Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold379
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: 429249
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 418 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:200309 original size:33 final size:33
Alignment explanation
Indices: 200269--200335 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
200259 GCCAAGGAAA
***
200269 TGTATCGACACATTTTTCTGTGTATCGATACAT
1 TGTATCGACACATGGATCTGTGTATCGATACAT
* *
200302 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGACACATGGATCTGTGTATCGATACAT
200335 T
1 T
200336 CGGAAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGACACATGGATCTGTGTATCGATACAT
Found at i:202872 original size:31 final size:28
Alignment explanation
Indices: 202789--202861 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
202779 CTTCACAATC
* * ***
202789 GGGGATGCTCCAACCCCGTTA-ATCATC
1 GGGGATACTCCAACCCCGTTATTTCCGA
202816 GGGGATACTCCAACCCCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTATTTCCGA
202844 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
202862 ACTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 20 0.50
28 20 0.50
ACGTcount: A:0.22, C:0.34, G:0.23, T:0.21
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCGA
Found at i:202971 original size:53 final size:53
Alignment explanation
Indices: 202675--203017 Score: 208
Period size: 51 Copynumber: 6.5 Consensus size: 53
202665 TTCTCAATTC
* * * ** *
202675 TCCACAATCGGGGATATTCCAACTCCGATTTTATTT-TTAAAACACTAA-TTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTT
* *
202726 TCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAAACACCAATTT-T
* * * * *** * *
202781 T-CACAATCGGGGATGCTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTAT-TTC-CAAAAACACCAA-----TT-TT
* * * *** *
202839 TCC--GA--GGGGATACTCCAACCCCGACTTTATTTCC-AAAATATTGACTTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTT
* *
202887 T-CATAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTT
1 TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTT
* * *
202938 TCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTT
1 TCC-ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTT
* * *
202992 T-CACAATCGAGGACACTCCAACCCCG
1 TCCATAATCGGGGATACTCCAACCCCG
203018 TTACTTCCGA
Statistics
Matches: 221, Mismatches: 49, Indels: 43
0.71 0.16 0.14
Matches are distributed among these distances:
47 1 0.00
48 3 0.01
49 2 0.01
51 69 0.31
52 24 0.11
53 50 0.23
54 40 0.18
55 19 0.09
56 2 0.01
57 5 0.02
58 4 0.02
59 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (53 bp):
TCCATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTT
Found at i:203108 original size:79 final size:79
Alignment explanation
Indices: 202948--203203 Score: 237
Period size: 79 Copynumber: 3.2 Consensus size: 79
202938 TCCTTTAATC
* * * * * * * * *
202948 GGGGATACTCCAACTCCGATTTTATTTCCAAAAAT-ACCAATTTTTCACAATCGAGGACACTCCA
1 GGGGATACTCCAACCCCGACTTTA-TTCC-CAAATCATCGATTTCTCACAACCGGGGATACTCCA
* *
203012 ACCCCGTTACTTCCGA
64 ACCCCGTTATTTTCGA
* * * **
203028 GGGGATACTCCAACCCCGGCTTTATTCCCAAAAT-ATTGATTTCTCATAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGACTTTATTCCC-AAATCATCGATTTCTCACAACCGGGGATACTCCAA
203092 CCCCGTTATTTTCGA
65 CCCCGTTATTTTCGA
* * * ** * *
203107 GGGGATACTCCAATCCCGATTTTTTTTTCTAATCATCGATTTCTCACAACCGGGGATACTCCAGC
1 GGGGATACTCCAACCCCGACTTTATTCCCAAATCATCGATTTCTCACAACCGGGGATACTCCAAC
*
203172 CCCGTTATTTTCAA
66 CCCGTTATTTTCGA
* *
203186 GGGAACACTCCAACCCCG
1 GGGGATACTCCAACCCCG
203204 TTATTATCTC
Statistics
Matches: 144, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
78 3 0.02
79 120 0.83
80 21 0.15
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGACTTTATTCCCAAATCATCGATTTCTCACAACCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:204347 original size:20 final size:21
Alignment explanation
Indices: 204296--204347 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
204286 TTCTGTAATT
*
204296 TGTATCGATACAATAGCTTAA
1 TGTATCGATACAATAGCTAAA
**
204317 TGTATTAATAC-ATAAG-TAAA
1 TGTATCGATACAAT-AGCTAAA
204337 TGTATCGATAC
1 TGTATCGATAC
204348 TGGACCTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACAATAGCTAAA
Found at i:204410 original size:20 final size:20
Alignment explanation
Indices: 204385--204514 Score: 88
Period size: 20 Copynumber: 6.6 Consensus size: 20
204375 TTCTGAAAAA
204385 ATTGTATCGATACATTTTTC
1 ATTGTATCGATACATTTTTC
* **
204405 ATTGTATTGATACATTTTGG
1 ATTGTATCGATACATTTTTC
* * ** * * *
204425 GTT-T-TTGACCCAAATGTTA
1 ATTGTATCGATAC-ATTTTTC
204444 AT-GTATCGATACATTTTTC
1 ATTGTATCGATACATTTTTC
* *
204463 AATGTATCGATACATTTTTT
1 ATTGTATCGATACATTTTTC
*
204483 AATGTATCGATACATTCTTT-
1 ATTGTATCGATACATT-TTTC
*
204503 AATGTATCGATA
1 ATTGTATCGATA
204515 AATCCAGTTA
Statistics
Matches: 86, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
18 5 0.06
19 11 0.13
20 67 0.78
21 3 0.03
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTGTATCGATACATTTTTC
Found at i:205717 original size:20 final size:21
Alignment explanation
Indices: 205666--205717 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
205656 TTCTGTAATT
*
205666 TGTATCGATACAATAGCTTAA
1 TGTATCGATACAATAGCTAAA
**
205687 TGTATTAATAC-ATAAG-TAAA
1 TGTATCGATACAAT-AGCTAAA
205707 TGTATCGATAC
1 TGTATCGATAC
205718 TGGACCTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACAATAGCTAAA
Found at i:205780 original size:20 final size:20
Alignment explanation
Indices: 205755--205884 Score: 88
Period size: 20 Copynumber: 6.6 Consensus size: 20
205745 TTCTGAAAAA
205755 ATTGTATCGATACATTTTTC
1 ATTGTATCGATACATTTTTC
* **
205775 ATTGTATTGATACATTTTGG
1 ATTGTATCGATACATTTTTC
* * ** * * *
205795 GTT-T-TTGACCCAAATGTTA
1 ATTGTATCGATAC-ATTTTTC
205814 AT-GTATCGATACATTTTTC
1 ATTGTATCGATACATTTTTC
* *
205833 AATGTATCGATACATTTTTT
1 ATTGTATCGATACATTTTTC
*
205853 AATGTATCGATACATTCTTT-
1 ATTGTATCGATACATT-TTTC
*
205873 AATGTATCGATA
1 ATTGTATCGATA
205885 AATCCAGTTA
Statistics
Matches: 86, Mismatches: 19, Indels: 10
0.75 0.17 0.09
Matches are distributed among these distances:
18 5 0.06
19 11 0.13
20 67 0.78
21 3 0.03
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.46
Consensus pattern (20 bp):
ATTGTATCGATACATTTTTC
Found at i:207118 original size:20 final size:21
Alignment explanation
Indices: 207067--207118 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
207057 TTCTGCAATT
*
207067 TGTATCGATACAATAGCTTAA
1 TGTATCGATACAATAGCTAAA
**
207088 TGTATTAATAC-ATAAG-TAAA
1 TGTATCGATACAAT-AGCTAAA
207108 TGTATCGATAC
1 TGTATCGATAC
207119 TGGACCTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (21 bp):
TGTATCGATACAATAGCTAAA
Found at i:207181 original size:20 final size:20
Alignment explanation
Indices: 207156--207193 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
207146 TTCTGAAAAA
207156 ATTGTATCGATACATTTTTC
1 ATTGTATCGATACATTTTTC
*
207176 ATTGTATTGATACATTTT
1 ATTGTATCGATACATTTT
207194 GGGTTTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (20 bp):
ATTGTATCGATACATTTTTC
Found at i:207279 original size:20 final size:20
Alignment explanation
Indices: 207208--207279 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
207198 TTTTGACCCA
* *
207208 AATGTATCAATATATT-TTT
1 AATGTATCGATACATTCTTT
207227 CAATGTATCGATACATTCTTT
1 -AATGTATCGATACATTCTTT
*
207248 AATGTATTGATACATTCTTT
1 AATGTATCGATACATTCTTT
207268 AATGTATCGATA
1 AATGTATCGATA
207280 AATCCAGTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
20 44 0.94
21 3 0.06
ACGTcount: A:0.33, C:0.11, G:0.10, T:0.46
Consensus pattern (20 bp):
AATGTATCGATACATTCTTT
Found at i:211522 original size:90 final size:90
Alignment explanation
Indices: 211369--211544 Score: 325
Period size: 90 Copynumber: 2.0 Consensus size: 90
211359 GCTGCTAGAA
* *
211369 TAACCCAGAGAATAGGTTTACTTAGAGAAACACTTCTAACCTCTACTTTCATTTATCATGTACAT
1 TAACCCAGAGAATAGGTTTACTCAGAGAAACACTTCTAACATCTACTTTCATTTATCATGTACAT
211434 GTAGGTGATAATGAATGAACACTTC
66 GTAGGTGATAATGAATGAACACTTC
211459 TAACCCAGAGAATAGGTTTACTCAGAGAAACACTTCTAACATCTACTTTCATTTATCATGTACAT
1 TAACCCAGAGAATAGGTTTACTCAGAGAAACACTTCTAACATCTACTTTCATTTATCATGTACAT
*
211524 GTAGGTGATAATGAGTGAACA
66 GTAGGTGATAATGAATGAACA
211545 TTACCATCTA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (90 bp):
TAACCCAGAGAATAGGTTTACTCAGAGAAACACTTCTAACATCTACTTTCATTTATCATGTACAT
GTAGGTGATAATGAATGAACACTTC
Found at i:214547 original size:13 final size:13
Alignment explanation
Indices: 214529--214598 Score: 86
Period size: 13 Copynumber: 4.9 Consensus size: 13
214519 CATAAAGTGT
214529 TGTATCGATACAA
1 TGTATCGATACAA
214542 TGTATCGATACAA
1 TGTATCGATACAA
214555 TGTATCGATACATAA
1 TGTATCGATAC--AA
214570 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
214587 TGTATCGATACA
1 TGTATCGATACA
214599 TAAGTTTTGT
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
13 36 0.71
15 2 0.04
17 2 0.04
19 11 0.22
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:214579 original size:19 final size:18
Alignment explanation
Indices: 214507--214617 Score: 81
Period size: 13 Copynumber: 6.8 Consensus size: 18
214497 ATTTCAACGA
214507 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
214526 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
214542 --TGTATCGATAC--AA-
1 TTTGTATCGATACATAAG
214555 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
214571 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
214587 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
214603 TTTTGTATCGATACA
1 -TTTGTATCGATACA
214618 ATGTAAGCTA
Statistics
Matches: 79, Mismatches: 0, Indels: 26
0.75 0.00 0.25
Matches are distributed among these distances:
13 35 0.44
15 4 0.05
17 4 0.05
19 24 0.30
20 12 0.15
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:214582 original size:45 final size:46
Alignment explanation
Indices: 214509--214598 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 46
214499 TTCAACGATT
214509 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACAA
214555 TGTATCGATACAT-AAGTGTTGTATCGATACAATGTATCGATACA
1 TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACA
214599 TAAGTTTTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 31 0.70
46 13 0.30
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (46 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAATGTATCGATACAA
Found at i:214583 original size:32 final size:32
Alignment explanation
Indices: 214542--214622 Score: 153
Period size: 32 Copynumber: 2.5 Consensus size: 32
214532 ATCGATACAA
214542 TGTATCGATACAATGTATCGATACATAAGTGT
1 TGTATCGATACAATGTATCGATACATAAGTGT
*
214574 TGTATCGATACAATGTATCGATACATAAGTTT
1 TGTATCGATACAATGTATCGATACATAAGTGT
214606 TGTATCGATACAATGTA
1 TGTATCGATACAATGTA
214623 AGCTATTGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACAATGTATCGATACATAAGTGT
Found at i:214678 original size:13 final size:13
Alignment explanation
Indices: 214660--214684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
214650 ATTACTTAAA
214660 TGTATCGATACAT
1 TGTATCGATACAT
214673 TGTATCGATACA
1 TGTATCGATACA
214685 CTGATCTTTA
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:214735 original size:52 final size:52
Alignment explanation
Indices: 214695--214873 Score: 331
Period size: 52 Copynumber: 3.4 Consensus size: 52
214685 CTGATCTTTA
* *
214695 TATCGATACATGCAGGCAAATGTGCCCAGATGTATTGATACACTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
214747 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
*
214799 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
214851 TATCGATACATGCAGGCAAATTT
1 TATCGATACATGCAGGCAAATTT
214874 TCATATTTCG
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATG
Found at i:219731 original size:13 final size:13
Alignment explanation
Indices: 219713--219737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
219703 CATTATGCTT
219713 TGTATCGATACAA
1 TGTATCGATACAA
219726 TGTATCGATACA
1 TGTATCGATACA
219738 TGTTCATTAT
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:219752 original size:19 final size:20
Alignment explanation
Indices: 219728--219778 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
219718 CGATACAATG
**
219728 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
219747 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
219767 TATCGATACATG
1 TATCGATACATG
219779 AAACTAGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:219772 original size:20 final size:20
Alignment explanation
Indices: 219722--219778 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
219712 TTGTATCGAT
*
219722 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
219741 TC-ATTATATCGATACATGG
1 ACAATTGTATCGATACATGG
219760 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
219779 AAACTAGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:219850 original size:33 final size:32
Alignment explanation
Indices: 219808--219870 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
219798 TACCACTGTT
219808 TGTATCGATACATG-GCACATTGTATCGATATAA
1 TGTATCGATACATGTG-A-ATTGTATCGATATAA
219841 TGTATCGATACATGTTGAATTGTATCGATA
1 TGTATCGATACATG-TGAATTGTATCGATA
219871 CATTGCTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATGTGAATTGTATCGATATAA
Found at i:222006 original size:79 final size:77
Alignment explanation
Indices: 221800--222017 Score: 222
Period size: 79 Copynumber: 2.8 Consensus size: 77
221790 ACAGGGCTTT
* **
221800 AGTATCCCTGATTATGGAAAATAGATGTTCTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAA
1 AGTATCCCCGATTATAAAAAATAGATGTT-TAGAAATAAAATCGGGGTT-GAGTATCCCCTCGAA
*
221865 AGTAACAGGGTTAG
64 AATAACAGGGTTAG
* * * * * * *
221879 AGTATCCCTGATTATAGAAAATCGATATTTTGAAAATAAAATCAGGGTTGTAGTATCCCCTTGAA
1 AGTATCCCCGATTATAAAAAATAGATGTTTAG-AAATAAAATCGGGGTTG-AGTATCCCCTCGAA
**
221944 AATAATTGGGTTAG
64 AATAACAGGGTTAG
* * *
221958 AGTATCCCCGATTGTAAAAAATTGATGCTTTAGAAATAAGGA-CGGGGTTGAAGTATCCCC
1 AGTATCCCCGATTATAAAAAATAGATG-TTTAGAAATAA-AATCGGGGTTG-AGTATCCCC
222018 GATTGTGAGA
Statistics
Matches: 117, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
78 3 0.03
79 109 0.93
80 5 0.04
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (77 bp):
AGTATCCCCGATTATAAAAAATAGATGTTTAGAAATAAAATCGGGGTTGAGTATCCCCTCGAAAA
TAACAGGGTTAG
Found at i:222045 original size:51 final size:50
Alignment explanation
Indices: 221951--222066 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 50
221941 GAAAATAATT
** * *
221951 GGGTTAGAGTATCCCCGATTGTAAAAAATTGATGCTTTAGAAATAAGGACG
1 GGGTT-GAGTATCCCCGATTGTAAAAAATCAATACTTTAGAAATAAAGACG
* * * * *
222002 GGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGTCG
1 GGGTTG-AGTATCCCCGATTGTAAAAAATCAATACTTTAGAAATAAAGACG
222053 GGGTTGAGTATCCC
1 GGGTTGAGTATCCC
222067 TTCAGAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
50 9 0.16
51 46 0.84
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (50 bp):
GGGTTGAGTATCCCCGATTGTAAAAAATCAATACTTTAGAAATAAAGACG
Found at i:222092 original size:28 final size:28
Alignment explanation
Indices: 222054--222122 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
222044 ATAAAGTCGG
*
222054 GGTT-GAGTATCCCTTCA-GAAATAATGA
1 GGTTGGAGTATCCC-TAATGAAATAATGA
*
222081 GGTTGGAGTATCCCTAATGAAATAATGG
1 GGTTGGAGTATCCCTAATGAAATAATGA
222109 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
222123 CGATTGTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 6 0.16
28 32 0.84
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (28 bp):
GGTTGGAGTATCCCTAATGAAATAATGA
Found at i:222169 original size:51 final size:51
Alignment explanation
Indices: 222109--222224 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 51
222099 GAAATAATGG
* *
222109 GGTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTGGAAATAAAATCG-
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTAGAAATAAAACCGA
** * *
222159 GAGTTGGAGTATCATCGATTGTGGAAAATTGATGTTTTAGAAATAAAACCGA
1 G-GTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTAGAAATAAAACCGA
222211 GGTTGGAGTATCCC
1 GGTTGGAGTATCCC
222225 TTTGGAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 54 0.96
52 1 0.02
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTAGAAATAAAACCGA
Found at i:222215 original size:157 final size:158
Alignment explanation
Indices: 221943--222235 Score: 367
Period size: 157 Copynumber: 1.9 Consensus size: 158
221933 ATCCCCTTGA
* * * *
221943 AAATAATTGGGTTAGAGTATCCCCGATTGTAAAAAATTGATGCTTTAGAAATAAGGACGGGGTTG
1 AAATAATGGGGTTAGAGTATCCCCGATTGTAAAAAATTGATACTTTAGAAATAAGAACGGAGTTG
* * ** *
222008 AAGTATCCCCGATTGTGAGAAATCAATATTTTGGAAATAAAGTCGGGGTT-GAGTATCCCTTCAG
66 AAGTATCACCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTCAG
222072 AAATAATGAGGTTGGAGTATCCCTAATG
131 AAATAATGAGGTTGGAGTATCCCTAATG
* * * *
222100 AAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATATTTTGGAAATAA-AATCGGAGTT
1 AAATAATGGGGTTAGAGTATCCCCGATTGTAAAAAATTGATACTTTAGAAATAAGAA-CGGAGTT
* * ** * *
222164 GGAGTATCATCGATTGTG-GAAAATTGATGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTT
65 GAAGTATCACCGATTGTGAG-AAATCAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTC
*
222228 GGAAATAA
129 AGAAATAA
222236 CGGGGTTATA
Statistics
Matches: 113, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
156 2 0.02
157 93 0.82
158 18 0.16
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (158 bp):
AAATAATGGGGTTAGAGTATCCCCGATTGTAAAAAATTGATACTTTAGAAATAAGAACGGAGTTG
AAGTATCACCGATTGTGAGAAATCAATATTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTCAG
AAATAATGAGGTTGGAGTATCCCTAATG
Found at i:222317 original size:51 final size:51
Alignment explanation
Indices: 222245--222349 Score: 165
Period size: 51 Copynumber: 2.1 Consensus size: 51
222235 ACGGGGTTAT
* *
222245 AGTATCCACGATAGTGGAAAATCGATGTTTTGGAAATAAAATCGAGGTTGG
1 AGTATCCACGATAGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTTGG
* * *
222296 AGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAATCGAGGTTGG
1 AGTATCCACGATAGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTTGG
222347 AGT
1 AGT
222350 TTCTCTCGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.10, G:0.26, T:0.30
Consensus pattern (51 bp):
AGTATCCACGATAGTGAAAAATCGATGTTTTAGAAATAAAATCGAGGTTGG
Found at i:222317 original size:130 final size:130
Alignment explanation
Indices: 222079--222349 Score: 393
Period size: 130 Copynumber: 2.1 Consensus size: 130
222069 CAGAAATAAT
* * * * *
222079 GAGGTTGGAGTATCCCTAATGAAATAATGGGGTTGGAGTATCCCCGATTGTGAAAAATTGATATT
1 GAGGTTGGAGTATCCCTAATGAAATAACGGGGTTAGAGTATCCACGATAGTGAAAAATCGATATT
* *
222144 TTGGAAATAAAATCGGAGTTGGAGTATCATCGATTGTGGAAAATTGATGTTTTAGAAATAAAACC
66 TTGGAAATAAAATCGGAGTTGGAGTATCACCGATTGTGAAAAATTGATGTTTTAGAAATAAAACC
* * * *
222209 GAGGTTGGAGTATCCCT-TTGGAAATAACGGGGTTATAGTATCCACGATAGTGGAAAATCGATGT
1 GAGGTTGGAGTATCCCTAAT-GAAATAACGGGGTTAGAGTATCCACGATAGTGAAAAATCGATAT
*
222273 TTTGGAAATAAAATC-GAGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTTTTAGAAATAAAA
65 TTTGGAAATAAAATCGGA-GTTGGAGTATCACCGATTGTGAAAAATTGATGTTTTAGAAATAAAA
*
222337 TC
129 CC
222339 GAGGTTGGAGT
1 GAGGTTGGAGT
222350 TTCTCTCGAA
Statistics
Matches: 126, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
129 3 0.02
130 123 0.98
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.30
Consensus pattern (130 bp):
GAGGTTGGAGTATCCCTAATGAAATAACGGGGTTAGAGTATCCACGATAGTGAAAAATCGATATT
TTGGAAATAAAATCGGAGTTGGAGTATCACCGATTGTGAAAAATTGATGTTTTAGAAATAAAACC
Found at i:231449 original size:16 final size:16
Alignment explanation
Indices: 231428--231473 Score: 92
Period size: 16 Copynumber: 2.9 Consensus size: 16
231418 GTAGTTACGG
231428 GCTGGAAGCTGCTGCT
1 GCTGGAAGCTGCTGCT
231444 GCTGGAAGCTGCTGCT
1 GCTGGAAGCTGCTGCT
231460 GCTGGAAGCTGCTG
1 GCTGGAAGCTGCTG
231474 GCTGGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.13, C:0.24, G:0.39, T:0.24
Consensus pattern (16 bp):
GCTGGAAGCTGCTGCT
Found at i:231454 original size:13 final size:14
Alignment explanation
Indices: 231428--231480 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 14
231418 GTAGTTACGG
231428 GCTGGAAGCTGCTGCT
1 GCTGGAA-C-GCTGCT
231444 GCTGGAAGCTGCTGCT
1 GCTGGAA-C-GCTGCT
231460 GCTGGAA-GCTGCT
1 GCTGGAACGCTGCT
231473 GGCTGGAA
1 -GCTGGAA
231481 TTTATTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.17
14 7 0.19
16 23 0.64
ACGTcount: A:0.15, C:0.23, G:0.40, T:0.23
Consensus pattern (14 bp):
GCTGGAACGCTGCT
Found at i:232009 original size:86 final size:86
Alignment explanation
Indices: 231855--232069 Score: 313
Period size: 86 Copynumber: 2.5 Consensus size: 86
231845 CCTCTTGCGC
* * *
231855 ATTGCTTTGTCCTCATCATTGCTATTTTGCTTTTCCACGTTACTTTGTCTTCCACTTTCTTCAGT
1 ATTGCTTTGTCTTCATCATTGCTGTTTT--TTTTTCACGTTACTTTGTCTTCCACTTTCTTCAGT
231920 GTTGCTTTGCTTTGCTATTCCAT
64 GTTGCTTTGCTTTGCTATTCCAT
* ** * *
231943 GTTGCTTTGTCTTCATCATAACTGTTTTTTTTTCACGTTACTTTGTCTTCCACTTTTTTCATTGT
1 ATTGCTTTGTCTTCATCATTGCTGTTTTTTTTTCACGTTACTTTGTCTTCCACTTTCTTCAGTGT
*
232008 TGCTTTGCTTTGCTGTTCCAT
66 TGCTTTGCTTTGCTATTCCAT
232029 ATTGCTTTGTCTTCATCATTGCTGTTTTTTTTCTTCACGTT
1 ATTGCTTTGTCTTCATCATTGCTG-TTTTTTT-TTCACGTT
232070 GGCTTCCACT
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
86 75 0.66
87 7 0.06
88 31 0.27
ACGTcount: A:0.11, C:0.22, G:0.13, T:0.54
Consensus pattern (86 bp):
ATTGCTTTGTCTTCATCATTGCTGTTTTTTTTTCACGTTACTTTGTCTTCCACTTTCTTCAGTGT
TGCTTTGCTTTGCTATTCCAT
Found at i:232275 original size:14 final size:14
Alignment explanation
Indices: 232247--232439 Score: 93
Period size: 14 Copynumber: 14.9 Consensus size: 14
232237 TGAAATGTTT
*
232247 ATGAAATG-CATGC
1 ATGAAATGAAATGC
232260 ATGAAATGAAATGC
1 ATGAAATGAAATGC
*
232274 ATGAAATGAAAAT-T
1 ATGAAATG-AAATGC
232288 ATG---TGAAATGC
1 ATGAAATGAAATGC
* *
232299 ATG-CATGAATTG-
1 ATGAAATGAAATGC
* **
232311 -TTACGTGAAATGC
1 ATGAAATGAAATGC
232324 ATGAAATGAAAATGC
1 ATGAAATG-AAATGC
*
232339 ATG-CATG-AA-GC
1 ATGAAATGAAATGC
* **
232350 TTGAAATG---TTT
1 ATGAAATGAAATGC
*
232361 ATGAAATG-CATGC
1 ATGAAATGAAATGC
232374 ATGAAATGAAATGC
1 ATGAAATGAAATGC
232388 ATGAAATGAAAATG-
1 ATGAAATG-AAATGC
232402 ATG---TGAAATGC
1 ATGAAATGAAATGC
232413 ATGAAATGAAAATGC
1 ATGAAATG-AAATGC
*
232428 ATG-CATGAAATG
1 ATGAAATGAAATG
232440 TTACGTGAAA
Statistics
Matches: 140, Mismatches: 20, Indels: 40
0.70 0.10 0.20
Matches are distributed among these distances:
10 9 0.06
11 22 0.16
12 12 0.09
13 28 0.20
14 42 0.30
15 27 0.19
ACGTcount: A:0.44, C:0.08, G:0.22, T:0.26
Consensus pattern (14 bp):
ATGAAATGAAATGC
Found at i:232298 original size:25 final size:25
Alignment explanation
Indices: 232266--232336 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
232256 ATGCATGAAA
*
232266 TGAAATGCATGAAATGAAAATTATG
1 TGAAATGCATGAAATGAAAATTACG
* **
232291 TGAAATGCATG-CATGAATTGTTACG
1 TGAAATGCATGAAATGAA-AATTACG
232316 TGAAATGCATGAAATGAAAAT
1 TGAAATGCATGAAATGAAAAT
232337 GCATGCATGA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 5 0.14
25 27 0.73
26 5 0.14
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (25 bp):
TGAAATGCATGAAATGAAAATTACG
Found at i:232358 original size:114 final size:115
Alignment explanation
Indices: 232204--232415 Score: 390
Period size: 114 Copynumber: 1.8 Consensus size: 115
232194 AAATGCATGT
232204 ATGCATGAAATGAAAATTTGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGA
1 ATGCATGAAATGAAAA-TTGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGA
*
232269 AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAATTGTTACGTGAA
65 AATGCATGAAATGAAAATGATGTGAAATGCATGCATGAATTGTTACGTGAA
*
232320 ATGCATGAAATGAAAA-TGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAA
1 ATGCATGAAATGAAAATTGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGAA
232384 ATGCATGAAATGAAAATGATGTGAAATGCATG
66 ATGCATGAAATGAAAATGATGTGAAATGCATG
232416 AAATGAAAAT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
114 78 0.83
116 16 0.17
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.27
Consensus pattern (115 bp):
ATGCATGAAATGAAAATTGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGAA
ATGCATGAAATGAAAATGATGTGAAATGCATGCATGAATTGTTACGTGAA
Found at i:232451 original size:114 final size:113
Alignment explanation
Indices: 232208--232439 Score: 347
Period size: 114 Copynumber: 2.0 Consensus size: 113
232198 GCATGTATGC
232208 ATGAAATGAAAATTTGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGAAATG
1 ATGAAATGAAAA--TGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGAAATG
* * * * *
232273 CATGAAATGAAAATTATGTGAAATGCATGCATGAATTGTTACGTGAAATG
64 CATGAAATGAAAATGATGTGAAATGCATGAATGAAATGATACATGAAATG
*
232323 CATGAAATGAAAATGCATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAAATGC
1 -ATGAAATGAAAATGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGAAATGC
*
232388 ATGAAATGAAAATGATGTGAAATGCATGAAATGAAAATGCATGCATGAAATG
65 ATGAAATGAAAATGATGTGAAATGCATG-AATG-AAATG-ATACATGAAATG
232440 TTACGTGAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
114 78 0.74
115 3 0.03
116 16 0.15
117 9 0.08
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (113 bp):
ATGAAATGAAAATGCATGCATGAAGCATGAAATGTTTATGAAATGCATGCATGAAATGAAATGCA
TGAAATGAAAATGATGTGAAATGCATGAATGAAATGATACATGAAATG
Found at i:232569 original size:21 final size:20
Alignment explanation
Indices: 232530--232573 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
232520 TTTTATAAAA
*
232530 TTTTTATTTTAATTTATTTAT
1 TTTTTATTTTAATTAATTT-T
232551 TTTTTATGTTTAA-TAATTTT
1 TTTTTAT-TTTAATTAATTTT
232571 TTT
1 TTT
232574 ATAAACTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 12 0.57
22 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (20 bp):
TTTTTATTTTAATTAATTTT
Found at i:232989 original size:43 final size:42
Alignment explanation
Indices: 232938--234006 Score: 1005
Period size: 42 Copynumber: 25.4 Consensus size: 42
232928 AAGATAAAAT
* * *
232938 AGGCAGACTTAGGGAAAAAAAAGTCTCAAGGGTCAAAGCCGAC
1 AGGCAGACTAAGGG-AAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * *
232981 AAGCAGACTAAGGGATAGGAAAGTCTCCAGGATCAAAGCCGAC
1 AGGCAGACTAAGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * *
233024 AGGCAGACTTA-GGACTAGGAAAGTTTCCAAGGTCAAAGCCGAC
1 AGGCAGACTAAGGGA--AGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * *
233067 AAGCAGACTTAGGGAA-AGAAAGTCTCTAGGGTTAAAGCCGAC
1 AGGCAGACTAAGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGAC
* *
233109 AGGCAGACTTAGGGATAGAAAAGTCTCCAAGGTCAAAGCCGAC
1 AGGCAGACTAAGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGAC
* *
233152 AGGCAGACTAAGGGATAGAAAAGTCTCGAGGGTCAAAGCCGAT
1 AGGCAGACTAAGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * * * *
233195 AGGCAAACTGAAAGAAAGGAGAGTTTCCAGGGTCAAAGCCGAC
1 AGGCAGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * ** * *
233238 AGGTAGAATGAA-GGTTGAAAAGTCTCTAGGGTCAAAGCCAAC
1 AGGCAGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * *
233280 AGGCAGACTAAGTGATGAAAAGTCTCTAGGGTCAAAGCCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * *
233322 AGGCAGACTGAGGGTAGAAAAGTCTCCCGGGTCAAAGCCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * * *
233364 AGGCAGATTGAGGGAAAAAAAGTCTCTAGGGTCAAAGCTGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* *
233406 AAGCAGACTAAGGGAAGAAAAGTCTCCAGGATCAAAGCCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
*
233448 AGGCAGACTGAAGGGAAGGAAAGTCTCCAGGGTCAAAGCCGAC
1 AGGCAGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * * *
233491 AGGCAAACTGAAAGGTAGGAAAGTCTCCAGGGTGAAA-CCGAC
1 AGGCAGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * *
233533 AAGCAGACTAAGGGTAGAAAAGTCTCCAAGGTCAAAGTCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* *
233575 AGGCAGACTAAGGGATAGGAAAGTCTCCAGGGTTAAA-CCGAC
1 AGGCAGACTAAGGGA-AGAAAAGTCTCCAGGGTCAAAGCCGAC
* *
233617 AGGCAGACTAAGGGAAGGAAAGTCTCTAGGGTCAAAGCCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * * * *
233659 AAGCAGACTGAGGGAAGGAAAGTCTCCAAGGTCAAAGCTGAT
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * *
233701 AGGCAGACTGAAGGGTAGGAAAGTTTCCAGGGTTAAA-CCGAC
1 AGGCAGACT-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
** * * * *
233743 AGGTGGACTACGGGAAGGAAAGTCTCCAGGGTTAAA-CTGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * * * * *
233784 AGACGGACTAAGGGTAGAAAAGTTTCTAGGGAT-GAAGCCAAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGG-TCAAAGCCGAC
* ** * * *
233826 AGGTAGACTTAAAATG-AGATAA-TCTCTAGGG----AGGCGAC
1 AGGCAGAC-T-AAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* * * *
233864 AGGCAGACTGAGGGAAAAGAAAGTCTCTAGGGTCAAAGTCGAC
1 AGGCAGACTAAGGGAAGA-AAAGTCTCCAGGGTCAAAGCCGAC
* * * * * *
233907 AGGTAGACTAGGGGAAGGAAAGTCTCCAAGGACGAAGCCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
* *
233949 AGGCAGACTAAGGGATGAAAAGTCTCCAAGGTCAAAGCCGAC
1 AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
233991 AGGCAGACTAAGGGAA
1 AGGCAGACTAAGGGAA
234007 AATAGAAAAG
Statistics
Matches: 849, Mismatches: 153, Indels: 49
0.81 0.15 0.05
Matches are distributed among these distances:
36 2 0.00
37 3 0.00
38 14 0.02
39 9 0.01
41 98 0.12
42 404 0.48
43 308 0.36
44 11 0.01
ACGTcount: A:0.37, C:0.18, G:0.31, T:0.14
Consensus pattern (42 bp):
AGGCAGACTAAGGGAAGAAAAGTCTCCAGGGTCAAAGCCGAC
Found at i:249042 original size:2 final size:2
Alignment explanation
Indices: 249037--249062 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
249027 AAAATACAAA
249037 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
249063 CCCTAAGGAT
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:251006 original size:43 final size:44
Alignment explanation
Indices: 250881--251019 Score: 142
Period size: 43 Copynumber: 3.2 Consensus size: 44
250871 TTATTGCTAT
250881 TTTGCTTTTCCATGTTACTTTGTCTTCCACTTTCTTCATTGTTGC
1 TTTG-TTTTCCATGTTACTTTGTCTTCCACTTTCTTCATTGTTGC
* * * *** *
250926 TTTGCTTTGC-TGTTCCATGTTG-CTTTGTC-TTCATCATTGTTG-
1 TTTGTTTTCCATGTTAC-T-TTGTCTTCCACTTTCTTCATTGTTGC
* *
250968 TTTTTTTTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGC
1 TTTGTTTTCCATGTTACTTTGTCTTCCACTTTCTTCATTGTTGC
251012 TTTGTTTT
1 TTTGTTTT
251020 GCTGTTCCAT
Statistics
Matches: 71, Mismatches: 17, Indels: 13
0.70 0.17 0.13
Matches are distributed among these distances:
41 3 0.04
42 12 0.17
43 33 0.46
44 16 0.23
45 7 0.10
ACGTcount: A:0.08, C:0.22, G:0.13, T:0.58
Consensus pattern (44 bp):
TTTGTTTTCCATGTTACTTTGTCTTCCACTTTCTTCATTGTTGC
Found at i:251023 original size:86 final size:87
Alignment explanation
Indices: 250886--251063 Score: 313
Period size: 86 Copynumber: 2.1 Consensus size: 87
250876 GCTATTTTGC
* *
250886 TTTTCCATGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTGCTGTTCCATGTTGCTT
1 TTTTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTGCTGTTCCATATTGCTT
*
250951 TGTCTTCATCATTG-TTGTTTT
66 TGTCTTCATCATTGCTGGTTTT
*
250972 TTTTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGTTTTGCTGTTCCATATTGCTT
1 TTTTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTGCTGTTCCATATTGCTT
251037 TGTCTTCATCATTGCTGGTTTT
66 TGTCTTCATCATTGCTGGTTTT
251059 TTTTC
1 TTTTC
251064 TTCACGTTGG
Statistics
Matches: 87, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
86 76 0.87
87 11 0.13
ACGTcount: A:0.08, C:0.21, G:0.13, T:0.57
Consensus pattern (87 bp):
TTTTCCACGTTACTTTGTCTTCCACTTTCTTCATTGTTGCTTTGCTTTGCTGTTCCATATTGCTT
TGTCTTCATCATTGCTGGTTTT
Found at i:251049 original size:43 final size:42
Alignment explanation
Indices: 250916--251050 Score: 130
Period size: 43 Copynumber: 3.1 Consensus size: 42
250906 TCCACTTTCT
*
250916 TCATTGTTGCTTTGCTTTGCTGTTCCATGTTGCTTTGTCTTCA
1 TCATTGTTGCTTTGTTTTGCTGTTCCAT-TTGCTTTGTCTTCA
* * * * *** *
250959 TCATTGTTG-TTTTTTTTCCACGTTAC-TTTGTCTTCCACTTTCT
1 TCATTGTTGCTTTGTTTTGC-TGTTCCATTTG-CTTTGTC-TTCA
251002 TCATTGTTGCTTTGTTTTGCTGTTCCATATTGCTTTGTCTTCA
1 TCATTGTTGCTTTGTTTTGCTGTTCCAT-TTGCTTTGTCTTCA
251045 TCATTG
1 TCATTG
251051 CTGGTTTTTT
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
41 3 0.04
42 12 0.17
43 38 0.55
44 13 0.19
45 3 0.04
ACGTcount: A:0.09, C:0.21, G:0.15, T:0.56
Consensus pattern (42 bp):
TCATTGTTGCTTTGTTTTGCTGTTCCATTTGCTTTGTCTTCA
Found at i:251281 original size:29 final size:30
Alignment explanation
Indices: 251223--251293 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 30
251213 AATGAAAATT
251223 TGCATGCATGAAGCATGAAATATTTATGAAA
1 TGCATGCATGAA-CATGAAATATTTATGAAA
*
251254 TGCATGCATGAA-ATGAAA-ATTATGTGAAA
1 TGCATGCATGAACATGAAATATT-TATGAAA
251283 TGCATGCATGA
1 TGCATGCATGA
251294 TTTGTTACGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
28 3 0.08
29 23 0.61
31 12 0.32
ACGTcount: A:0.41, C:0.10, G:0.21, T:0.28
Consensus pattern (30 bp):
TGCATGCATGAACATGAAATATTTATGAAA
Found at i:251349 original size:100 final size:103
Alignment explanation
Indices: 251205--251420 Score: 296
Period size: 100 Copynumber: 2.1 Consensus size: 103
251195 AAATGCATGT
251205 ATGCATGAAATGAAAATTTGCATGCATGAAGCATGAAATATTTATGAAATGCATGCATGAAATGA
1 ATGCATGAAATGAAAA-TTGCATGCATGAAGCATGAAATATTTATGAAATGCATGCATGAAATG-
* * **
251270 AAAT-TATG-TG-AAATGCATGCATGATTTGTTACGTGAA
64 AAATGCACGATGAAAATGCATGCATGAAATGTTACGTGAA
* * *
251307 ATGCATGAAATGAAAA-TGTATGCATGAAGCTTGAAATGTTTATGAAATGCATGCATGAAATGAA
1 ATGCATGAAATGAAAATTGCATGCATGAAGCATGAAATATTTATGAAATGCATGCATGAAATGAA
251371 ATGCACGAAATGAAAATGCATGCATGAAATGTTACGTGAA
66 ATGCACG--ATGAAAATGCATGCATGAAATGTTACGTGAA
*
251411 ATGTATGAAA
1 ATGCATGAAA
251421 GTATGCATGC
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
99 4 0.04
100 45 0.45
102 16 0.16
103 2 0.02
104 34 0.34
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (103 bp):
ATGCATGAAATGAAAATTGCATGCATGAAGCATGAAATATTTATGAAATGCATGCATGAAATGAA
ATGCACGATGAAAATGCATGCATGAAATGTTACGTGAA
Found at i:251361 original size:50 final size:50
Alignment explanation
Indices: 251205--251371 Score: 171
Period size: 50 Copynumber: 3.3 Consensus size: 50
251195 AAATGCATGT
* *
251205 ATGCATGAAATGAAAATTTGCATGCATGAAGCATGAAATATTTATGAAATGC
1 ATGCATGAAATGAAAA--TGTATGCATGAAGCATGAAATGTTTATGAAATGC
* * * ** *
251257 ATGCATGAAATGAAAAT-TATG--TGAAATGCATG-CATGATTTGTTACGTGAA
1 ATGCATGAAATGAAAATGTATGCATG-AA-GCATGAAATG-TTTATGAAATG-C
*
251307 ATGCATGAAATGAAAATGTATGCATGAAGCTTGAAATGTTTATGAAATGC
1 ATGCATGAAATGAAAATGTATGCATGAAGCATGAAATGTTTATGAAATGC
251357 ATGCATGAAATGAAA
1 ATGCATGAAATGAAA
251372 TGCACGAAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
47 2 0.02
48 4 0.04
49 15 0.16
50 33 0.36
51 15 0.16
52 21 0.23
53 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGCATGAAATGAAAATGTATGCATGAAGCATGAAATGTTTATGAAATGC
Found at i:251380 original size:14 final size:15
Alignment explanation
Indices: 251357--251390 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
251347 TATGAAATGC
*
251357 ATGCATGAAATG-AA
1 ATGCACGAAATGAAA
251371 ATGCACGAAATGAAA
1 ATGCACGAAATGAAA
251386 ATGCA
1 ATGCA
251391 TGCATGAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (15 bp):
ATGCACGAAATGAAA
Found at i:255671 original size:19 final size:19
Alignment explanation
Indices: 255644--255706 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
255634 AGCGATACAT
255644 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
255663 TGTAGCGAT---ACA--T-
1 TGTATCGATACAACACTTA
255676 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
255695 TGTATCGATACA
1 TGTATCGATACA
255707 GTTACTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 8 0.22
14 1 0.03
16 6 0.17
18 1 0.03
19 20 0.56
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:255671 original size:32 final size:32
Alignment explanation
Indices: 255631--255706 Score: 143
Period size: 32 Copynumber: 2.4 Consensus size: 32
255621 GCAGTAGCTT
255631 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTAGCGATACATTGTATCGATACAACACTTA
255663 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTAGCGATACATTGTATCGATACAACACTTA
*
255695 TGTATCGATACA
1 TGTAGCGATACA
255707 GTTACTGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (32 bp):
TGTAGCGATACATTGTATCGATACAACACTTA
Found at i:256634 original size:101 final size:101
Alignment explanation
Indices: 256399--257162 Score: 956
Period size: 101 Copynumber: 7.7 Consensus size: 101
256389 ATATGCAGCT
* * * * * * * * * *
256399 AGCGATATTGGGCTCAAAGATG-CGAAGAATGACAATGTGCTGATTCATGGCTAGCGACATTAGA
1 AGCGACATTGGTCTTAAAGATGACGAAG-GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
* * * **
256463 CTTGAAGAAGAA--TGCCAATGTGTTGAGACAAGGCC
65 CTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* * *** * * * *
256498 AACGACATTAGG-CTT-AGGAATGTTAAAGATGCCAATACGCTGATTCAAGGCCAACGATAGTGG
1 AGCGACATT-GGTCTTAAAG-ATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
* *
256561 ACTTAAGGATGAAGGTGCCAATGTGCTAATTCAAGGCC
64 ACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* **
256599 AGTGACATTGGT-TTGAAAGATGACGAAGGCACCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 AGCGACATTGGTCTT-AAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
*
256663 CTTAAAGATGAAGTTGCCAATGTGCTGATTCAAGGCC
65 CTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
256700 AACGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
256765 TTAAAGATGAAGGTGCTAATGTGCTGATTCAAGGCC
66 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
256801 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
256866 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCC
66 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
*
256902 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGAC
1 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
256967 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
66 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* * * *
257003 AGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTTAAGGCCAGCGATATTGGAC
1 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
257068 -T-----T----GTGCCAATGTGCTGATTTAAGGCC
66 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
* * * *
257094 AACGACATTGTTCTT-AA-A-GAC-AAGGTGCCAATATGTTGATTCAAGGCCAGTGATATTGGAC
1 AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
257155 TTAGAAGA
66 TTA-AAGA
257163 AGATGCCACC
Statistics
Matches: 588, Mismatches: 61, Indels: 37
0.86 0.09 0.05
Matches are distributed among these distances:
87 36 0.06
88 4 0.01
89 1 0.00
90 2 0.00
91 35 0.06
95 1 0.00
98 2 0.00
99 48 0.08
100 10 0.02
101 445 0.76
102 4 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (101 bp):
AGCGACATTGGTCTTAAAGATGACGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCC
Found at i:257207 original size:31 final size:27
Alignment explanation
Indices: 257169--257227 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 27
257159 AAGAAGATGC
257169 CACCAACTTGTGTGGGCTTTTGAAAGGGTTG
1 CACCAACTTGTGT--GCTTTT-AAA-GGTTG
257200 CACCAACTTGTGTGCTTTTAAAGGTTG
1 CACCAACTTGTGTGCTTTTAAAGGTTG
257227 C
1 C
257228 CACTGACTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 6 0.21
28 3 0.11
29 6 0.21
31 13 0.46
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (27 bp):
CACCAACTTGTGTGCTTTTAAAGGTTG
Found at i:257259 original size:30 final size:29
Alignment explanation
Indices: 257179--257274 Score: 115
Period size: 30 Copynumber: 3.3 Consensus size: 29
257169 CACCAACTTG
**
257179 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTGAAAGGG-TGCCACTGACT
* *
257208 TGTGTGCTTTT-AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAGGGTGCCACTGACT
*
257236 TATGGGCTTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTTG-AAAGGGTGCCACTGACT
257266 TGTGGGCTT
1 TGTGGGCTT
257275 AAAAGGAGAA
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 2 0.04
28 20 0.36
29 10 0.18
30 24 0.43
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (29 bp):
TGTGGGCTTTTGAAAGGGTGCCACTGACT
Found at i:257364 original size:34 final size:32
Alignment explanation
Indices: 257247--257702 Score: 360
Period size: 33 Copynumber: 14.4 Consensus size: 32
257237 ATGGGCTTTT
* * *
257247 GAAAAGGGTGCCACTGACTTGTGGGCTTAAAAG
1 GAAAA-GGTGCCACGGAGTTGTGGACTTAAAAG
* *
257280 GAGAAAGATGCCACCGAGTTGTGGACTTAAAAGG
1 GA-AAAGGTGCCACGGAGTTGTGGACTTAAAA-G
257314 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
257346 GAACAAGGATGCCACGGAGTTGTGGACTTAAAA-
1 GAA-AAGG-TGCCACGGAGTTGTGGACTTAAAAG
* *
257379 G----GGTGCCACAGAGTTGTGGACTGAAAAG
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *
257407 GAACAAGGATGCCATGGAGTTGTAGACTTAAAA-
1 GAA-AAGG-TGCCACGGAGTTGTGGACTTAAAAG
** *
257440 G----GGTGCCACAAAGTTGCGGACTTAAAA-
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
* *
257467 G----GGTGCCACAGAGTTGTGGGCTTTAAAAAG
1 GAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAG
*
257497 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
*
257528 G----GGTGCCACAGAGTTGTGGACTTTGAAAAAG
1 GAAAAGGTGCCACGGAGTTGTGGAC-TT--AAAAG
* *
257559 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 GAAAAGGTGCCACGGAGTTGTGGAC-TT-AAAAG
* * *
257593 AAAAATGTGCCACAGAGTTGTGGACTTAAAAGG
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G
* *
257626 GAAAAGATGCCACGGAGTTGTAGACTTAAAAGG
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAA-G
* * * **
257659 GAAAAGATGCCACTGAGTCGTGGACTTGGAA-
1 GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
*
257690 GAAAAGATGCCAC
1 GAAAAGGTGCCAC
257703 TAAGTCGTAG
Statistics
Matches: 354, Mismatches: 42, Indels: 56
0.78 0.09 0.12
Matches are distributed among these distances:
27 78 0.22
28 9 0.03
29 4 0.01
30 4 0.01
31 13 0.04
32 12 0.03
33 118 0.33
34 95 0.27
35 21 0.06
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (32 bp):
GAAAAGGTGCCACGGAGTTGTGGACTTAAAAG
Found at i:257392 original size:27 final size:27
Alignment explanation
Indices: 257350--257550 Score: 186
Period size: 27 Copynumber: 6.9 Consensus size: 27
257340 TAAAAGGAAC
* *
257350 AAGGATGCCACGGAGTTGTGGACTTAA
1 AAGGGTGCCACAGAGTTGTGGACTTAA
*
257377 AAGGGTGCCACAGAGTTGTGGACTGAA
1 AAGGGTGCCACAGAGTTGTGGACTTAA
** *
257404 AAGGAACAAGGATGCCATGGAGTTGTAGACTTAA
1 AA-G-----GG-TGCCACAGAGTTGTGGACTTAA
* *
257438 AAGGGTGCCACAAAGTTGCGGACTTAA
1 AAGGGTGCCACAGAGTTGTGGACTTAA
*
257465 AAGGGTGCCACAGAGTTGTGGGCTTTAAA
1 AAGGGTGCCACAGAGTTGTGGAC-TT-AA
*
257494 AAGAAAAAGGTGCCACGGAGTTGTGGACTTAA
1 AAG-----GGTGCCACAGAGTTGTGGACTTAA
257526 AAGGGTGCCACAGAGTTGTGGACTT
1 AAGGGTGCCACAGAGTTGTGGACTT
257551 TGAAAAAGAA
Statistics
Matches: 142, Mismatches: 18, Indels: 28
0.76 0.10 0.15
Matches are distributed among these distances:
27 84 0.59
28 5 0.04
29 5 0.04
32 5 0.04
33 5 0.04
34 38 0.27
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (27 bp):
AAGGGTGCCACAGAGTTGTGGACTTAA
Found at i:257396 original size:61 final size:61
Alignment explanation
Indices: 257315--257468 Score: 247
Period size: 61 Copynumber: 2.5 Consensus size: 61
257305 CTTAAAAGGG
* *
257315 AAAA-GGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGATGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGATGCCACGGAGTTGTAGACTT
* *
257375 AAAAGGGTGCCACAGAGTTGTGGACTGAAAAGGAACAAGGATGCCATGGAGTTGTAGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGATGCCACGGAGTTGTAGACTT
* *
257436 AAAAGGGTGCCACAAAGTTGCGGACTTAAAAGG
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGG
257469 GTGCCACAGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
60 4 0.05
61 82 0.95
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.19
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAACAAGGATGCCACGGAGTTGTAGACTT
Found at i:257469 original size:88 final size:88
Alignment explanation
Indices: 257363--257626 Score: 307
Period size: 88 Copynumber: 2.9 Consensus size: 88
257353 GATGCCACGG
* * *
257363 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TGAAAAGGAACAAGGATGCCATGGAGT
1 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAAGAAAAAGG-TGCCACGGAGT
257427 TGTAGACTTAAAAGGGTGCCACAA
65 TGTAGACTTAAAAGGGTGCCACAA
* * *
257451 AGTTGCGGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTT
1 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAAGAAAAAGGTGCCACGGAGTT
* *
257516 GTGGACTTAAAAGGGTGCCACAG
66 GTAGACTTAAAAGGGTGCCACAA
* * *
257539 AGTTGTGGACTTTGAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTG-AAAAGAAAAATGTGC
1 AGTTGTGGAC-TT--AAAAG-----GGTGCCACAGAGTTGTGGAC-TTGAAAAAGAAAAAGGTGC
* *
257603 CACAGAGTTGTGGACTTAAAAGGG
57 CACGGAGTTGTAGACTTAAAAGGG
257627 AAAAGATGCC
Statistics
Matches: 153, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
88 76 0.50
89 14 0.09
91 5 0.03
96 56 0.37
97 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (88 bp):
AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTGAAAAAGAAAAAGGTGCCACGGAGTT
GTAGACTTAAAAGGGTGCCACAA
Found at i:257506 original size:61 final size:62
Alignment explanation
Indices: 257436--257571 Score: 220
Period size: 61 Copynumber: 2.2 Consensus size: 62
257426 TTGTAGACTT
* *
257436 AAAAGGGTGCCACAAAGTTGCGGACTTAAAAGGGTGCCACAGAGTTGTGGGCTTT-AAAAAG
1 AAAAAGGTGCCACAAAGTTGCGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAAG
** *
257497 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAAG
1 AAAAAGGTGCCACAAAGTTGCGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAAG
257559 AAAAAGGTGCCAC
1 AAAAAGGTGCCAC
257572 GGAGTTGTGG
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
61 50 0.72
62 19 0.28
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (62 bp):
AAAAAGGTGCCACAAAGTTGCGGACTTAAAAGGGTGCCACAGAGTTGTGGACTTTGAAAAAG
Found at i:257694 original size:31 final size:31
Alignment explanation
Indices: 257626--257821 Score: 216
Period size: 31 Copynumber: 6.3 Consensus size: 31
257616 ACTTAAAAGG
* * * **
257626 GAAAAGATGCCACGGAGTTGTAGACTTAAAA
1 GAAAAGATGCCACTGAGTCGTGGACTTGGAA
257657 GGGAAAAGATGCCACTGAGTCGTGGACTTGGAA
1 --GAAAAGATGCCACTGAGTCGTGGACTTGGAA
* * *
257690 GAAAAGATGCCACTAAGTCGTAGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTGGAA
*
257721 -AAGAGATGCCACTGAGTCGTGGACTTTGGGAA
1 GAAAAGATGCCACTGAGTCGTGGAC-TT-GGAA
* * *
257753 -AAAAGACGCCACTGGGTCATGGACTTGGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTGGAA
*
257783 GAAAAGATGCCACTGAGTCGTGGACTTTGAA
1 GAAAAGATGCCACTGAGTCGTGGACTTGGAA
*
257814 GAAGAGAT
1 GAAAAGAT
257822 TTGAAGAATT
Statistics
Matches: 139, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
30 25 0.18
31 65 0.47
32 23 0.17
33 26 0.19
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (31 bp):
GAAAAGATGCCACTGAGTCGTGGACTTGGAA
Found at i:266075 original size:13 final size:13
Alignment explanation
Indices: 266057--266082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
266047 AAATTCCCAG
266057 ATGTATCGATACA
1 ATGTATCGATACA
266070 ATGTATCGATACA
1 ATGTATCGATACA
266083 TTGAATAATG
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:266162 original size:19 final size:19
Alignment explanation
Indices: 266134--266194 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
266124 AGTGATACAT
266134 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
266153 TGTGTCGAT--AA-A--T-
1 TGTATCGATACAACACTTA
266166 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
266185 TGTATCGATA
1 TGTATCGATA
266195 TAGTTACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 8 0.24
14 1 0.03
15 2 0.06
16 2 0.06
17 2 0.06
18 1 0.03
19 18 0.53
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:266173 original size:32 final size:32
Alignment explanation
Indices: 266127--266194 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
266117 GCTTTGTAGT
* *
266127 GATACATTGTATCGATACAACACTTATGTGTC
1 GATAAATTGTATCGATACAACACTTATGTATC
266159 GATAAATTGTATCGATACAACACTTATGTATC
1 GATAAATTGTATCGATACAACACTTATGTATC
266191 GATA
1 GATA
266195 TAGTTACTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
GATAAATTGTATCGATACAACACTTATGTATC
Found at i:266405 original size:12 final size:12
Alignment explanation
Indices: 266388--266415 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
266378 AACCATTTTC
266388 GTCCCCACATAT
1 GTCCCCACATAT
266400 GTCCCCACATAT
1 GTCCCCACATAT
266412 GTCC
1 GTCC
266416 ACTCCTCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.21, C:0.43, G:0.11, T:0.25
Consensus pattern (12 bp):
GTCCCCACATAT
Found at i:266509 original size:20 final size:21
Alignment explanation
Indices: 266484--266522 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
266474 GTGTCTACAA
266484 ATGTATCGATACAT-TGAAGG
1 ATGTATCGATACATCTGAAGG
266504 ATGTATCGATACATCTGAA
1 ATGTATCGATACATCTGAA
266523 AAACCCATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.31
Consensus pattern (21 bp):
ATGTATCGATACATCTGAAGG
Found at i:266569 original size:13 final size:13
Alignment explanation
Indices: 266551--266589 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
266541 ATAATATTCT
*
266551 TTGTATCGATACG
1 TTGTATCGATACA
266564 TTGTATCGATACA
1 TTGTATCGATACA
266577 TTGTATCGATACA
1 TTGTATCGATACA
266590 AGGGTTACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:268523 original size:22 final size:23
Alignment explanation
Indices: 268483--268527 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
268473 TTTTTAATCG
* *
268483 TTTATCAAGGGGGAGAATTTTTT
1 TTTATCAAGAGGGAAAATTTTTT
268506 TTTATCAA-AGGGAAAATTTTTT
1 TTTATCAAGAGGGAAAATTTTTT
268528 AACGAGAGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.31, C:0.04, G:0.20, T:0.44
Consensus pattern (23 bp):
TTTATCAAGAGGGAAAATTTTTT
Found at i:269138 original size:19 final size:19
Alignment explanation
Indices: 269114--269185 Score: 117
Period size: 19 Copynumber: 3.7 Consensus size: 19
269104 ATTGATACAA
269114 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
269133 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
269153 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
269172 TGTATCGATACATG
1 TGTATCGATACATG
269186 AAACTGGCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 31 0.65
20 17 0.35
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:269163 original size:39 final size:38
Alignment explanation
Indices: 269110--269185 Score: 143
Period size: 39 Copynumber: 2.0 Consensus size: 38
269100 TTGTATTGAT
269110 ACAATGTATCGATACATGTTCATTGTATCGATACATGG
1 ACAATGTATCGATACATGTTCATTGTATCGATACATGG
269148 ACAATTGTATCGATACATGTTCATTGTATCGATACATG
1 ACAA-TGTATCGATACATGTTCATTGTATCGATACATG
269186 AAACTGGCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
38 4 0.11
39 33 0.89
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.36
Consensus pattern (38 bp):
ACAATGTATCGATACATGTTCATTGTATCGATACATGG
Found at i:269255 original size:31 final size:30
Alignment explanation
Indices: 269217--269279 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 30
269207 CCACTGTTTG
269217 TATCGATACATG-GCACATTGTATCGATACAT
1 TATCGATACATGTG-A-ATTGTATCGATACAT
269248 TATCGATACATGTTGAATTGTATCGATACAT
1 TATCGATACATG-TGAATTGTATCGATACAT
269279 T
1 T
269280 GCTCCTAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
31 28 0.93
32 1 0.03
33 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (30 bp):
TATCGATACATGTGAATTGTATCGATACAT
Found at i:278605 original size:20 final size:20
Alignment explanation
Indices: 278561--278613 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
278551 TACTCTAAAG
* *
278561 AATGTATCGATACATTTATA
1 AATGTATCGATACATTGAAA
*
278581 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
*
278601 AATGTATTGATAC
1 AATGTATCGATAC
278614 TTCTAGGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:285097 original size:21 final size:18
Alignment explanation
Indices: 285080--285117 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
285070 CAAAAGATGG
285080 CATAAAAAAAAATCAAGA
1 CATAAAAAAAAATCAAGA
*
285098 CATGAAAAAAAATCAAGA
1 CATAAAAAAAAATCAAGA
285116 CA
1 CA
285118 ATCCTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.68, C:0.13, G:0.08, T:0.11
Consensus pattern (18 bp):
CATAAAAAAAAATCAAGA
Found at i:285989 original size:20 final size:20
Alignment explanation
Indices: 285964--286101 Score: 133
Period size: 20 Copynumber: 6.8 Consensus size: 20
285954 GTAAAAGGAC
285964 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
285984 AGAATGTATCAATACATTCA
1 AGAATGTATCGATACATTGA
* *
286004 TA-CATGTATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
286024 A-AGATGTATCGATATATTGA
1 AGA-ATGTATCGATACATTGA
286044 A-AGATGTATCGATACATCT-A
1 AGA-ATGTATCGATACAT-TGA
*
286064 GGTAATGTATCGATACATTGGA
1 AG-AATGTATCGATACATT-GA
286086 AG-ATGTATCGATACAT
1 AGAATGTATCGATACAT
286102 CTGGGTAAAA
Statistics
Matches: 101, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.01
20 81 0.80
21 16 0.16
22 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:286097 original size:61 final size:60
Alignment explanation
Indices: 285967--286101 Score: 177
Period size: 61 Copynumber: 2.2 Consensus size: 60
285957 AAAGGACAGA
*
285967 ATGTATCGATACATTGAAGAATGTATCAATACATTCATACATGTATCGATATATTGAAAG
1 ATGTATCGATACATTGAAGAATGTATCAATACATTCATACATGTATCGATACATTGAAAG
* * *
286027 ATGTATCGATATATTGAA-AGATGTATCGATACA-TCTAGGTA-ATGTATCGATACATTGGAAG
1 ATGTATCGATACATTGAAGA-ATGTATCAATACATTC-A--TACATGTATCGATACATTGAAAG
286088 ATGTATCGATACAT
1 ATGTATCGATACAT
286102 CTGGGTAAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 3 0.05
60 30 0.45
61 31 0.47
62 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (60 bp):
ATGTATCGATACATTGAAGAATGTATCAATACATTCATACATGTATCGATACATTGAAAG
Found at i:291159 original size:32 final size:33
Alignment explanation
Indices: 291116--291183 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
291106 ACAAGAGGGG
291116 AAAGAAAGGAAAAGAAAAATAGAG-AAA-AAAAT
1 AAAGAAAGGAAAAGAAAAA-AGAGAAAAGAAAAT
* *
291148 AAAGGAAGGAAAAGAAAAAAGGGAAAAGAAAAT
1 AAAGAAAGGAAAAGAAAAAAGAGAAAAGAAAAT
291181 AAA
1 AAA
291184 AAAAATTGTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 3 0.09
32 21 0.66
33 8 0.25
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (33 bp):
AAAGAAAGGAAAAGAAAAAAGAGAAAAGAAAAT
Found at i:291172 original size:14 final size:14
Alignment explanation
Indices: 291123--291179 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
291113 GGGAAAGAAA
291123 GGAAAAGAAAAATAG
1 GGAAAAGAAAAA-AG
*
291138 AGAAAA-AAATAAAGG
1 GGAAAAGAAA-AAA-G
291153 AAGGAAAAGAAAAAAG
1 --GGAAAAGAAAAAAG
291169 GGAAAAGAAAA
1 GGAAAAGAAAA
291180 TAAAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 15 0.43
15 8 0.23
16 1 0.03
17 8 0.23
18 3 0.09
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (14 bp):
GGAAAAGAAAAAAG
Found at i:292422 original size:8 final size:8
Alignment explanation
Indices: 292409--292434 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
292399 TGTTTAATTT
292409 ATTTTTAA
1 ATTTTTAA
292417 ATTTTTAA
1 ATTTTTAA
292425 ATTTTTAA
1 ATTTTTAA
292433 AT
1 AT
292435 GATCTGCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTTAA
Found at i:294905 original size:18 final size:17
Alignment explanation
Indices: 294882--294915 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
294872 AGAATTTACT
294882 GAAACCCCTACTTGCAAG
1 GAAA-CCCTACTTGCAAG
*
294900 GAAACCTTACTTGCAA
1 GAAACCCTACTTGCAA
294916 TCTTACTCTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.35, C:0.29, G:0.15, T:0.21
Consensus pattern (17 bp):
GAAACCCTACTTGCAAG
Found at i:295607 original size:34 final size:34
Alignment explanation
Indices: 295568--295684 Score: 164
Period size: 34 Copynumber: 3.4 Consensus size: 34
295558 TAAAATATCT
* * * *
295568 TGCTTACCTAACGCATTACCTAAGACACTTAATA
1 TGCTTACCTAACACATCACCTAACACACCTAATA
295602 TGCTTACCTAACACATCACC-AACACACCTAATA
1 TGCTTACCTAACACATCACCTAACACACCTAATA
*
295635 TACTTTACCTAACACATCACCTAACACACCTAATA
1 TGC-TTACCTAACACATCACCTAACACACCTAATA
*
295670 TGTTTACCTAACACA
1 TGCTTACCTAACACA
295685 CTTAACAAAG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
33 13 0.18
34 47 0.64
35 14 0.19
ACGTcount: A:0.38, C:0.32, G:0.04, T:0.26
Consensus pattern (34 bp):
TGCTTACCTAACACATCACCTAACACACCTAATA
Found at i:300374 original size:34 final size:35
Alignment explanation
Indices: 300334--300414 Score: 128
Period size: 34 Copynumber: 2.3 Consensus size: 35
300324 AATATCTCGC
*
300334 TCACCTAACACATTACCTAACACACCTAATATACT
1 TCACCTAACACATCACCTAACACACCTAATATACT
* *
300369 T-ACCTAACACATCACCTAATACACCTAATATGCT
1 TCACCTAACACATCACCTAACACACCTAATATACT
300403 TCACCTAACACA
1 TCACCTAACACA
300415 CCTAATATGC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
34 31 0.74
35 11 0.26
ACGTcount: A:0.40, C:0.35, G:0.01, T:0.25
Consensus pattern (35 bp):
TCACCTAACACATCACCTAACACACCTAATATACT
Found at i:300406 original size:23 final size:23
Alignment explanation
Indices: 300380--300459 Score: 110
Period size: 22 Copynumber: 3.6 Consensus size: 23
300370 ACCTAACACA
*
300380 TCACCTAATACACCTAATATGCT
1 TCACCTAACACACCTAATATGCT
300403 TCACCTAACACACCTAATATGC-
1 TCACCTAACACACCTAATATGCT
* *
300425 TCACTTAATACACCTAATATG-T
1 TCACCTAACACACCTAATATGCT
*
300447 TTACCTAACACAC
1 TCACCTAACACAC
300460 TTTACAAGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.58
23 21 0.42
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (23 bp):
TCACCTAACACACCTAATATGCT
Found at i:302458 original size:8 final size:8
Alignment explanation
Indices: 302434--302464 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
302424 GTAGAAACTA
302434 AAAAAAAT
1 AAAAAAAT
302442 AAAATAAAT
1 AAAA-AAAT
302451 AAAAAAAT
1 AAAAAAAT
302459 AAAAAA
1 AAAAAA
302465 TCATTAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (8 bp):
AAAAAAAT
Found at i:306909 original size:21 final size:20
Alignment explanation
Indices: 306883--306934 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
306873 TTCTACAATT
**
306883 TGTATCGATACAATAACTTTA
1 TGTATCGATAC-ATAACTGAA
* *
306904 TGTATCAATACATAAGTGAA
1 TGTATCGATACATAACTGAA
306924 TGTATCGATAC
1 TGTATCGATAC
306935 TGGACCCTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAACTGAA
Found at i:307056 original size:20 final size:20
Alignment explanation
Indices: 307028--307075 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
307018 AACCCAAATG
*
307028 TATCAATATATTTTTCAATA
1 TATCGATATATTTTTCAATA
*
307048 TATCGATATATTTTTTAATA
1 TATCGATATATTTTTCAATA
307068 TATCGATA
1 TATCGATA
307076 AATCCAGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (20 bp):
TATCGATATATTTTTCAATA
Found at i:309579 original size:97 final size:97
Alignment explanation
Indices: 309454--309650 Score: 234
Period size: 97 Copynumber: 2.0 Consensus size: 97
309444 CTCCGTTTTC
* ** * *
309454 TTTAAACTCGTCAAGACTAAAATTTTATTTTTGCTTAAATTGTTAACCTCGGGGATACTCTAACT
1 TTTAAACTCGTCAAGACTAAAATCTTATTTTTGCCCAAATTGTTAACCTCGGGGATACTCCAACC
* * *
309519 CTATTCTTTTGAGGGGATACTCTAACCCCATT
66 CCATTCCTTTGAGGGGATAATCTAACCCCATT
* * * *** *
309551 TTTAAACTTC-TCAAGATTTAAATCTTATTTTTTCCCAAATTGTTATTGTTGGGGATACTCCAAC
1 TTTAAAC-TCGTCAAGACTAAAATCTTATTTTTGCCCAAATTGTTAACCTCGGGGATACTCCAAC
*
309615 CCCATTCCTTTGAGGGGATAATCTAACCTCATT
65 CCCATTCCTTTGAGGGGATAATCTAACCCCATT
309648 TTT
1 TTT
309651 TAACCAAAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
97 81 0.98
98 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.41
Consensus pattern (97 bp):
TTTAAACTCGTCAAGACTAAAATCTTATTTTTGCCCAAATTGTTAACCTCGGGGATACTCCAACC
CCATTCCTTTGAGGGGATAATCTAACCCCATT
Found at i:310720 original size:31 final size:31
Alignment explanation
Indices: 310685--310759 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
310675 CTTGTTCACT
* * *
310685 AATATTTTTTGTTATGCGAATGTCATCATGC
1 AATATATTTCGTTATGCGAATCTCATCATGC
**
310716 AATATATTTCGTTATGCGGGTCTCATCATGC
1 AATATATTTCGTTATGCGAATCTCATCATGC
310747 AATATATTTCGTT
1 AATATATTTCGTT
310760 TTAACAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (31 bp):
AATATATTTCGTTATGCGAATCTCATCATGC
Found at i:313488 original size:20 final size:19
Alignment explanation
Indices: 313441--313490 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
313431 TATGCTTTGC
** *
313441 ATCGATACATGTTCATTGT
1 ATCGATACATGGACATTAT
*
313460 ATTGATACATGGACAATTAT
1 ATCGATACATGGAC-ATTAT
313480 ATCGATACATG
1 ATCGATACATG
313491 AAACTGGCAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (19 bp):
ATCGATACATGGACATTAT
Found at i:313544 original size:20 final size:19
Alignment explanation
Indices: 313519--313572 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
313509 CTACCACTGT
313519 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGTG-A-A
*
313539 TTGTATCAATACATGTTGAA
1 TTGTATCGATACATG-TGAA
313559 TTGTATCGATACAT
1 TTGTATCGATACAT
313573 TGCTTCTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 28 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (19 bp):
TTGTATCGATACATGTGAA
Found at i:322871 original size:20 final size:20
Alignment explanation
Indices: 322842--322899 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
322832 ATGTACTCTA
322842 AAAAATGTATCGATACATTC
1 AAAAATGTATCGATACATTC
* * *
322862 ATATATGTATCGATACATTG
1 AAAAATGTATCGATACATTC
322882 AAAAATGTATCGATACAT
1 AAAAATGTATCGATACAT
322900 CTGGGTAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (20 bp):
AAAAATGTATCGATACATTC
Found at i:324362 original size:44 final size:44
Alignment explanation
Indices: 324297--324384 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
324287 AGTGTACTCC
*
324297 ACAGTTTCCAGGACCAAAACTGCTGAGAGAAAGGCACTGAAACA
1 ACAGTTTCCAGGACCAAAACTGCAGAGAGAAAGGCACTGAAACA
*
324341 ACAGTTTCCAGGACCAGAACTGCAGAGAGAAAGGCACTGAAACA
1 ACAGTTTCCAGGACCAAAACTGCAGAGAGAAAGGCACTGAAACA
324385 CAGCACGACC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.12
Consensus pattern (44 bp):
ACAGTTTCCAGGACCAAAACTGCAGAGAGAAAGGCACTGAAACA
Found at i:325650 original size:13 final size:13
Alignment explanation
Indices: 325632--325659 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
325622 GCGATCAATT
325632 ATAATAAATATTA
1 ATAATAAATATTA
325645 ATAATAAATATTA
1 ATAATAAATATTA
325658 AT
1 AT
325660 GATGAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATAAATATTA
Found at i:330094 original size:20 final size:20
Alignment explanation
Indices: 330069--330119 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
330059 TAACTAGATG
**
330069 TATCGATATGTTGAAAAATA
1 TATCGATACATTGAAAAATA
330089 TATCGATACATTGAAAAATA
1 TATCGATACATTGAAAAATA
330109 TATCGATACAT
1 TATCGATACAT
330120 CTAGGTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (20 bp):
TATCGATACATTGAAAAATA
Found at i:330159 original size:20 final size:20
Alignment explanation
Indices: 330134--330231 Score: 94
Period size: 20 Copynumber: 4.8 Consensus size: 20
330124 GTAAAAGGAC
330134 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
330154 AGAATGTGTCGATACATTCA
1 AGAATGTATCGATACATTGA
*
330174 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
330194 A-AGATGTATCGATAGATCT-A
1 AGA-ATGTATCGATACAT-TGA
*
330214 GGTAATGTATCGATACAT
1 AG-AATGTATCGATACAT
330232 CTGGGTACAA
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 47 0.73
21 15 0.23
22 1 0.02
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:332841 original size:20 final size:20
Alignment explanation
Indices: 332816--332858 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
332806 CACTCTATGG
332816 TCAATGTTTAAGCTAGCATC
1 TCAATGTTTAAGCTAGCATC
332836 TCAATGTTTAAGCTAGCATC
1 TCAATGTTTAAGCTAGCATC
332856 TCA
1 TCA
332859 TAAGCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (20 bp):
TCAATGTTTAAGCTAGCATC
Found at i:334354 original size:98 final size:99
Alignment explanation
Indices: 334239--334484 Score: 252
Period size: 97 Copynumber: 2.5 Consensus size: 99
334229 AATTTTATTT
* * * *
334239 ATCGAAAATATTCCAACCCCA-TCTTCCGAAGAGATACTCCAACACCATTTTTTTAAAC-TCGTC
1 ATCGAAGATACTCCAACCCCATTCTTTCGAAGGGATACTCCAACACCATTTTTTTAAACTTC-TC
* **
334302 AAGACTT-AAATTTTATTTTTGCTTAAATTATCAAC
65 AAGA-TTGAAATCTTATTTTTGCCCAAATTATCAAC
* * * * * * *
334337 CTCGAAGATACTCCAACCCTATTCTTTTGAGGGGATACT-CTA-ACCATGTTTTTAAACTTCTTA
1 ATCGAAGATACTCCAACCCCATTCTTTCGAAGGGATACTCCAACACCATTTTTTTAAACTTCTCA
* * *
334400 AGATTGAAATCTTATTTTTTCCCAAATTGTCATC
66 AGATTGAAATCTTATTTTTGCCCAAATTATCAAC
* * *
334434 ATCGAAGATACTCTAACCCCATTCTTTCG-AGGGATGCTCCAACCCCATTTT
1 ATCGAAGATACTCCAACCCCATTCTTTCGAAGGGATACTCCAACACCATTTT
334485 CAACCAAAAA
Statistics
Matches: 117, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
96 9 0.08
97 68 0.58
98 27 0.23
99 13 0.11
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.35
Consensus pattern (99 bp):
ATCGAAGATACTCCAACCCCATTCTTTCGAAGGGATACTCCAACACCATTTTTTTAAACTTCTCA
AGATTGAAATCTTATTTTTGCCCAAATTATCAAC
Found at i:336776 original size:33 final size:34
Alignment explanation
Indices: 336732--336801 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 34
336722 ACAAGAGGGG
*
336732 AAAGAAAGGAAAAGAAAAATAGAGAAAA-AAAAT
1 AAAGAAAGGAAAAGAAAAAAAGAGAAAAGAAAAT
* *
336765 AAAGGAAGGAAAAGAAAAAAAGGGAAAAGAAAAT
1 AAAGAAAGGAAAAGAAAAAAAGAGAAAAGAAAAT
336799 AAA
1 AAA
336802 AAAAATTTAC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 25 0.76
34 8 0.24
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.04
Consensus pattern (34 bp):
AAAGAAAGGAAAAGAAAAAAAGAGAAAAGAAAAT
Found at i:336787 original size:14 final size:15
Alignment explanation
Indices: 336732--336797 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
336722 ACAAGAGGGG
336732 AAAGAAAGGAAAAGAA
1 AAAG-AAGGAAAAGAA
* * *
336748 AAATAGAGAAAAAAAA
1 AAAGA-AGGAAAAGAA
336764 TAAAGGAAGGAAAAGAA
1 -AAA-GAAGGAAAAGAA
336781 AAA-AAGGGAAAAGAA
1 AAAGAA-GGAAAAGAA
336796 AA
1 AA
336798 TAAAAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.05
15 12 0.30
16 14 0.35
17 11 0.28
18 1 0.03
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAAGAAGGAAAAGAA
Found at i:336790 original size:15 final size:15
Alignment explanation
Indices: 336739--336797 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
336729 GGGAAAGAAA
*
336739 GGAAAAGAAAAATAG
1 GGAAAAGAAAAAAAG
*
336754 AGAAAA-AAAATAAAGG
1 GGAAAAGAAAA-AAA-G
336770 AAGGAAAAGAAAAAAAG
1 --GGAAAAGAAAAAAAG
336787 GGAAAAGAAAA
1 GGAAAAGAAAA
336798 TAAAAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
14 4 0.11
15 18 0.50
16 1 0.03
17 1 0.03
18 8 0.22
19 4 0.11
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (15 bp):
GGAAAAGAAAAAAAG
Found at i:338609 original size:16 final size:16
Alignment explanation
Indices: 338588--338618 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
338578 TTTATTTTTT
338588 AAATTTCAAGGATTTC
1 AAATTTCAAGGATTTC
338604 AAATTTCAAGGATTT
1 AAATTTCAAGGATTT
338619 GATGTACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (16 bp):
AAATTTCAAGGATTTC
Found at i:341118 original size:35 final size:34
Alignment explanation
Indices: 341035--341152 Score: 155
Period size: 34 Copynumber: 3.4 Consensus size: 34
341025 TAAAATATCT
* * * *
341035 TGCTCACCTAACGCATTACCTAACACATCTAATA
1 TGCTTACCTAACACATCACCTAACACACCTAATA
341069 TGCTTACCTAACACATCACCTAACACACCTAATA
1 TGCTTACCTAACACATCACCTAACACACCTAATA
* * *
341103 TACTTTACCTAACACACCACCTAATACACCTAATA
1 TGC-TTACCTAACACATCACCTAACACACCTAATA
*
341138 TGCTCACCTAACACA
1 TGCTTACCTAACACA
341153 CCTAATATGT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 43 0.58
35 31 0.42
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.25
Consensus pattern (34 bp):
TGCTTACCTAACACATCACCTAACACACCTAATA
Found at i:341147 original size:22 final size:22
Alignment explanation
Indices: 341120--341175 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
341110 CCTAACACAC
*
341120 CACCTAATACACCTAATATGCT
1 CACCTAACACACCTAATATGCT
*
341142 CACCTAACACACCTAATATGTT
1 CACCTAACACACCTAATATGCT
*
341164 TACCTAACACAC
1 CACCTAACACAC
341176 TTAACAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.34, G:0.04, T:0.25
Consensus pattern (22 bp):
CACCTAACACACCTAATATGCT
Found at i:345865 original size:34 final size:34
Alignment explanation
Indices: 345822--345905 Score: 132
Period size: 34 Copynumber: 2.4 Consensus size: 34
345812 TAAAATATCT
* *
345822 TGCTCACCTAACACATTACCTAACACACCTAATA
1 TGCTTACCTAACACATCACCTAACACACCTAATA
*
345856 TGCTTACCTAACACATCACCTAACACACTTAATA
1 TGCTTACCTAACACATCACCTAACACACCTAATA
345890 TGCTTCACCTAACACA
1 TGCTT-ACCTAACACA
345906 CCTAATATGC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 36 0.78
35 10 0.22
ACGTcount: A:0.37, C:0.35, G:0.04, T:0.25
Consensus pattern (34 bp):
TGCTTACCTAACACATCACCTAACACACCTAATA
Found at i:345928 original size:22 final size:23
Alignment explanation
Indices: 345871--345950 Score: 110
Period size: 22 Copynumber: 3.6 Consensus size: 23
345861 ACCTAACACA
*
345871 TCACCTAACACACTTAATATGCT
1 TCACCTAACACACCTAATATGCT
345894 TCACCTAACACACCTAATATGC-
1 TCACCTAACACACCTAATATGCT
* *
345916 TCACTTAATACACCTAATATG-T
1 TCACCTAACACACCTAATATGCT
*
345938 TTACCTAACACAC
1 TCACCTAACACAC
345951 TTAACAAGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
22 29 0.58
23 21 0.42
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (23 bp):
TCACCTAACACACCTAATATGCT
Found at i:347380 original size:141 final size:141
Alignment explanation
Indices: 347126--347380 Score: 411
Period size: 141 Copynumber: 1.8 Consensus size: 141
347116 ATTAGGCTAA
* * ** * *
347126 AACCACTTTCACTCTAGTGTCAAGGTTTATATTCATAATATAACCTCATAAAGGATACATAAATG
1 AACCACTTTCACCCTAGTGGCAAGGTCGATATTCATAAGATAACCTCAGAAAGGATACATAAATG
*
347191 CTAGCATACAGTACCATTGTATTTATCCCTAATGGCAGGGTCCAGAACATAGTTAGGTCAAATAA
66 CTAGCATACAGTACCATTGTATTCATCCCTAATGGCAGGGTCCAGAACATAGTTAGGTCAAATAA
347256 TACTAGACTAT
131 TACTAGACTAT
* ** *
347267 AACCACTTTCACCCTAGTGGCAAGGTCGATATTCATAAGGTAACCTCAGAAAGGATATGTTAATG
1 AACCACTTTCACCCTAGTGGCAAGGTCGATATTCATAAGATAACCTCAGAAAGGATACATAAATG
347332 CTAGCATACAGTACCATTGTATTCATCCCTAATGGCAGGGTCCAGAACA
66 CTAGCATACAGTACCATTGTATTCATCCCTAATGGCAGGGTCCAGAACA
347381 GTAGCTAAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
141 103 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (141 bp):
AACCACTTTCACCCTAGTGGCAAGGTCGATATTCATAAGATAACCTCAGAAAGGATACATAAATG
CTAGCATACAGTACCATTGTATTCATCCCTAATGGCAGGGTCCAGAACATAGTTAGGTCAAATAA
TACTAGACTAT
Found at i:352637 original size:20 final size:20
Alignment explanation
Indices: 352589--352640 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
352579 TTTTGACTTA
*
352589 AATGTATCAATATATTTTTT
1 AATGTATCGATATATTTTTT
352609 AATGTATCGATATATTTTTT
1 AATGTATCGATATATTTTTT
352629 AATGTATCGATA
1 AATGTATCGATA
352641 AATCCAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.50
Consensus pattern (20 bp):
AATGTATCGATATATTTTTT
Found at i:355144 original size:97 final size:97
Alignment explanation
Indices: 355019--355215 Score: 234
Period size: 97 Copynumber: 2.0 Consensus size: 97
355009 CTCCGTTTTC
* ** *
355019 TTTAAACTTATCAAGACTAAAATTTTATTTTTGCTTAAATTGTTAACCTCGGGGATACTCTAA-C
1 TTTAAACTTATCAAGACTAAAATCTTATTTTTGCCCAAATTGTTAACCTCGGGGATACTCCAACC
* * *
355083 TCTATTCTTTTGAGGAGATACTCTAACCTCATT
66 TC-ATTCTTCTGAGGAGATAATCCAACCTCATT
* * * * ***
355116 TTTAAACTTCTCAAGATTTAAATCTTATTTTTTCCCAAATTGTTATTGTCGGGGATACTCCAACC
1 TTTAAACTTATCAAGACTAAAATCTTATTTTTGCCCAAATTGTTAACCTCGGGGATACTCCAACC
* *
355181 TCATTCTTCTGAGGGGATAATCCAACCTCGTT
66 TCATTCTTCTGAGGAGATAATCCAACCTCATT
355213 TTT
1 TTT
355216 CAACCAAAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
97 80 0.96
98 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.41
Consensus pattern (97 bp):
TTTAAACTTATCAAGACTAAAATCTTATTTTTGCCCAAATTGTTAACCTCGGGGATACTCCAACC
TCATTCTTCTGAGGAGATAATCCAACCTCATT
Found at i:356875 original size:90 final size:90
Alignment explanation
Indices: 356722--356897 Score: 325
Period size: 90 Copynumber: 2.0 Consensus size: 90
356712 GCTACTAGAA
356722 TAACCTAGAGAATAGGTTTACTCAGAGAAACACTTCTAACCACTACTTTCATTTATCATGTACAT
1 TAACCTAGAGAATAGGTTTACTCAGAGAAACACTTCTAACCACTACTTTCATTTATCATGTACAT
*
356787 GTAGGTGATAATGAATGAACACTTC
66 GTAGGTGATAATGAATAAACACTTC
* *
356812 TAACCTAGAGAATAGGTTTACTCAGAGAAACACTTCTAACCTCTACTTTCATTTGTCATGTACAT
1 TAACCTAGAGAATAGGTTTACTCAGAGAAACACTTCTAACCACTACTTTCATTTATCATGTACAT
356877 GTAGGTGATAATGAATAAACA
66 GTAGGTGATAATGAATAAACA
356898 TTACCATCTA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (90 bp):
TAACCTAGAGAATAGGTTTACTCAGAGAAACACTTCTAACCACTACTTTCATTTATCATGTACAT
GTAGGTGATAATGAATAAACACTTC
Found at i:361365 original size:20 final size:19
Alignment explanation
Indices: 361342--361414 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
361332 CACATTCAGA
*
361342 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
**
361362 TGTATTAATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
361381 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
361401 TGTATCGATACATG
1 TGTATCGATACATG
361415 AAACTGGCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
19 15 0.34
20 28 0.64
21 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:361481 original size:33 final size:32
Alignment explanation
Indices: 361444--361508 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
361434 TACCACTGTT
361444 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGTG-A-ATTGTATCGATACAA
361477 TGTATCGATACATGTTGAATTGTATCGATACA
1 TGTATCGATACATG-TGAATTGTATCGATACA
361509 TTGCTTCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATGTGAATTGTATCGATACAA
Found at i:361482 original size:13 final size:13
Alignment explanation
Indices: 361464--361488 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361454 CATGGCACAT
361464 TGTATCGATACAA
1 TGTATCGATACAA
361477 TGTATCGATACA
1 TGTATCGATACA
361489 TGTTGAATTG
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:367302 original size:20 final size:19
Alignment explanation
Indices: 367277--367365 Score: 73
Period size: 20 Copynumber: 4.8 Consensus size: 19
367267 TTTTCACAAT
367277 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATT-CTCA
*
367297 TTGTATTGAT--A----CA
1 TTGTATCGATACATTCTCA
367310 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATT-CTCA
* *
367330 TTGTATCGATAGATTTTACA
1 TTGTATCGATACATTCT-CA
*
367350 ATGTATCGATACATTC
1 TTGTATCGATACATTC
367366 AGGCATTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
13 11 0.20
15 1 0.02
18 1 0.02
19 1 0.02
20 40 0.74
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACATTCTCA
Found at i:367313 original size:13 final size:13
Alignment explanation
Indices: 367295--367325 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
367285 ATACATTGCT
*
367295 CATTGTATTGATA
1 CATTGTATCGATA
367308 CATTGTATCGATA
1 CATTGTATCGATA
367321 CATTG
1 CATTG
367326 CTCATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:367319 original size:33 final size:33
Alignment explanation
Indices: 367277--367340 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
367267 TTTTCACAAT
*
367277 TTGTATCGATACATTGCTCATTGTATTGATACA
1 TTGTATCGATACATTGCTCATTGTATCGATACA
367310 TTGTATCGATACATTGCTCATTGTATCGATA
1 TTGTATCGATACATTGCTCATTGTATCGATA
367341 GATTTTACAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.42
Consensus pattern (33 bp):
TTGTATCGATACATTGCTCATTGTATCGATACA
Found at i:368223 original size:12 final size:12
Alignment explanation
Indices: 368187--368216 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
368177 AAGACTCCCA
368187 TGCATTCTTGTT
1 TGCATTCTTGTT
368199 TGCATTCTTGTT
1 TGCATTCTTGTT
368211 TGCATT
1 TGCATT
368217 TCTGTTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.10, C:0.17, G:0.17, T:0.57
Consensus pattern (12 bp):
TGCATTCTTGTT
Found at i:369952 original size:51 final size:50
Alignment explanation
Indices: 369657--369978 Score: 236
Period size: 51 Copynumber: 6.3 Consensus size: 50
369647 TTTTCATCTT
* *
369657 GGGGATACTCCAATCTCGGTTTCATTTTCAAAACATCAATTTTTCTTAATC
1 GGGGATACTCCAATC-CGATTTCATTTTCAAAACATCAATTTTTCTCAATC
* * * * ** * *
369708 -GGGATACTCTAACTCCGATTTTA-TTTCTAAAGCATCGATTTACCGCAACC
1 GGGGATACTCCAA-TCCGATTTCATTTTC-AAAACATCAATTTTTCTCAATC
* * * * *
369758 GGGGATACTCTAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATC
1 GGGGATACTCCAAT-CCGATTTCATTTTCAAAACATCAATTTTTCTCAATC
* * * * * *
369809 AGGGATACTCCAACTCCGATTTTA-TTTCTAAAGCATCGATTTTCCTGCAACC
1 GGGGATACTCCAA-TCCGATTTCATTTTC-AAAACATCAATTTTTCT-CAATC
** * * * * *
369861 GGGGATACTCTTATCCCGGTTTCATCTCCACAACATCAATTTTTCTTAATC
1 GGGGATACTCCAAT-CCGATTTCATTTTCAAAACATCAATTTTTCTCAATC
* * * * * *
369912 GGGGATACTCCAACTCTGATTTTATTTTCAAAATACCAATTTTTCACAATT
1 GGGGATACTCCAA-TCCGATTTCATTTTCAAAACATCAATTTTTCTCAATC
369963 GGGGATACTCCAATCC
1 GGGGATACTCCAATCC
369979 CGTCATTTCA
Statistics
Matches: 201, Mismatches: 59, Indels: 23
0.71 0.21 0.08
Matches are distributed among these distances:
49 4 0.02
50 37 0.18
51 121 0.60
52 37 0.18
53 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.35
Consensus pattern (50 bp):
GGGGATACTCCAATCCGATTTCATTTTCAAAACATCAATTTTTCTCAATC
Found at i:369954 original size:103 final size:101
Alignment explanation
Indices: 369657--369938 Score: 456
Period size: 103 Copynumber: 2.8 Consensus size: 101
369647 TTTTCATCTT
* * * * *
369657 GGGGATACTCCAATCTCGGTTTCATTTTCAAAACATCAATTTTTCTTAATCGGGATACTCTAACT
1 GGGGATACTCTAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATCGGGATACTCCAACT
*
369722 CCGATTTTATTTCTAAAGCATCGATTTACCGCAACC
66 CCGATTTTATTTCTAAAGCATCGATTTTCCGCAACC
369758 GGGGATACTCTAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATCAGGGATACTCCAAC
1 GGGGATACTCTAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATC-GGGATACTCCAAC
369823 TCCGATTTTATTTCTAAAGCATCGATTTTCCTGCAACC
65 TCCGATTTTATTTCTAAAGCATCGATTTTCC-GCAACC
* *
369861 GGGGATACTCTTATCCCGGTTTCATCTCCACAACATCAATTTTTCTTAATCGGGGATACTCCAAC
1 GGGGATACTCTAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATC-GGGATACTCCAAC
*
369926 TCTGATTTTATTT
65 TCCGATTTTATTT
369939 TCAAAATACC
Statistics
Matches: 169, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
101 47 0.28
102 42 0.25
103 80 0.47
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (101 bp):
GGGGATACTCTAATCCCGGTTTCATCTCCAAAACATCAATTTTTCTTAATCGGGATACTCCAACT
CCGATTTTATTTCTAAAGCATCGATTTTCCGCAACC
Found at i:369995 original size:28 final size:27
Alignment explanation
Indices: 369963--370036 Score: 96
Period size: 28 Copynumber: 2.7 Consensus size: 27
369953 TTTCACAATT
*
369963 GGGGATACTCCAATCCCGTCA-TTTCA
1 GGGGATACTCCAACCCCGTCATTTTCA
*
369989 TCGGGGATACTCCAACCCCGTTATTTTCGA
1 --GGGGATACTCCAACCCCGTCATTTTC-A
370019 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
370037 ACTTTATATC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 37 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.24
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTCATTTTCA
Found at i:370119 original size:110 final size:109
Alignment explanation
Indices: 369963--370163 Score: 294
Period size: 110 Copynumber: 1.8 Consensus size: 109
369953 TTTCACAATT
* * * *
369963 GGGGATACTCCAATCCCGTCATTTCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACT
1 GGGGATACTCCAACCCCGTCATGTCATCAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACT
370028 CCAACCCCGACTTTATATCCAAAATATTGATTCTTTCATAATCG
66 CCAACCCCGACTTTATATCCAAAATATTGATTCTTTCATAATCG
* * * *
370072 GGGGAGTACTCTAACCCCGTTATGTCATCAGGGATACTCCCATCCCGTTATTTCCGAGGGGATAC
1 GGGGA-TACTCCAACCCCGTCATGTCATCAGGGATACTCCAACCCCGTTATTTCCGAGGGGATAC
* * *
370137 TCCAACCCCGATTTTATTTCTAAAATA
65 TCCAACCCCGACTTTATATCCAAAATA
370164 CCAATTTTTC
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
109 5 0.06
110 75 0.94
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.30
Consensus pattern (109 bp):
GGGGATACTCCAACCCCGTCATGTCATCAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACT
CCAACCCCGACTTTATATCCAAAATATTGATTCTTTCATAATCG
Found at i:370146 original size:28 final size:28
Alignment explanation
Indices: 370072--370146 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
370062 TTCATAATCG
*
370072 GGGGAGTACTCTAACCCCGTTATGTCATCA
1 GGGGA-TACTCCAACCCCGTTATGTCA-CA
* * *
370102 -GGGATACTCCCATCCCGTTATTTC-CGA
1 GGGGATACTCCAACCCCGTTATGTCAC-A
370129 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
370147 ATTTTATTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 31 0.84
29 4 0.11
ACGTcount: A:0.21, C:0.32, G:0.23, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATGTCACA
Found at i:370199 original size:51 final size:50
Alignment explanation
Indices: 370130--370248 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 50
370120 TATTTCCGAG
* * * * *
370130 GGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATC
1 GGGATACTCTAACCCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
* *
370180 GAGGATACTCTAACTCCGATTTTAGTTCCAAAACACCAATTTCTCATAATC
1 G-GGATACTCTAACCCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
370231 GGAGATACTCTAACCCCG
1 GG-GATACTCTAACCCCG
370249 TTATTTTCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
50 2 0.03
51 57 0.97
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (50 bp):
GGGATACTCTAACCCCGATTTTAGTTCCAAAACACCAATTTCTCACAATC
Found at i:370394 original size:80 final size:80
Alignment explanation
Indices: 370310--370458 Score: 185
Period size: 80 Copynumber: 1.9 Consensus size: 80
370300 TTTTCACAAT
* * ** * *
370310 CGGGGATACTCTAACCTCGATTTTATTTTTTAGAA-CATCGA-TTTTCCATAATCGGGGATATTC
1 CGGGGATACTCCAACCCCGACCTTA-TTTTTA-AAGCATCGATTTTTCCACAATCGGGGATACTC
370373 CAACCTAGTTATTTTCA
64 CAACCTAGTTATTTTCA
* * *
370390 CGGGGATACTCCAACCCCGGCCTTATTTTTAAAGCATCGATTTTTTCACAATCGGGGATACTCTA
1 CGGGGATACTCCAACCCCGACCTTATTTTTAAAGCATCGATTTTTCCACAATCGGGGATACTCCA
370455 ACCT
66 ACCT
370459 CGATTTTATT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
78 2 0.03
79 12 0.21
80 44 0.76
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (80 bp):
CGGGGATACTCCAACCCCGACCTTATTTTTAAAGCATCGATTTTTCCACAATCGGGGATACTCCA
ACCTAGTTATTTTCA
Found at i:370407 original size:132 final size:131
Alignment explanation
Indices: 370102--370506 Score: 498
Period size: 132 Copynumber: 3.1 Consensus size: 131
370092 TATGTCATCA
* * ***
370102 GGGATACTCCCATCCC-GTTATTTCCGA-GGGGATACTCCAACCCCGATTTTATTTCTAAA--AT
1 GGGATACT-CCAACCCAGTTATTTTC-ACGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCAT
* * * * ** * * *
370163 ACCAATTTTTCACAATCGAGGATACTCTAA-CTCCGATTTTA-GTTCCAAAACACCAATTTCTCA
64 -CGATTTTTTCACAATCGGGGATACTCTAACCT-CGATTTTATTTTTTAGAACACGATTTTC-CA
370226 TAATCG
126 TAATCG
* * * * *
370232 GAGATACTCTAACCCCGTTATTTTCACGGGGATACTTCGACCCCGGCCTTATTTCTAAAGCATCG
1 GGGATACTCCAACCCAGTTATTTTCACGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCG
370297 ATTTTTTCACAATCGGGGATACTCTAACCTCGATTTTATTTTTTAGAACATCGATTTTCCATAAT
66 ATTTTTTCACAATCGGGGATACTCTAACCTCGATTTTATTTTTTAGAACA-CGATTTTCCATAAT
370362 CG
130 CG
* * *
370364 GGGATATTCCAACCTAGTTATTTTCACGGGGATACTCCAACCCCGGCCTTATTTTTAAAGCATCG
1 GGGATACTCCAACCCAGTTATTTTCACGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCG
370429 ATTTTTTCACAATCGGGGATACTCTAACCTCGATTTTATTTTTTAGAACACCGATTTTCCATAAT
66 ATTTTTTCACAATCGGGGATACTCTAACCTCGATTTTATTTTTTAGAACA-CGATTTTCCATAAT
370494 CG
130 CG
*
370496 AGGATACTCCA
1 GGGATACTCCA
370507 GCCCTGTTGT
Statistics
Matches: 239, Mismatches: 29, Indels: 12
0.85 0.10 0.04
Matches are distributed among these distances:
129 6 0.03
130 42 0.18
131 34 0.14
132 151 0.63
133 6 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (131 bp):
GGGATACTCCAACCCAGTTATTTTCACGGGGATACTCCAACCCCGGCCTTATTTCTAAAGCATCG
ATTTTTTCACAATCGGGGATACTCTAACCTCGATTTTATTTTTTAGAACACGATTTTCCATAATC
G
Found at i:372582 original size:4 final size:4
Alignment explanation
Indices: 372573--372597 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
372563 TATTTTGAGG
372573 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
372598 GTTTTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Done.