Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 1 of 25
Found at i:355 original size:52 final size:51
Alignment explanation
Indices: 299--575 Score: 147
Period size: 53 Copynumber: 5.3 Consensus size: 51
289 AAAACCAGGA
299 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAACGATAAAACCAGAG
1 TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAACGATAAAACC-GAG
** *** * * * *** *
351 TTGGAGTATCCCCTCGAAAGT--AACGGGGTTGGAGTATCCCCGATGAAATAACGAGG
1 TTGGAGTAT-CCC-CGATTGTGGAA--AAATTAGTGTTTTAACGAT-AAA-ACCGA-G
* * * *
407 TTGGAGTATCCTCGATTGTGGAAAAATT-GTATTTTTGGAA--ATAAAATCGGG
1 TTGGAGTATCCCCGATTGTGGAAAAATTAGT-GTTTT--AACGATAAAACCGAG
* ** * * *
458 TTGGAGTCTCCCCGATTAAAGG-AAAATTGGCGTTTTGAA-AATAAAACC-AGG
1 TTGGAGTATCCCCGATT-GTGGAAAAATTAGTGTTTT-AACGATAAAACCGA-G
509 ATTGGAGTATCCCCCGATTGTGGAAAAATTAGTGTTTTAACGATAAAACCGTAG
1 -TTGGAGTAT-CCCCGATTGTGGAAAAATTAGTGTTTTAACGATAAAACCG-AG
563 TTGGAGTATCCCC
1 TTGGAGTATCCCC
576 TCGAAAATAA
Statistics
Matches: 163, Mismatches: 40, Indels: 44
0.66 0.16 0.18
Matches are distributed among these distances:
50 3 0.02
51 34 0.21
52 33 0.20
53 44 0.27
54 27 0.17
55 8 0.05
56 14 0.09
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAACGATAAAACCGAG
Found at i:390 original size:28 final size:27
Alignment explanation
Indices: 350--417 Score: 93
Period size: 28 Copynumber: 2.4 Consensus size: 27
340 TAAAACCAGA
*
350 GTTGGAGTATCCCC-TCGAAAGTAACGGG
1 GTTGGAGTATCCCCAT-GAAA-TAACGAG
378 GTTGGAGTATCCCCGATGAAATAACGAG
1 GTTGGAGTATCCCC-ATGAAATAACGAG
406 GTTGGAGTATCC
1 GTTGGAGTATCC
418 TCGATTGTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 32 0.86
29 4 0.11
30 1 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCATGAAATAACGAG
Found at i:474 original size:51 final size:52
Alignment explanation
Indices: 405--575 Score: 152
Period size: 51 Copynumber: 3.3 Consensus size: 52
395 GAAATAACGA
* * * * *
405 GGTTGGAGTATCCTCGATTGTGGAAAAATTGTATTTTTGGAAATAAAATC-G
1 GGTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCAG
* ** *
456 GGTTGGAGTCTCCCCGATTAAAGG-AAAATTGGCGTTTTGAAAATAAAACCAG
1 GGTTGGAGTATCCCCGATT-GTGGAAAAATTGGAGTTTTGAAAATAAAACCAG
* * * *
508 GATTGGAGTATCCCCCGATTGTGGAAAAATTAGTGTTTT-AACGATAAAACC-G
1 GGTTGGAGTAT-CCCCGATTGTGGAAAAATTGGAGTTTTGAA-AATAAAACCAG
*
560 TAGTTGGAGTATCCCC
1 -GGTTGGAGTATCCCC
576 TCGAAAATAA
Statistics
Matches: 96, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
51 38 0.40
52 21 0.22
53 37 0.39
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGGAAAAATTGGAGTTTTGAAAATAAAACCAG
Found at i:594 original size:28 final size:26
Alignment explanation
Indices: 562--630 Score: 86
Period size: 26 Copynumber: 2.6 Consensus size: 26
552 TAAAACCGTA
*
562 GTTGGAGTATCCCCTC-GAAAATAACGGG
1 GTTGGAGTATCCCCGCTG--AATAAC-GG
*
590 GTTGGAGTATCCCCGCTGATTAACGG
1 GTTGGAGTATCCCCGCTGAATAACGG
616 GTTGGAGTATCCCCG
1 GTTGGAGTATCCCCG
631 ATTGTGAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 17 0.45
27 5 0.13
28 15 0.39
29 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.25
Consensus pattern (26 bp):
GTTGGAGTATCCCCGCTGAATAACGG
Found at i:3064 original size:13 final size:13
Alignment explanation
Indices: 3046--3071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3036 ACAAAGATCC
3046 ATGTATCGATACA
1 ATGTATCGATACA
3059 ATGTATCGATACA
1 ATGTATCGATACA
3072 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3067 original size:33 final size:33
Alignment explanation
Indices: 3025--3091 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3015 AAAATTTCCA
***
3025 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3058 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
3091 A
1 A
3092 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:3135 original size:19 final size:18
Alignment explanation
Indices: 3111--3178 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
3101 CAGTAGCTAA
3111 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
3130 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
3145 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
3162 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
3179 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:3151 original size:13 final size:13
Alignment explanation
Indices: 3133--3157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3123 ACAATACTTA
3133 TGTATCGATACAT
1 TGTATCGATACAT
3146 TGTATCGATACA
1 TGTATCGATACA
3158 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3155 original size:32 final size:32
Alignment explanation
Indices: 3114--3176 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3104 TAGCTAATTA
*
3114 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
3146 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
3177 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:3258 original size:21 final size:21
Alignment explanation
Indices: 3234--3290 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3224 CATTTGTAGG
3234 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
3255 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
3276 ATGTATCGATACATT
1 ATGTATCGATACATT
3291 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:3301 original size:1 final size:1
Alignment explanation
Indices: 3295--3346 Score: 77
Period size: 1 Copynumber: 52.0 Consensus size: 1
3285 TACATTTAAA
***
3295 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCAATTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3347 CAAACACTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.04, C:0.02, G:0.00, T:0.94
Consensus pattern (1 bp):
T
Found at i:3347 original size:20 final size:20
Alignment explanation
Indices: 3295--3349 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
3285 TACATTTAAA
3295 TTTTTTTTTTTTTTT---TT
1 TTTTTTTTTTTTTTTCAATT
3312 TTTTTTTTTTTTTTTCAATT
1 TTTTTTTTTTTTTTTCAATT
3332 TTTTTTTTTTTTTTTCAA
1 TTTTTTTTTTTTTTTCAA
3350 ACACTTTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 15 0.43
20 20 0.57
ACGTcount: A:0.07, C:0.04, G:0.00, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTTTTTTTCAATT
Found at i:4028 original size:55 final size:55
Alignment explanation
Indices: 3944--4445 Score: 561
Period size: 55 Copynumber: 8.9 Consensus size: 55
3934 ATAAATTGTA
* * * *
3944 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTCGTGTGGGCTTTAAAAGGTG
** * *
3999 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGTG
** * * * **
4054 TCCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTGAAAATAAAAAGCA
1 TCCTGCTCTTTGA-GGACTGAAAAATGCCACCAACTCGTGTGGGC-TT-----TAAAAGGTG
4115 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAAC-CTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTC-GTGTGGGCTTTAAAAGGTG
* * * * **
4170 T-C-GTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGC-TT-----TAAAAGGTG
4229 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAAC-CTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTC-GTGTGGGCTTTAAAAGGTG
*
4284 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAAC-CTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTC-GTGTGGGCTTTAAAAGGTG
4339 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAAC-CTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTC-GTGTGGGCTTTAAAAGGTG
* *
4394 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTT-AAAA
4446 TAAAAAGCAT
Statistics
Matches: 389, Mismatches: 36, Indels: 43
0.83 0.08 0.09
Matches are distributed among these distances:
53 36 0.09
54 4 0.01
55 249 0.64
56 9 0.02
59 7 0.02
60 5 0.01
61 78 0.20
62 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTCGTGTGGGCTTTAAAAGGTG
Found at i:4234 original size:114 final size:116
Alignment explanation
Indices: 3999--4464 Score: 727
Period size: 116 Copynumber: 4.1 Consensus size: 116
3989 TTGAAAGGCG
** * *
3999 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
* *
4064 T-AGGGACT-GAAAGGTGCCACCAACTTGTGTAGGCTTTGAAAATAAAAAGCA
66 TGA-GGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
*
4115 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGT-C-GTTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
4178 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
4229 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
** * * **
4294 TGAGGACTAAAAAATGCCACCAACCTGTGTGGGC-TT-----TAAAAGGTG
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
4339 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
4404 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
66 TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
4455 TCCTGCTCTT
1 TCCTGCTCTT
4465 CAGGTATCCC
Statistics
Matches: 320, Mismatches: 20, Indels: 20
0.89 0.06 0.06
Matches are distributed among these distances:
110 102 0.32
111 2 0.01
114 103 0.32
115 9 0.03
116 104 0.32
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (116 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
TGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCA
Found at i:4279 original size:27 final size:27
Alignment explanation
Indices: 4249--4389 Score: 66
Period size: 27 Copynumber: 5.1 Consensus size: 27
4239 TGAGGACTGA
4249 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
* *** ** * * * **
4276 AAAAGGTGTCCTGCTCTTTGAGGACTAA
1 AAAATGCCACCAAC-CTGTGTGGGCTTT
4304 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
* *** ** * * * **
4331 AAAAGGTGTCCTGCTCTTTGAGGACTGA
1 AAAATGCCACCAAC-CTGTGTGGGCTTT
4359 AAAATGCCACCAACCTGTGTGGGCTTT
1 AAAATGCCACCAACCTGTGTGGGCTTT
4386 AAAA
1 AAAA
4390 GGTGTCCTGC
Statistics
Matches: 68, Mismatches: 44, Indels: 4
0.59 0.38 0.03
Matches are distributed among these distances:
27 36 0.53
28 32 0.47
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.26
Consensus pattern (27 bp):
AAAATGCCACCAACCTGTGTGGGCTTT
Found at i:4399 original size:110 final size:110
Alignment explanation
Indices: 3944--4445 Score: 652
Period size: 110 Copynumber: 4.5 Consensus size: 110
3934 ATAAATTGTA
* * * * * *
3944 TCCTGCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCGTCCTGCTCT
1 TCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAAGCATCCTGCTCT
** * *
4008 TTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
65 TTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
** *
4054 TCCTGCTCTTT-AGGGACTGAAAGGTGCCACCAACTTGTGTAGGCTTTGAAAATAAAAAGCATCC
1 TCCTGCTCTTTGA-GGACTGAAAAATGCCACCAACTTGTGTGGGC-TT-----TAAAAAGCATCC
4118 TGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
59 TGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
* *
4170 T-C-GTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAATAAAAAGCATCCT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGC-TT-----TAAAAAGCATCCT
4233 GCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
60 GCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
* * * **
4284 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTT
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCATCCTGCTCTT
4349 TGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
66 TGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
* *
4394 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAA
4446 TAAAAAGCAT
Statistics
Matches: 351, Mismatches: 30, Indels: 22
0.87 0.07 0.05
Matches are distributed among these distances:
109 1 0.00
110 140 0.40
111 5 0.01
114 106 0.30
115 5 0.01
116 94 0.27
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (110 bp):
TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGCATCCTGCTCTT
TGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
Found at i:7981 original size:1 final size:1
Alignment explanation
Indices: 7975--8053 Score: 104
Period size: 1 Copynumber: 79.0 Consensus size: 1
7965 CCTTCTCTTC
* * *
7975 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
8040 GAGAAAAGAAAAAA
1 AAAAAAAAAAAAAA
8054 CCTACTTAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.92, C:0.04, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:9103 original size:55 final size:55
Alignment explanation
Indices: 9018--9973 Score: 1385
Period size: 55 Copynumber: 17.3 Consensus size: 55
9008 TCCGCTTTTT
9018 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
9073 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
9128 AGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
9183 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA--TTTTCC
* * *
9239 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*** *
9295 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCCTTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
9350 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
9405 AATCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
*** *
9461 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCCTTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTCC
* *
9516 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
9571 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
9626 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
9681 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
9736 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
*
9791 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * * * *
9846 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* * *
9901 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-T
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
* *
9956 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
9974 TACAATTTAT
Statistics
Matches: 839, Mismatches: 47, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
54 7 0.01
55 673 0.80
56 157 0.19
57 2 0.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:9261 original size:27 final size:26
Alignment explanation
Indices: 9175--9261 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
9165 AAGTTGGTGG
9175 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
9201 CACCTCTCAAAG-CCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCC-CA-AAG-AGCAGGA
9230 CACCTTTTCAGTCCCCAAAGAGCAGGA
1 CACC-TTTCAGTCCCCAAAGAGCAGGA
9257 CACCT
1 CACCT
9262 CTCAAAGCCC
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
26 11 0.24
27 10 0.22
28 8 0.18
29 10 0.22
30 6 0.13
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:9652 original size:26 final size:26
Alignment explanation
Indices: 9567--9707 Score: 70
Period size: 26 Copynumber: 5.2 Consensus size: 26
9557 TGGTGGCATT
9567 TTTCAGTCCTCAAAGAGCAGGACACC
1 TTTCAGTCCTCAAAGAGCAGGACACC
* * * ** **
9593 TTTCAAAGCCCACACAAGTTGGTGG-CATT
1 TTTC--AGTCCTCA-AAG-AGCAGGACACC
9622 TTTCAGTCCTCAAAGAGCAGGACACC
1 TTTCAGTCCTCAAAGAGCAGGACACC
* * * ** **
9648 TTTCAAAGCCCACACAAGTTGGTGG-CATT
1 TTTC--AGTCCTCA-AAG-AGCAGGACACC
9677 TTTCAGTCCTCAAAGAGCAGGACACC
1 TTTCAGTCCTCAAAGAGCAGGACACC
9703 TTTCA
1 TTTCA
9708 AAGCCCACAC
Statistics
Matches: 77, Mismatches: 28, Indels: 20
0.62 0.22 0.16
Matches are distributed among these distances:
25 6 0.08
26 23 0.30
27 12 0.16
28 12 0.16
29 18 0.23
30 6 0.08
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (26 bp):
TTTCAGTCCTCAAAGAGCAGGACACC
Found at i:9730 original size:165 final size:166
Alignment explanation
Indices: 9018--9973 Score: 1534
Period size: 165 Copynumber: 5.8 Consensus size: 166
9008 TCCGCTTTTT
*
9018 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAA
*
9082 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAACGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
9146 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
9183 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCCCAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCCTCAA
* *
9248 AGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
*
9313 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCC-TTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
9349 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAA
1 -AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
* *
9414 AGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
*
9479 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCC-TTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
9515 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAA
1 -AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAA
*
9580 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTTCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
**
9644 CACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTTC
130 CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
*
9681 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTT-CAGTCCTCAA
*
9745 AGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGA
65 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
9809 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
130 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * * *
9846 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
* * * * *
9911 GAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TACTCCTCAATGAGCAGGA
66 GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGA
9974 TACAATTTAT
Statistics
Matches: 745, Mismatches: 36, Indels: 20
0.93 0.04 0.02
Matches are distributed among these distances:
164 6 0.01
165 356 0.48
166 277 0.37
167 106 0.14
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (166 bp):
AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACTTTTCAGTCCTCAAA
GAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCCAGTCCTCAAAGAGCAGGAC
ACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:9901 original size:29 final size:29
Alignment explanation
Indices: 9754--9901 Score: 71
Period size: 29 Copynumber: 5.3 Consensus size: 29
9744 AAGAACAGGA
*
9754 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
* * * * * * *
9783 CA-TTTTC-CAGTCCTCA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
9809 CACCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCT-TTCAAAGCCCACACAAGTGGGTGG
** * * *
9838 CACCTTTC-ATTCCC-CA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
9864 CACTTTTCAAAGCCCACACAAGTGGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
9893 CACCTTTCA
1 CACCTTTCA
9902 GTCCTCAAAG
Statistics
Matches: 78, Mismatches: 29, Indels: 24
0.60 0.22 0.18
Matches are distributed among these distances:
26 17 0.22
27 15 0.19
28 22 0.28
29 24 0.31
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTGGGTGG
Found at i:10576 original size:1 final size:1
Alignment explanation
Indices: 10570--10619 Score: 73
Period size: 1 Copynumber: 50.0 Consensus size: 1
10560 AAAGTGTTTG
***
10570 AAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10620 TTTTAATGTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.94, C:0.00, G:0.02, T:0.04
Consensus pattern (1 bp):
A
Found at i:10591 original size:19 final size:19
Alignment explanation
Indices: 10567--10619 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
10557 GATAAAGTGT
10567 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
10586 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
10605 ---AAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
10620 TTTTAATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
16 15 0.44
19 19 0.56
ACGTcount: A:0.89, C:0.00, G:0.04, T:0.08
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:10648 original size:21 final size:21
Alignment explanation
Indices: 10624--10680 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
10614 AAAAAATTTT
10624 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
10645 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
10666 AATGTATCGATACAT
1 AATGTATCGATACAT
10681 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:10760 original size:19 final size:19
Alignment explanation
Indices: 10736--10803 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
10726 AATTCAACAA
10736 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
10755 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
10770 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
10787 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
10804 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:10775 original size:13 final size:13
Alignment explanation
Indices: 10757--10781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10747 ACATAAGTTT
10757 TGTATCGATACAA
1 TGTATCGATACAA
10770 TGTATCGATACA
1 TGTATCGATACA
10782 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10779 original size:32 final size:32
Alignment explanation
Indices: 10738--10800 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10728 TTCAACAATT
*
10738 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
10770 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
10801 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:10861 original size:13 final size:13
Alignment explanation
Indices: 10843--10868 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
10833 CATTTTTCTG
10843 TGTATCGATACAT
1 TGTATCGATACAT
10856 TGTATCGATACAT
1 TGTATCGATACAT
10869 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:10865 original size:33 final size:33
Alignment explanation
Indices: 10823--10889 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10813 GCCAAGGAAA
***
10823 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
10856 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
10889 T
1 T
10890 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:13410 original size:52 final size:52
Alignment explanation
Indices: 13337--13718 Score: 261
Period size: 52 Copynumber: 7.3 Consensus size: 52
13327 TTATTTTCGA
*
13337 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
13389 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
13441 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
* * *** * * *** **
13493 GAGGATACTCCAAC-CTCGTTATTTCATCG-GGGATACTCCAACCCCGTT--ACTTTC
1 GGGGATACTCCAACTC-CGGT-TTT-AT-GTTCAAAACACCAA--TTTTTCCACAATC
*
13547 GAGGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 --GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
13601 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
13653 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
*
13705 GAGGATACTCCAAC
1 GGGGATACTCCAAC
13719 CTCGTTATTT
Statistics
Matches: 257, Mismatches: 46, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
51 27 0.11
52 147 0.57
53 33 0.13
54 28 0.11
55 5 0.02
56 16 0.06
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATGTTCAAAACACCAATTTTTCCACAATC
Found at i:13490 original size:104 final size:103
Alignment explanation
Indices: 13337--13717 Score: 402
Period size: 104 Copynumber: 3.6 Consensus size: 103
13327 TTATTTTCGA
* * *
13337 GGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCCAA
13402 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
65 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
13441 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
* * * * ** * *
13504 AA-CCTCG--TTATTTCATCGGGGATACTCCAA--CCCCGTTACTTTC
63 AATCCTGGTTTTATTT--TC---AAAACGCCAATTTTCCTTTA--ATC
* * *
13547 GAGGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 --GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCC
13612 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
63 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
13653 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
13716 AA
63 AA
13718 CCTCGTTATT
Statistics
Matches: 226, Mismatches: 28, Indels: 46
0.75 0.09 0.15
Matches are distributed among these distances:
101 6 0.03
102 4 0.02
103 6 0.03
104 91 0.40
105 26 0.12
106 18 0.08
107 13 0.06
108 48 0.21
109 6 0.03
110 2 0.01
111 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (103 bp):
GGGGATACTCCAACTCCGATTTTATCTTAAAACACCAATTTTTCCACAATCGAGGATACTCCAAT
CCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
Found at i:13526 original size:28 final size:30
Alignment explanation
Indices: 13490--13562 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 30
13480 ATTTTTCACA
* *
13490 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
13518 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
13548 A--GGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
13563 TCCGGTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:13604 original size:212 final size:212
Alignment explanation
Indices: 13222--13785 Score: 1004
Period size: 212 Copynumber: 2.6 Consensus size: 212
13212 AATTCTCCAC
* * *
13222 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAATACCAATTTCTTCACAATCGGGGA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TTCACAATCGAGGA
* * *
13287 TACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAAC
62 TACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAAC
13351 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
127 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
13416 TCAAAACGCCAATTTTCCTTT
192 TCAAAACGCCAATTTTCCTTT
13437 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
13502 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
13567 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
131 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
13632 AACGCCAATTTTCCTTT
196 AACGCCAATTTTCCTTT
13649 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
* *
13714 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
*
13779 GCTTTAT
131 GTTTTAT
13786 TCCCAAAATA
Statistics
Matches: 339, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
211 28 0.08
212 280 0.83
215 31 0.09
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
AACGCCAATTTTCCTTT
Found at i:13738 original size:28 final size:28
Alignment explanation
Indices: 13702--13778 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
13692 ATTTTTCACA
* * *
13702 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
13730 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
13758 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
13779 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:14992 original size:30 final size:30
Alignment explanation
Indices: 14905--15083 Score: 175
Period size: 30 Copynumber: 6.0 Consensus size: 30
14895 TGTAGACTTT
* * * **
14905 AAAAGGGTTCCACGAAATCATGGACTTCAA
1 AAAAGGGTGCCACGAAGTTATGGACTTTGA
* * *
14935 AAAAAGGTGCCACGGAGTGATGGACTTTGA
1 AAAAGGGTGCCACGAAGTTATGGACTTTGA
*
14965 AAAAGGGTGCCACGGAGTTATGGACTTTGA
1 AAAAGGGTGCCACGAAGTTATGGACTTTGA
* * * *
14995 AAAAGAGTACCACGAAGTTGTTGACTTTG-
1 AAAAGGGTGCCACGAAGTTATGGACTTTGA
** *
15024 AAAAGGGTGCCATAAAGTTGTGGACTTTGA
1 AAAAGGGTGCCACGAAGTTATGGACTTTGA
15054 ATAAA-GGTGCCACTG-AGTTATGGACTTTGA
1 A-AAAGGGTGCCAC-GAAGTTATGGACTTTGA
15084 GAAGGTTACT
Statistics
Matches: 124, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.19
30 97 0.78
31 3 0.02
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.25
Consensus pattern (30 bp):
AAAAGGGTGCCACGAAGTTATGGACTTTGA
Found at i:15080 original size:59 final size:57
Alignment explanation
Indices: 14899--15088 Score: 177
Period size: 59 Copynumber: 3.2 Consensus size: 57
14889 TACAATTGTA
* * ** *
14899 GACTTT-AAAAGGGTTCCACGAAA-TCATGGACTTCAAAAAAAGGTGCCACGGAGTGATG
1 GACTTTGAAAAGGGTGCCAC-AAAGTTATGGACTT-TGAAAAAGGTGCCAC-GAGTTATG
** * * *
14957 GACTTTGAAAAAGGGTGCCACGGAGTTATGGACTTTGAAAAAGAGTACCACGAAGTTGTT
1 GACTTTG-AAAAGGGTGCCACAAAGTTATGGACTTTGAAAAAG-GTGCCACG-AGTTATG
* *
15017 GACTTTGAAAAGGGTGCCATAAAGTTGTGGACTTTGAATAAAGGTGCCACTGAGTTATG
1 GACTTTGAAAAGGGTGCCACAAAGTTATGGACTTTGAA-AAAGGTGCCAC-GAGTTATG
*
15076 GACTTTGAGAAGG
1 GACTTTGAAAAGG
15089 TTACTCTATT
Statistics
Matches: 107, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
58 6 0.06
59 58 0.54
60 43 0.40
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.25
Consensus pattern (57 bp):
GACTTTGAAAAGGGTGCCACAAAGTTATGGACTTTGAAAAAGGTGCCACGAGTTATG
Found at i:19752 original size:29 final size:29
Alignment explanation
Indices: 19710--19771 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
19700 CATTTGCTCG
19710 CCATCTCCCATTTGTCGACAAAAGGTCAA
1 CCATCTCCCATTTGTCGACAAAAGGTCAA
*
19739 CCATCTCCCATTTGTCGACAAAAGGTCAG
1 CCATCTCCCATTTGTCGACAAAAGGTCAA
19768 CCAT
1 CCAT
19772 GGATTGGACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.29, C:0.32, G:0.15, T:0.24
Consensus pattern (29 bp):
CCATCTCCCATTTGTCGACAAAAGGTCAA
Found at i:22357 original size:21 final size:22
Alignment explanation
Indices: 22297--22382 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
22287 AGTGATTTTA
* *
22297 TATCGATACATGAATAGTGATA
1 TATCGATACATGAACAGTGATG
**
22319 CGT-GAT-CTATGAACAGTGATG
1 TATCGATAC-ATGAACAGTGATG
22340 TATCGATACATGAA-AGTGATG
1 TATCGATACATGAACAGTGATG
22361 TATCGATACATGAACAGTGATG
1 TATCGATACATGAACAGTGATG
22383 AATAGTGATG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 36 0.67
22 16 0.30
23 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (22 bp):
TATCGATACATGAACAGTGATG
Found at i:22374 original size:43 final size:43
Alignment explanation
Indices: 22297--22382 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
22287 AGTGATTTTA
*
22297 TATCGATACATGAATAGTGATACGTGATCTATGAACAGTGATG
1 TATCGATACATGAATAGTGATACATGATCTATGAACAGTGATG
**
22340 TATCGATACATGAA-AGTGATGTATCGATAC-ATGAACAGTGATG
1 TATCGATACATGAATAGTGATACAT-GAT-CTATGAACAGTGATG
22383 AATAGTGATG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 7 0.18
43 30 0.79
44 1 0.03
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (43 bp):
TATCGATACATGAATAGTGATACATGATCTATGAACAGTGATG
Found at i:22389 original size:10 final size:10
Alignment explanation
Indices: 22370--22400 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
22360 GTATCGATAC
22370 ATGAACAGTG
1 ATGAACAGTG
*
22380 ATGAATAGTG
1 ATGAACAGTG
22390 ATGAACAGTG
1 ATGAACAGTG
22400 A
1 A
22401 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:22447 original size:19 final size:19
Alignment explanation
Indices: 22423--22459 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22413 GCTACTACCA
*
22423 ATGTATCGATACATATTTT
1 ATGTATCGATACAAATTTT
22442 ATGTATCGATACAAATTT
1 ATGTATCGATACAAATTT
22460 GGCTACTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACAAATTTT
Found at i:22488 original size:53 final size:53
Alignment explanation
Indices: 22424--22560 Score: 213
Period size: 53 Copynumber: 2.6 Consensus size: 53
22414 CTACTACCAA
*
22424 TGTATCGATACATATTTTATGTATCGATACAAATTTGGCTACTGCCAATG-AC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGTAC
* *
22476 TTGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTTCCAATGTAC
1 -TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGTAC
*
22530 TATATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
22561 TATGCAATCT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
53 62 0.81
54 15 0.19
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGTAC
Found at i:22593 original size:20 final size:20
Alignment explanation
Indices: 22548--22601 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
22538 TACATATTTG
*
22548 TGTGTATCGATACTATGCAA
1 TGTGTATCGATACTATGAAA
* *
22568 TCTGTATCGATAC-ATTTAAA
1 TGTGTATCGATACTA-TGAAA
22588 TGTGTATCGATACT
1 TGTGTATCGATACT
22602 TTTCAGGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTGTATCGATACTATGAAA
Found at i:22666 original size:21 final size:21
Alignment explanation
Indices: 22640--22680 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
22630 GTCAACCTTG
22640 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
22661 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
22681 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:25463 original size:51 final size:52
Alignment explanation
Indices: 25349--25473 Score: 153
Period size: 51 Copynumber: 2.4 Consensus size: 52
25339 ATAGATGCAT
* *
25349 TGAAGAATGTATCGATAAATTTGGATCAAAAACGCAGAATATATCAATACAA
1 TGAAAAATGTATCGATAAATTTGGATCAAAAACGCAGAATATATCAATAAAA
* * * * * * *
25401 TAAAAAATGTATCGATACATTTGGGTCAAAATC-TAGAATGTATCGATAAAA
1 TGAAAAATGTATCGATAAATTTGGATCAAAAACGCAGAATATATCAATAAAA
*
25452 TGAAAAATGTATCGATATATTT
1 TGAAAAATGTATCGATAAATTT
25474 TCTTTCCAAA
Statistics
Matches: 62, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
51 34 0.55
52 28 0.45
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.30
Consensus pattern (52 bp):
TGAAAAATGTATCGATAAATTTGGATCAAAAACGCAGAATATATCAATAAAA
Found at i:29360 original size:139 final size:140
Alignment explanation
Indices: 29110--29386 Score: 427
Period size: 139 Copynumber: 2.0 Consensus size: 140
29100 TGCTTACAAT
* * *
29110 TGTATCGATACATGCAGGTAAATTTTCATATTTCATGATATTTTCTTCCTTTGCCAAATGAGTTT
1 TGTATCGATACATGCAGGCAAATTTTCATATTTCATGACATTTTCTTCCTTTGCCAAATGAGGTT
*
29175 TTTGCATTATAAGTGATCAGGATTCATATCAAATCTCAATTGTCACA-ATCAAAACCAATCTTGA
66 TTTGCATCATAAGTGATCAGGATTCATATCAAATCTCAATTGTCACATATCAAAACCAATCTTGA
29239 TCATTTTTAA
131 TCATTTTTAA
*
29249 TGTATCGATACATGCAGGCAAATTTTCATATTTCATGACATTTTCTT-TTTCTGCCAAAT-ACGG
1 TGTATCGATACATGCAGGCAAATTTTCATATTTCATGACATTTTCTTCCTT-TGCCAAATGA-GG
* * *
29312 TTTTTGCATCATAAGTGATC-GAGATTCATTTCAAATCTCAATTGTCACATGTCAAAACTAATCT
64 TTTTTGCATCATAAGTGATCAG-GATTCATATCAAATCTCAATTGTCACATATCAAAACCAATCT
29376 TGATCATTTTT
128 TGATCATTTTT
29387 GAAGCTAAAG
Statistics
Matches: 126, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
138 4 0.03
139 99 0.79
140 23 0.18
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (140 bp):
TGTATCGATACATGCAGGCAAATTTTCATATTTCATGACATTTTCTTCCTTTGCCAAATGAGGTT
TTTGCATCATAAGTGATCAGGATTCATATCAAATCTCAATTGTCACATATCAAAACCAATCTTGA
TCATTTTTAA
Found at i:30336 original size:22 final size:22
Alignment explanation
Indices: 30308--30349 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
30298 ATAAGCTTAA
*
30308 GGATTTCACCAAAATTATCAAC
1 GGATTTCACCAAAATCATCAAC
30330 GGATTTCACCAAAATCATCA
1 GGATTTCACCAAAATCATCA
30350 TTTTGATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (22 bp):
GGATTTCACCAAAATCATCAAC
Found at i:40901 original size:20 final size:20
Alignment explanation
Indices: 40876--40929 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
40866 GTTTGAAGCA
*
40876 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
40896 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
*
40916 ATATATCGATACAA
1 ATGTATCGATACAA
40930 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:40983 original size:20 final size:19
Alignment explanation
Indices: 40958--41031 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 19
40948 CTGCCAGTTT
40958 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTG-G
* *
40978 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTG-G
*
40997 CATGTATCGTTAC-ATCTGG
1 CATGTATCGATACAAT-TGG
*
41016 CTGTGTATCGATACAA
1 C-ATGTATCGATACAA
41032 ATAAGGGTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.02
19 14 0.33
20 26 0.62
21 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (19 bp):
CATGTATCGATACAATTGG
Found at i:41002 original size:19 final size:20
Alignment explanation
Indices: 40958--41010 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
40948 CTGCCAGTTT
**
40958 CATGTATCGATACAATTGTG
1 CATGTATCGATACAATTGAA
*
40978 CATGTATTGATACAA-TGAA
1 CATGTATCGATACAATTGAA
*
40997 CATGTATCGTTACA
1 CATGTATCGATACA
41011 TCTGGCTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:46051 original size:20 final size:20
Alignment explanation
Indices: 46001--46051 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
45991 ATTTATAATT
*
46001 TATATAAATAAAATATAAAA
1 TATATAAATTAAATATAAAA
* *
46021 TATA-ATGATTAAATTTAAAA
1 TATATA-AATTAAATATAAAA
46041 TATATAAATTA
1 TATATAAATTA
46052 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 23 0.92
21 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
TATATAAATTAAATATAAAA
Found at i:46633 original size:15 final size:16
Alignment explanation
Indices: 46604--46646 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
46594 TTTAAAGTTT
*
46604 TAATATAAATTAAAAA
1 TAATATAAATAAAAAA
46620 TAATA-AAATAAAAAA
1 TAATATAAATAAAAAA
46635 TATATATTAAAT
1 TA-ATA-TAAAT
46647 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 11 0.48
16 8 0.35
18 4 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
TAATATAAATAAAAAA
Found at i:46704 original size:23 final size:21
Alignment explanation
Indices: 46664--46706 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
46654 TATTTCAATT
*
46664 AATAATATAATAATTTTAAAA
1 AATAATATAATAAATTTAAAA
46685 AATAATATTTAATAAATTTAAA
1 AATAATA--TAATAAATTTAAA
46707 TTTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
23 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AATAATATAATAAATTTAAAA
Found at i:48993 original size:2 final size:2
Alignment explanation
Indices: 48986--49033 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
48976 TAACCATCTA
*
48986 AT AT AT AT AT AT AT AT AT AT AT AT AT AG 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
49028 AT AT AT
1 AT AT AT
49034 GAATGTGTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51191 original size:13 final size:13
Alignment explanation
Indices: 51173--51198 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51163 CATTTTGGGA
51173 TGTATCGATACAT
1 TGTATCGATACAT
51186 TGTATCGATACAT
1 TGTATCGATACAT
51199 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:51195 original size:33 final size:32
Alignment explanation
Indices: 51153--51216 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
51143 TACAAGCCAA
*
51153 TGTATCGATACATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
51186 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
51217 AACAGTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:51355 original size:20 final size:20
Alignment explanation
Indices: 51332--51372 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
51322 CTGTGCAATC
*
51332 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTTCAAGG
*
51352 TGTATCGATACTTTTCAAGG
1 TGTATCGATACATTTCAAGG
51372 T
1 T
51373 TTTGACCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTCAAGG
Found at i:53799 original size:13 final size:13
Alignment explanation
Indices: 53781--53805 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53771 ATAAACCCTT
53781 TGTATCGATACAC
1 TGTATCGATACAC
53794 TGTATCGATACA
1 TGTATCGATACA
53806 GAGAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:54523 original size:13 final size:13
Alignment explanation
Indices: 54505--54530 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54495 TACAGCAAGT
54505 ATGTATCGATACA
1 ATGTATCGATACA
54518 ATGTATCGATACA
1 ATGTATCGATACA
54531 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:58290 original size:13 final size:13
Alignment explanation
Indices: 58272--58296 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58262 TTTTCCAGAT
58272 TGTATCGATACAA
1 TGTATCGATACAA
58285 TGTATCGATACA
1 TGTATCGATACA
58297 TTACTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:59164 original size:21 final size:21
Alignment explanation
Indices: 59139--59190 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
59129 TTGTATAAAT
59139 TTTGTATTAAAGGGAAGAACA
1 TTTGTATTAAAGGGAAGAACA
59160 TTTGTATTAAAGGGAAGAACA
1 TTTGTATTAAAGGGAAGAACA
59181 TTTGTATTAA
1 TTTGTATTAA
59191 GGGGGAGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (21 bp):
TTTGTATTAAAGGGAAGAACA
Found at i:60145 original size:13 final size:13
Alignment explanation
Indices: 60127--60152 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60117 TACAGCAAGT
60127 ATGTATCGATACA
1 ATGTATCGATACA
60140 ATGTATCGATACA
1 ATGTATCGATACA
60153 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:66790 original size:33 final size:32
Alignment explanation
Indices: 66753--66816 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
66743 TACAAGCCAA
* *
66753 TGTATCGATATATTTTGGGATGTATCGATACAT
1 TGTATCGATACATCTTGGG-TGTATCGATACAT
*
66786 TGTATCGATACATCTTGTGTGTATCGATACA
1 TGTATCGATACATCTTGGGTGTATCGATACA
66817 AACAGTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (32 bp):
TGTATCGATACATCTTGGGTGTATCGATACAT
Found at i:66791 original size:13 final size:13
Alignment explanation
Indices: 66773--66798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
66763 TATTTTGGGA
66773 TGTATCGATACAT
1 TGTATCGATACAT
66786 TGTATCGATACAT
1 TGTATCGATACAT
66799 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:66905 original size:20 final size:21
Alignment explanation
Indices: 66858--66910 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
66848 GCCAATGATC
*
66858 TGTATCGATACATTCTTTACA
1 TGTATCGATACATTCTGTACA
*
66879 AGTATCGATACATT-TGGT-CA
1 TGTATCGATACATTCT-GTACA
66899 TGTATCGATACA
1 TGTATCGATACA
66911 ATGTATAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTCTGTACA
Found at i:68876 original size:57 final size:57
Alignment explanation
Indices: 68770--68877 Score: 148
Period size: 57 Copynumber: 1.9 Consensus size: 57
68760 TTTAATTTTT
* *
68770 AAGCCTTTGACAATGGTAAGATAATAATTTTGGACCTTAGCAAATGGTTGAATTCTC
1 AAGCCTTTGACAATGGTAAGATAATAATTTTGGACCTCAGCAAACGGTTGAATTCTC
* *
68827 AAGCCTTT-AGCAATAGG-AAGATAATAATTTTGGACCTCGGTAAACGGTTGA
1 AAGCCTTTGA-CAAT-GGTAAGATAATAATTTTGGACCTCAGCAAACGGTTGA
68878 GGCATAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
56 1 0.02
57 42 0.93
58 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.31
Consensus pattern (57 bp):
AAGCCTTTGACAATGGTAAGATAATAATTTTGGACCTCAGCAAACGGTTGAATTCTC
Found at i:76100 original size:4 final size:4
Alignment explanation
Indices: 76091--76151 Score: 113
Period size: 4 Copynumber: 15.2 Consensus size: 4
76081 AGTTGTCATT
*
76091 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GACA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
76139 GAAA GAAA GAAA G
1 GAAA GAAA GAAA G
76152 CAACTGCAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:76265 original size:2 final size:2
Alignment explanation
Indices: 76258--76291 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
76248 TTAATCTTTG
76258 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
76292 TTCCAGATTG
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:77712 original size:2 final size:2
Alignment explanation
Indices: 77701--77729 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
77691 ATCCACCGCC
77701 TA TA TA -A 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
77730 AAAGGAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:79044 original size:12 final size:13
Alignment explanation
Indices: 79012--79056 Score: 56
Period size: 12 Copynumber: 3.4 Consensus size: 13
79002 TGAGTCTCGA
79012 AAAATAATAATCAT
1 AAAATAATAAT-AT
79026 AAGAATAATAATAT
1 AA-AATAATAATAT
*
79040 -AAATAATAATAA
1 AAAATAATAATAT
79052 AAAAT
1 AAAAT
79057 GACTTGGCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.36
13 5 0.18
14 4 0.14
15 9 0.32
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AAAATAATAATAT
Found at i:81081 original size:14 final size:14
Alignment explanation
Indices: 81059--81099 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
81049 TATTATTTAA
81059 TATTATAAAAATAT
1 TATTATAAAAATAT
*
81073 TATT-TTAAAATAT
1 TATTATAAAAATAT
*
81086 TAATATAAAAATAT
1 TATTATAAAAATAT
81100 AAATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATTATAAAAATAT
Found at i:81118 original size:15 final size:16
Alignment explanation
Indices: 81098--81128 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
81088 ATATAAAAAT
81098 ATAAAT-ATTTTAATA
1 ATAAATAATTTTAATA
81113 ATAAATAATTTTAATA
1 ATAAATAATTTTAATA
81129 TTTTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATAATTTTAATA
Found at i:81159 original size:27 final size:24
Alignment explanation
Indices: 81017--81147 Score: 103
Period size: 24 Copynumber: 5.6 Consensus size: 24
81007 GTAATTAATA
* *
81017 AATATTAATATAA-TTTATTATTTT
1 AATAATAA-ATAATTTTAATATTTT
* *
81041 AATAA-AAATATTATTTAATATTAT
1 AATAATAAATAAT-TTTAATATTTT
* * * *
81065 AA-AA-ATATTATTTTAAAATATT
1 AATAATAAATAATTTTAATATTTT
* *
81087 AAT-ATAAA-AATATAAATATTTT
1 AATAATAAATAATTTTAATATTTT
81109 AATAATAAATAATTTTAATATTTT
1 AATAATAAATAATTTTAATATTTT
*
81133 AATAATCAATAATTT
1 AATAATAAATAATTT
81148 GATATTTATT
Statistics
Matches: 82, Mismatches: 19, Indels: 12
0.73 0.17 0.11
Matches are distributed among these distances:
22 26 0.32
23 15 0.18
24 41 0.50
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (24 bp):
AATAATAAATAATTTTAATATTTT
Found at i:81367 original size:7 final size:7
Alignment explanation
Indices: 81339--81402 Score: 51
Period size: 7 Copynumber: 9.1 Consensus size: 7
81329 TCCCTTTGAA
81339 ATTATAT
1 ATTATAT
*
81346 AATATAT
1 ATTATAT
81353 CATT-TAT
1 -ATTATAT
81360 ATTATAT
1 ATTATAT
*
81367 ATTACAT
1 ATTATAT
*
81374 ATTATACA
1 ATTATA-T
81382 ATTAT-T
1 ATTATAT
*
81388 TTTATAT
1 ATTATAT
*
81395 AATATAT
1 ATTATAT
81402 A
1 A
81403 AATAATTATT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
6 7 0.16
7 30 0.68
8 7 0.16
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (7 bp):
ATTATAT
Found at i:85816 original size:14 final size:14
Alignment explanation
Indices: 85797--85825 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
85787 TTTCTTACAA
85797 ATATTCATATAACC
1 ATATTCATATAACC
85811 ATATTCATATAACC
1 ATATTCATATAACC
85825 A
1 A
85826 GAATTTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
ATATTCATATAACC
Found at i:88484 original size:32 final size:32
Alignment explanation
Indices: 88448--88508 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
88438 GTGAGTCAAG
88448 ACCAGGCTCATCATCGAATGATCCTGTAAGTT
1 ACCAGGCTCATCATCGAATGATCCTGTAAGTT
* * *
88480 ACCAGGTTCATCATCGTATGATCTTGTAA
1 ACCAGGCTCATCATCGAATGATCCTGTAA
88509 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (32 bp):
ACCAGGCTCATCATCGAATGATCCTGTAAGTT
Found at i:90077 original size:2 final size:2
Alignment explanation
Indices: 90072--90101 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
90062 AAAAAAAAAA
90072 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
90102 GGCTTAAGCT
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:90903 original size:2 final size:2
Alignment explanation
Indices: 90896--90920 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
90886 TTTAGTAAAA
90896 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
90921 ATTTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:92174 original size:27 final size:28
Alignment explanation
Indices: 92109--92180 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
92099 ACACGATATG
92109 AAAATAATTAAAATATAATACAACATAA
1 AAAATAATTAAAATATAATACAACATAA
**
92137 AAAATAATTAAAATATAATATGACAT-A
1 AAAATAATTAAAATATAATACAACATAA
92164 AAAATAATTAAAATATA
1 AAAATAATTAAAATATA
92181 CCATGATATG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
27 18 0.43
28 24 0.57
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (28 bp):
AAAATAATTAAAATATAATACAACATAA
Found at i:92186 original size:27 final size:28
Alignment explanation
Indices: 92109--92198 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 28
92099 ACACGATATG
**
92109 AAAATAATTAAAATATAATACAACATAA
1 AAAATAATTAAAATATAATATGACATAA
92137 AAAATAATTAAAATATAATATGACAT-A
1 AAAATAATTAAAATATAATATGACATAA
** *
92164 AAAATAATTAAAATATACCATGATATGAA
1 AAAATAATTAAAATATAATATGACAT-AA
92193 AAAATA
1 AAAATA
92199 GTAAGATCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (28 bp):
AAAATAATTAAAATATAATATGACATAA
Found at i:92194 original size:28 final size:28
Alignment explanation
Indices: 92109--92195 Score: 113
Period size: 28 Copynumber: 3.1 Consensus size: 28
92099 ACACGATATG
** *
92109 AAAATAATTAAAATATAATACAACATAA
1 AAAATAATTAAAATATAATATGACATGA
92137 AAAATAATTAAAATATAATATGACAT-A
1 AAAATAATTAAAATATAATATGACATGA
** *
92164 AAAATAATTAAAATATACCATGATATGA
1 AAAATAATTAAAATATAATATGACATGA
92192 AAAA
1 AAAA
92196 ATAGTAAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
27 24 0.45
28 29 0.55
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.26
Consensus pattern (28 bp):
AAAATAATTAAAATATAATATGACATGA
Found at i:92570 original size:22 final size:22
Alignment explanation
Indices: 92544--92589 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
92534 TCATTTAATT
92544 ATCATTGATGAGAAAAAAGTTA
1 ATCATTGATGAGAAAAAAGTTA
*
92566 ATCATTGATGAGAAAAAATTTA
1 ATCATTGATGAGAAAAAAGTTA
92588 AT
1 AT
92590 TTTATGCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.15, T:0.30
Consensus pattern (22 bp):
ATCATTGATGAGAAAAAAGTTA
Found at i:93421 original size:25 final size:28
Alignment explanation
Indices: 93392--93444 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 28
93382 ATACGTCATT
*
93392 AATACAATATGA-A-AAAAATA-ATTAA
1 AATACAACATGATATAAAAATATATTAA
93417 AATACAACATGATATAAAAATATATTAA
1 AATACAACATGATATAAAAATATATTAA
93445 CACAATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 11 0.46
26 1 0.04
27 7 0.29
28 5 0.21
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (28 bp):
AATACAACATGATATAAAAATATATTAA
Found at i:94520 original size:53 final size:53
Alignment explanation
Indices: 94455--94558 Score: 190
Period size: 53 Copynumber: 2.0 Consensus size: 53
94445 AAATATCAAA
94455 GTATTTTCTTCATTAGATAAGTACAGAACTTTAGAGAGAATCTTAGAATAAAG
1 GTATTTTCTTCATTAGATAAGTACAGAACTTTAGAGAGAATCTTAGAATAAAG
* *
94508 GTATTTTTTTCATTAGATAAGTACAGCACTTTAGAGAGAATCTTAGAATAA
1 GTATTTTCTTCATTAGATAAGTACAGAACTTTAGAGAGAATCTTAGAATAA
94559 CAATTTCCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (53 bp):
GTATTTTCTTCATTAGATAAGTACAGAACTTTAGAGAGAATCTTAGAATAAAG
Found at i:96043 original size:12 final size:12
Alignment explanation
Indices: 96023--96055 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
96013 GCGATTTATT
96023 TTTTAAAAAT-A
1 TTTTAAAAATAA
96034 TTTATAAAAATAA
1 TTT-TAAAAATAA
96047 TTTTAAAAA
1 TTTTAAAAA
96056 ATATAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.15
12 13 0.65
13 4 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTTTAAAAATAA
Found at i:97198 original size:2 final size:2
Alignment explanation
Indices: 97186--97224 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
97176 GGAAATAAGC
* *
97186 TA TA CA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
97225 GAAAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:97809 original size:21 final size:22
Alignment explanation
Indices: 97769--97810 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
97759 TTGGTTGGAT
97769 AAAATTTCTGTAAGTAGAGATC
1 AAAATTTCTGTAAGTAGAGATC
* *
97791 AAAATTTTTTTAA-TAGAGAT
1 AAAATTTCTGTAAGTAGAGAT
97811 AAACAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.05, G:0.14, T:0.38
Consensus pattern (22 bp):
AAAATTTCTGTAAGTAGAGATC
Found at i:98630 original size:3 final size:3
Alignment explanation
Indices: 98622--98662 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
98612 CTATAAGTTT
98622 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
98663 CAGCAAGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:98975 original size:49 final size:49
Alignment explanation
Indices: 98903--99004 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
98893 AATAATAAAA
*
98903 GTCTAAACTAGAAGCATGCATGCAAACATCATGTAATTTAATTAATCAG
1 GTCTAAACTAGAAGCATGCATGCAAACATCATGTAATTTAATTAATCAC
* *
98952 GTCTACACTAGAAGCATGCATGCAAACATCGTGTAATTTAATTAATCAC
1 GTCTAAACTAGAAGCATGCATGCAAACATCATGTAATTTAATTAATCAC
99001 GTCT
1 GTCT
99005 TATACCAAAC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (49 bp):
GTCTAAACTAGAAGCATGCATGCAAACATCATGTAATTTAATTAATCAC
Found at i:99681 original size:35 final size:36
Alignment explanation
Indices: 99642--99713 Score: 85
Period size: 35 Copynumber: 2.0 Consensus size: 36
99632 TTAAATTATG
99642 TGTATATATAATAAATAATTAAAA-A-ATACTAAAAT
1 TGTATATATAATAAATAA-TAAAATATATACTAAAAT
* ** *
99677 TGTATTTATGTTAAATAATAAAATATATATTAAAAT
1 TGTATATATAATAAATAATAAAATATATACTAAAAT
99713 T
1 T
99714 ATAGTTAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
34 5 0.16
35 16 0.52
36 10 0.32
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (36 bp):
TGTATATATAATAAATAATAAAATATATACTAAAAT
Found at i:99726 original size:36 final size:34
Alignment explanation
Indices: 99653--99733 Score: 99
Period size: 36 Copynumber: 2.3 Consensus size: 34
99643 GTATATATAA
* * *
99653 TAAATAATTAAAAAATACTAAAATTGTATTTATGT
1 TAAATAA-TAAAAAATACTAAAATTATAGTTAGGT
*
99688 TAAATAATAAAATATATATTAAAATTATAGTTAGGT
1 TAAATAATAAAA-A-ATACTAAAATTATAGTTAGGT
99724 TAAATAATAA
1 TAAATAATAA
99734 TAATTAAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 5 0.12
35 8 0.20
36 27 0.68
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.38
Consensus pattern (34 bp):
TAAATAATAAAAAATACTAAAATTATAGTTAGGT
Found at i:99968 original size:12 final size:12
Alignment explanation
Indices: 99951--99975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
99941 ATAACAATAT
99951 AAAAAAGATCAC
1 AAAAAAGATCAC
99963 AAAAAAGATCAC
1 AAAAAAGATCAC
99975 A
1 A
99976 TGGGTAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAAGATCAC
Found at i:101639 original size:14 final size:14
Alignment explanation
Indices: 101620--101648 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
101610 ATGAAGAATC
101620 ATTACTAAAAAACG
1 ATTACTAAAAAACG
101634 ATTACTAAAAAACG
1 ATTACTAAAAAACG
101648 A
1 A
101649 ATGTCTCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ATTACTAAAAAACG
Found at i:102771 original size:20 final size:20
Alignment explanation
Indices: 102723--102799 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
102713 GATACACCTT
*
102723 CAAATGTATCGATACATAATG
1 CAAATGTATCGATACATAA-C
* *
102744 CACA-GTATCGATACATGAC
1 CAAATGTATCGATACATAAC
* *
102763 CAAATGTATCGATACTTACAA
1 CAAATGTATCGATACATA-AC
*
102784 AAAATGTATCGATACA
1 CAAATGTATCGATACA
102800 GGTGATTGGC
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
19 3 0.07
20 24 0.53
21 18 0.40
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
CAAATGTATCGATACATAAC
Found at i:102901 original size:33 final size:32
Alignment explanation
Indices: 102841--102902 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
102831 CTTAACTGTT
* *
102841 TGTATCGATACACACAAGATGTATCGATATAA
1 TGTATAGATACACACAAAATGTATCGATATAA
*
102873 TGTATAGATACATCCCAAAATGTATCGATA
1 TGTATAGATACA-CACAAAATGTATCGATA
102903 CATTGGCTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATAGATACACACAAAATGTATCGATATAA
Found at i:104288 original size:49 final size:49
Alignment explanation
Indices: 104218--104758 Score: 265
Period size: 49 Copynumber: 11.3 Consensus size: 49
104208 GCATGACCCT
* * *
104218 AAAGACTGAGTTTTAGTTAGTTTTGATAGAAAGTACAAAACTAACTCTA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTCTA
* * * *
104267 AAAAACTCGATTTTGGTTAGTTTTGATGGAAAGTACAAAACTAACTTTGA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTCT-A
*** * * * *
104317 AAA-ACTCAATTTCAATTGATTTTTGAT-GAATAGTAAAAAACTAGCTTTA
1 AAAGACTCAATTTTGGTT-AGTTTTGATAGAA-AGTACAAAACTAACTCTA
*** * * * * *
104366 GAAA-ACTTTGTTTTAGTAAGTTTTGAT-GAAAGGTAAAAAACTTACCCTA
1 -AAAGACTCAATTTTGGTTAGTTTTGATAGAAA-GTACAAAACTAACTCTA
* * ** *
104415 AAAGGCAT-AACTTTGGTTAGTTTTGAT-GATAAAAACAAAAATAA-TCCTA
1 AAAGAC-TCAATTTTGGTTAGTTTTGATAGA-AAGTACAAAACTAACT-CTA
* * * * *
104464 AAAGACTCAATTTTAGTTAGTTTTGACAAAAAATATAAAACTAA-TCTTA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTC-TA
* * * * *
104513 AAAAACTTAATTTT-ATTAATTTTAATAGAAAGTACAAAACTAACTCTA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTCTA
* * * *
104561 AAAAACTAAATTTT-G--A----CGA-A-ATAG-ACAAAAGC-AAC-CTTA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAA-CTAACTC-TA
* * *
104600 AAAGACTCGATTTTGG-T-G-TTTAATAGAAAGTATAAAACTAAC-CGTA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTC-TA
* * *
104646 AAAGACTTAATTTTGGTT-GATTTTGATA-ATAAGTAAAAAAACTAACCCTA
1 AAAGACTCAATTTTGGTTAG-TTTTGATAGA-AAGT-ACAAAACTAACTCTA
** * * *
104696 AAAGACTTGATTTTGGTTAGTTTTGATAAAAAGTACAAAATTTAC-CTTA
1 AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTC-TA
*
104745 AAAGACTCGATTTT
1 AAAGACTCAATTTT
104759 CTCATGAAAA
Statistics
Matches: 383, Mismatches: 76, Indels: 66
0.73 0.14 0.13
Matches are distributed among these distances:
38 1 0.00
39 22 0.06
40 5 0.01
41 1 0.00
42 1 0.00
43 1 0.00
44 1 0.00
45 4 0.01
46 26 0.07
47 2 0.01
48 45 0.12
49 188 0.49
50 83 0.22
51 3 0.01
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (49 bp):
AAAGACTCAATTTTGGTTAGTTTTGATAGAAAGTACAAAACTAACTCTA
Found at i:104698 original size:50 final size:50
Alignment explanation
Indices: 104633--104735 Score: 154
Period size: 50 Copynumber: 2.1 Consensus size: 50
104623 TAGAAAGTAT
* *
104633 AAAACTAACCGTAAAAGACTTAATTTTGGTT-GATTTTGATAATAAGTAAA
1 AAAACTAACCCTAAAAGACTTAATTTTGGTTAG-TTTTGATAAAAAGTAAA
* *
104683 AAAACTAACCCTAAAAGACTTGATTTTGGTTAGTTTTGATAAAAAGTACA
1 AAAACTAACCCTAAAAGACTTAATTTTGGTTAGTTTTGATAAAAAGTAAA
104733 AAA
1 AAA
104736 TTTACCTTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
50 47 0.98
51 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.32
Consensus pattern (50 bp):
AAAACTAACCCTAAAAGACTTAATTTTGGTTAGTTTTGATAAAAAGTAAA
Found at i:106184 original size:13 final size:13
Alignment explanation
Indices: 106166--106192 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
106156 ATACACCAAG
106166 AATGTATCGATAC
1 AATGTATCGATAC
106179 AATGTATCGATAC
1 AATGTATCGATAC
106192 A
1 A
106193 CCAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:106190 original size:32 final size:34
Alignment explanation
Indices: 106149--106213 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 34
106139 TAGCCAAACT
*
106149 TGTATCGATACACC-AAGAA-TGTATCGATACAA
1 TGTATCGATACACCAAAAAATTGTATCGATACAA
106181 TGTATCGATACACCAAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAAATTGTATCGATACA
106214 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 14 0.47
33 4 0.13
34 12 0.40
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (34 bp):
TGTATCGATACACCAAAAAATTGTATCGATACAA
Found at i:107824 original size:15 final size:14
Alignment explanation
Indices: 107797--107823 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
107787 TTGCATGAGT
107797 TTTGAATTTTTTTC
1 TTTGAATTTTTTTC
107811 TTTGAATTTTTTT
1 TTTGAATTTTTTT
107824 TATTTTTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTGAATTTTTTTC
Found at i:108287 original size:7 final size:7
Alignment explanation
Indices: 108275--108324 Score: 59
Period size: 7 Copynumber: 7.1 Consensus size: 7
108265 AGAAAAAAAG
108275 AAAGAAA
1 AAAGAAA
108282 AAAGAAAA
1 AAAG-AAA
108290 AAAGAAA
1 AAAGAAA
108297 AAAGAAA
1 AAAGAAA
108304 AAA-AAA
1 AAAGAAA
*
108310 GGAA-AAA
1 -AAAGAAA
108317 AAAGAAA
1 AAAGAAA
108324 A
1 A
108325 CTAAGGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 5 0.13
7 26 0.68
8 7 0.18
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:108289 original size:19 final size:18
Alignment explanation
Indices: 108265--108324 Score: 86
Period size: 17 Copynumber: 3.3 Consensus size: 18
108255 AATAATAGAG
108265 AGAAAAAAAGAAAGAAAAA
1 AGAAAAAAAGAAA-AAAAA
*
108284 AGAAAAAAAGAAAAAAGA
1 AGAAAAAAAGAAAAAAAA
*
108302 A-AAAAAAAGGAAAAAAA
1 AGAAAAAAAGAAAAAAAA
108319 AGAAAA
1 AGAAAA
108325 CTAAGGTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.41
18 9 0.24
19 13 0.35
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAGAAAAAAAA
Found at i:108295 original size:15 final size:15
Alignment explanation
Indices: 108270--108307 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
108260 TAGAGAGAAA
108270 AAAAGAAAGAAAAAAG
1 AAAA-AAAGAAAAAAG
108286 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
108301 AAAAAAA
1 AAAAAAA
108308 AAGGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:108299 original size:27 final size:28
Alignment explanation
Indices: 108265--108324 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 28
108255 AATAATAGAG
108265 AGAAAAAAAGAAAGAAAAAA-G-AAAAAA
1 AGAAAAAAAGAAA-AAAAAAGGAAAAAAA
108292 AG-AAAAAAGAAAAAAAAAGGAAAAAAA
1 AGAAAAAAAGAAAAAAAAAGGAAAAAAA
108319 AGAAAA
1 AGAAAA
108325 CTAAGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 6 0.20
26 11 0.37
27 10 0.33
28 3 0.10
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (28 bp):
AGAAAAAAAGAAAAAAAAAGGAAAAAAA
Found at i:108301 original size:26 final size:27
Alignment explanation
Indices: 108268--108324 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
108258 AATAGAGAGA
108268 AAAAAAGAAAGAAAAAA-G-AAAAAAAG
1 AAAAAAGAAA-AAAAAAGGAAAAAAAAG
108294 AAAAAAGAAAAAAAAAGGAAAAAAAAG
1 AAAAAAGAAAAAAAAAGGAAAAAAAAG
108321 AAAA
1 AAAA
108325 CTAAGGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
25 6 0.21
26 11 0.38
27 12 0.41
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (27 bp):
AAAAAAGAAAAAAAAAGGAAAAAAAAG
Found at i:108942 original size:168 final size:168
Alignment explanation
Indices: 108663--108966 Score: 502
Period size: 168 Copynumber: 1.8 Consensus size: 168
108653 TTTGTAAACA
* * *
108663 TAGGGACTAAATTGCAAAAAACCCAAACACCTTTCTTTGAATGATCCATGCTTGGCCGAATATTG
1 TAGGGACTAAATTGCAAAAAACCCAAAAACCTTTCTTTGAAGGATCCATACTTGGCCGAATATTG
* * *
108728 ATGAGGATTTTTGCCATGTTTGGTTGTTGATTCCAAGCTGATTTCATATCTTGATCA-TGTATTT
66 ATAAGGATTTTTGCCAAGTTTGGTTGTTGATTCCAAGCTAATTTCATATCTTGAT-AGTGTATTT
108792 TTATGTTATTTGGGATTAAAAATGCAAATTTAACAAGTT
130 TTATGTTATTTGGGATTAAAAATGCAAATTTAACAAGTT
* * *
108831 TAGGGACTAAATTGCAAAAAACCTAAAAACTTTTCTTTGAAGGATCCATACTTGGTCGAATATTG
1 TAGGGACTAAATTGCAAAAAACCCAAAAACCTTTCTTTGAAGGATCCATACTTGGCCGAATATTG
*
108896 ATAAGGATTTTTGCCAAGTTTGGTTGTTGATTCCAAGCTAATTTCATGTCTTGATAGTGTATTTT
66 ATAAGGATTTTTGCCAAGTTTGGTTGTTGATTCCAAGCTAATTTCATATCTTGATAGTGTATTTT
108961 TATGTT
131 TATGTT
108967 GTTTTTGTTG
Statistics
Matches: 125, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
167 1 0.01
168 124 0.99
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (168 bp):
TAGGGACTAAATTGCAAAAAACCCAAAAACCTTTCTTTGAAGGATCCATACTTGGCCGAATATTG
ATAAGGATTTTTGCCAAGTTTGGTTGTTGATTCCAAGCTAATTTCATATCTTGATAGTGTATTTT
TATGTTATTTGGGATTAAAAATGCAAATTTAACAAGTT
Found at i:109161 original size:54 final size:54
Alignment explanation
Indices: 109079--109187 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
109069 TTTTGTATGA
109079 TACATATTTAATATATTCAATATGTAATTTTATGAATTTCCATGAAACTTGGTG
1 TACATATTTAATATATTCAATATGTAATTTTATGAATTTCCATGAAACTTGGTG
109133 TACATATTTAATATATTCAATATGTAATTTTATGAATTTCCATGAAACTTGGTG
1 TACATATTTAATATATTCAATATGTAATTTTATGAATTTCCATGAAACTTGGTG
109187 T
1 T
109188 TTTTTTATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (54 bp):
TACATATTTAATATATTCAATATGTAATTTTATGAATTTCCATGAAACTTGGTG
Found at i:109412 original size:8 final size:8
Alignment explanation
Indices: 109399--109433 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
109389 TGAAATTTTC
109399 AAAAATAA
1 AAAAATAA
109407 AAAAATAA
1 AAAAATAA
109415 AAAAATAA
1 AAAAATAA
109423 AATAAA-AA
1 AA-AAATAA
109431 AAA
1 AAA
109434 TTCTTTTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 1 0.04
8 22 0.85
9 3 0.12
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:109424 original size:13 final size:13
Alignment explanation
Indices: 109408--109432 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109398 CAAAAATAAA
109408 AAAATAAAAAAAT
1 AAAATAAAAAAAT
109421 AAAATAAAAAAA
1 AAAATAAAAAAA
109433 ATTCTTTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATAAAAAAAT
Found at i:113690 original size:58 final size:58
Alignment explanation
Indices: 113619--113930 Score: 271
Period size: 58 Copynumber: 5.4 Consensus size: 58
113609 TAAGTTATGC
* *
113619 AAAATAACCTAAATGACTTTAAATGCATAAAAATTACATAATAGGCCCTATATCATGG
1 AAAATAACCTAAATGACTTTAAATGCATAAAAATTACATAATAGTCCCTAAATCATGG
* * *
113677 AAAATAACTTAAATGAACTTAAAATGCATAAAAATTACATAA-AGTCCCTAAATAATGG
1 AAAATAACCTAAATG-ACTTTAAATGCATAAAAATTACATAATAGTCCCTAAATCATGG
** * * *
113735 AAAATAACCTAAATGACCCTAAAAGATATAAAAATTACA-AATAGTCCCTAAATCATGA
1 AAAATAACCTAAATGACTTTAAATG-CATAAAAATTACATAATAGTCCCTAAATCATGG
* * * * *
113793 AAAATTACCTAAA--AATCCTAGATGCA-ATAAAATTACA-AGATAGTCCCTAAATCATGA
1 AAAATAACCTAAATGACT-TTAAATGCATA-AAAATTACATA-ATAGTCCCTAAATCATGG
* ** * * * *
113850 AAAATGACCTAAAT-ACCTAAAAATGCA-AGAAAATTACGTAATAATCCCTAGATCATAG
1 AAAATAACCTAAATGA-CTTTAAATGCATA-AAAATTACATAATAGTCCCTAAATCATGG
* * * *
113908 AAATTGACCTAAATAACCTTAAA
1 AAAATAACCTAAATGACTTTAAA
113931 ATTTATGGAG
Statistics
Matches: 210, Mismatches: 34, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
55 1 0.00
56 12 0.06
57 43 0.20
58 126 0.60
59 28 0.13
ACGTcount: A:0.51, C:0.16, G:0.09, T:0.25
Consensus pattern (58 bp):
AAAATAACCTAAATGACTTTAAATGCATAAAAATTACATAATAGTCCCTAAATCATGG
Found at i:113728 original size:29 final size:28
Alignment explanation
Indices: 113638--113854 Score: 95
Period size: 29 Copynumber: 7.5 Consensus size: 28
113628 TAAATGACTT
*
113638 TAAATGCAT-AAAAATTACATAATAGGCCC
1 TAAAT-CATGAAAAATTACATAA-AGACCC
* * * * * *
113667 TATATCATGGAAAATAACTTAAATGAACT
1 TAAATCATGAAAAATTACATAAA-GACCC
*
113696 TAAAATGCAT-AAAAATTACATAAAGTCCC
1 T-AAAT-CATGAAAAATTACATAAAGACCC
* * * *
113725 TAAATAATGGAAAATAACCTAAATGACCC
1 TAAATCATGAAAAATTACATAAA-GACCC
** * *
113754 TAAAAGATATAAAAATTACA-AATAGTCCC
1 TAAATCAT-GAAAAATTACATAA-AGACCC
* * *
113783 TAAATCATGAAAAATTACCTAAAAATCC
1 TAAATCATGAAAAATTACATAAAGACCC
* *
113811 TAGATGCA--ATAAAATTACA-AGATAGTCCC
1 TAAAT-CATGA-AAAATTACATA-A-AGACCC
113840 TAAATCATGAAAAAT
1 TAAATCATGAAAAAT
113855 GACCTAAATA
Statistics
Matches: 134, Mismatches: 39, Indels: 30
0.66 0.19 0.15
Matches are distributed among these distances:
27 4 0.03
28 46 0.34
29 58 0.43
30 23 0.17
31 3 0.02
ACGTcount: A:0.51, C:0.15, G:0.09, T:0.25
Consensus pattern (28 bp):
TAAATCATGAAAAATTACATAAAGACCC
Found at i:113812 original size:28 final size:28
Alignment explanation
Indices: 113781--113870 Score: 64
Period size: 28 Copynumber: 3.2 Consensus size: 28
113771 ACAAATAGTC
113781 CCTAAATCATGAAAAATTACCTAAAAAT
1 CCTAAATCATGAAAAATTACCTAAAAAT
* *
113809 CCTAGATGCA--ATAAAATTA-C-AAGATAGT
1 CCTAAAT-CATGA-AAAATTACCTAA-A-AAT
* *
113837 CCCTAAATCATGAAAAATGACCTAAATA-
1 -CCTAAATCATGAAAAATTACCTAAAAAT
113865 CCTAAA
1 CCTAAA
113871 AATGCAAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 19
0.65 0.08 0.26
Matches are distributed among these distances:
26 2 0.04
27 9 0.19
28 17 0.36
29 14 0.30
30 3 0.06
31 2 0.04
ACGTcount: A:0.50, C:0.19, G:0.08, T:0.23
Consensus pattern (28 bp):
CCTAAATCATGAAAAATTACCTAAAAAT
Found at i:113898 original size:115 final size:114
Alignment explanation
Indices: 113707--113920 Score: 260
Period size: 115 Copynumber: 1.9 Consensus size: 114
113697 AAAATGCATA
*
113707 AAAATTACATAAAGTCCCTAAATAATGGAAAATAACCTAAATGACCCTAAAAGATATAAAAATTA
1 AAAATTACATAAAGTCCCTAAATAATGAAAAATAACCTAAATGACCCTAAAAGATATAAAAATTA
*
113772 CAAATAGTCCCTAAATCATGAAAAATT-ACCTAAAAATCCTAGATGCAAT
66 CAAATAATCCCTAAATCAT-AAAAATTGACCTAAAAATCCTAGATGCAAT
* *
113821 AAAATTACA-AGATAGTCCCTAAATCATGAAAAATGACCTAAAT-A-CCTAAAA-ATGCA-AGAA
1 AAAATTACATA-A-AGTCCCTAAATAATGAAAAATAACCTAAATGACCCTAAAAGAT--ATA-AA
* * *
113881 AATTACGTAATAATCCCTAGATCATAGAAATTGACCTAAA
61 AATTAC-AAATAATCCCTAAATCATAAAAATTGACCTAAA
113921 TAACCTTAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
112 2 0.02
113 9 0.10
114 26 0.30
115 49 0.57
ACGTcount: A:0.51, C:0.17, G:0.09, T:0.23
Consensus pattern (114 bp):
AAAATTACATAAAGTCCCTAAATAATGAAAAATAACCTAAATGACCCTAAAAGATATAAAAATTA
CAAATAATCCCTAAATCATAAAAATTGACCTAAAAATCCTAGATGCAAT
Found at i:117550 original size:78 final size:78
Alignment explanation
Indices: 117415--117565 Score: 239
Period size: 78 Copynumber: 1.9 Consensus size: 78
117405 ACAACGGGGC
* * * * *
117415 TGGAGTATCCCCAATTATGGAAAATCGGTGTTTTGAAAATAAAATTGGGGTTAGAGTATTCCCTC
1 TGGAATATCCCCAATTATAGAAAATCAGTGTTTTGAAAATAAAATTAGGGTTAGAGTATCCCCTC
117480 GAAAATAACAGGG
66 GAAAATAACAGGG
* *
117493 TGGAATATCCCTAATTATAGAAAATCAGTGTTTTGAAAATAAAATTAGGGTTGGAGTATCCCCTC
1 TGGAATATCCCCAATTATAGAAAATCAGTGTTTTGAAAATAAAATTAGGGTTAGAGTATCCCCTC
117558 GAAAATAA
66 GAAAATAA
117566 TGGGGTTAGA
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (78 bp):
TGGAATATCCCCAATTATAGAAAATCAGTGTTTTGAAAATAAAATTAGGGTTAGAGTATCCCCTC
GAAAATAACAGGG
Found at i:117594 original size:78 final size:77
Alignment explanation
Indices: 117407--117711 Score: 240
Period size: 79 Copynumber: 3.9 Consensus size: 77
117397 TGGGGATAAC
* * * * * * *
117407 AACGGGGCTGGAGTATCCCCAATTATGGAAAATCGGTGTTTTGAAAATAAAATTGGGGTTAGAGT
1 AACGGGGTTAGAGTAT-CCCGATTGT-GAAAATCAGTGTTTTGAAAATAAAATTAGGGTTGGAGT
*
117472 ATTCCCTCGAAAAT
64 ATCCCCTCGAAAAT
* * * * *
117486 AACAGGG-TGGAATATCCCTAATTATAGAAAATCAGTGTTTTGAAAATAAAATTAGGGTTGGAGT
1 AACGGGGTTAGAGTATCCC-GATTGT-GAAAATCAGTGTTTTGAAAATAAAATTAGGGTTGGAGT
117550 ATCCCCTCGAAAAT
64 ATCCCCTCGAAAAT
* * * *** *
117564 AATGGGGTTAGAGCATCTCCGATTGTGAAAAATC-GATGCTTT-AGAAATAAGGCTGGGGTTGGA
1 AACGGGGTTAGAGTATC-CCGATTGTG-AAAATCAG-TGTTTTGA-AAATAAAATTAGGGTTGGA
* * *
117627 GTATCCTCACAAAAAT
62 GTATCCCCTCGAAAAT
* * * *
117643 AACGGGGTTAGAGTATCCCCGATTGTGAGGAATCAATATTTTGGAAATAAAACTTA-GGTTGGAG
1 AACGGGGTTAGAGTAT-CCCGATTGTGA-AAATCAGTGTTTTGAAAATAAAA-TTAGGGTTGGAG
117707 TATCC
63 TATCC
117712 TTGATTGTGG
Statistics
Matches: 182, Mismatches: 33, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
77 3 0.02
78 70 0.38
79 105 0.58
80 4 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (77 bp):
AACGGGGTTAGAGTATCCCGATTGTGAAAATCAGTGTTTTGAAAATAAAATTAGGGTTGGAGTAT
CCCCTCGAAAAT
Found at i:117781 original size:79 final size:76
Alignment explanation
Indices: 117698--117903 Score: 261
Period size: 79 Copynumber: 2.6 Consensus size: 76
117688 AATAAAACTT
* *
117698 AGGTTGGAGTATCCTTGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCT
1 AGGTTGGAGTATCCCTGATTGTGAAAAATT-ATGTTTT-GAAATAAAACCGGGGTTGGAGTATC-
*
117763 CCAT-GGAAATAAC
63 CCATCGAAAATAAC
* * *
117776 GAGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATC
1 -AGGTTGGAGTATCCCTGATTGTGAAAAATTA-TGTTTTG-AAATAAAACCGGGGTTGGAGTATC
117841 CCATCGAAAATAAC
63 CCATCGAAAATAAC
*
117855 AGGGTTGGAGTATCCCTGATTGTAAAAAATTTATGTTTTGGAAATAAAA
1 A-GGTTGGAGTATCCCTGATTGTGAAAAA-TTATGTTTT-GAAATAAAA
117904 ACAAGAATGA
Statistics
Matches: 112, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
78 7 0.06
79 101 0.90
80 4 0.04
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (76 bp):
AGGTTGGAGTATCCCTGATTGTGAAAAATTATGTTTTGAAATAAAACCGGGGTTGGAGTATCCCA
TCGAAAATAAC
Found at i:117821 original size:130 final size:130
Alignment explanation
Indices: 117584--117841 Score: 306
Period size: 130 Copynumber: 2.0 Consensus size: 130
117574 GAGCATCTCC
** * *
117584 GATTGTGAAAAATCGATGCTTTAGAAATAAGGCTGGGGTTGGAGTATCCTCACAAAAATAACGGG
1 GATTGTGAAAAATCGATGCTTTAGAAATAAAACCGGGGTTGGAGTATCCTCACAAAAATAACGAG
* ** * *
117649 GTTAGAGTATCCCCGATTGTGAGGAATCAATATTTTGGAAATAAAA-CTTAGGTTGGAGTATCCT
66 GTTAGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATC-GAGGTTGGAGTATCCT
117713 T
130 T
* * * *
117714 GATTGTGGAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTAT-CTC-CATGGAAATAACG
1 GATTGTGAAAAATCGATGCTTTAGAAATAAAACCGGGGTTGGAGTATCCTCACA--AAAATAACG
* * * * *
117777 AGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCC
64 AGGTTAGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGAGGTTGGAGTATCC
117842 CATCGAAAAT
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
128 2 0.02
129 3 0.03
130 101 0.94
131 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.29
Consensus pattern (130 bp):
GATTGTGAAAAATCGATGCTTTAGAAATAAAACCGGGGTTGGAGTATCCTCACAAAAATAACGAG
GTTAGAGTATCCCCGATTATGAAAAATCAATATTTTGAAAATAAAATCGAGGTTGGAGTATCCTT
Found at i:118071 original size:50 final size:50
Alignment explanation
Indices: 117992--118087 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 50
117982 TGGCCTATAT
*
117992 AGGGTCCTAAGAGGGTTCCGAGGCCGATTGGAGTTACGAGGGAACACTGG
1 AGGGTCCTAAGAGGGTTCCGAGGCAGATTGGAGTTACGAGGGAACACTGG
** * *
118042 AGGGTCCTAAGAGGGTTTTGAGGCAGATTGGGGTTATGAGGGAACA
1 AGGGTCCTAAGAGGGTTCCGAGGCAGATTGGAGTTACGAGGGAACA
118088 TCGAGTGTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.25, C:0.14, G:0.41, T:0.21
Consensus pattern (50 bp):
AGGGTCCTAAGAGGGTTCCGAGGCAGATTGGAGTTACGAGGGAACACTGG
Found at i:120335 original size:29 final size:30
Alignment explanation
Indices: 120302--120375 Score: 123
Period size: 29 Copynumber: 2.5 Consensus size: 30
120292 AAAAATGCTT
*
120302 GAATGTATCGATACATCTGGGT-AAACCTA
1 GAATGTATCGATACATCTGGGTAAAACCCA
*
120331 GAATGCATCGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACATCTGGGTAAAACCCA
120361 GAATGTATCGATACA
1 GAATGTATCGATACA
120376 ATGAACAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 21 0.51
30 20 0.49
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.24
Consensus pattern (30 bp):
GAATGTATCGATACATCTGGGTAAAACCCA
Done.