Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015161.1 Kokia drynarioides strain JFW-HI SEQ_130205, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 994981
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 641 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:718076 original size:2 final size:2
Alignment explanation
Indices: 718069--718098 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
718059 TTTATTATTC
718069 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
718099 GTGTGTGTGT
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:732788 original size:28 final size:27
Alignment explanation
Indices: 732748--732837 Score: 94
Period size: 28 Copynumber: 3.3 Consensus size: 27
732738 ATCCTCATTA
* *
732748 TGTTAAAGGAAGCCTTTGTGGCTGATTC
1 TGTTAAAAGAAGCCTTTGTGG-TTATTC
*
732776 TGTTAAAAGAAGCCTTTGTAGTTTATTC
1 TGTTAAAAGAAGCCTTTGT-GGTTATTC
*
732804 TG--AAAATGAAGCCTTCGTGGTTATCTC
1 TGTTAAAA-GAAGCCTTTGTGGTTAT-TC
732831 TGTTAAA
1 TGTTAAA
732838 GAATTTGTGG
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
26 9 0.17
27 14 0.27
28 25 0.48
29 4 0.08
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (27 bp):
TGTTAAAAGAAGCCTTTGTGGTTATTC
Found at i:732832 original size:27 final size:26
Alignment explanation
Indices: 732780--732832 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
732770 TGATTCTGTT
* *
732780 AAAAGAAGCCTTTGTAGTTTATTCTG
1 AAAAGAAGCCTTCGTAGGTTATTCTG
732806 AAAATGAAGCCTTCGT-GGTTATCTCTG
1 AAAA-GAAGCCTTCGTAGGTTAT-TCTG
732833 TTAAAGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (26 bp):
AAAAGAAGCCTTCGTAGGTTATTCTG
Found at i:754524 original size:19 final size:19
Alignment explanation
Indices: 754500--754537 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
754490 CACATCCCAT
*
754500 TTTTTAAGTAGTTAATTAA
1 TTTTTAAGTAATTAATTAA
*
754519 TTTTTAATTAATTAATTAA
1 TTTTTAAGTAATTAATTAA
754538 GTTAGTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTAAGTAATTAATTAA
Found at i:756353 original size:24 final size:24
Alignment explanation
Indices: 756318--756365 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
756308 AAGGAGGAAG
756318 CTATATGACAATTT-TACTGCAAAA
1 CTATATGACAATTTAT-CTGCAAAA
*
756342 CTATATGGCAATTTATCTGCAAAA
1 CTATATGACAATTTATCTGCAAAA
756366 ATATGTGGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (24 bp):
CTATATGACAATTTATCTGCAAAA
Found at i:763238 original size:13 final size:13
Alignment explanation
Indices: 763220--763244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
763210 AGAGGTGTAC
763220 GATGATATATATT
1 GATGATATATATT
763233 GATGATATATAT
1 GATGATATATAT
763245 GTGAAATATA
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
GATGATATATATT
Found at i:771372 original size:2 final size:2
Alignment explanation
Indices: 771365--771394 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
771355 AGCCTTTGGA
771365 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
771395 AGTCTTTGAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:774605 original size:14 final size:14
Alignment explanation
Indices: 774586--774619 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
774576 GGTGTCTTAC
774586 TGTTCATCTATTAT
1 TGTTCATCTATTAT
*
774600 TGTTCATCTTTTAT
1 TGTTCATCTATTAT
774614 T-TTCAT
1 TGTTCAT
774620 TTCATTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.62
Consensus pattern (14 bp):
TGTTCATCTATTAT
Found at i:775609 original size:24 final size:24
Alignment explanation
Indices: 775530--775618 Score: 72
Period size: 24 Copynumber: 3.7 Consensus size: 24
775520 TTTCAGAAAT
* * *
775530 TTAGCTCATACGAGCCCAAACAAAA
1 TTAGCTCTTACGAGCCCAGA-TAAA
* **
775555 TTAGCTCATACGAGCCCAGATAGG
1 TTAGCTCTTACGAGCCCAGATAAA
* * *
775579 GTGGCTCTTACGAGCTCAGATAAA
1 TTAGCTCTTACGAGCCCAGATAAA
775603 TTAGCTCATT-CGAGCC
1 TTAGCTC-TTACGAGCC
775619 TAGACAGAGT
Statistics
Matches: 50, Mismatches: 13, Indels: 3
0.76 0.20 0.05
Matches are distributed among these distances:
24 29 0.58
25 21 0.42
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGATAAA
Found at i:777573 original size:23 final size:23
Alignment explanation
Indices: 777547--777598 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
777537 AACCTGGGTT
*
777547 GTTGACATTGACTAACCTT-ACAC
1 GTTGACATTGACCAA-CTTGACAC
* *
777570 GTTGACTTTGACCAACTTGACCC
1 GTTGACATTGACCAACTTGACAC
777593 GTTGAC
1 GTTGAC
777599 CGTTGACTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (23 bp):
GTTGACATTGACCAACTTGACAC
Found at i:778247 original size:23 final size:23
Alignment explanation
Indices: 778122--778247 Score: 108
Period size: 23 Copynumber: 5.5 Consensus size: 23
778112 AATTGGACCT
* * *
778122 GACCCGTTGATTTTGATCGACCC
1 GACCCGTTGACTTTGACCAACCC
* * *
778145 GACCCATTAACTTTGACCAACCT
1 GACCCGTTGACTTTGACCAACCC
* * * *
778168 AACCTGTTGAATATGACCAACCC
1 GACCCGTTGACTTTGACCAACCC
* **
778191 GACCCGTTGGCTTTGATTAACCC
1 GACCCGTTGACTTTGACCAACCC
* *
778214 AACCCGTTGACTTTGACCAACTC
1 GACCCGTTGACTTTGACCAACCC
*
778237 GACCCATTGAC
1 GACCCGTTGAC
778248 CGTTAACTTG
Statistics
Matches: 76, Mismatches: 27, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 76 1.00
ACGTcount: A:0.25, C:0.33, G:0.16, T:0.26
Consensus pattern (23 bp):
GACCCGTTGACTTTGACCAACCC
Found at i:778932 original size:4 final size:4
Alignment explanation
Indices: 778919--778990 Score: 83
Period size: 4 Copynumber: 18.2 Consensus size: 4
778909 CAATTTAAAT
* * * * * *
778919 TATA -ATA TATA TATA TATA TATA CATA CATA CATA CATA CATA CATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
778966 TATA TATA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA TATA T
778991 GAATGAATAT
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
3 3 0.05
4 62 0.95
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (4 bp):
TATA
Found at i:783793 original size:23 final size:23
Alignment explanation
Indices: 783714--783780 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
783704 TGATCGACTT
*
783714 GACCCATTGACTTTGACCAACCC
1 GACCCATTGACTTTGACTAACCC
* *
783737 GACCCGTTGACTTTGATTAACCC
1 GACCCATTGACTTTGACTAACCC
*
783760 GACCCATTGACTTTAACTAAC
1 GACCCATTGACTTTGACTAAC
783781 TCAACCCGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.27, C:0.33, G:0.13, T:0.27
Consensus pattern (23 bp):
GACCCATTGACTTTGACTAACCC
Found at i:785036 original size:2 final size:2
Alignment explanation
Indices: 785029--785055 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
785019 AATTATAAAT
785029 TA 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 T
785056 GAATGAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:791008 original size:23 final size:23
Alignment explanation
Indices: 790954--791083 Score: 109
Period size: 23 Copynumber: 5.6 Consensus size: 23
790944 CCTGAATTAG
* *
790954 ACCCGACCCATTGATTTTGA-TCG
1 ACCCGACCCATTGACTTTGACT-A
**
790977 ACTTGACCCATTGACTTTGACTA
1 ACCCGACCCATTGACTTTGACTA
* * * * *
791000 ACCCAACCCGTTGAATTTAATCCA
1 ACCCGACCCATTGACTTTGA-CTA
* * *
791024 ACTCGACCCGTTGACTTTGATTA
1 ACCCGACCCATTGACTTTGACTA
791047 ACCCGACCCATTGACTTTGACTA
1 ACCCGACCCATTGACTTTGACTA
* *
791070 ACTCGACCTATTGA
1 ACCCGACCCATTGA
791084 TCGTTAACTT
Statistics
Matches: 83, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
23 64 0.77
24 19 0.23
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (23 bp):
ACCCGACCCATTGACTTTGACTA
Found at i:791038 original size:47 final size:46
Alignment explanation
Indices: 790954--791083 Score: 125
Period size: 47 Copynumber: 2.8 Consensus size: 46
790944 CCTGAATTAG
* * * * * *
790954 ACCCGACCCATTGATTTTGATCGACTTGACCCATTGACTTTGACTA
1 ACCCAACCCATTGAATTTAACCAACTCGACCCATTGACTTTGACTA
* * *
791000 ACCCAACCCGTTGAATTTAATCCAACTCGACCCGTTGACTTTGATTA
1 ACCCAACCCATTGAATTTAA-CCAACTCGACCCATTGACTTTGACTA
* * * * *
791047 ACCCGACCCATTGACTTTGACTAACTCGACCTATTGA
1 ACCCAACCCATTGAATTTAACCAACTCGACCCATTGA
791084 TCGTTAACTT
Statistics
Matches: 67, Mismatches: 16, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
46 30 0.45
47 37 0.55
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (46 bp):
ACCCAACCCATTGAATTTAACCAACTCGACCCATTGACTTTGACTA
Found at i:796220 original size:27 final size:26
Alignment explanation
Indices: 796189--796252 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 26
796179 TTTATCGAGG
*
796189 TTATTAATTTATTGATAAA-TAATTATT
1 TTATTAATTTATCGATAAATTAA-TA-T
796216 TTATTAATTTATCGATAAATTAATAT
1 TTATTAATTTATCGATAAATTAATAT
796242 TTATTAATTTA
1 TTATTAATTTA
796253 GAGAATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 12 0.34
27 20 0.57
28 3 0.09
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATTAATAT
Found at i:797659 original size:8 final size:8
Alignment explanation
Indices: 797642--797678 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
797632 CGACCTTTCC
797642 TTTTTC-T
1 TTTTTCTT
797649 TTTTTCTT
1 TTTTTCTT
797657 TTTTTCTTT
1 TTTTTC-TT
797666 TTTTTCTT
1 TTTTTCTT
797674 TTTTT
1 TTTTT
797679 TTTGTGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 6 0.21
8 14 0.50
9 8 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTCTT
Found at i:797667 original size:9 final size:9
Alignment explanation
Indices: 797648--797679 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
797638 TTCCTTTTTC
797648 TTTTTTC-T
1 TTTTTTCTT
797656 TTTTTTCTT
1 TTTTTTCTT
797665 TTTTTTCTT
1 TTTTTTCTT
797674 TTTTTT
1 TTTTTT
797680 TTGTGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:799226 original size:16 final size:16
Alignment explanation
Indices: 799205--799236 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
799195 ATGATTTTTT
*
799205 ATGTTAAAGGACTAAA
1 ATGTTAAAGGAATAAA
799221 ATGTTAAAGGAATAAA
1 ATGTTAAAGGAATAAA
799237 TTTGTAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (16 bp):
ATGTTAAAGGAATAAA
Found at i:804502 original size:21 final size:21
Alignment explanation
Indices: 804454--804503 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
804444 GGAGTTTTTA
*
804454 GTATCGGTAGAAGCATGACAT
1 GTATCGATAGAAGCATGACAT
* *
804475 GTTTCGATAGAAGTCAT-ACTT
1 GTATCGATAGAAG-CATGACAT
804496 GTATCGAT
1 GTATCGAT
804504 TATATTGCCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (21 bp):
GTATCGATAGAAGCATGACAT
Found at i:810409 original size:23 final size:23
Alignment explanation
Indices: 810383--810445 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
810373 TGATGATGGC
*
810383 AAAATAAAAATACATATAT-GAAT
1 AAAATAAAAATA-ATATATACAAT
*
810406 AAAA-ATAAAATAAATAAATACAAT
1 AAAATA-AAAAT-AATATATACAAT
*
810430 TAAATAAAAATAATAT
1 AAAATAAAAATAATAT
810446 CAATCCATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
22 1 0.03
23 18 0.56
24 12 0.38
25 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAATAAAAATAATATATACAAT
Found at i:810591 original size:10 final size:10
Alignment explanation
Indices: 810576--810645 Score: 68
Period size: 11 Copynumber: 6.5 Consensus size: 10
810566 TGCATGAATT
*
810576 AAAAAATACA
1 AAAAAATAAA
*
810586 AAAAAATATA
1 AAAAAATAAA
810596 AAAAAATAAA
1 AAAAAATAAA
810606 ATAAAAATAAA
1 A-AAAAATAAA
*
810617 GATAAAATAAA
1 -AAAAAATAAA
810628 TAAATAAATAAA
1 -AAA-AAATAAA
810640 ATAAAA
1 A-AAAA
810646 GAGACTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.37
11 22 0.43
12 10 0.20
ACGTcount: A:0.80, C:0.01, G:0.01, T:0.17
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:810599 original size:11 final size:9
Alignment explanation
Indices: 810576--810645 Score: 61
Period size: 10 Copynumber: 7.2 Consensus size: 9
810566 TGCATGAATT
810576 AAAAAATACA
1 AAAAAATA-A
810586 AAAAAATATA
1 AAAAAATA-A
810596 AAAAAATAAA
1 AAAAAAT-AA
810606 ATAAAAATAA
1 A-AAAAATAA
810616 AGATAAAAT-A
1 A-A-AAAATAA
*
810626 AATAAATAA
1 AAAAAATAA
*
810635 ATAAAATAA
1 AAAAAATAA
810644 AA
1 AA
810646 GAGACTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
8 4 0.08
9 10 0.20
10 24 0.48
11 12 0.24
ACGTcount: A:0.80, C:0.01, G:0.01, T:0.17
Consensus pattern (9 bp):
AAAAAATAA
Found at i:810599 original size:19 final size:21
Alignment explanation
Indices: 810576--810640 Score: 66
Period size: 21 Copynumber: 3.1 Consensus size: 21
810566 TGCATGAATT
*
810576 AAAAAATACAA-AAAAATATA
1 AAAAAATAAAATAAAAATATA
810596 AAAAAATAAAATAAAAATA-A
1 AAAAAATAAAATAAAAATATA
810616 AGATAAAAT-AAATAAATAA-ATA
1 A-A-AAAATAAAATAAA-AATATA
810638 AAA
1 AAA
810641 TAAAAGAGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
20 13 0.33
21 17 0.44
22 9 0.23
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.17
Consensus pattern (21 bp):
AAAAAATAAAATAAAAATATA
Found at i:810606 original size:25 final size:26
Alignment explanation
Indices: 810578--810635 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
810568 CATGAATTAA
*
810578 AAAATACAAAA-AAATATAAAA-AAAT
1 AAAATA-AAAATAAAGATAAAATAAAT
810603 AAAATAAAAATAAAGATAAAATAAAT
1 AAAATAAAAATAAAGATAAAATAAAT
810629 -AAATAAA
1 AAAATAAA
810636 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 22 0.73
26 4 0.13
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (26 bp):
AAAATAAAAATAAAGATAAAATAAAT
Found at i:810638 original size:17 final size:17
Alignment explanation
Indices: 810593--810644 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
810583 ACAAAAAAAT
*
810593 ATAAAAAAATAAAAT-A
1 ATAAATAAATAAAATAA
810609 A-AAATAAAGATAAAATAA
1 ATAAAT-AA-ATAAAATAA
810627 ATAAATAAATAAAATAA
1 ATAAATAAATAAAATAA
810644 A
1 A
810645 AGAGACTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 3 0.10
16 3 0.10
17 17 0.55
18 4 0.13
19 4 0.13
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (17 bp):
ATAAATAAATAAAATAA
Found at i:810655 original size:23 final size:23
Alignment explanation
Indices: 810593--810647 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
810583 ACAAAAAAAT
810593 ATAAAA-AAATAAAATAAAAATAAAG
1 ATAAAAGAAAT-AAAT--AAATAAAG
*
810618 ATAAAATAAATAAATAAATAAA-
1 ATAAAAGAAATAAATAAATAAAG
810640 ATAAAAGA
1 ATAAAAGA
810648 GACTAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 7 0.25
23 7 0.25
25 10 0.36
26 4 0.14
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (23 bp):
ATAAAAGAAATAAATAAATAAAG
Found at i:818575 original size:27 final size:27
Alignment explanation
Indices: 818533--818603 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
818523 GCAGGATGTA
*
818533 GCTCATTCGAGTTCAGAACAGAGTATT
1 GCTCATTCGAGCTCAGAACAGAGTATT
* *
818560 GCTCATTTGAGCTCAGAACAGATTATT
1 GCTCATTCGAGCTCAGAACAGAGTATT
* *
818587 GCTCCTACGAGC-CAGAA
1 GCTCATTCGAGCTCAGAA
818604 ATAGAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
26 5 0.13
27 33 0.87
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.27
Consensus pattern (27 bp):
GCTCATTCGAGCTCAGAACAGAGTATT
Found at i:818628 original size:28 final size:28
Alignment explanation
Indices: 818586--818740 Score: 186
Period size: 28 Copynumber: 5.6 Consensus size: 28
818576 AACAGATTAT
*
818586 TGCTCC-TACGAGCCAGAAATAGAATAA
1 TGCTCCTTTCGAGCCAGAAATAGAATAA
818613 TGCTCCTTTCGAGCCAGAAATAGAATAA
1 TGCTCCTTTCGAGCCAGAAATAGAATAA
* * * * *
818641 TGTTCCTTTTGAGCCATAAACAAAATAA
1 TGCTCCTTTCGAGCCAGAAATAGAATAA
* * *
818669 TGCTCCTTTTGAGCCAGAAACAAAATAA
1 TGCTCCTTTCGAGCCAGAAATAGAATAA
* *
818697 TGCTCTTTTCGAGCCAGAGATAGAATAA
1 TGCTCCTTTCGAGCCAGAAATAGAATAA
* *
818725 TGTTCTTTTCGAGCCA
1 TGCTCCTTTCGAGCCA
818741 CAGTCTAGAA
Statistics
Matches: 113, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 6 0.05
28 107 0.95
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (28 bp):
TGCTCCTTTCGAGCCAGAAATAGAATAA
Found at i:818760 original size:29 final size:29
Alignment explanation
Indices: 818605--818773 Score: 127
Period size: 28 Copynumber: 6.0 Consensus size: 29
818595 GAGCCAGAAA
* **
818605 TAGAATAATGCTCCTTTCGAGCCAGA-AA
1 TAGAATAATGCTCTTTTCGAGCCAGAGTC
* * **
818633 TAGAATAATGTTCCTTTT-GAGCCATAAAC
1 TAGAATAATGCT-CTTTTCGAGCCAGAGTC
* **
818662 -AAAATAATGCTCCTTTT-GAGCCAGAAAC
1 TAGAATAATGCT-CTTTTCGAGCCAGAGTC
* *
818690 -AAAATAATGCTCTTTTCGAGCCAGAG-A
1 TAGAATAATGCTCTTTTCGAGCCAGAGTC
* *
818717 TAGAATAATGTTCTTTTCGAGCCACAGTC
1 TAGAATAATGCTCTTTTCGAGCCAGAGTC
* *
818746 TAGAATATTGCTC-TTACGAGCCAGAGTC
1 TAGAATAATGCTCTTTTCGAGCCAGAGTC
818774 CAACTCACAT
Statistics
Matches: 119, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
27 5 0.04
28 98 0.82
29 16 0.13
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (29 bp):
TAGAATAATGCTCTTTTCGAGCCAGAGTC
Found at i:818767 original size:84 final size:83
Alignment explanation
Indices: 818583--818770 Score: 234
Period size: 84 Copynumber: 2.2 Consensus size: 83
818573 CAGAACAGAT
* * *
818583 TATTGCTCCTACGAGCCAGAAATAGAATAATGCTCCTTTCGAGCCAGAAATAGAATAATGTTCCT
1 TATTGCTCTTACGAGCCAGAAACAAAATAATGCTCCTTTCGAGCCAGAAATAGAATAATGTTCCT
*
818648 TTTGAGCCATAAACAAAA
66 TTTGAGCCACAAACAAAA
* ** * *
818666 TAATGCTCCTTTTGAGCCAGAAACAAAATAATGCTCTTTTCGAGCCAGAGATAGAATAATGTT-C
1 TATTGCT-CTTACGAGCCAGAAACAAAATAATGCTCCTTTCGAGCCAGAAATAGAATAATGTTCC
** *
818730 TTTTCGAGCCACAGTCTAGAA
65 TTTT-GAGCCACAAAC-AAAA
818751 TATTGCTCTTACGAGCCAGA
1 TATTGCTCTTACGAGCCAGA
818771 GTCCAACTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
83 11 0.13
84 67 0.77
85 9 0.10
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (83 bp):
TATTGCTCTTACGAGCCAGAAACAAAATAATGCTCCTTTCGAGCCAGAAATAGAATAATGTTCCT
TTTGAGCCACAAACAAAA
Found at i:820937 original size:25 final size:25
Alignment explanation
Indices: 820890--820937 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
820880 AACGAAACTC
*
820890 AATATAAACCCTAAATTTGAAACCT
1 AATATAAACCCTAAATCTGAAACCT
*
820915 AATATAAACTCTAAACTCT-AAAC
1 AATATAAACCCTAAA-TCTGAAAC
820938 TCTTTCCTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 18 0.90
26 2 0.10
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (25 bp):
AATATAAACCCTAAATCTGAAACCT
Found at i:838354 original size:36 final size:36
Alignment explanation
Indices: 838313--838404 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 36
838303 TATTCAAAGA
*
838313 AGGAATTGTTTGTTCTTCATCAATGTCAATATTAGG
1 AGGAATTGTTTGTTCTTCATCAATGTCAATATTAAG
* *
838349 AGGAATTATTTGTTTTTCATCAATGTCAATATTAAG
1 AGGAATTGTTTGTTCTTCATCAATGTCAATATTAAG
838385 AGGAATTGTTTGTTCTTCAT
1 AGGAATTGTTTGTTCTTCAT
838405 TAAGACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (36 bp):
AGGAATTGTTTGTTCTTCATCAATGTCAATATTAAG
Found at i:842242 original size:23 final size:24
Alignment explanation
Indices: 842186--842247 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
842176 TTGTCTGCAA
*
842186 CTTTTTTCTTTTTATCTGTAAGTTTT
1 CTTTTTTCTTTCT-T-TGTAAGTTTT
842212 CTTTTTTCTTTCTTTGTAA-TTTT
1 CTTTTTTCTTTCTTTGTAAGTTTT
842235 -TTTGTTTCTTTCT
1 CTTT-TTTCTTTCT
842248 GTCAGACTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
22 3 0.09
23 13 0.38
24 5 0.15
25 1 0.03
26 12 0.35
ACGTcount: A:0.08, C:0.13, G:0.06, T:0.73
Consensus pattern (24 bp):
CTTTTTTCTTTCTTTGTAAGTTTT
Found at i:844877 original size:20 final size:19
Alignment explanation
Indices: 844852--844890 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
844842 TCTAATGAAT
*
844852 ATTGGAAATGTGAAACGACG
1 ATTGGAAACGTGAAA-GACG
844872 ATTGGAAACGTGAAAGACG
1 ATTGGAAACGTGAAAGACG
844891 GTAATAATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.41, C:0.10, G:0.31, T:0.18
Consensus pattern (19 bp):
ATTGGAAACGTGAAAGACG
Found at i:854774 original size:7 final size:7
Alignment explanation
Indices: 854762--854787 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
854752 AATGGGAATT
854762 GAGAAGG
1 GAGAAGG
854769 GAGAAGG
1 GAGAAGG
854776 GAGAAGG
1 GAGAAGG
854783 GAGAA
1 GAGAA
854788 CTTCAACCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (7 bp):
GAGAAGG
Found at i:857148 original size:13 final size:13
Alignment explanation
Indices: 857130--857156 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
857120 GTACAGGAAC
857130 TAAATCGTATAAG
1 TAAATCGTATAAG
857143 TAAATCGTATAAG
1 TAAATCGTATAAG
857156 T
1 T
857157 GATAAAAGTT
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:0.44, C:0.07, G:0.15, T:0.33
Consensus pattern (13 bp):
TAAATCGTATAAG
Found at i:863900 original size:32 final size:32
Alignment explanation
Indices: 863859--863919 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
863849 AAGTCTGCAC
863859 CTGCAAAGAGAGAAGAGACAACCATTTAACAT
1 CTGCAAAGAGAGAAGAGACAACCATTTAACAT
*
863891 CTGCAAAGAGAGAAGAGACAGCCATTTAA
1 CTGCAAAGAGAGAAGAGACAACCATTTAA
863920 GTTGTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (32 bp):
CTGCAAAGAGAGAAGAGACAACCATTTAACAT
Found at i:865286 original size:29 final size:29
Alignment explanation
Indices: 865254--865588 Score: 190
Period size: 29 Copynumber: 11.6 Consensus size: 29
865244 TCGAACTTCT
* *
865254 TAAAATCATATTTTGATCCTAAACTTTCC
1 TAAAATCACATTTTGACCCTAAACTTTCC
* * *
865283 TAAAATTACATTTTAACCCCTAAACTTT-T
1 TAAAATCACATTTTGA-CCCTAAACTTTCC
* *
865312 TAAAAAAT-ATATTTTGATCCTAAACTTTTCC
1 T--AAAATCACATTTTGACCCTAAAC-TTTCC
* * *
865343 -AAAAACACATTTTTACCCCAAAC--T-C
1 TAAAATCACATTTTGACCCTAAACTTTCC
* * * * *
865368 AAAAATTATATTTT-TCCCTAAACTTT-T
1 TAAAATCACATTTTGACCCTAAACTTTCC
865395 TCAAAATCACATTTTGACCCCTAAACTTTTCC
1 T-AAAATCACATTTTGA-CCCTAAAC-TTTCC
* *
865427 -AAAATCACATTTTGACCTTTAAACTTTTC
1 TAAAATCACATTTTGACC-CTAAACTTTCC
* * * * *
865456 TAAAATTATATTTTAACCCCCACACTTT-C
1 TAAAATCACATTTTGA-CCCTAAACTTTCC
* *
865485 TCAAAATCATATTTTGA-CCTCGAAC-TTCC
1 T-AAAATCACATTTTGACCCT-AAACTTTCC
* * *
865514 TAAAACCACATTTTAACCCTAAACTTTCA
1 TAAAATCACATTTTGACCCTAAACTTTCC
* * * *
865543 TAATATCACCTTTTTACCCTAAACTTTTC
1 TAAAATCACATTTTGACCCTAAACTTTCC
* *
865572 TAAAATTACGTTTTGAC
1 TAAAATCACATTTTGAC
865589 ATTAAATTCT
Statistics
Matches: 231, Mismatches: 53, Indels: 44
0.70 0.16 0.13
Matches are distributed among these distances:
25 8 0.03
26 11 0.05
27 1 0.00
28 34 0.15
29 88 0.38
30 79 0.34
31 10 0.04
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAAATCACATTTTGACCCTAAACTTTCC
Found at i:865307 original size:30 final size:30
Alignment explanation
Indices: 865254--865588 Score: 184
Period size: 30 Copynumber: 11.6 Consensus size: 30
865244 TCGAACTTCT
* *
865254 TAAAATCATATTTTGA-TCCTAAACTTTCC
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* * *
865283 TAAAATTACATTTTAACCCCTAAACTTT-T
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* *
865312 TAAAAAAT-ATATTTTGA-TCCTAAACTTTTCC
1 T--AAAATCACATTTTGACCCCTAAAC-TTTCC
* *
865343 -AAAAACACATTTTTACCCC-AAAC--T-C
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* * * * *
865368 AAAAATTATATTTT--TCCCTAAACTTT-T
1 TAAAATCACATTTTGACCCCTAAACTTTCC
865395 TCAAAATCACATTTTGACCCCTAAACTTTTCC
1 T-AAAATCACATTTTGACCCCTAAAC-TTTCC
** *
865427 -AAAATCACATTTTGACCTTTAAACTTTTC
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* * * * *
865456 TAAAATTATATTTTAACCCCCACACTTT-C
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* * *
865485 TCAAAATCATATTTTGACCTC-GAAC-TTCC
1 T-AAAATCACATTTTGACCCCTAAACTTTCC
* * *
865514 TAAAACCACATTTT-AACCCTAAACTTTCA
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* * * *
865543 TAATATCACCTTTTTA-CCCTAAACTTTTC
1 TAAAATCACATTTTGACCCCTAAACTTTCC
* *
865572 TAAAATTACGTTTTGAC
1 TAAAATCACATTTTGAC
865589 ATTAAATTCT
Statistics
Matches: 230, Mismatches: 53, Indels: 45
0.70 0.16 0.14
Matches are distributed among these distances:
24 3 0.01
25 5 0.02
26 11 0.05
27 4 0.02
28 31 0.13
29 79 0.34
30 89 0.39
31 8 0.03
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.39
Consensus pattern (30 bp):
TAAAATCACATTTTGACCCCTAAACTTTCC
Found at i:865400 original size:54 final size:55
Alignment explanation
Indices: 865255--865421 Score: 169
Period size: 59 Copynumber: 2.9 Consensus size: 55
865245 CGAACTTCTT
** * *
865255 AAAATCATATTTTGATCCTAAAC-TTTCCTAAAATTACATTTTAACCCCTAAACTTTTTAA
1 AAAAT-ATATTTT-ATCCTAAACTTTTCC-AAAAACACATTTTGACCCCTAAAC---TCAA
*
865315 AAAATATATTTTGATCCTAAACTTTTCCAAAAACACATTTTTACCCC-AAACTCAA
1 AAAATATATTTT-ATCCTAAACTTTTCCAAAAACACATTTTGACCCCTAAACTCAA
* * *
865370 AAATTATATTTT-TCCCTAAACTTTTTCAAAATCACATTTTGACCCCTAAACT
1 AAAATATATTTTAT-CCTAAACTTTTCCAAAAACACATTTTGACCCCTAAACT
865422 TTTCCAAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
53 1 0.01
54 29 0.30
55 19 0.20
58 4 0.04
59 33 0.34
60 10 0.10
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (55 bp):
AAAATATATTTTATCCTAAACTTTTCCAAAAACACATTTTGACCCCTAAACTCAA
Found at i:865470 original size:113 final size:114
Alignment explanation
Indices: 865271--865540 Score: 257
Period size: 113 Copynumber: 2.4 Consensus size: 114
865261 ATATTTTGAT
* *
865271 CCTAAACTTTCCTAAAATTACATTTTAACCCCTAAACTTTTTAAAAAATATATTTTGATCCTAAA
1 CCTAAACTTTCCTAAAATCACATTTTAACCCCTAAACTTTTTAAAAAATACATTTTGATCCTAAA
865336 CTTTTCCAAAAACACATTTTT-ACCCCAAACTCAAAAATTATATTTTTC
66 CTTTTCCAAAAACACATTTTTAACCCCAAACTCAAAAATTATATTTTTC
* * **
865384 CCTAAACTTT-TTCAAAATCACATTTTGACCCCTAAAC-TTTTCCAAAATCACATTTTGA-CCTT
1 CCTAAACTTTCCT-AAAATCACATTTTAACCCCTAAACTTTTTAAAAAAT-ACATTTTGATCC--
* ** * * * * **
865446 TAAACTTTTCTAAAATTATA-TTTTAACCCCCACACTTTCTCAAAATCATATTTTGA
62 TAAACTTTTCCAAAAACACATTTTTAA-CCCCAAAC--TC-AAAAATTATATTTTTC
* *
865502 CCTCGAAC-TTCCTAAAACCACATTTTAA-CCCTAAACTTT
1 CCT-AAACTTTCCTAAAATCACATTTTAACCCCTAAACTTT
865541 CATAATATCA
Statistics
Matches: 126, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
112 12 0.10
113 44 0.35
114 17 0.13
115 7 0.06
117 10 0.08
118 32 0.25
119 4 0.03
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (114 bp):
CCTAAACTTTCCTAAAATCACATTTTAACCCCTAAACTTTTTAAAAAATACATTTTGATCCTAAA
CTTTTCCAAAAACACATTTTTAACCCCAAACTCAAAAATTATATTTTTC
Found at i:869422 original size:29 final size:29
Alignment explanation
Indices: 869390--869454 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
869380 TTCATACATA
*
869390 CATTCTTACTCATAATCATATCATATAAT
1 CATTCTTACTCATAATCATACCATATAAT
869419 CATTCTTACTCATAATCATACCATATAAT
1 CATTCTTACTCATAATCATACCATATAAT
869448 CATTCTT
1 CATTCTT
869455 TCGTAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (29 bp):
CATTCTTACTCATAATCATACCATATAAT
Found at i:869435 original size:16 final size:15
Alignment explanation
Indices: 869372--869454 Score: 61
Period size: 16 Copynumber: 5.6 Consensus size: 15
869362 TACAAAATTG
869372 ATCATTCTT-TCATA
1 ATCATTCTTATCATA
869386 CATACATTCTTACTCATA
1 -AT-CATTCTTA-TCATA
869404 ATCATATC--AT-ATA
1 ATCAT-TCTTATCATA
869417 ATCATTCTTACTCATA
1 ATCATTCTTA-TCATA
* *
869433 ATCATAC-CAT-ATA
1 ATCATTCTTATCATA
869446 ATCATTCTT
1 ATCATTCTT
869455 TCGTAAATTT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
12 2 0.04
13 17 0.31
14 3 0.05
15 5 0.09
16 19 0.35
17 4 0.07
18 5 0.09
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (15 bp):
ATCATTCTTATCATA
Found at i:872537 original size:50 final size:50
Alignment explanation
Indices: 872478--872673 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 50
872468 CACAAAAAAT
* * * *
872478 TACCAAAAAAGATGTGAAAGGAAAGGTTGAGGCCGCAACAGCGAACCCGA
1 TACCTAAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCCGA
* * * *
872528 TACCTAAAAAGATGTGATGGGAAAGATTAAGGCCGCAACGGCAAACCCAA
1 TACCTAAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCCGA
* * * * ** * * *
872578 TACCTTAGAAGATGCGATGGGAAAGATTGAGGTTGCCATGGCGAATCCGA
1 TACCTAAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCCGA
** * * * *
872628 TACC-ATGAAGATATGAAGGGGAAGGTTGAGGCCGCAACGGTGAACC
1 TACCTAAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACC
872674 TAGCACCTTA
Statistics
Matches: 114, Mismatches: 32, Indels: 1
0.78 0.22 0.01
Matches are distributed among these distances:
49 29 0.25
50 85 0.75
ACGTcount: A:0.37, C:0.18, G:0.30, T:0.15
Consensus pattern (50 bp):
TACCTAAAAAGATGTGAAGGGAAAGATTGAGGCCGCAACGGCGAACCCGA
Found at i:874839 original size:30 final size:29
Alignment explanation
Indices: 874768--875086 Score: 317
Period size: 29 Copynumber: 10.9 Consensus size: 29
874758 TGCATTAAAA
* *
874768 GACCCTCAAAC-TTTCCTAAAATCATATTTT
1 GACCCT-AAACTTTTCC-AAAATTACATTTT
* *
874798 GACTCTAAACTTTTCTAAAATTACATTTT
1 GACCCTAAACTTTTCCAAAATTACATTTT
* * *
874827 AACCTTTAAACTTTTCAAAAATTACATTTT
1 GACC-CTAAACTTTTCCAAAATTACATTTT
*
874857 -ACCCTAAATTTTTCC-AAATTCACATTTT
1 GACCCTAAACTTTTCCAAAATT-ACATTTT
* *
874885 TACCCTAAACTTTTCAAAAATTACATTTT
1 GACCCTAAACTTTTCCAAAATTACATTTT
* *
874914 -ACCCCAAACTTTTCCAAAATCACATTTT
1 GACCCTAAACTTTTCCAAAATTACATTTT
*
874942 CACCCTCAAACTTTTCCAAAATTACATTTT
1 GACCCT-AAACTTTTCCAAAATTACATTTT
* *
874972 GACTCCTAAAATTTTCTAAAATTACATTTT
1 GAC-CCTAAACTTTTCCAAAATTACATTTT
* * * *
875002 GACCCTCACAC-TTCCCAAAATCATATTTT
1 GACCCT-AAACTTTTCCAAAATTACATTTT
* * *
875031 AACCCTAAAC-TTTCCTAAAACTACCTTTT
1 GACCCTAAACTTTTCC-AAAATTACATTTT
*
875060 TACCCTAAACTTTTCCAAAATTACATT
1 GACCCTAAACTTTTCCAAAATTACATT
875087 AACCCTAAAT
Statistics
Matches: 241, Mismatches: 37, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
27 5 0.02
28 48 0.20
29 93 0.39
30 92 0.38
31 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (29 bp):
GACCCTAAACTTTTCCAAAATTACATTTT
Found at i:875112 original size:26 final size:27
Alignment explanation
Indices: 874802--875112 Score: 117
Period size: 30 Copynumber: 10.9 Consensus size: 27
874792 TATTTTGACT
* *
874802 CTAAACTTTTCTAAAATTACATTTTAACC
1 CTAAACTTCTCCAAAATTACA--TTAACC
* * * *
874831 TTTAAACTTTTCAAAAATTACATTTTACC
1 -CTAAACTTCTCCAAAATTACA-TTAACC
* * *
874860 CTAAATTTTTCC-AAATTCACATTTTTACC
1 CTAAACTTCTCCAAAATT-ACA--TTAACC
* * *
874889 CTAAACTTTTCAAAAATTACATTTTACC
1 CTAAACTTCTCCAAAATTACA-TTAACC
* * * *
874917 CCAAACTTTTCCAAAATCACATTTTCACC
1 CTAAACTTCTCCAAAATTACA--TTAACC
* *
874946 CTCAAACTTTTCCAAAATTACATTTTGACTC
1 CT-AAACTTCTCCAAAATTACA--TTAAC-C
* * * *
874977 CTAAAATTTTCTAAAATTACATTTTGACC
1 CTAAACTTCTCCAAAATTACA--TTAACC
* **
875006 CTCACACTTC-CCAAAATCATATTTTAACC
1 CT-AAACTTCTCCAAAAT--TACATTAACC
* * *
875035 CTAAACTT-TCCTAAAACTACCTTTTTACC
1 CTAAACTTCTCC-AAAATTA-C-ATTAACC
*
875064 CTAAACTTTTCCAAAATTACATTAACC
1 CTAAACTTCTCCAAAATTACATTAACC
* *
875091 CTAAA-TTCTCCGAAATTTCATT
1 CTAAACTTCTCCAAAATTACATT
875113 TTCAACCCAT
Statistics
Matches: 233, Mismatches: 34, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
26 14 0.06
27 17 0.07
28 45 0.19
29 73 0.31
30 79 0.34
31 5 0.02
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.39
Consensus pattern (27 bp):
CTAAACTTCTCCAAAATTACATTAACC
Found at i:876803 original size:45 final size:45
Alignment explanation
Indices: 876745--876850 Score: 117
Period size: 45 Copynumber: 2.3 Consensus size: 45
876735 GTATAAAAGT
876745 GTGGTTGCAAGATACCACGACATCAT-TTCGGTTATG-TATAAGACC
1 GTGGTTG-AAGATACCACGACATCATATTCGG-TATGTTATAAGACC
* * *
876790 GTGGTTGAGAGATACTACGGCATCATATTTGGTATGTTATAAGACC
1 GTGGTTGA-AGATACCACGACATCATATTCGGTATGTTATAAGACC
* *
876836 TTAGTTGAAAGATAC
1 GTGGTTG-AAGATAC
876851 TTTGGCATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
45 26 0.50
46 24 0.46
47 1 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (45 bp):
GTGGTTGAAGATACCACGACATCATATTCGGTATGTTATAAGACC
Found at i:876849 original size:46 final size:46
Alignment explanation
Indices: 876748--876863 Score: 128
Period size: 46 Copynumber: 2.5 Consensus size: 46
876738 TAAAAGTGTG
* * * *
876748 GTTGCAAGATACCACGACATCAT-TTCGGTTATGTATAAGACCGTG
1 GTTGAAAGATACTACGGCATCATATTCGGTTATGTATAAGACCGTA
* * *
876793 GTTGAGAGATACTACGGCATCATATTTGG-TATGTTATAAGACCTTA
1 GTTGAAAGATACTACGGCATCATATTCGGTTATG-TATAAGACCGTA
**
876839 GTTGAAAGATACTTTGGCATCATAT
1 GTTGAAAGATACTACGGCATCATAT
876864 CAATACTGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
45 23 0.39
46 36 0.61
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (46 bp):
GTTGAAAGATACTACGGCATCATATTCGGTTATGTATAAGACCGTA
Found at i:880242 original size:18 final size:17
Alignment explanation
Indices: 880219--880253 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
880209 CCTTACTGTG
880219 TTTTTGGATCAAAAATTA
1 TTTTT-GATCAAAAATTA
*
880237 TTTTTGCTCAAAAATTA
1 TTTTTGATCAAAAATTA
880254 AAATCTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTTTGATCAAAAATTA
Found at i:888403 original size:16 final size:16
Alignment explanation
Indices: 888382--888412 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
888372 AATTAATATA
*
888382 ATAAAATAATTAAAAC
1 ATAAAAAAATTAAAAC
888398 ATAAAAAAATTAAAA
1 ATAAAAAAATTAAAA
888413 GCGGTCATCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAAAAAATTAAAAC
Found at i:894123 original size:19 final size:19
Alignment explanation
Indices: 894099--894152 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
894089 ACCATTTATC
894099 GTTGATCGTTGACTTGACT
1 GTTGATCGTTGACTTGACT
894118 GTTGATCGTTGATCATTGACT
1 GTTGATCGTTGA-C-TTGACT
* *
894139 -TTGACCATTGACTT
1 GTTGATCGTTGACTT
894153 CACCGTTGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 10 0.32
21 6 0.19
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.43
Consensus pattern (19 bp):
GTTGATCGTTGACTTGACT
Found at i:894605 original size:30 final size:30
Alignment explanation
Indices: 894570--894626 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
894560 GCCGCTTGAG
894570 GTGTGTTTCTATCCGTGCTACATATTTGTT
1 GTGTGTTTCTATCCGTGCTACATATTTGTT
* * *
894600 GTGTGTTTCTTTCTGTGCTTCATATTT
1 GTGTGTTTCTATCCGTGCTACATATTT
894627 ATTATGTGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.11, C:0.16, G:0.19, T:0.54
Consensus pattern (30 bp):
GTGTGTTTCTATCCGTGCTACATATTTGTT
Found at i:894678 original size:15 final size:14
Alignment explanation
Indices: 894660--894707 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
894650 CTGTGTGATA
894660 TTATTATGTGTTGTG
1 TTATT-TGTGTTGTG
*
894675 TTATTTGTG-TGATT
1 TTATTTGTGTTG-TG
894689 TTAATTTGTGTTGTG
1 TT-ATTTGTGTTGTG
894704 TTAT
1 TTAT
894708 CACATGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.07
14 9 0.32
15 15 0.54
16 2 0.07
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (14 bp):
TTATTTGTGTTGTG
Found at i:894683 original size:29 final size:29
Alignment explanation
Indices: 894651--894707 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
894641 TTCCATACAC
894651 TGTGTGATATT-ATTATGTGTTGTGTTATT
1 TGTGTGATATTAATT-TGTGTTGTGTTATT
*
894680 TGTGTGATTTTAATTTGTGTTGTGTTAT
1 TGTGTGATATTAATTTGTGTTGTGTTAT
894708 CACATGTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.88
30 3 0.12
ACGTcount: A:0.16, C:0.00, G:0.25, T:0.60
Consensus pattern (29 bp):
TGTGTGATATTAATTTGTGTTGTGTTATT
Found at i:898603 original size:29 final size:29
Alignment explanation
Indices: 898571--898628 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
898561 TTCCACACCT
*
898571 TGTGTGATATTATTATGTGTTGGGTTATC
1 TGTGTGATATTAATATGTGTTGGGTTATC
* * *
898600 TGTGTGATTTTAATCTGTGTTGTGTTATC
1 TGTGTGATATTAATATGTGTTGGGTTATC
898629 GCATGTTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (29 bp):
TGTGTGATATTAATATGTGTTGGGTTATC
Found at i:901123 original size:14 final size:14
Alignment explanation
Indices: 901104--901140 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
901094 TAACTTAACA
901104 TATATTTTAATATT
1 TATATTTTAATATT
*
901118 TATATTATAATATT
1 TATATTTTAATATT
*
901132 AATATTTTA
1 TATATTTTA
901141 TTCAACTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATTTTAATATT
Found at i:901705 original size:19 final size:21
Alignment explanation
Indices: 901681--901721 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
901671 AAACTTAATC
901681 AAATAATT-TATTTTA-ATAT
1 AAATAATTATATTTTATATAT
*
901700 AAATAATTATCTTTTATATAT
1 AAATAATTATATTTTATATAT
901721 A
1 A
901722 TATATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 6 0.32
21 5 0.26
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATAATTATATTTTATATAT
Found at i:907727 original size:30 final size:29
Alignment explanation
Indices: 907682--907746 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
907672 TTTCAAAAAA
*
907682 TAATTAATTATGAGAAATCA-TATTTATAT
1 TAATTAATTATGAGAAAACACT-TTTATAT
*
907711 TAATTATATTTTGAGAAAACACTTTTATAT
1 TAATTA-ATTATGAGAAAACACTTTTATAT
907741 TAATTA
1 TAATTA
907747 CGTTATATGG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 6 0.19
30 25 0.78
31 1 0.03
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (29 bp):
TAATTAATTATGAGAAAACACTTTTATAT
Found at i:909018 original size:71 final size:71
Alignment explanation
Indices: 908902--909041 Score: 280
Period size: 71 Copynumber: 2.0 Consensus size: 71
908892 CTTGCGAAGA
908902 ATAGGGGAGTTTTAATAATTGAAACGCATAGAAGCAACACTTTGACCCACTCTTTTCCTTTTTAG
1 ATAGGGGAGTTTTAATAATTGAAACGCATAGAAGCAACACTTTGACCCACTCTTTTCCTTTTTAG
908967 GTGGGG
66 GTGGGG
908973 ATAGGGGAGTTTTAATAATTGAAACGCATAGAAGCAACACTTTGACCCACTCTTTTCCTTTTTAG
1 ATAGGGGAGTTTTAATAATTGAAACGCATAGAAGCAACACTTTGACCCACTCTTTTCCTTTTTAG
909038 GTGG
66 GTGG
909042 TGCCGGGTCC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (71 bp):
ATAGGGGAGTTTTAATAATTGAAACGCATAGAAGCAACACTTTGACCCACTCTTTTCCTTTTTAG
GTGGGG
Found at i:909631 original size:2 final size:2
Alignment explanation
Indices: 909624--909668 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
909614 ACCTTGTTTT
909624 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
909666 TA T
1 TA T
909669 TGTATTAACT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:917886 original size:17 final size:17
Alignment explanation
Indices: 917864--917898 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
917854 GGAGAATGTG
917864 GGTTCGAGTGAGTTGAA
1 GGTTCGAGTGAGTTGAA
917881 GGTTCGAGTGAGTTGAA
1 GGTTCGAGTGAGTTGAA
917898 G
1 G
917899 TGCATTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.06, G:0.43, T:0.29
Consensus pattern (17 bp):
GGTTCGAGTGAGTTGAA
Found at i:922707 original size:25 final size:25
Alignment explanation
Indices: 922674--922724 Score: 86
Period size: 25 Copynumber: 2.0 Consensus size: 25
922664 AATTAAAAAG
922674 GACAAAAGAATTACAAACA-AATAAA
1 GACAAAAGAATTACAAA-AGAATAAA
922699 GACAAAAGAATTACAAAAGAATAAA
1 GACAAAAGAATTACAAAAGAATAAA
922724 G
1 G
922725 TATATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 24 0.96
ACGTcount: A:0.67, C:0.10, G:0.12, T:0.12
Consensus pattern (25 bp):
GACAAAAGAATTACAAAAGAATAAA
Found at i:923624 original size:52 final size:53
Alignment explanation
Indices: 923544--923782 Score: 193
Period size: 52 Copynumber: 4.6 Consensus size: 53
923534 AAAAAAAAAG
* * * *
923544 GGTCCAATGACTAAGTGTTATCGTGAGTAGATGAATCCTTTACGGATTTTGAA
1 GGTCCAATGACTAAGTGTCATTGTGAGTATATGAATCCTTTACGGATTTTAAA
* * *
923597 -TTCCAATGACTAAGCGTCATTGTGAGTATATGAAATCCTTTATGGA-TTTAAA
1 GGTCCAATGACTAAGTGTCATTGTGAGTATATG-AATCCTTTACGGATTTTAAA
** * * *
923649 GGTCTGATGACTAAGTGTCATTGTGAGTATATGGATCTTTTACTGA--TTAAGA
1 GGTCCAATGACTAAGTGTCATTGTGAGTATATGAATCCTTTACGGATTTTAA-A
* ** * * * * *** *
923701 GGTCCGATGACTCTGTGTTATAGTGAGTATACGAATCCCTCGTGGATTAT-AA
1 GGTCCAATGACTAAGTGTCATTGTGAGTATATGAATCCTTTACGGATTTTAAA
*
923753 GGTCCGATGACTATA-TGTCATTGTGAGTAT
1 GGTCCAATGACTA-AGTGTCATTGTGAGTAT
923783 TAAATGAAAT
Statistics
Matches: 147, Mismatches: 33, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
51 4 0.03
52 101 0.69
53 41 0.28
54 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (53 bp):
GGTCCAATGACTAAGTGTCATTGTGAGTATATGAATCCTTTACGGATTTTAAA
Found at i:934153 original size:26 final size:26
Alignment explanation
Indices: 934124--934176 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
934114 TCTGAAGTTA
934124 AAATTATATTATATATTGAATATAGT
1 AAATTATATTATATATTGAATATAGT
934150 AAATTATATTATATATTGAATATAGT
1 AAATTATATTATATATTGAATATAGT
934176 A
1 A
934177 CAAATGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (26 bp):
AAATTATATTATATATTGAATATAGT
Found at i:940416 original size:2 final size:2
Alignment explanation
Indices: 940409--940434 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
940399 AATAGTTTGA
940409 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
940435 TAATCATCTA
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:943781 original size:29 final size:29
Alignment explanation
Indices: 943749--943806 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
943739 GAATTGGATC
943749 AAATCAAAATTTCATG-ATTA-AATTGCACA
1 AAATCAAAATTT-ATGTA-TACAATTGCACA
*
943778 AAATCAAAGTTTATGTATACAATTGCACA
1 AAATCAAAATTTATGTATACAATTGCACA
943807 TTAAATCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.31
Consensus pattern (29 bp):
AAATCAAAATTTATGTATACAATTGCACA
Found at i:943825 original size:31 final size:29
Alignment explanation
Indices: 943769--943827 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
943759 TTCATGATTA
*
943769 AATTGCACAAAATCAAAGTTTATGTATAC
1 AATTGCACAAAATCAAAGTTCATGTATAC
*
943798 AATTGCACATTAAATCATAGTTCATGTATA
1 AATTGCACA--AAATCAAAGTTCATGTATA
943828 GTTTTGGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 9 0.35
31 17 0.65
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (29 bp):
AATTGCACAAAATCAAAGTTCATGTATAC
Found at i:945186 original size:27 final size:27
Alignment explanation
Indices: 945091--945257 Score: 144
Period size: 27 Copynumber: 6.3 Consensus size: 27
945081 ATGGCAACTA
*
945091 GGGTAGTCCATTGGGACAATAAACTC-
1 GGGTAGTCCATTGGGACAGTAAACTCG
* * * *
945117 GAGTAGTCCATTGGAACAATAAACTTG
1 GGGTAGTCCATTGGGACAGTAAACTCG
****
945144 GGGTAGTCTGCGGGGACAGTAAACTCG
1 GGGTAGTCCATTGGGACAGTAAACTCG
* *
945171 GGGTAGTCCGTTGGGACAAG-AAGCTCG
1 GGGTAGTCCATTGGGAC-AGTAAACTCG
* * *
945198 GGGTAGTCTATCGGGACAGTATACTC-
1 GGGTAGTCCATTGGGACAGTAAACTCG
* *
945224 GGGTAGTCCATCGAGACAGTAAA-TGCG
1 GGGTAGTCCATTGGGACAGTAAACT-CG
945251 GGGTAGT
1 GGGTAGT
945258 TCACCAAGAT
Statistics
Matches: 113, Mismatches: 23, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
25 1 0.01
26 46 0.41
27 64 0.57
28 2 0.02
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (27 bp):
GGGTAGTCCATTGGGACAGTAAACTCG
Found at i:945252 original size:26 final size:27
Alignment explanation
Indices: 945195--945257 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
945185 GACAAGAAGC
* * *
945195 TCGGGGTAGTCTATCGGGACAGTATAC
1 TCGGGGTAGTCCATCGAGACAGTATAA
945222 TC-GGGTAGTCCATCGAGACAGTA-AA
1 TCGGGGTAGTCCATCGAGACAGTATAA
945247 TGCGGGGTAGT
1 T-CGGGGTAGT
945258 TCACCAAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 2 0.06
26 20 0.65
27 9 0.29
ACGTcount: A:0.24, C:0.17, G:0.35, T:0.24
Consensus pattern (27 bp):
TCGGGGTAGTCCATCGAGACAGTATAA
Found at i:951409 original size:51 final size:51
Alignment explanation
Indices: 951333--951435 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 51
951323 AAAAAACAAC
*
951333 TTGAGGTTTGATATTTGCGATAAAATCAAATATAACTGACGAGGAGGGAAG
1 TTGAGGTCTGATATTTGCGATAAAATCAAATATAACTGACGAGGAGGGAAG
*
951384 TTGAGGTCTGATATTTGCGATAAAATCAAATGTAACTGACGAGGAGGGAAG
1 TTGAGGTCTGATATTTGCGATAAAATCAAATATAACTGACGAGGAGGGAAG
951435 T
1 T
951436 GGTTTTTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.36, C:0.09, G:0.28, T:0.27
Consensus pattern (51 bp):
TTGAGGTCTGATATTTGCGATAAAATCAAATATAACTGACGAGGAGGGAAG
Found at i:958102 original size:44 final size:44
Alignment explanation
Indices: 958037--958120 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
958027 GTCCACGGAT
* * *
958037 ACCAATTCAATTGAAAATTTACTCAAAAATCATTTGTATACAAC
1 ACCAATTCAATTGAAAATTTACTAAAAAATAACTTGTATACAAC
958081 ACCAATTCAATT-AAAATTTTACTAAAAAATAACTTGTATA
1 ACCAATTCAATTGAAAA-TTTACTAAAAAATAACTTGTATA
958121 TGTATTAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 4 0.11
44 32 0.89
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.33
Consensus pattern (44 bp):
ACCAATTCAATTGAAAATTTACTAAAAAATAACTTGTATACAAC
Found at i:959821 original size:6 final size:6
Alignment explanation
Indices: 959810--959834 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
959800 AATAGTAGTG
959810 GGAGAA GGAGAA GGAGAA GGAGAA G
1 GGAGAA GGAGAA GGAGAA GGAGAA G
959835 AGGCCTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAGAA
Found at i:967733 original size:19 final size:20
Alignment explanation
Indices: 967711--967748 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
967701 CCAATTTACA
*
967711 ACTCAATTA-AATATTTCAT
1 ACTCAATTACAACATTTCAT
*
967730 ACTCATTTACAACATTTCA
1 ACTCAATTACAACATTTCA
967749 AACTATCAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (20 bp):
ACTCAATTACAACATTTCAT
Found at i:968223 original size:8 final size:8
Alignment explanation
Indices: 968210--968252 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
968200 CAAATAACCA
968210 ATATACAT
1 ATATACAT
968218 ATATAC--
1 ATATACAT
968224 ATATACAT
1 ATATACAT
*
968232 ACATACAT
1 ATATACAT
*
968240 ATATATAT
1 ATATACAT
968248 ATATA
1 ATATA
968253 ACCTACCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
6 6 0.20
8 24 0.80
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (8 bp):
ATATACAT
Found at i:968229 original size:14 final size:14
Alignment explanation
Indices: 968210--968250 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
968200 CAAATAACCA
968210 ATATACATATATAC
1 ATATACATATATAC
*
968224 ATATACATACATAC
1 ATATACATATATAC
*
968238 ATATATATATATA
1 ATATACATATATA
968251 TAACCTACCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (14 bp):
ATATACATATATAC
Found at i:971811 original size:13 final size:13
Alignment explanation
Indices: 971793--971817 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
971783 TGTCAACTCA
971793 TTTTTTCATTTCT
1 TTTTTTCATTTCT
971806 TTTTTTCATTTC
1 TTTTTTCATTTC
971818 ACTTTTATTT
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTCATTTCT
Found at i:974834 original size:10 final size:11
Alignment explanation
Indices: 974821--974867 Score: 60
Period size: 12 Copynumber: 4.2 Consensus size: 11
974811 AAAAATTCAC
974821 AAAAAGAAAG-
1 AAAAAGAAAGA
974831 AAAAAGAAAGA
1 AAAAAGAAAGA
*
974842 AGAAAAAAAAGA
1 A-AAAAGAAAGA
974854 AAAAAGAAAAGA
1 AAAAAG-AAAGA
974866 AA
1 AA
974868 TATATTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 10 0.31
11 5 0.16
12 17 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:974852 original size:16 final size:16
Alignment explanation
Indices: 974821--974863 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
974811 AAAAATTCAC
974821 AAAAAGAAAGAAAAAGA
1 AAAAAGAAA-AAAAAGA
*
974838 AAGAAGAAAAAAAAGA
1 AAAAAGAAAAAAAAGA
974854 AAAAAGAAAA
1 AAAAAGAAAA
974864 GAAATATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:979643 original size:14 final size:15
Alignment explanation
Indices: 979608--979645 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
979598 ATAATTTTTA
979608 TATTGAATTTTGAAT
1 TATTGAATTTTGAAT
979623 TGA-TGAATTTT-AAT
1 T-ATTGAATTTTGAAT
979637 TATTGAATT
1 TATTGAATT
979646 AAAAGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.05
14 10 0.48
15 9 0.43
16 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
TATTGAATTTTGAAT
Found at i:983195 original size:21 final size:20
Alignment explanation
Indices: 983171--983222 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
983161 AATAAAAATC
*
983171 ATAAAAAAATATAGAAACTAT
1 ATAAAAATATATAGAAA-TAT
* *
983192 ATAAAATTAT-TAGAAATTT
1 ATAAAAATATATAGAAATAT
983211 ATAAAAATATAT
1 ATAAAAATATAT
983223 TTGAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 11 0.42
20 7 0.27
21 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (20 bp):
ATAAAAATATATAGAAATAT
Found at i:983223 original size:21 final size:20
Alignment explanation
Indices: 983189--983250 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
983179 ATATAGAAAC
983189 TATATAAAATTATTAGAAATT
1 TATA-AAAATTATTAGAAATT
* *
983210 TATAAAAATATATTTGAATTT
1 TATAAAAAT-TATTAGAAATT
*
983231 TATTAAAAATTATTAAAAAT
1 TA-TAAAAATTATTAGAAAT
983251 ATAAAAAACA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.15
21 22 0.65
22 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TATAAAAATTATTAGAAATT
Found at i:985323 original size:12 final size:12
Alignment explanation
Indices: 985306--985425 Score: 88
Period size: 12 Copynumber: 10.2 Consensus size: 12
985296 CCAAACAATC
*
985306 AAAATAGCAACA
1 AAAATAACAACA
*
985318 AAAATAACAGC-
1 AAAATAACAACA
*
985329 AAAACAA-AA-A
1 AAAATAACAACA
* *
985339 AAAATAGCAAAA
1 AAAATAACAACA
*
985351 AAAATAACAGCA
1 AAAATAACAACA
*
985363 AAAATAACAAAAA
1 AAAATAAC-AACA
*
985376 AAAACAACAACA
1 AAAATAACAACA
985388 AAAATAACAACA
1 AAAATAACAACA
** *
985400 TCAA-AACAATA
1 AAAATAACAACA
985411 AAAA-AAGCAACA
1 AAAATAA-CAACA
985423 AAA
1 AAA
985426 TAGAAAAAAA
Statistics
Matches: 83, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
10 6 0.07
11 18 0.22
12 50 0.60
13 9 0.11
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:985348 original size:33 final size:33
Alignment explanation
Indices: 985306--985425 Score: 125
Period size: 37 Copynumber: 3.5 Consensus size: 33
985296 CCAAACAATC
985306 AAAATAGCAACAAAAATAACAGCAAAACAAAAA
1 AAAATAGCAACAAAAATAACAGCAAAACAAAAA
*
985339 AAAATAGCAAAAAAAATAACAGCAAAAATAACAAAAA
1 AAAATAGCAACAAAAATAACAGC---AA-AACAAAAA
* * * *
985376 AAAACAACAACAAAAATAACAACATCAAAACAATAA
1 AAAATAGCAACAAAAAT---AACAGCAAAACAAAAA
985412 AAAA-AGCAACAAAA
1 AAAATAGCAACAAAA
985426 TAGAAAAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
33 22 0.30
35 9 0.12
36 13 0.18
37 24 0.33
40 5 0.07
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (33 bp):
AAAATAGCAACAAAAATAACAGCAAAACAAAAA
Found at i:985397 original size:15 final size:15
Alignment explanation
Indices: 985313--985405 Score: 56
Period size: 15 Copynumber: 6.5 Consensus size: 15
985303 ATCAAAATAG
985313 CAACAAAAATAACAGCA
1 CAACAAAAATAACA--A
*
985330 AAACAAAAA-AA-AA
1 CAACAAAAATAACAA
* * * *
985343 TAGCAAAAAAAATAA
1 CAACAAAAATAACAA
*
985358 CAGCAAAAAT---AA
1 CAACAAAAATAACAA
985370 CAA-AAAAA-AACAA
1 CAACAAAAATAACAA
985383 CAACAAAAATAACAA
1 CAACAAAAATAACAA
*
985398 CATCAAAA
1 CAACAAAA
985406 CAATAAAAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
11 5 0.08
12 4 0.06
13 13 0.21
14 7 0.11
15 23 0.37
16 2 0.03
17 8 0.13
ACGTcount: A:0.74, C:0.16, G:0.03, T:0.06
Consensus pattern (15 bp):
CAACAAAAATAACAA
Found at i:985416 original size:25 final size:25
Alignment explanation
Indices: 985313--985397 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 25
985303 ATCAAAATAG
**
985313 CAACAAAAATAAC--AGCAAAACAA
1 CAACAAAAATAACAAAAAAAAACAA
* *
985336 -AA-AAAAATAGC-AAAAAAAATAA
1 CAACAAAAATAACAAAAAAAAACAA
*
985358 CAGCAAAAATAACAAAAAAAAACAA
1 CAACAAAAATAACAAAAAAAAACAA
985383 CAACAAAAATAACAA
1 CAACAAAAATAACAA
985398 CATCAAAACA
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
21 8 0.16
22 9 0.18
23 1 0.02
24 8 0.16
25 24 0.48
ACGTcount: A:0.75, C:0.15, G:0.04, T:0.06
Consensus pattern (25 bp):
CAACAAAAATAACAAAAAAAAACAA
Found at i:985451 original size:19 final size:20
Alignment explanation
Indices: 985401--985454 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
985391 ATAACAACAT
985401 CAAAACAATAAAAAAAGCAA
1 CAAAACAATAAAAAAAGCAA
* * * *
985421 CAAAA-TAGAAAAAAA-TAC
1 CAAAACAATAAAAAAAGCAA
985439 CAAAACAATAAAAAAA
1 CAAAACAATAAAAAAA
985455 AAACACCAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
18 6 0.22
19 16 0.59
20 5 0.19
ACGTcount: A:0.76, C:0.13, G:0.04, T:0.07
Consensus pattern (20 bp):
CAAAACAATAAAAAAAGCAA
Found at i:985462 original size:22 final size:21
Alignment explanation
Indices: 985348--985489 Score: 84
Period size: 21 Copynumber: 7.0 Consensus size: 21
985338 AAAAATAGCA
*
985348 AAAAAAATAACAGC-AAA-AAT
1 AAAAAAA-AACACCAAAACAAT
*
985368 AACAAAAAAA-AACAACAACAA-
1 AA-AAAAAAACACCAA-AACAAT
* * *
985389 AAATAACAACATCAAAACAAT
1 AAAAAAAAACACCAAAACAAT
* *
985410 -AAAAAAAGCA--ACAA-AAT
1 AAAAAAAAACACCAAAACAAT
* *
985427 AGAAAAAAATACCAAAACAAT
1 AAAAAAAAACACCAAAACAAT
*
985448 AAAAAAAAAACACCAAAACAGT
1 -AAAAAAAAACACCAAAACAAT
* *
985470 AAAGAACAACACCAAAACAA
1 AAAAAAAAACACCAAAACAA
985490 ATATATAATT
Statistics
Matches: 93, Mismatches: 18, Indels: 21
0.70 0.14 0.16
Matches are distributed among these distances:
17 3 0.03
18 10 0.11
19 2 0.02
20 25 0.27
21 33 0.35
22 20 0.22
ACGTcount: A:0.73, C:0.17, G:0.04, T:0.06
Consensus pattern (21 bp):
AAAAAAAAACACCAAAACAAT
Found at i:985762 original size:19 final size:18
Alignment explanation
Indices: 985735--985779 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
985725 ATAACTTTAA
985735 AAATTTTATATTTTATAAT
1 AAATTTTAT-TTTTATAAT
* *
985754 AATTTTTATTTTTCTAAT
1 AAATTTTATTTTTATAAT
985772 AAATTTTA
1 AAATTTTA
985780 AATATTTTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTTTATTTTTATAAT
Found at i:994912 original size:18 final size:18
Alignment explanation
Indices: 994889--994933 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
994879 TATGTTTTCA
*
994889 AATAATATGT-TAATTAAT
1 AATAATAT-TATAATAAAT
994907 AATAATATTATAATAAAT
1 AATAATATTATAATAAAT
994925 AATAATATT
1 AATAATATT
994934 TTATTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AATAATATTATAATAAAT
Done.