTTAAAATCAATATAAATAATTTA
3041538 TATATTATTAATGTATGACATTTTTTTTTAAAATCAATATAAATAATTTA
1 TATATTATTAATGTATGA-A-TTTTTTTTAAAATCAATATAAATAATTTA
3041588 TATATTA
1 TATATTA
3041595 ATAAATAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
45 17 0.35
47 1 0.02
49 7 0.14
50 24 0.49
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.52
Consensus pattern (48 bp):
TATATTATTAATGTATGAATTTTTTTTAAAATCAATATAAATAATTTA
Found at i:3042060 original size:27 final size:26
Alignment explanation
Indices: 3042007--3042060 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
3041997 ATTATGTTTT
* ** *
3042007 AAAATATCATTGAATTTTTTTACAAA
1 AAAATATAATTGAATTTCATTAAAAA
3042033 AAAATAATAATTGAATTTCATTAAAAA
1 AAAAT-ATAATTGAATTTCATTAAAAA
3042060 A
1 A
3042061 GAGGAAAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.54, C:0.06, G:0.04, T:0.37
Consensus pattern (26 bp):
AAAATATAATTGAATTTCATTAAAAA
Found at i:3044324 original size:21 final size:20
Alignment explanation
Indices: 3044299--3044337 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
3044289 ATAAAATAGT
3044299 AAATTAAATAATAATATTTTG
1 AAATTAAAT-ATAATATTTTG
3044320 AAATTAAATATAAT-TTTT
1 AAATTAAATATAATATTTT
3044338 TATTTAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 5 0.28
21 9 0.50
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
AAATTAAATATAATATTTTG
Found at i:3044338 original size:20 final size:21
Alignment explanation
Indices: 3044299--3044338 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3044289 ATAAAATAGT
3044299 AAATTAAATAATAATATTTTG
1 AAATTAAATAATAATATTTTG
*
3044320 AAATTAAAT-ATAATTTTTT
1 AAATTAAATAATAATATTTT
3044339 ATTTAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (21 bp):
AAATTAAATAATAATATTTTG
Found at i:3048206 original size:24 final size:24
Alignment explanation
Indices: 3048156--3048207 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3048146 TCCTCTGCCT
* *
3048156 CCTCCTCTTCTTCTACTGAGATTA
1 CCTCCTCTTCTTCTACTCAGATCA
3048180 CCTCCTCTTCTTCTACTCAG-TCCA
1 CCTCCTCTTCTTCTACTCAGAT-CA
3048204 CCTC
1 CCTC
3048208 AGCTTCTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.13, C:0.42, G:0.06, T:0.38
Consensus pattern (24 bp):
CCTCCTCTTCTTCTACTCAGATCA
Found at i:3061094 original size:150 final size:150
Alignment explanation
Indices: 3060823--3061122 Score: 555
Period size: 150 Copynumber: 2.0 Consensus size: 150
3060813 ATCTTGTGAT
3060823 CCTTTGGCTCCATTTCCAATGTACCTTTCATAAAAATATAATAATAAAAGAAATAAAAACTTAAT
1 CCTTTGGCTCCATTTCCAATGTACCTTTCATAAAAATATAATAATAAAAGAAATAAAAACTTAAT
*
3060888 CACAGAGAAGAATTAGCATAGAAATTCAAGATAAGCTTAGATAATGTAAAACAGAAGCATCACAG
66 CACAGAGAAGAATTAGCATAGAAATTAAAGATAAGCTTAGATAATGTAAAACAGAAGCATCACAG
* * *
3060953 GCTGCATTCCAGAAAGAGAC
131 ACTACATTCCAGAAACAGAC
3060973 CCTTTGGCTCCATTTCCAATGTACCTTTCATAAAAATATAATAATAAAAGAAATAAAAACTTAAT
1 CCTTTGGCTCCATTTCCAATGTACCTTTCATAAAAATATAATAATAAAAGAAATAAAAACTTAAT
*
3061038 CACAGAGAAGAATTAGCATAGAAATTAAAGATAAGCTTAGATAATGTCAAACAGAAGCATCACAG
66 CACAGAGAAGAATTAGCATAGAAATTAAAGATAAGCTTAGATAATGTAAAACAGAAGCATCACAG
3061103 ACTACATTCCAGAAACAGAC
131 ACTACATTCCAGAAACAGAC
3061123 GATTACCAGT
Statistics
Matches: 145, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
150 145 1.00
ACGTcount: A:0.46, C:0.17, G:0.13, T:0.24
Consensus pattern (150 bp):
CCTTTGGCTCCATTTCCAATGTACCTTTCATAAAAATATAATAATAAAAGAAATAAAAACTTAAT
CACAGAGAAGAATTAGCATAGAAATTAAAGATAAGCTTAGATAATGTAAAACAGAAGCATCACAG
ACTACATTCCAGAAACAGAC
Found at i:3064378 original size:24 final size:24
Alignment explanation
Indices: 3064346--3064397 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
3064336 GAACATTATA
3064346 ACATGTATGGACACACAACGACCT
1 ACATGTATGGACACACAACGACCT
*
3064370 ACATGTATGGACACACAACGGCCT
1 ACATGTATGGACACACAACGACCT
3064394 ACAT
1 ACAT
3064398 AACCAACAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (24 bp):
ACATGTATGGACACACAACGACCT
Found at i:3077943 original size:32 final size:32
Alignment explanation
Indices: 3077902--3077967 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
3077892 GTTAATCCAT
3077902 CCAAATCAGTCCTCAAAATCACCCAAACAAAA
1 CCAAATCAGTCCTCAAAATCACCCAAACAAAA
*
3077934 CCAAATCAGTCCTCAAAATCACCCAAACAGAA
1 CCAAATCAGTCCTCAAAATCACCCAAACAAAA
3077966 CC
1 CC
3077968 GAACAACTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.47, C:0.36, G:0.05, T:0.12
Consensus pattern (32 bp):
CCAAATCAGTCCTCAAAATCACCCAAACAAAA
Found at i:3081860 original size:18 final size:18
Alignment explanation
Indices: 3081837--3081876 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
3081827 ATATTCACGT
3081837 CCGCGACACCCGCAGTGA
1 CCGCGACACCCGCAGTGA
3081855 CCGCGACACCCGCAGTGA
1 CCGCGACACCCGCAGTGA
3081873 CCGC
1 CCGC
3081877 AATAGCCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.47, G:0.28, T:0.05
Consensus pattern (18 bp):
CCGCGACACCCGCAGTGA
Found at i:3095765 original size:18 final size:18
Alignment explanation
Indices: 3095742--3095783 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3095732 CCCCCTTAAT
3095742 CTTCCCCGAGAAATCAAC
1 CTTCCCCGAGAAATCAAC
** *
3095760 CTTCCCTTAGAGATCAAC
1 CTTCCCCGAGAAATCAAC
3095778 CTTCCC
1 CTTCCC
3095784 TAACAACCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.40, G:0.10, T:0.24
Consensus pattern (18 bp):
CTTCCCCGAGAAATCAAC
Found at i:3098761 original size:30 final size:30
Alignment explanation
Indices: 3098726--3098791 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
3098716 AATGATAACT
3098726 AAAACAATAGCAATTGGATCCATCGCAAGA
1 AAAACAATAGCAATTGGATCCATCGCAAGA
* *
3098756 AAAACAATAGCAATTTGATCCATTGCAAGA
1 AAAACAATAGCAATTGGATCCATCGCAAGA
3098786 AAAACA
1 AAAACA
3098792 TGTTCCTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.50, C:0.18, G:0.14, T:0.18
Consensus pattern (30 bp):
AAAACAATAGCAATTGGATCCATCGCAAGA
Found at i:3107256 original size:10 final size:9
Alignment explanation
Indices: 3107241--3107269 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3107231 GATTTTACTC
3107241 AAAAAAATA
1 AAAAAAATA
3107250 AAAAAAATA
1 AAAAAAATA
3107259 AAAAAAA-A
1 AAAAAAATA
3107267 AAA
1 AAA
3107270 CTTGATTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.20
9 16 0.80
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (9 bp):
AAAAAAATA
Found at i:3118622 original size:20 final size:20
Alignment explanation
Indices: 3118597--3118643 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3118587 TGTTTTTCAT
3118597 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
*
3118617 ATTTTAAACACTTTAAACAT
1 ATTTTAAACACTTTAAACAC
3118637 ATTTTAA
1 ATTTTAA
3118644 TTAACAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:3121093 original size:22 final size:22
Alignment explanation
Indices: 3121036--3121105 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
3121026 TTCTCTCCCC
* *
3121036 AGTGTT-ATAACACTTTTATATC
1 AGTGTTGAT-ACACTTTTGTATT
*
3121058 AGTG-TGAATGCACTTTTGTATT
1 AGTGTTG-ATACACTTTTGTATT
*
3121080 AGTGTTGATACACTTTAGTATT
1 AGTGTTGATACACTTTTGTATT
3121102 AGTG
1 AGTG
3121106 CTAAGTCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 1 0.03
22 35 0.88
23 4 0.10
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.44
Consensus pattern (22 bp):
AGTGTTGATACACTTTTGTATT
Found at i:3127718 original size:31 final size:31
Alignment explanation
Indices: 3127660--3127718 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3127650 AAATATTTAA
* *
3127660 AAAATATATATTTTTAAGTGATGATAAAGTT
1 AAAATATATATTTTTAACTGATAATAAAGTT
3127691 AAAATATATATTTTTACACTGA-AATAAA
1 AAAATATATATTTTTA-ACTGATAATAAA
3127719 AATAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.39
Consensus pattern (31 bp):
AAAATATATATTTTTAACTGATAATAAAGTT
Found at i:3127728 original size:30 final size:31
Alignment explanation
Indices: 3127660--3127728 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
3127650 AAATATTTAA
* * **
3127660 AAAATATATATTTTTAAGTGATGATAAAGTT
1 AAAATATATATTTTTAACTGATAATAAAAAT
3127691 AAAATATATATTTTTACACTGA-AATAAAAAT
1 AAAATATATATTTTTA-ACTGATAATAAAAAT
3127722 -AAATATA
1 AAAATATA
3127729 GTTAATAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.21
31 22 0.67
32 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.38
Consensus pattern (31 bp):
AAAATATATATTTTTAACTGATAATAAAAAT
Found at i:3127747 original size:28 final size:29
Alignment explanation
Indices: 3127716--3127770 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
3127706 ACACTGAAAT
3127716 AAAAATAAA-TATAGTTAATAAGTTAAGA
1 AAAAATAAATTATAGTTAATAAGTTAAGA
*
3127744 AAAAATAAATTATATTTAATAAGTTAA
1 AAAAATAAATTATAGTTAATAAGTTAA
3127771 AACAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (29 bp):
AAAAATAAATTATAGTTAATAAGTTAAGA
Found at i:3131167 original size:10 final size:10
Alignment explanation
Indices: 3131152--3131176 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3131142 GATTTGACCT
3131152 AAAATTATCC
1 AAAATTATCC
3131162 AAAATTATCC
1 AAAATTATCC
3131172 AAAAT
1 AAAAT
3131177 GGGTGGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (10 bp):
AAAATTATCC
Found at i:3134245 original size:20 final size:20
Alignment explanation
Indices: 3134217--3134258 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
3134207 ATCAGATTGT
*
3134217 CCAGGGGGTACCGATTCCCC
1 CCAGAGGGTACCGATTCCCC
3134237 CCAGAGGGTACCGATTCCCC
1 CCAGAGGGTACCGATTCCCC
3134257 CC
1 CC
3134259 TGTCTAACGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.43, G:0.26, T:0.14
Consensus pattern (20 bp):
CCAGAGGGTACCGATTCCCC
Found at i:3137907 original size:54 final size:53
Alignment explanation
Indices: 3137839--3138143 Score: 173
Period size: 54 Copynumber: 5.5 Consensus size: 53
3137829 GGTGCTTGAT
*
3137839 TTTAGATTGTAGCACAGAGGTGCTCAATCAT-TCCGATGCACAGAGGTGCCAG
1 TTTAGATTGAAGCACAGAGGTGCTCAATCATATCCGATGCACAGAGGTGCCAG
* ** * *
3137891 AATTTAGATTGAAGCACAGAGGTGCTCAGTCATAGTTGGCTGCACAGAGGTGTCAG
1 --TTTAGATTGAAGCACAGAGGTGCTCAATCATA-TCCGATGCACAGAGGTGCCAG
* * * ** * * *
3137947 TCCTCGATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGGTGTCAG
1 T-TTAGATTGAAGCACAGAGGTGCTCAATCATATCCGATGCACAGAGGTGCCAG
*** ** * * *** *
3138001 CTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTTAACTGCACAGAGGTGTCAG
1 -TTTAGATTGAAGCACAGAGGTGCTCAATCA----TATCCGA-TGCACAGAGGTGCCAG
* * ** * * *
3138060 TTCTCGATT-AAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAGGTGTCAG
1 TT-TAGATTGAAGCACAGAGGTGCTCAATCA-TATCCGATGCACAGAGGTGCCAG
* *
3138114 CTCTCGATTGAAGCACAGAGGTGCTCAATC
1 -TTTAGATTGAAGCACAGAGGTGCTCAATC
3138144 GTTAATTCTA
Statistics
Matches: 207, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
54 95 0.46
55 53 0.26
56 17 0.08
58 24 0.12
59 18 0.09
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (53 bp):
TTTAGATTGAAGCACAGAGGTGCTCAATCATATCCGATGCACAGAGGTGCCAG
Found at i:3138100 original size:113 final size:113
Alignment explanation
Indices: 3137930--3138140 Score: 352
Period size: 113 Copynumber: 1.9 Consensus size: 113
3137920 TCATAGTTGG
3137930 CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGG
1 CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGG
*
3137995 TGTCAGCTCCCGGCTGAAGCACAGAGGTGCTCAGTCATTTTTTTTTAA
66 TGTCAGCTCCCGACTGAAGCACAGAGGTGCTCAGTCATTTTTTTTTAA
* * *
3138043 CTGCACAGAGGTGTCAGTTCTCGATT-AAGCACAGAGGTGCTCAATCACTTTTGGCTACACAGAG
1 CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCA-TCTTAGCTACACAGAG
* *
3138107 GTGTCAGCTCTCGATTGAAGCACAGAGGTGCTCA
65 GTGTCAGCTCCCGACTGAAGCACAGAGGTGCTCA
3138141 ATCGTTAATT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 21 0.23
113 70 0.77
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.26
Consensus pattern (113 bp):
CTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAGAGGTGCTCAATCATCTTAGCTACACAGAGG
TGTCAGCTCCCGACTGAAGCACAGAGGTGCTCAGTCATTTTTTTTTAA
Found at i:3138394 original size:81 final size:81
Alignment explanation
Indices: 3138259--3138416 Score: 271
Period size: 81 Copynumber: 2.0 Consensus size: 81
3138249 GCGAGTTACA
*
3138259 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGTTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
* *
3138324 CTGAGCCGGTTGCACC
66 CCGAGCCAGTTGCACC
* *
3138340 AAGAATGGTTCGCACACGAAATGGCGGATCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
1 AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
3138405 CCGAGCCAGTTG
66 CCGAGCCAGTTG
3138417 TGCAAGAGAC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (81 bp):
AAGAATGGTTCGCACACGAAATGGCGGAGCAACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CCGAGCCAGTTGCACC
Found at i:3149145 original size:23 final size:20
Alignment explanation
Indices: 3149100--3149145 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 20
3149090 AATTAAATTT
*
3149100 ATTCAAAGTTTTAAAAAATA
1 ATTCAAAGTTTTAAAAAAGA
3149120 ATTCAAAGTCCTTTAACAAAAGA
1 ATTCAAAGT--TTTAA-AAAAGA
3149143 ATT
1 ATT
3149146 TGAGCACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
22 5 0.23
23 8 0.36
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.33
Consensus pattern (20 bp):
ATTCAAAGTTTTAAAAAAGA
Found at i:3149389 original size:20 final size:21
Alignment explanation
Indices: 3149364--3149403 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
3149354 CTTTGTAAAG
3149364 TAGTATCGATACCA-TAGGCA
1 TAGTATCGATACCATTAGGCA
3149384 TAGTATCGATACCATTAGGC
1 TAGTATCGATACCATTAGGC
3149404 TCCAATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (21 bp):
TAGTATCGATACCATTAGGCA
Found at i:3153195 original size:73 final size:73
Alignment explanation
Indices: 3152980--3153260 Score: 270
Period size: 72 Copynumber: 3.9 Consensus size: 73
3152970 AGTTTTAAAG
* * * ** *
3152980 GGAAAAATATCTCAAGTGAGATGAAATTTTGTTTCGAGAGAAACTGTCTTGAGCAAGACAGAAA-
1 GGAAAAATATCTCAAGGGAGATG-AATTTTTTTTCGAGAGAAACTGTCTCGAGTGAGACAAAAAT
* **
3153044 -ACTTTCAA
65 TATTTTTGA
* * *
3153052 GGGAAAATATCTCAAGGGAGATGAATTTTTATTTTGAGAGAAACTGTCTCAAGTGAGACTAAAAA
1 GGAAAAATATCTCAAGGGAGATGAATTTTT-TTTCGAGAGAAACTGTCTCGAGTGAGAC-AAAAA
*
3153117 --CTTTTTGA
64 TTATTTTTGA
* * ** *
3153125 GGCAAAATATCTCAAGGGAGATGAATTTTTTTTGGAGAGAAACCATGTCGAGTGAGACAAAAATT
1 GGAAAAATATCTCAAGGGAGATGAATTTTTTTTCGAGAGAAACTGTCTCGAGTGAGACAAAAATT
3153190 ATTTTTGA
66 ATTTTTGA
* * * * *
3153198 GGAAAAACTATATCCA--GTGA-GAATTTTGTTTCGAGAGAAACTGTCTCGAGTAAGACAAAAAT
1 GGAAAAA-TATCTCAAGGGAGATGAATTTTTTTTCGAGAGAAACTGTCTCGAGTGAGACAAAAAT
3153260 T
65 T
3153261 TGAAGTAAAA
Statistics
Matches: 174, Mismatches: 30, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
71 48 0.28
72 70 0.40
73 50 0.29
74 6 0.03
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (73 bp):
GGAAAAATATCTCAAGGGAGATGAATTTTTTTTCGAGAGAAACTGTCTCGAGTGAGACAAAAATT
ATTTTTGA
Found at i:3155298 original size:21 final size:21
Alignment explanation
Indices: 3155252--3155292 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3155242 TTGTTAAAAT
3155252 AAAA-TAATTATTTTATCACA
1 AAAAGTAATTATTTTATCACA
*
3155272 AAAAGTAATT-TTTTTTCACA
1 AAAAGTAATTATTTTATCACA
3155292 A
1 A
3155293 TTAAGTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAGTAATTATTTTATCACA
Found at i:3155648 original size:197 final size:197
Alignment explanation
Indices: 3155412--3155917 Score: 700
Period size: 197 Copynumber: 2.6 Consensus size: 197
3155402 ACTTTTTTAC
* * *
3155412 TGTGACTAAATAATTTTGTTGCAATTTGTTATTGTGAAAGAATATTATTTGTCACATTTTTTTAT
1 TGTGAATAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
*
3155477 AATGAGAAATTAATATTTGTTACAAATTGTTATTTTGATTAAATAAATTTGTCACAA-TTTTTAT
66 AATGAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTTAT
* * *
3155541 TTTGACAAAATATTGAGACGAAATAAATTTGACATAACTGTTTACTTTGACTAAATTTA-ACGTG
131 TTTGACAAAATATTGAGACAAAATAAATTTGACATAAATGTTTACTTTGAATAAATTTATAC--G
3155605 TTAT
194 TTAT
* * * *
3155609 TGTGAATAAATCATTTTGTTACAATTTTTTATTGTGAAAGAATATTACTTGTCACAATTCTTTAT
1 TGTGAATAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
* * *
3155674 GATGAGAAATTAATATTTGTTATAAATTATTATTTTGATTAAATAAATTTGTCAGAATTTTTTAT
66 AATGAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTTAT
* * *
3155739 TTTGACAAAATATTGTGACAAAATAAATTTGACATAAATTTTTATTTTGAATAAATTTATTACGT
131 TTTGACAAAATATTGAGACAAAATAAATTTGACATAAATGTTTACTTTGAATAAATTTA-TACGT
3155804 TAT
195 TAT
* * * * *
3155807 TGT-AACTAAATAAATTTGTTACAATTTGTTATTATGAAATAATA--ATTTTTCATAATTTTTTA
1 TGTGAA-TAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTA
* * *
3155869 TATTGAGAAATTAATAATTGTTATAAATTGTTATTATG-TCTAAATAAAT
65 TAATGAGAAATTAATATTTGTTATAAATTGTTATTTTGAT-TAAATAAAT
3155918 ATCGAAATCC
Statistics
Matches: 273, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
195 1 0.00
196 56 0.21
197 113 0.41
198 101 0.37
200 2 0.01
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.46
Consensus pattern (197 bp):
TGTGAATAAATAATTTTGTTACAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTAT
AATGAGAAATTAATATTTGTTATAAATTGTTATTTTGATTAAATAAATTTGTCACAATTTTTTAT
TTTGACAAAATATTGAGACAAAATAAATTTGACATAAATGTTTACTTTGAATAAATTTATACGTT
AT
Found at i:3155725 original size:98 final size:97
Alignment explanation
Indices: 3155418--3155752 Score: 233
Period size: 98 Copynumber: 3.4 Consensus size: 97
3155408 TTACTGTGAC
* ** * * * *
3155418 TAAATAATTTTGTTGCAATTTGTTATTGTGA-AAGAATATTATTTGTCACATTTTTTTATAATGA
1 TAAATAAATTTGTCACAATTTTTTATTGTGACAA-AATATTA-TTGTCACAATTATTTATGATGA
* *
3155482 GAAATTAATATTTGTTACAAATTGTTATTTTGAT
64 GAAATTAATATTTGTTATAAATTATTATTTTGAT
* * * * *
3155516 TAAATAAATTTGTCACAA-TTTTTATTTTGACAAAATATTGA--GACGA-AATAAATT-TGA-CA
1 TAAATAAATTTGTCACAATTTTTTATTGTGACAAAATATT-ATTGTC-ACAATTATTTATGATGA
* * * * *
3155575 TAACTGT-TTACTTTG--ACTAAATTTAACGTGTTATTGTGAA
64 GAAAT-TAATA-TTTGTTA-TAAA-TT-A----TTATTTTGAT
* * * *
3155615 TAAATCATTTTGTTACAATTTTTTATTGTGA-AAGAATATTACTTGTCACAATTCTTTATGATGA
1 TAAATAAATTTGTCACAATTTTTTATTGTGACAA-AATATTA-TTGTCACAATTATTTATGATGA
3155679 GAAATTAATATTTGTTATAAATTATTATTTTGAT
64 GAAATTAATATTTGTTATAAATTATTATTTTGAT
* *
3155713 TAAATAAATTTGTCAGAATTTTTTATTTTGACAAAATATT
1 TAAATAAATTTGTCACAATTTTTTATTGTGACAAAATATT
3155753 GTGACAAAAT
Statistics
Matches: 175, Mismatches: 38, Indels: 48
0.67 0.15 0.18
Matches are distributed among these distances:
92 1 0.01
93 9 0.05
94 9 0.05
95 6 0.03
96 1 0.01
97 16 0.09
98 58 0.33
99 28 0.16
100 17 0.10
101 1 0.01
102 8 0.05
103 10 0.06
104 10 0.06
105 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (97 bp):
TAAATAAATTTGTCACAATTTTTTATTGTGACAAAATATTATTGTCACAATTATTTATGATGAGA
AATTAATATTTGTTATAAATTATTATTTTGAT
Found at i:3155824 original size:100 final size:98
Alignment explanation
Indices: 3155516--3155839 Score: 261
Period size: 100 Copynumber: 3.3 Consensus size: 98
3155506 TTATTTTGAT
* * *
3155516 TAAATAAATTTGTCACAA-TTTTTATTTTGACAAAATATTGAGACGAAATAAATTTGACATAACT
1 TAAATAAATTTGTCACAATTTTTTATTTTGACAAAATATTGTGACAAAATAAATTTGACATAAAT
* *
3155580 GTTTACTTTGACTAAATTTA--ACGTGTTATTGTGAA
66 TTTTA-TTTGAATAAATTTATTAC--GTTATTGT-AA
* * * * * * * *** *
3155615 TAAATCATTTTGTTACAATTTTTTATTGTGA-AAGAATATTACTTGTCACAATTCTTTATGATGA
1 TAAATAAATTTGTCACAATTTTTTATTTTGACAA-AATATT--GTGACAAAATAAATT-TGA-CA
* ** * *
3155679 GAAATTAATATTTGTTATAAA-TTATTA--TT-TTG-AT
61 TAAATTTTTATTTG-AATAAATTTATTACGTTATTGTAA
*
3155713 TAAATAAATTTGTCAGAATTTTTTATTTTGACAAAATATTGTGACAAAATAAATTTGACATAAAT
1 TAAATAAATTTGTCACAATTTTTTATTTTGACAAAATATTGTGACAAAATAAATTTGACATAAAT
3155778 TTTTATTTTGAATAAATTTATTACGTTATTGTAA
66 TTTTA-TTTGAATAAATTTATTACGTTATTGTAA
* *
3155812 CTAAATAAATTTGTTACAATTTGTTATT
1 -TAAATAAATTTGTCACAATTTTTTATT
3155840 ATGAAATAAT
Statistics
Matches: 167, Mismatches: 41, Indels: 33
0.69 0.17 0.14
Matches are distributed among these distances:
94 13 0.08
95 13 0.08
96 9 0.05
97 2 0.01
98 36 0.22
99 20 0.12
100 44 0.26
101 2 0.01
102 7 0.04
103 10 0.06
104 10 0.06
105 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (98 bp):
TAAATAAATTTGTCACAATTTTTTATTTTGACAAAATATTGTGACAAAATAAATTTGACATAAAT
TTTTATTTGAATAAATTTATTACGTTATTGTAA
Found at i:3155864 original size:31 final size:31
Alignment explanation
Indices: 3155822--3155906 Score: 84
Period size: 33 Copynumber: 2.7 Consensus size: 31
3155812 CTAAATAAAT
*
3155822 TTGTTACAATTTGTTATTATGAAA-TAATAA
1 TTGTTATAATTTGTTATTATGAAATTAATAA
* *
3155852 TTTTTCATAATTTTTTA-TATTGAGAAATTAATAA
1 TTGTT-ATAATTTGTTATTA-T--GAAATTAATAA
*
3155886 TTGTTATAAATTGTTATTATG
1 TTGTTATAATTTGTTATTATG
3155907 TCTAAATAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
30 6 0.14
31 11 0.26
33 14 0.33
34 12 0.28
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.52
Consensus pattern (31 bp):
TTGTTATAATTTGTTATTATGAAATTAATAA
Found at i:3157501 original size:3 final size:3
Alignment explanation
Indices: 3157493--3157530 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3157483 TTTTCTTAAG
3157493 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3157531 TAAAGCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3161287 original size:2 final size:2
Alignment explanation
Indices: 3161282--3161313 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3161272 ATGCGATACG
3161282 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
3161314 GACCATAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3167758 original size:10 final size:10
Alignment explanation
Indices: 3167722--3167829 Score: 57
Period size: 10 Copynumber: 11.1 Consensus size: 10
3167712 TGTAAAACCC
3167722 ATAATAAT-A
1 ATAATAATAA
* * *
3167731 TTATTAATAT
1 ATAATAATAA
3167741 ATAATAATAA
1 ATAATAATAA
*
3167751 ATACTAAT--
1 ATAATAATAA
*
3167759 GTAATAATAA
1 ATAATAATAA
* * *
3167769 ACAATATTATG
1 ATAATAATA-A
*
3167780 TTAATAATAA
1 ATAATAATAA
*
3167790 ATAAAAATAA
1 ATAATAATAA
3167800 A-AATAA-AA
1 ATAATAATAA
3167808 ATAATAGAATAA
1 ATAAT--AATAA
3167820 ATAA-AATAA
1 ATAATAATAA
3167829 A
1 A
3167830 ATAAAATGAA
Statistics
Matches: 71, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
8 9 0.13
9 19 0.27
10 29 0.41
11 8 0.11
12 6 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
ATAATAATAA
Found at i:3167765 original size:18 final size:20
Alignment explanation
Indices: 3167742--3167793 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 20
3167732 TATTAATATA
*
3167742 TAATAATAAATACTA-ATG-
1 TAATAATAAATAATATATGT
*
3167760 TAATAATAAACAATATTATGT
1 TAATAATAAATAATA-TATGT
3167781 TAATAATAAATAA
1 TAATAATAAATAA
3167794 AAATAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 13 0.46
20 3 0.11
21 12 0.43
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
TAATAATAAATAATATATGT
Found at i:3167767 original size:21 final size:21
Alignment explanation
Indices: 3167741--3167799 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
3167731 TTATTAATAT
3167741 ATAATAATAAATACTAATG-TA
1 ATAATAATAAATA-TAATGTTA
*
3167762 ATAATAA-ACAATATTATGTTA
1 ATAATAATA-AATATAATGTTA
*
3167783 ATAATAAATAAAAATAA
1 ATAAT-AATAAATATAA
3167800 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 5 0.16
21 18 0.58
22 7 0.23
23 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (21 bp):
ATAATAATAAATATAATGTTA
Found at i:3167799 original size:6 final size:6
Alignment explanation
Indices: 3167782--3167835 Score: 54
Period size: 6 Copynumber: 8.2 Consensus size: 6
3167772 ATATTATGTT
*
3167782 AATAATA AATAAA AATAAA AATAAA AATAATA GAATAAA TAAAATAA AATAAA
1 AATAA-A AATAAA AATAAA AATAAA AATAA-A -AATAAA -AATA-AA AATAAA
3167835 A
1 A
3167836 TGAAATTCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
6 21 0.51
7 13 0.32
8 7 0.17
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:3168810 original size:20 final size:20
Alignment explanation
Indices: 3168771--3168824 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
3168761 ATATTAGGAT
*
3168771 CAGTATCGATATCTTAAGG-C
1 CAGTATCGATA-CTGAAGGCC
3168791 CAGTATCGATACTGACAGGCC
1 CAGTATCGATACTGA-AGGCC
*
3168812 CAATATCGATACT
1 CAGTATCGATACT
3168825 AATGTCCTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 3 0.10
20 14 0.47
21 13 0.43
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGTATCGATACTGAAGGCC
Found at i:3169301 original size:237 final size:237
Alignment explanation
Indices: 3168886--3169356 Score: 906
Period size: 237 Copynumber: 2.0 Consensus size: 237
3168876 GGGTTATGAG
*
3168886 TGTTGGGAAATAAACGAGTAACAAGTAATTTCCCTATAACCATATTAGTGAGAATACGAAATAAA
1 TGTTGGGAAATAAACGAGTAACAAGTAATTTCCCTATAACCAGATTAGTGAGAATACGAAATAAA
3168951 AGCGGAAAAATAATACCCGAAAAATTGATAACGGAGTTCAGCCAATTGTGCTTACGTCTCCGAAC
66 AGCGGAAAAATAATACCCGAAAAATTGATAACGGAGTTCAGCCAATTGTGCTTACGTCTCCGAAC
3169016 TGCTGCAGATCTTTTACTAAAGAGAAAAAATTACAGGTGTTTACAAAACACACTTGAGAGAGAAC
131 TGCTGCAGATCTTTTACTAAAGAGAAAAAATTACAGGTGTTTACAAAACACACTTGAGAGAGAAC
3169081 TGGAAGATTTTGGGATGATTTTGAAGCTAAATGAGCTAGGGT
196 TGGAAGATTTTGGGATGATTTTGAAGCTAAATGAGCTAGGGT
* *
3169123 TGTTGGGAAATAAACGAGTAACAAGTAATTTCCCTGTAGCCAGATTAGTGAGAATACGAAATAAA
1 TGTTGGGAAATAAACGAGTAACAAGTAATTTCCCTATAACCAGATTAGTGAGAATACGAAATAAA
*
3169188 AGCGGAAAAATAATACCCGAAAAATTGATAACGGAGTTCAGCCAATTGTGCTTACGTCTCCGGAC
66 AGCGGAAAAATAATACCCGAAAAATTGATAACGGAGTTCAGCCAATTGTGCTTACGTCTCCGAAC
3169253 TGCTGCAGATCTTTTACTAAAGAGAAAAAATTACAGGTGTTTACAAAACACACTTGAGAGAGAAC
131 TGCTGCAGATCTTTTACTAAAGAGAAAAAATTACAGGTGTTTACAAAACACACTTGAGAGAGAAC
3169318 TGGAAGATTTTGGGATGATTTTGAAGCTAAATGAGCTAG
196 TGGAAGATTTTGGGATGATTTTGAAGCTAAATGAGCTAG
3169357 AGTATTTATA
Statistics
Matches: 230, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
237 230 1.00
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (237 bp):
TGTTGGGAAATAAACGAGTAACAAGTAATTTCCCTATAACCAGATTAGTGAGAATACGAAATAAA
AGCGGAAAAATAATACCCGAAAAATTGATAACGGAGTTCAGCCAATTGTGCTTACGTCTCCGAAC
TGCTGCAGATCTTTTACTAAAGAGAAAAAATTACAGGTGTTTACAAAACACACTTGAGAGAGAAC
TGGAAGATTTTGGGATGATTTTGAAGCTAAATGAGCTAGGGT
Found at i:3174448 original size:22 final size:22
Alignment explanation
Indices: 3174400--3174480 Score: 83
Period size: 22 Copynumber: 3.6 Consensus size: 22
3174390 CAGTGTTATA
* *
3174400 ACACTTTTGTATCAGTGCAAATG
1 ACACTTTTGTATTAGTGCTAA-G
* *
3174423 -CACTTTTGTATTAGTGTTGAG
1 ACACTTTTGTATTAGTGCTAAG
*
3174444 ACACTTTAGTATTAGTGCTAAG
1 ACACTTTTGTATTAGTGCTAAG
*
3174466 ACACTTCTGTGATTA
1 ACACTTTTGT-ATTA
3174481 AGTAGCAAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
21 1 0.02
22 42 0.89
23 4 0.09
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (22 bp):
ACACTTTTGTATTAGTGCTAAG
Found at i:3177020 original size:13 final size:13
Alignment explanation
Indices: 3177002--3177047 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
3176992 CAAAGGGATG
3177002 TAAACGAACACAA
1 TAAACGAACACAA
*
3177015 TAAACG-A-AC-G
1 TAAACGAACACAA
3177025 TAAACGAACACAA
1 TAAACGAACACAA
*
3177038 TAAATGAACA
1 TAAACGAACA
3177048 TAAATGAACG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
10 6 0.22
11 3 0.11
12 3 0.11
13 15 0.56
ACGTcount: A:0.59, C:0.20, G:0.11, T:0.11
Consensus pattern (13 bp):
TAAACGAACACAA
Found at i:3177028 original size:23 final size:23
Alignment explanation
Indices: 3177001--3177056 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3176991 ACAAAGGGAT
3177001 GTAAACGAACACAATAAACGAAC
1 GTAAACGAACACAATAAACGAAC
*
3177024 GTAAACGAACACAATAAATGAAC
1 GTAAACGAACACAATAAACGAAC
* *
3177047 ATAAATGAAC
1 GTAAACGAAC
3177057 GTAAATGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.12
Consensus pattern (23 bp):
GTAAACGAACACAATAAACGAAC
Found at i:3177236 original size:14 final size:14
Alignment explanation
Indices: 3177217--3177283 Score: 70
Period size: 14 Copynumber: 5.1 Consensus size: 14
3177207 AGATTGGACT
3177217 AAACATAAATGAAC
1 AAACATAAATGAAC
*
3177231 AAACATAAACGAAC
1 AAACATAAATGAAC
*
3177245 GAACATAAATG---
1 AAACATAAATGAAC
3177256 -AACATAAATGAAC
1 AAACATAAATGAAC
* *
3177269 GAACATAAACGAAC
1 AAACATAAATGAAC
3177283 A
1 A
3177284 TATTATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
10 10 0.23
14 34 0.77
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.12
Consensus pattern (14 bp):
AAACATAAATGAAC
Found at i:3177268 original size:24 final size:24
Alignment explanation
Indices: 3177232--3177285 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
3177222 TAAATGAACA
*
3177232 AACATAAACGAACGAACATAAATG
1 AACATAAACGAACGAACATAAACG
*
3177256 AACATAAATGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
3177280 AACATA
1 AACATA
3177286 TTATTAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.17, G:0.11, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:3178113 original size:13 final size:13
Alignment explanation
Indices: 3178092--3178128 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3178082 TGTATTCAAA
*
3178092 AAATATAAAACTT
1 AAATTTAAAACTT
3178105 AAATTTAAAACTT
1 AAATTTAAAACTT
3178118 AAATCTTAAAA
1 AAAT-TTAAAA
3178129 TATATAATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTTAAAACTT
Found at i:3179173 original size:7 final size:7
Alignment explanation
Indices: 3179161--3179200 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
3179151 CTATGGTTGA
3179161 TTATTTT
1 TTATTTT
3179168 TTATTTT
1 TTATTTT
3179175 TTATTTT
1 TTATTTT
*
3179182 TTACTTT
1 TTATTTT
3179189 TTATTTT
1 TTATTTT
3179196 TTATT
1 TTATT
3179201 AACTTTTAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (7 bp):
TTATTTT
Found at i:3179399 original size:6 final size:6
Alignment explanation
Indices: 3179390--3179419 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3179380 TTCTCATTCT
3179390 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC
1 CTTTCC CTTTCC CTTTCC CTTTCC CTTTCC
3179420 AGATAGGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CTTTCC
Found at i:3182617 original size:21 final size:21
Alignment explanation
Indices: 3182590--3182648 Score: 91
Period size: 21 Copynumber: 2.8 Consensus size: 21
3182580 GTCCGAGTTA
3182590 CCCGCGACGGCCGCAATAGCG
1 CCCGCGACGGCCGCAATAGCG
* * *
3182611 TCCGCGACGACCGCAGTAGCG
1 CCCGCGACGGCCGCAATAGCG
3182632 CCCGCGACGGCCGCAAT
1 CCCGCGACGGCCGCAAT
3182649 CACAGGAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.42, G:0.32, T:0.07
Consensus pattern (21 bp):
CCCGCGACGGCCGCAATAGCG
Found at i:3186718 original size:3 final size:3
Alignment explanation
Indices: 3186705--3186757 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
3186695 GTCGAAAAAA
*
3186705 TAT TAAT TAT TAT TAT TAT TAT TAT TAT T-T ATAT TAT TAT TAT CAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
*
3186751 TAA TAT T
1 TAT TAT T
3186758 TTAATTACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.88
4 4 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3188283 original size:30 final size:31
Alignment explanation
Indices: 3188237--3188352 Score: 123
Period size: 30 Copynumber: 3.8 Consensus size: 31
3188227 TTTTTATGTA
3188237 ATTACTTTTCAGTCCTTTAAGTTTCTTTTTTT
1 ATTACTTTT-AGTCCTTTAAGTTTCTTTTTTT
*
3188269 ATTA-TTTTAGTCCTTTAAGTTT-TTGTTCTT
1 ATTACTTTTAGTCCTTTAAGTTTCTT-TTTTT
* * *
3188299 ATTATTTTTAGTCCTTTAAGTCTCTGTTTTT
1 ATTACTTTTAGTCCTTTAAGTTTCTTTTTTT
* * *
3188330 GTTA-TTTTGGTCC-TCAAGTTTCT
1 ATTACTTTTAGTCCTTTAAGTTTCT
3188353 GTTAATCATA
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
29 10 0.14
30 30 0.41
31 28 0.38
32 5 0.07
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.60
Consensus pattern (31 bp):
ATTACTTTTAGTCCTTTAAGTTTCTTTTTTT
Found at i:3188311 original size:31 final size:31
Alignment explanation
Indices: 3188237--3188337 Score: 125
Period size: 31 Copynumber: 3.3 Consensus size: 31
3188227 TTTTTATGTA
*
3188237 ATTACTTTTCAGTCCTTTAAGTTTCTT-TTTTT
1 ATTA-TTTTTAGTCCTTTAAGTTT-TTGTTTTT
*
3188269 ATTA-TTTTAGTCCTTTAAGTTTTTGTTCTT
1 ATTATTTTTAGTCCTTTAAGTTTTTGTTTTT
* *
3188299 ATTATTTTTAGTCCTTTAAGTCTCTGTTTTT
1 ATTATTTTTAGTCCTTTAAGTTTTTGTTTTT
*
3188330 GTTATTTT
1 ATTATTTT
3188338 GGTCCTCAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
29 2 0.03
30 25 0.41
31 30 0.49
32 4 0.07
ACGTcount: A:0.16, C:0.12, G:0.09, T:0.63
Consensus pattern (31 bp):
ATTATTTTTAGTCCTTTAAGTTTTTGTTTTT
Found at i:3189119 original size:15 final size:16
Alignment explanation
Indices: 3189089--3189121 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
3189079 CAACTTTTTG
3189089 TCTTAAAAAATGAATTT
1 TCTTAAAAAA-GAATTT
3189106 TCTTAAAAAA-AATTT
1 TCTTAAAAAAGAATTT
3189121 T
1 T
3189122 AAAAGACGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
17 10 0.62
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
TCTTAAAAAAGAATTT
Found at i:3190179 original size:30 final size:30
Alignment explanation
Indices: 3190145--3190206 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
3190135 ATCTTGCTTG
*
3190145 TACTAACTTATTTTTCTCTTTTGTTTGTGT
1 TACTAACTCATTTTTCTCTTTTGTTTGTGT
*
3190175 TACTAACTCGTTTTTCTCTTTTGTTTGTGT
1 TACTAACTCATTTTTCTCTTTTGTTTGTGT
3190205 TA
1 TA
3190207 TTTTTCATCA
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:0.13, C:0.15, G:0.11, T:0.61
Consensus pattern (30 bp):
TACTAACTCATTTTTCTCTTTTGTTTGTGT
Found at i:3193615 original size:20 final size:20
Alignment explanation
Indices: 3193590--3193645 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3193580 GAATGCAATT
3193590 AGGGTATCGATACATAGTAG
1 AGGGTATCGATACATAGTAG
*
3193610 AGGGTATCGATACCTAGTAG
1 AGGGTATCGATACATAGTAG
*
3193630 AGGGTACCGATACATA
1 AGGGTATCGATACATA
3193646 CCTTAATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (20 bp):
AGGGTATCGATACATAGTAG
Found at i:3199992 original size:64 final size:66
Alignment explanation
Indices: 3199871--3199993 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 66
3199861 CCATTCAACA
* *
3199871 GGTATCGATACCCTCTTAAATGAAAAAGAATAACAGAATATAGGGAGGGTATCGATACCCCAGTT
1 GGTACCGATACCCTCTTAAATGAAAAAGAATAACAGAATATAAGGAGGGTATCGATACCCCAGTT
3199936 G
66 G
* * * **
3199937 GGTACCGATACCCTCTTGAATG-AAAA-ACTAATAGAATATAATTAGGGTATCGATACC
1 GGTACCGATACCCTCTTAAATGAAAAAGAATAACAGAATATAAGGAGGGTATCGATACC
3199994 TACCTTAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
64 26 0.52
65 4 0.08
66 20 0.40
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (66 bp):
GGTACCGATACCCTCTTAAATGAAAAAGAATAACAGAATATAAGGAGGGTATCGATACCCCAGTT
G
Found at i:3200561 original size:21 final size:21
Alignment explanation
Indices: 3200535--3200597 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
3200525 GTCGAGGGTT
3200535 TCATAGGTCATTCGGGACAAC
1 TCATAGGTCATTCGGGACAAC
* * *
3200556 TCATAGGTCCTTCGGAACATAT
1 TCATAGGTCATTCGGGACA-AC
*
3200578 TCACAGGTCATTCGGGACAA
1 TCATAGGTCATTCGGGACAA
3200598 ATTTCATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 17 0.49
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (21 bp):
TCATAGGTCATTCGGGACAAC
Found at i:3201282 original size:2 final size:2
Alignment explanation
Indices: 3201275--3201333 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
3201265 CATATACCAA
3201275 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
3201317 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
3201334 CAATAAAGTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3202095 original size:18 final size:19
Alignment explanation
Indices: 3202060--3202096 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3202050 CACGGAATGT
3202060 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
3202080 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
3202097 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:3206013 original size:23 final size:21
Alignment explanation
Indices: 3205986--3206028 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
3205976 ATATAAAAAA
3205986 TTAT-TTTTTATTAAATATTTT
1 TTATATTTTTATTAAAT-TTTT
*
3206007 TTATATTTTTATTTAATTTTT
1 TTATATTTTTATTAAATTTTT
3206028 T
1 T
3206029 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATATTTTTATTAAATTTTT
Found at i:3209685 original size:30 final size:28
Alignment explanation
Indices: 3209662--3209716 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3209652 CGGTGATCGG
3209662 TATATTTACCGATCTAACACCGGTCAGAT
1 TATATTTACCGATCTAACACCGGT-AGAT
* *
3209691 TATATTTCCCGATCTAACACCCGTAG
1 TATATTTACCGATCTAACACCGGTAG
3209717 CAGTAAAGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (28 bp):
TATATTTACCGATCTAACACCGGTAGAT
Found at i:3215606 original size:17 final size:18
Alignment explanation
Indices: 3215563--3215603 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3215553 AAATTATATT
3215563 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
3215580 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
3215598 ATTAAA
1 AGTAAA
3215604 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:3217799 original size:2 final size:2
Alignment explanation
Indices: 3217794--3217827 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3217784 TAATAATTTC
3217794 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
3217828 CAATTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3220836 original size:59 final size:59
Alignment explanation
Indices: 3220744--3220928 Score: 316
Period size: 59 Copynumber: 3.1 Consensus size: 59
3220734 GTATTTAACC
* *
3220744 CATTATTCTTTTACTTTCATACTAATTAGTTTTAACCATGCACTTCTACAACTCCAATA
1 CATTATTCTTTTACTTTCATACAAATTAGTTTTAACCATGCACTTCTACAACTCAAATA
3220803 CATTATTCTTTTACTTTCATACAAATTAGTTTTAACCATGCACTTCTACAACTCAAATA
1 CATTATTCTTTTACTTTCATACAAATTAGTTTTAACCATGCACTTCTACAACTCAAATA
* **
3220862 CATTATTCTTTTACTTTCATACCAATTAGCATTAACCATGCACTTCTACAACTCAAATA
1 CATTATTCTTTTACTTTCATACAAATTAGTTTTAACCATGCACTTCTACAACTCAAATA
3220921 CATGTATT
1 CAT-TATT
3220929 TATCATTAAT
Statistics
Matches: 120, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
59 116 0.97
60 4 0.03
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (59 bp):
CATTATTCTTTTACTTTCATACAAATTAGTTTTAACCATGCACTTCTACAACTCAAATA
Found at i:3222626 original size:2 final size:2
Alignment explanation
Indices: 3222621--3222669 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
3222611 ATTTTTTCTT
3222621 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3222663 TA TA TA T
1 TA TA TA T
3222670 GGATAATTAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3224183 original size:20 final size:20
Alignment explanation
Indices: 3224147--3224185 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3224137 CTTTGGTATA
*
3224147 GATACCCACCTGTTGATATC
1 GATACCCACCTGCTGATATC
3224167 GATACCC-CCTGACTGATAT
1 GATACCCACCTG-CTGATAT
3224186 GGGCTATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (20 bp):
GATACCCACCTGCTGATATC
Found at i:3226514 original size:58 final size:58
Alignment explanation
Indices: 3226443--3226558 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
3226433 ACAAAGTCTA
* * *
3226443 TGGTTACCTTGTCCCATTTTCACTGAGGAATCGAAATGACCTGAAGCAAACATGAGGG
1 TGGTTACCCTGTCCCATTTCCACTGAGGAATCGAAATGACCTAAAGCAAACATGAGGG
* *
3226501 TGGTTACCCTGTCCCATTTCCACTGAGGAATCGATATGACCTAAAGTAAACATGAGGG
1 TGGTTACCCTGTCCCATTTCCACTGAGGAATCGAAATGACCTAAAGCAAACATGAGGG
3226559 AACCTGTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (58 bp):
TGGTTACCCTGTCCCATTTCCACTGAGGAATCGAAATGACCTAAAGCAAACATGAGGG
Found at i:3232845 original size:4 final size:4
Alignment explanation
Indices: 3232836--3235416 Score: 5092
Period size: 4 Copynumber: 647.8 Consensus size: 4
3232826 CTTTTCTAAA
3232836 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3232884 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3232932 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3232980 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233028 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233076 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233124 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233172 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233220 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233268 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233316 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233364 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233412 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233460 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233508 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233556 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233604 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233650 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233698 ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233744 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233792 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233840 A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233886 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233934 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3233982 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234030 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234078 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234126 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234174 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234222 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234270 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234318 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234366 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234414 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234462 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234510 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234558 ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234604 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234652 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234700 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234748 ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234794 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234842 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234890 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234938 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3234986 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235034 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235082 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235130 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235178 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235226 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235274 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235322 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
3235370 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
3235417 ATACCTAACT
Statistics
Matches: 2567, Mismatches: 0, Indels: 20
0.99 0.00 0.01
Matches are distributed among these distances:
2 10 0.00
4 2557 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:3239528 original size:22 final size:22
Alignment explanation
Indices: 3239503--3239572 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
3239493 TAAGTTGTTT
3239503 TGGATTGAATATTGGACTATTG
1 TGGATTGAATATTGGACTATTG
* * * *
3239525 TGGATT-AAT-TT-AAGTTGTTT
1 TGGATTGAATATTGGA-CTATTG
*
3239545 TGGATTGAATATTGGGCTATTG
1 TGGATTGAATATTGGACTATTG
3239567 TGGATT
1 TGGATT
3239573 AATTTAAGTT
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 6 0.17
22 17 0.49
ACGTcount: A:0.24, C:0.03, G:0.27, T:0.46
Consensus pattern (22 bp):
TGGATTGAATATTGGACTATTG
Found at i:3239537 original size:42 final size:42
Alignment explanation
Indices: 3239490--3239582 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
3239480 TTTTCGGTTG
3239490 ATTTAAGTTGTTTTGGATTGAATATTGGACTATTGTGGATTA
1 ATTTAAGTTGTTTTGGATTGAATATTGGACTATTGTGGATTA
*
3239532 ATTTAAGTTGTTTTGGATTGAATATTGGGCTATTGTGGATTA
1 ATTTAAGTTGTTTTGGATTGAATATTGGACTATTGTGGATTA
3239574 ATTTAAGTT
1 ATTTAAGTT
3239583 TTGAATGTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (42 bp):
ATTTAAGTTGTTTTGGATTGAATATTGGACTATTGTGGATTA
Found at i:3244377 original size:22 final size:21
Alignment explanation
Indices: 3244340--3244398 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
3244330 AGTAATTTTG
3244340 ATAATTTATTTAAAAAATAAAT
1 ATAATTTA-TTAAAAAATAAAT
3244362 ATATATTTATTAAAAAATAAAT
1 ATA-ATTTATTAAAAAATAAAT
*
3244384 ATAACTT-TTAAAAAA
1 ATAATTTATTAAAAAA
3244399 ATCTTTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 8 0.23
21 3 0.09
22 19 0.54
23 5 0.14
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATTTATTAAAAAATAAAT
Found at i:3246394 original size:61 final size:61
Alignment explanation
Indices: 3246311--3246427 Score: 207
Period size: 61 Copynumber: 1.9 Consensus size: 61
3246301 TAAATCACAA
* *
3246311 TATATTTTAAATGCTTTACTCTTCAAATCATTCGAGGTTGACTCATCGCAAGTCGTCCTCG
1 TATATTTTAAATACTTTACTCTTCAAATCATTCGAGGTTGACTCATCACAAGTCGTCCTCG
*
3246372 TATATTTTAAATACTTTGCTCTTCAAATCATTCGAGGTTGACTCATCACAAGTCGT
1 TATATTTTAAATACTTTACTCTTCAAATCATTCGAGGTTGACTCATCACAAGTCGT
3246428 TATCATATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.38
Consensus pattern (61 bp):
TATATTTTAAATACTTTACTCTTCAAATCATTCGAGGTTGACTCATCACAAGTCGTCCTCG
Found at i:3246637 original size:24 final size:25
Alignment explanation
Indices: 3246566--3246631 Score: 116
Period size: 25 Copynumber: 2.7 Consensus size: 25
3246556 ACTACACAAG
3246566 TATAATTTAAAAATCTATTCAATCA
1 TATAATTTAAAAATCTATTCAATCA
3246591 TATAATTTAAAAATCTATTCAATCA
1 TATAATTTAAAAATCTATTCAATCA
*
3246616 TATAGTTT-AAAATCTA
1 TATAATTTAAAAATCTA
3246632 AACAATGGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 8 0.20
25 32 0.80
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.41
Consensus pattern (25 bp):
TATAATTTAAAAATCTATTCAATCA
Found at i:3246889 original size:14 final size:14
Alignment explanation
Indices: 3246872--3246907 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3246862 AAATCTAGGG
*
3246872 TTTGAGGTTAAAAC
1 TTTGAGATTAAAAC
3246886 TTTGAGATTAAAAC
1 TTTGAGATTAAAAC
*
3246900 TCTGAGAT
1 TTTGAGAT
3246908 CATTAAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.19, T:0.36
Consensus pattern (14 bp):
TTTGAGATTAAAAC
Found at i:3250168 original size:3 final size:3
Alignment explanation
Indices: 3250160--3250229 Score: 50
Period size: 3 Copynumber: 22.3 Consensus size: 3
3250150 TTAGTTATGC
* * ** *
3250160 TAA TAA TAA TAG TAA TGA TAA TAA TTAA TAA TTC TAA TTAC TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA TAA TAA
* *
3250207 TAA TAGT TAT TAA TAA TAA TAA T
1 TAA TA-A TAA TAA TAA TAA TAA T
3250230 TAATTATAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
3 45 0.87
4 7 0.13
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:3250207 original size:19 final size:19
Alignment explanation
Indices: 3250178--3250230 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3250168 ATAGTAATGA
3250178 TAATAATTAATAATTCTAAT
1 TAATAA-TAATAATTCTAAT
* ** *
3250198 TACTAATAATAATAGTTAT
1 TAATAATAATAATTCTAAT
3250217 TAATAATAATAATT
1 TAATAATAATAATT
3250231 AATTATAAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATAATAATAATTCTAAT
Found at i:3250210 original size:13 final size:13
Alignment explanation
Indices: 3250160--3250238 Score: 52
Period size: 16 Copynumber: 5.7 Consensus size: 13
3250150 TTAGTTATGC
*
3250160 TAATAATAAT-AG
1 TAATAATAATAAT
*
3250172 TAATGATAATAAT
1 TAATAATAATAAT
* *
3250185 TAATAATTCTAATTAC
1 TAATAA---TAATAAT
3250201 TAATAATAATAGTTAT
1 TAATAATAATA---AT
3250217 TAATAATAATAAT
1 TAATAATAATAAT
*
3250230 TAATTATAA
1 TAATAATAA
3250239 ACAATTAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
12 9 0.17
13 20 0.38
16 23 0.44
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.41
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:3259786 original size:3 final size:3
Alignment explanation
Indices: 3259771--3259816 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
3259761 TAAATACACT
* *
3259771 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3259817 TTTTTTTAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 1 0.03
3 37 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3260129 original size:105 final size:105
Alignment explanation
Indices: 3259953--3260229 Score: 333
Period size: 105 Copynumber: 2.6 Consensus size: 105
3259943 TCGTTAGATT
** * *
3259953 GAACAAGTTCTTCTCATTATGAAC-TTCTTTTTTCTCGTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTTC-TCCTT-T--AGGACGAGTTCTTCTCATTATGAACTC
* * * *
3260017 TTTTGGAAATGTTGATCCAAATCCTTTTGCGGTGGACTTAGAAA-
62 TTCTGGAAATGTTGATCCAAATCCATCTGCGGT-GAATTAGAAAG
* *
3260061 GAACATGTTTTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
* * ** * *
3260126 GGAAATGTTGGTTCACCTCCATCTGTGGTGAATTTGAAAG
66 GGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
* *
3260166 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTC
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTC
3260230 ATTAGAAATG
Statistics
Matches: 147, Mismatches: 20, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
104 8 0.05
105 110 0.75
107 1 0.01
108 25 0.17
109 3 0.02
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.41
Consensus pattern (105 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGACGAGTTCTTCTCATTATGAACTCTTCT
GGAAATGTTGATCCAAATCCATCTGCGGTGAATTAGAAAG
Found at i:3260228 original size:16 final size:16
Alignment explanation
Indices: 3260174--3260229 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
3260164 AGGAACAAGT
3260174 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
* *
3260190 T-TTCTCCTTTATGATGAGT
1 TCTTCT-CATTATGA--A-C
3260209 TCTTCTCATTATGAAC
1 TCTTCTCATTATGAAC
3260225 TCTTC
1 TCTTC
3260230 ATTAGAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 1 0.03
18 1 0.03
19 8 0.26
20 4 0.13
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.48
Consensus pattern (16 bp):
TCTTCTCATTATGAAC
Found at i:3260555 original size:225 final size:223
Alignment explanation
Indices: 3260166--3260603 Score: 657
Period size: 225 Copynumber: 2.0 Consensus size: 223
3260156 AATTTGAAAG
*
3260166 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTATGATGAGTTCTTCTCATTATGAACTCTTCA
1 GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
* * * * * * *
3260231 TTAGAAATGTCGATCCCTCAAGCGAGGCGTCACTGATTCGAAATGTCGTGAATCAAGTGATAGGT
66 TGAGAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAAGT
* *
3260296 CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTTTCATTATGAAC
131 CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
3260361 TCTCCATTGAAAATGTTGATGCGAATTT
196 TCTCCATTGAAAATGTTGATGCGAATTT
3260389 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCGTT-GGATGAGTTCTTCTCATTATGAACT
1 GAACAAGTTCTTCTCATTATGAAC-T-TTC-TCCT--TTAGGATGAGTTCTTCTCATTATGAACT
* * *
3260453 C-TCCTGA-AAATATCAATCCCTCAAGCGAGGTGTCACTGATTCAAAATGTCATAAATCGAGTGA
61 CTTCATGAGAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGA
* * *
3260516 TAAGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGAATGAGTTCTTCTCATTA
126 TAAGTCAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTA
*
3260581 TGAACTCTCCATTGGAAATGTTG
191 TGAACTCTCCATTGAAAATGTTG
3260604 GTTCACCTCC
Statistics
Matches: 193, Mismatches: 17, Indels: 8
0.89 0.08 0.04
Matches are distributed among these distances:
223 24 0.12
224 1 0.01
225 133 0.69
226 8 0.04
227 25 0.13
228 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (223 bp):
GAACAAGTTCTTCTCATTATGAACTTTCTCCTTTAGGATGAGTTCTTCTCATTATGAACTCTTCA
TGAGAAATATCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATAAATCAAGTGATAAGT
CAAAAAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGAATGAGTTCTTCTCATTATGAAC
TCTCCATTGAAAATGTTGATGCGAATTT
Found at i:3261509 original size:9 final size:9
Alignment explanation
Indices: 3261489--3261533 Score: 53
Period size: 9 Copynumber: 5.4 Consensus size: 9
3261479 TTTTCATTTC
3261489 TTTTTTCA-
1 TTTTTTCAT
3261497 -TTTTTCAT
1 TTTTTTCAT
3261505 TTTTTT--T
1 TTTTTTCAT
*
3261512 CTTTTTCAT
1 TTTTTTCAT
3261521 TTTTTTCAT
1 TTTTTTCAT
3261530 TTTT
1 TTTT
3261534 CATCTTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
7 13 0.42
9 18 0.58
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:3261556 original size:32 final size:32
Alignment explanation
Indices: 3261463--3261558 Score: 115
Period size: 32 Copynumber: 2.9 Consensus size: 32
3261453 CAAACCCTCC
3261463 TTTTTC-TCTTTTTATTTTTTCATTTCTTTTTTCA
1 TTTTTCATCTTTTTATTTTTTC--TT-TTTTTTCA
* *
3261497 TTTTTCAT-TTTTTTTCTTTTTCATTTTTTTCA
1 TTTTTCATCTTTTTAT-TTTTTCTTTTTTTTCA
*
3261529 TTTTTCATCTTTTTATTTGTTCTTTTTTTT
1 TTTTTCATCTTTTTATTTTTTCTTTTTTTT
3261559 TCTTCAAGCA
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
32 28 0.52
33 7 0.13
34 12 0.22
35 7 0.13
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.78
Consensus pattern (32 bp):
TTTTTCATCTTTTTATTTTTTCTTTTTTTTCA
Found at i:3261558 original size:16 final size:16
Alignment explanation
Indices: 3261471--3261558 Score: 90
Period size: 16 Copynumber: 5.3 Consensus size: 16
3261461 CCTTTTTCTC
3261471 TTTTTATTTTTTCATTTCT
1 TTTTTA-TTTTTCA-TT-T
3261490 TTTTTCATTTTTCATTT
1 TTTTT-ATTTTTCATTT
*
3261507 TTTTTCTTTTTCATTT
1 TTTTTATTTTTCATTT
* *
3261523 TTTTCATTTTTCA-TC
1 TTTTTATTTTTCATTT
3261538 TTTTTATTTGTTC-TTT
1 TTTTTATTT-TTCATTT
3261554 TTTTT
1 TTTTT
3261559 TCTTCAAGCA
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.15
16 30 0.50
17 6 0.10
18 2 0.03
19 12 0.20
20 1 0.02
ACGTcount: A:0.09, C:0.11, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTTCATTT
Found at i:3274530 original size:3 final size:3
Alignment explanation
Indices: 3274515--3274572 Score: 91
Period size: 3 Copynumber: 19.7 Consensus size: 3
3274505 TAAATACACT
*
3274515 TAA TAA TAC TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3274563 T-T TAA TAA TA
1 TAA TAA TAA TA
3274573 TTTTTTAACT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3276722 original size:30 final size:30
Alignment explanation
Indices: 3276688--3276759 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
3276678 TTGGCCTAGG
3276688 AGTATCGATACTATTGTACTATTATATAGT
1 AGTATCGATACTATTGTACTATTATATAGT
3276718 AGTATCGATACTATTGTACTATTATATAGT
1 AGTATCGATACTATTGTACTATTATATAGT
3276748 AGTATCGATACT
1 AGTATCGATACT
3276760 CCTTTGAGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (30 bp):
AGTATCGATACTATTGTACTATTATATAGT
Found at i:3279584 original size:33 final size:35
Alignment explanation
Indices: 3279542--3279614 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
3279532 TTCATGTACA
* *
3279542 AAATTCCAAAACAC-TT-GTTACATTCTAAACTCC
1 AAATTCCAAAACACTTTAATTACATTCTAAACCCC
*
3279575 AAATTCCAAAATACTTTAATTACATTCTAAACCCC
1 AAATTCCAAAACACTTTAATTACATTCTAAACCCC
3279610 AAATT
1 AAATT
3279615 AAAGTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 13 0.37
34 2 0.06
35 20 0.57
ACGTcount: A:0.42, C:0.25, G:0.01, T:0.32
Consensus pattern (35 bp):
AAATTCCAAAACACTTTAATTACATTCTAAACCCC
Found at i:3279658 original size:35 final size:35
Alignment explanation
Indices: 3279619--3279722 Score: 156
Period size: 35 Copynumber: 3.0 Consensus size: 35
3279609 CAAATTAAAG
*
3279619 TATTTTAAAATTTGGGGTTTAAAATATAATTGAAT
1 TATTTTAGAATTTGGGGTTTAAAATATAATTGAAT
*
3279654 TATTTTAGAATTTGGGGTTTAAAATGTAATTGAAT
1 TATTTTAGAATTTGGGGTTTAAAATATAATTGAAT
* *
3279689 TATTTTAGAATTTAGGGTTTAGAATGA-AATTGAA
1 TATTTTAGAATTTGGGGTTTAAAAT-ATAATTGAA
3279723 GAATGTGTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (35 bp):
TATTTTAGAATTTGGGGTTTAAAATATAATTGAAT
Found at i:3287081 original size:41 final size:40
Alignment explanation
Indices: 3287001--3287131 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
3286991 AGTTTCTAAA
* * *
3287001 TTCGCAACTCGAATTTGACAATTTCGTAACACGAATTTCCTTT
1 TTCGCAACTCGATTTTTA-AA-TTCGTAACACGAGTTTCC-TT
*
3287044 TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCCTT
1 TTCGCAACTCGATTTTTAAATTCGTAACACGAGTTTCCTT
** * **
3287084 TTCGCAACAAGATTTTCT-AATTCGTAACGCGAGTTTCAAT
1 TTCGCAACTCGATTTT-TAAATTCGTAACACGAGTTTCCTT
3287124 TTCGCAAC
1 TTCGCAAC
3287132 AGGAATTTCG
Statistics
Matches: 77, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
40 42 0.55
41 17 0.22
42 2 0.03
43 16 0.21
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGATTTTTAAATTCGTAACACGAGTTTCCTT
Done.