Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold337
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: 762055
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 499 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:700738 original size:19 final size:18
Alignment explanation
Indices: 700714--700781 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
700704 CAGTAACTAA
700714 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
700733 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
700748 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
700765 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
700782 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:700754 original size:13 final size:13
Alignment explanation
Indices: 700736--700760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
700726 ACAATACTTA
700736 TGTATCGATACAT
1 TGTATCGATACAT
700749 TGTATCGATACA
1 TGTATCGATACA
700761 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:700758 original size:32 final size:32
Alignment explanation
Indices: 700717--700779 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
700707 TAACTAATTA
*
700717 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
700749 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
700780 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:700861 original size:21 final size:21
Alignment explanation
Indices: 700837--700893 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
700827 CATTTGTAGG
700837 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCCACAA
*
700858 ATGTATCGATACATTCTACAA
1 ATGTATCGATACATTCCACAA
700879 ATGTATCGATACATT
1 ATGTATCGATACATT
700894 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (21 bp):
ATGTATCGATACATTCCACAA
Found at i:700935 original size:14 final size:14
Alignment explanation
Indices: 700896--700937 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
700886 GATACATTTA
700896 AATTTTTTTTTTT-
1 AATTTTTTTTTTTC
*
700909 -TTTTTTTTTTTTC
1 AATTTTTTTTTTTC
700922 AATTTTTTTTTTTC
1 AATTTTTTTTTTTC
700936 AA
1 AA
700938 ACACTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.44
14 14 0.56
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (14 bp):
AATTTTTTTTTTTC
Found at i:702291 original size:15 final size:15
Alignment explanation
Indices: 702252--702298 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
702242 TCTTTTCTAG
*
702252 TTCAACAATTTTCTT
1 TTCAACAATTTTCAT
*
702267 TTCAAGAATTTT-AT
1 TTCAACAATTTTCAT
*
702281 TTCAACAAATTTTGAT
1 TTCAAC-AATTTTCAT
702297 TT
1 TT
702299 ATTTTCTTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.22
15 17 0.63
16 4 0.15
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (15 bp):
TTCAACAATTTTCAT
Found at i:704357 original size:20 final size:20
Alignment explanation
Indices: 704332--704384 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
704322 TGAGCATATA
* *
704332 ATGTATCGATATAAT-TCTTC
1 ATGTATCGATACAATGTC-CC
*
704352 ATGTATTGATACAATGTCCC
1 ATGTATCGATACAATGTCCC
704372 ATGTATCGATACA
1 ATGTATCGATACA
704385 TTTCACTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 26 0.93
21 2 0.07
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATGTCCC
Found at i:704438 original size:20 final size:20
Alignment explanation
Indices: 704413--704466 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
704403 TTGCCAATTT
*
704413 TATGTATCGATACAATTG-AG
1 TATGTATCGATACAA-TGAAC
*
704433 TATGTATCAATACAATGAAC
1 TATGTATCGATACAATGAAC
704453 T-TGTATCGATACAA
1 TATGTATCGATACAA
704467 AGCATAATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
TATGTATCGATACAATGAAC
Found at i:709739 original size:20 final size:20
Alignment explanation
Indices: 709688--709741 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
709678 AATAAAAAGT
*
709688 TATTTTTATATTAAAATTTATA
1 TATTTTTA-ATT-AAATTTAAA
*
709710 TATTTATAATTAAATTTAAA
1 TATTTTTAATTAAATTTAAA
*
709730 TTTTTTTAATTA
1 TATTTTTAATTA
709742 TTATATATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 18 0.64
21 3 0.11
22 7 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTTTAATTAAATTTAAA
Found at i:710078 original size:2 final size:2
Alignment explanation
Indices: 710071--710110 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
710061 GTTAACCATT
* *
710071 TA TA TA TA TA TA TC TA TA TG TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
710111 GGTCAATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:716080 original size:13 final size:13
Alignment explanation
Indices: 716062--716086 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
716052 CAAAGATCAG
716062 TGTATCGATACAA
1 TGTATCGATACAA
716075 TGTATCGATACA
1 TGTATCGATACA
716087 TGTGAGTAAT
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:716169 original size:13 final size:13
Alignment explanation
Indices: 716151--716175 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
716141 CAAAAAAATA
716151 TGTATCGATACAT
1 TGTATCGATACAT
716164 TGTATCGATACA
1 TGTATCGATACA
716176 ACATTTTATG
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:716171 original size:33 final size:33
Alignment explanation
Indices: 716129--716195 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
716119 AGTAGCTTAA
716129 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
716162 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
716195 A
1 A
716196 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:716605 original size:25 final size:25
Alignment explanation
Indices: 716577--716627 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
716567 TATTAAACTC
716577 ATATTCTTATTAATTTATAATTATT
1 ATATTCTTATTAATTTATAATTATT
* * * *
716602 ATATTGTTATTATTTTTTATTTATT
1 ATATTCTTATTAATTTATAATTATT
716627 A
1 A
716628 ATTTTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
ATATTCTTATTAATTTATAATTATT
Found at i:719449 original size:19 final size:21
Alignment explanation
Indices: 719427--719466 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
719417 GAGGTGTTGG
719427 ACATA-CT-AAAATGCATGAA
1 ACATAGCTCAAAATGCATGAA
719446 ACATAGCTCAAAATGCATGAA
1 ACATAGCTCAAAATGCATGAA
719467 TATGGGCTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.20
Consensus pattern (21 bp):
ACATAGCTCAAAATGCATGAA
Found at i:720544 original size:20 final size:20
Alignment explanation
Indices: 720511--720551 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
720501 AAAGGTCAAA
*
720511 ACCTTGAAAAGTATCGATAC
1 ACCTTCAAAAGTATCGATAC
*
720531 ACCTTCAAATGTATCGATAC
1 ACCTTCAAAAGTATCGATAC
720551 A
1 A
720552 GATTGCACAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (20 bp):
ACCTTCAAAAGTATCGATAC
Found at i:720579 original size:13 final size:13
Alignment explanation
Indices: 720561--720585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
720551 AGATTGCACA
720561 GTATCGATACATT
1 GTATCGATACATT
720574 GTATCGATACAT
1 GTATCGATACAT
720586 GACCAAATGT
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):
GTATCGATACATT
Found at i:720699 original size:20 final size:20
Alignment explanation
Indices: 720660--720707 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
720650 ACTGTTTGTC
*
720660 TCGATACA-CACAAGATGTA
1 TCGATACATCACAAAATGTA
*
720679 TCGATACATCCCAAAATGTA
1 TCGATACATCACAAAATGTA
720699 TCGATACAT
1 TCGATACAT
720708 TGGCTTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.25
Consensus pattern (20 bp):
TCGATACATCACAAAATGTA
Found at i:725524 original size:20 final size:21
Alignment explanation
Indices: 725495--725535 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
725485 TGTTTTTGAT
725495 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
725514 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
725536 AAGAAATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:725685 original size:13 final size:13
Alignment explanation
Indices: 725667--725705 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
725657 ATAATCCCCT
725667 TGTATCGATACAG
1 TGTATCGATACAG
725680 TGTATCGATACTA-
1 TGTATCGATAC-AG
725693 TGTATCGATACAG
1 TGTATCGATACAG
725706 AGAATACTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:732371 original size:13 final size:13
Alignment explanation
Indices: 732353--732377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
732343 AGATTGCACA
732353 GTATCGATACATT
1 GTATCGATACATT
732366 GTATCGATACAT
1 GTATCGATACAT
732378 GACCAAATGT
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):
GTATCGATACATT
Found at i:732390 original size:20 final size:21
Alignment explanation
Indices: 732365--732417 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
732355 ATCGATACAT
*
732365 TGTATCGATACATG-ACCA-AA
1 TGTATCGATACATGTA-AAGAA
*
732385 TGTATCGATACTTGTAAAGAA
1 TGTATCGATACATGTAAAGAA
732406 TGTATCGATACA
1 TGTATCGATACA
732418 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATGTAAAGAA
Found at i:733388 original size:20 final size:20
Alignment explanation
Indices: 733363--733416 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
733353 ATTTACCTGC
733363 ATGTATCGATACATTGAATA
1 ATGTATCGATACATTGAATA
*
733383 ATGTATCGATACCTTGAATA
1 ATGTATCGATACATTGAATA
*
733403 ATGTATTGATACAT
1 ATGTATCGATACAT
733417 CTAGGTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTGAATA
Found at i:733461 original size:19 final size:19
Alignment explanation
Indices: 733437--733484 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
733427 TACCCATATT
*
733437 TATCGATACAATGA-TAATG
1 TATCGATACAA-AACTAATG
*
733456 TATCGATACAAAACTTATG
1 TATCGATACAAAACTAATG
733475 TATCGATACA
1 TATCGATACA
733485 TTTATCGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (19 bp):
TATCGATACAAAACTAATG
Found at i:736852 original size:13 final size:13
Alignment explanation
Indices: 736834--736859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
736824 TACACAAAGT
736834 ATGTATCGATACA
1 ATGTATCGATACA
736847 ATGTATCGATACA
1 ATGTATCGATACA
736860 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:736857 original size:32 final size:33
Alignment explanation
Indices: 736816--736879 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
736806 TAGCCAAACT
**
736816 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
736848 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
736880 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:739109 original size:21 final size:21
Alignment explanation
Indices: 739076--739125 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
739066 TTGCAAGTTG
*
739076 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
739098 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
739119 AAATAAA
1 AAATAAA
739126 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:743044 original size:13 final size:13
Alignment explanation
Indices: 743026--743063 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
743016 CATTTTTCTT
743026 TGTATCGATACAA
1 TGTATCGATACAA
*
743039 TGTATCGATACAC
1 TGTATCGATACAA
743052 TGTATCGATACA
1 TGTATCGATACA
743064 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:743218 original size:20 final size:20
Alignment explanation
Indices: 743175--743220 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
743165 AAATCTTTTG
743175 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
743196 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
743216 CAAAA
1 CAAAA
743221 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:744921 original size:39 final size:40
Alignment explanation
Indices: 744854--744944 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
744844 GAGATTTTTT
* * *
744854 TTTAGTAAAAGGGGAGAATGCATAAATTTGCTAAAATTA-
1 TTTAGTTAAGGGGGAGAATGCACAAATTTGCTAAAATTAC
* * *
744893 TCTTA-TTAAGGGGGAGAATGTACGAATTTGTTAAAATTAC
1 T-TTAGTTAAGGGGGAGAATGCACAAATTTGCTAAAATTAC
744933 TTTAGTTAAGGG
1 TTTAGTTAAGGG
744945 AGAAAGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.74
40 11 0.26
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.34
Consensus pattern (40 bp):
TTTAGTTAAGGGGGAGAATGCACAAATTTGCTAAAATTAC
Found at i:745585 original size:13 final size:13
Alignment explanation
Indices: 745567--745592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
745557 TGCACAAAGT
745567 ATGTATCGATACA
1 ATGTATCGATACA
745580 ATGTATCGATACA
1 ATGTATCGATACA
745593 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:745595 original size:32 final size:33
Alignment explanation
Indices: 745549--745612 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
745539 GTAGCAAACT
* **
745549 TGTATCGATGCACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
745581 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
745613 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:746451 original size:30 final size:30
Alignment explanation
Indices: 746390--746451 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
746380 GTAACCTTTC
* * *
746390 TTCAAAGTCCACGACTCAGTGACATCTCTT
1 TTCAAAGTCCACAACTCAGTGACACCCCTT
*
746420 TTCAAAGTCCACAACTCCA-TGGCACCCCTT
1 TTCAAAGTCCACAACT-CAGTGACACCCCTT
746450 TT
1 TT
746452 AACCTTTTAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.26, C:0.34, G:0.11, T:0.29
Consensus pattern (30 bp):
TTCAAAGTCCACAACTCAGTGACACCCCTT
Found at i:746528 original size:62 final size:62
Alignment explanation
Indices: 746457--746800 Score: 424
Period size: 62 Copynumber: 5.6 Consensus size: 62
746447 CTTTTAACCT
* *
746457 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCTACACGAGTTGATGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
** * * *
746519 TTTAGTCCTCAAAGAATAGGATGCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * *
746581 TTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAACC
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * **
746643 TTTAGTCCTCAAAGAGCAGGATG-CTTTTT-TTTTCAAAGCCCATATGAGTTAGTGGTACTG
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
* * * * * *
746703 TTTTGTCCTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACATGAGTTGGT-GCTACCT
1 TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGC-ACCC
* *
746765 TTTAGTCCTCAAAGAGCAGGCACTCCATTTTCTTTT
1 TTTAGTCCTCAAAGAGCAGG-ACGCCTTTTTCTTTT
746801 TTCCTTTGTC
Statistics
Matches: 243, Mismatches: 35, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
60 44 0.18
61 12 0.05
62 175 0.72
63 12 0.05
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (62 bp):
TTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCC
Found at i:746746 original size:122 final size:124
Alignment explanation
Indices: 746454--746784 Score: 443
Period size: 122 Copynumber: 2.7 Consensus size: 124
746444 CCCCTTTTAA
* * *
746454 CCTTTTAGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCTACACGAGTTGATGGCACCC
1 CCTTTT-GTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAACC
** * *
746519 TTTAGTCCTCAAAGAATAGGATGCTTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGCAC
65 TTTAGTCCTCAAAGAGCAGGATGCTTTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCAC
* * *
746579 CCTTTAGTCCTCAAAGAGCAAGATGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAACCT
1 CCTTTTGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAACCT
* * *
746644 TTAGTCCTCAAAGAGCAGGATGC-TTTTT-TTTTCAAAGCCCATATGAGTTAGTGGTAC
66 TTAGTCCTCAAAGAGCAGGATGCTTTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCAC
** * * * * *
746701 TGTTTTGTCCTCAAAGAGCAGGACACCTTTTCCTTTTTAAAGCCCACATGAGTTGGT-GCTACCT
1 CCTTTTGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAACC-
746765 TTTAGTCCTCAAAGAGCAGG
65 TTTAGTCCTCAAAGAGCAGG
746785 CACTCCATTT
Statistics
Matches: 182, Mismatches: 23, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
121 5 0.03
122 92 0.51
123 5 0.03
124 75 0.41
125 5 0.03
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (124 bp):
CCTTTTGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAACCT
TTAGTCCTCAAAGAGCAGGATGCTTTTTTCTTTTCAAAGCCCACACGAGTTAGTGGCAC
Found at i:746843 original size:42 final size:41
Alignment explanation
Indices: 746769--747117 Score: 182
Period size: 42 Copynumber: 8.5 Consensus size: 41
746759 CTACCTTTTA
* ** *
746769 GTCCTCAAAGAGCAGG-CAC-TCCATTTTCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTATTTCCTTTTTTCCTTT
* *
746808 GTCCTTAAGGAGCAGGACGCACTTTATTTCCTTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCA-TTTATTTCC-TTTTTTCCTTT
* * * *
746851 GTCCTCAAAGTGTAGGACACATTTCGTTCTCC-TTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTT-ATT-TCCTTTTTTCCTTT
* * * * *
746893 ATCCTCAAAGAGCAAGG-CACACCTCATTTCTTTCTTTTCCTTTT
1 GTCCTCAAAGAGC-AGGACGCA-TTTATTTCCTT-TTTTCC-TTT
* * * *
746937 GTTCTCAAAGAGTAGGGCGCATTCCATTTCCTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATT-TATTTCCTTTTTTCCTTT
* ** * * *
746979 GTTCTTGAAGAGCATGACG----TACTT--TTTTTCCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTATTTCCTTTTTTCCTTT
* * *
747014 GTCCTCAAGGAGCAGGACAC-TTTACTTTTTCTTTTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTTA---TTTCCTTTTTTCCTTT
* * * *
747057 GTCTTTAAGGAGCAGGACCCATTTCATTCTCC-TTTTTCCTTT
1 GTCCTCAAAGAGCAGGACGCATTT-ATT-TCCTTTTTTCCTTT
* *
747099 TTCCTCAAAGAGTAGGACG
1 GTCCTCAAAGAGCAGGACG
747118 TACTCCTTTT
Statistics
Matches: 235, Mismatches: 51, Indels: 45
0.71 0.15 0.14
Matches are distributed among these distances:
35 23 0.10
37 3 0.01
38 2 0.01
39 14 0.06
40 2 0.01
41 4 0.02
42 78 0.33
43 78 0.33
44 30 0.13
45 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (41 bp):
GTCCTCAAAGAGCAGGACGCATTTATTTCCTTTTTTCCTTT
Found at i:746851 original size:43 final size:42
Alignment explanation
Indices: 746797--747117 Score: 170
Period size: 43 Copynumber: 7.7 Consensus size: 42
746787 CTCCATTTTC
* *
746797 TTTTTTCCTTTGTCCTTAAGGAGCAGGACGCACTTTATTTCCT
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGACGCA-TTTATTTCCT
* * * *
746840 TTTTTTCCTTTGTCCTCAAAGTGTAGGACACATTTCGTTCTCC-
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTT-ATT-TCCT
* * * *
746883 -TTTTTCCTTTATCCTCAAAGAGCAAGG-CACACCTCATTT-CT
1 TTTTTTCCTTTGTCCTCAAAGAGC-AGGACGCA-TTTATTTCCT
* * * *
746924 TTCTTTTCCTTTTGTTCTCAAAGAGTAGGGCGCATTCCATTTCC-
1 TT-TTTTCC-TTTGTCCTCAAAGAGCAGGACGCATT-TATTTCCT
* ** *
746968 TTTTTTCCTTTGTTCTTGAAGAGCATGACG----TA----CT
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTATTTCCT
* * *
747002 TTTTTTCCCTTTGTCCTCAAGGAGCAGGACAC-TTTACTTTTTCT
1 TTTTTT-CCTTTGTCCTCAAAGAGCAGGACGCATTTA--TTTCCT
* * * *
747046 TTTTTTCCTTTGTCTTTAAGGAGCAGGACCCATTTCATTCTCC-
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTT-ATT-TCCT
* *
747089 -TTTTTCCTTTTTCCTCAAAGAGTAGGACG
1 TTTTTTCCTTTGTCCTCAAAGAGCAGGACG
747118 TACTCCTTTT
Statistics
Matches: 214, Mismatches: 39, Indels: 51
0.70 0.13 0.17
Matches are distributed among these distances:
33 1 0.00
34 6 0.03
35 18 0.08
37 1 0.00
38 2 0.01
40 1 0.00
41 1 0.00
42 70 0.33
43 73 0.34
44 39 0.18
45 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (42 bp):
TTTTTTCCTTTGTCCTCAAAGAGCAGGACGCATTTATTTCCT
Found at i:746990 original size:86 final size:85
Alignment explanation
Indices: 746769--747116 Score: 223
Period size: 85 Copynumber: 4.2 Consensus size: 85
746759 CTACCTTTTA
* * *
746769 GTCCTCAAAGAGCAGG-CAC--TCCATTTTCTTTTTTCCTTTGTCCTTAAGGAGC-AGGACGCAC
1 GTCCTCAAAGAGTAGGACACATTCCATTTCCTTTTTTCCTTTGTCCTTAA-GAGCAAGGACACAC
* *
746830 TTTATTTCCTTTTTTTCCTTT
65 CTCATTTCCTTTTTTTCCTTT
* * * * *
746851 GTCCTCAAAGTGTAGGACACATTTCGTTCTCC-TTTTTCCTTTATCCTCAAAGAGCAAGG-CACA
1 GTCCTCAAAGAGTAGGACACATTCCATT-TCCTTTTTTCCTTTGTCCT-TAAGAGCAAGGACACA
746914 CCTCATTT-CTTTCTTTTCCTTTT
64 CCTCATTTCCTTT-TTTTCC-TTT
* * * * *
746937 GTTCTCAAAGAGTAGGGCGCATTCCATTTCCTTTTTTCCTTTGTTCTTGAAGAGC-ATG----AC
1 GTCCTCAAAGAGTAGGACACATTCCATTTCCTTTTTTCCTTTGTCCTT-AAGAGCAAGGACACAC
*
746997 GT-A----CTTTTTTTCCCTTT
65 CTCATTTCCTTTTTTT-CCTTT
* * * ** * * *
747014 GTCCTCAAGGAGCAGGACACTTTACTTTTTCTTTTTTTCCTTTGTCTTTAAGGAGC-AGGACCCA
1 GTCCTCAAAGAGTAGGACACATT-CCATTTCCTTTTTTCCTTTGTCCTTAA-GAGCAAGGACACA
**
747078 TTTCATTCTCC--TTTTTCCTTT
64 CCTCATT-TCCTTTTTTTCCTTT
*
747099 TTCCTCAAAGAGTAGGAC
1 GTCCTCAAAGAGTAGGAC
747117 GTACTCCTTT
Statistics
Matches: 205, Mismatches: 38, Indels: 43
0.72 0.13 0.15
Matches are distributed among these distances:
77 26 0.13
78 32 0.16
81 1 0.00
82 19 0.09
83 4 0.02
84 4 0.02
85 62 0.30
86 56 0.27
88 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (85 bp):
GTCCTCAAAGAGTAGGACACATTCCATTTCCTTTTTTCCTTTGTCCTTAAGAGCAAGGACACACC
TCATTTCCTTTTTTTCCTTT
Found at i:750483 original size:79 final size:79
Alignment explanation
Indices: 750397--750569 Score: 199
Period size: 79 Copynumber: 2.2 Consensus size: 79
750387 TCCACCATCA
* * **
750397 GGGATACTCCAA-CCTTAGTCTTATTT-TCAAAACATCGATTTTTTA-CAATCGAGGATACTCCA
1 GGGATACTCCAACCCTGA-TCTTATTTCT-AAAACACCGATTTTCCATC-ATCGAGGATACTCCA
* ***
750459 ACCCCGTTATTTTTGAG
63 ACCCCGCTATTTCCAAG
* * *
750476 GGGATACTCCAACCCTGATTTTATTTCTAAAACACCGATTTTCCATCATCGGGGATACTGCAACC
1 GGGATACTCCAACCCTGATCTTATTTCTAAAACACCGATTTTCCATCATCGAGGATACTCCAACC
750541 CCGCTATTTCCAAG
66 CCGCTATTTCCAAG
750555 GGGATACTCCAACCC
1 GGGATACTCCAACCC
750570 CATTTTTATC
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
79 74 0.93
80 6 0.08
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (79 bp):
GGGATACTCCAACCCTGATCTTATTTCTAAAACACCGATTTTCCATCATCGAGGATACTCCAACC
CCGCTATTTCCAAG
Found at i:750532 original size:130 final size:135
Alignment explanation
Indices: 750260--750541 Score: 344
Period size: 130 Copynumber: 2.1 Consensus size: 135
750250 TATTTCCAAC
* * * *
750260 GGGATACTCCAACCCTAGTTTTATTACTAAAAACATCGATTTTTTCACTATCGGGGATACTCTAC
1 GGGATACTCCAACCCTAGTCTTATTACTAAAAACATCGATTTTTTCACAATCGAGGATACTCAAC
* *
750325 TCCTGTTATTTTCAAGGGGATAGATACTCCAATCCCGATTTTATTTTTTAAAACACCAATTTTCC
66 TCCCGTTATTTTCAAGGGG--AGATACTCCAATCCCGATTTTATTTTCTAAAACACCAATTTTCC
750390 ACCATCA
129 ACCATCA
* * *
750397 GGGATACTCCAACCTTAGTCTTATT-TTCAAAACATCGATTTTTT-ACAATCGAGGATACTCCAA
1 GGGATACTCCAACCCTAGTCTTATTACTAAAAACATCGATTTTTTCACAATCGAGGATACT-CAA
** *
750460 C-CCCGTTATTTTTGA-GGG-GATACTCCAA-CCCTGATTTTA-TTTCTAAAACACCGATTTTCC
65 CTCCCGTTATTTTCAAGGGGAGATACTCCAATCCC-GATTTTATTTTCTAAAACACCAATTTTCC
* *
750520 ATCATCG
129 ACCATCA
*
750527 GGGATACTGCAACCC
1 GGGATACTCCAACCC
750542 CGCTATTTCC
Statistics
Matches: 127, Mismatches: 16, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
130 40 0.31
131 17 0.13
134 3 0.02
135 24 0.19
136 20 0.16
137 23 0.18
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.34
Consensus pattern (135 bp):
GGGATACTCCAACCCTAGTCTTATTACTAAAAACATCGATTTTTTCACAATCGAGGATACTCAAC
TCCCGTTATTTTCAAGGGGAGATACTCCAATCCCGATTTTATTTTCTAAAACACCAATTTTCCAC
CATCA
Found at i:752419 original size:155 final size:156
Alignment explanation
Indices: 752168--752512 Score: 367
Period size: 155 Copynumber: 2.2 Consensus size: 156
752158 TCTGGATAAG
**** *
752168 AAGAACGTGTTTTTGTTGCCAAATTGTGAAAAATTAAATATTCATACGAAATCTATGTTTGTCTT
1 AAGAACGTGTTTTTGTTGCCAAATCACAAAAAATTAAAGATTCATACGAAATCTATGTTTGTCTT
* * * * *
752233 ATATGACGTACAAACTTTCATTCTAAGGAAAAGAATAAAAAG-AAATCTTTTC-TTGGAAACC-A
66 ATATGACATACAAACCTTCATTCTAAAGAAAAGAATAAAAAGAAAAACTTTTCATAGGAAACCGA
752295 TAGCATCAATTTGTGTATCCCAAAGAA
131 -AGCATCAATTTGTGTATCCCAAAGAA
* * *
752322 AAGAACGTGTTTTTGTTGCTAAATCACAAAAAATTAAAGATT-ACTATGACAATCTGTGTTTGTC
1 AAGAACGTGTTTTTGTTGCCAAATCACAAAAAATTAAAGATTCA-TACGA-AATCTATGTTTGTC
** * * **
752386 TTATATGACATATGAACCTTGATTCTAAAGAAAATAATGGAAAGAAAAACTTTTCATAGGAAACC
64 TTATATGACATACAAACCTTCATTCTAAAGAAAAGAATAAAAAGAAAAACTTTTCATAGGAAACC
** * *
752451 GAAGCATCAATATCATATATCCCAATGAA
129 GAAGCATCAAT-TTGTGTATCCCAAAGAA
** * *
752480 GTGAACAT-TTGCTTGTTGCCAAATCACAAAAAA
1 AAGAACGTGTT-TTTGTTGCCAAATCACAAAAAA
752513 AAAATTGGAG
Statistics
Matches: 156, Mismatches: 28, Indels: 10
0.80 0.14 0.05
Matches are distributed among these distances:
153 1 0.01
154 40 0.26
155 48 0.31
156 9 0.06
157 19 0.12
158 39 0.25
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (156 bp):
AAGAACGTGTTTTTGTTGCCAAATCACAAAAAATTAAAGATTCATACGAAATCTATGTTTGTCTT
ATATGACATACAAACCTTCATTCTAAAGAAAAGAATAAAAAGAAAAACTTTTCATAGGAAACCGA
AGCATCAATTTGTGTATCCCAAAGAA
Found at i:753178 original size:157 final size:157
Alignment explanation
Indices: 752989--753277 Score: 397
Period size: 157 Copynumber: 1.8 Consensus size: 157
752979 AAAATTCATG
* * *
752989 TTTGTCTTATATGACAGACGAACTTTAATTTTATA-AAAAATGATGAG-AAAAAAGCTTTTCTTT
1 TTTGTCTTATATGACAGACAAACTTTAATTTTA-AGAAAAATGATAAGCAAAAAAGCCTTTC-TT
* *
753052 GGAAACCAAAG-AATCAATA-TAATGTATCTTAACGAGAAAAATGTGTTTTTGTTGCCAAATCAT
64 GGAAACCAAAGAAAT-AATACT-ATGTATCTTAACAAGAAAAATGTGTTTTTGTTGACAAATCAT
753115 GAAAAATTGAATATTCTTATGGGAATCCGCT
127 GAAAAATTGAATATTCTTATGGGAATCCGCT
* * * * *
753146 TTTGTTTTATATGATAGATAAACTTTGATTTTAAGGAAAATGATAAGCAAAAAAGCCTTTCTTGG
1 TTTGTCTTATATGACAGACAAACTTTAATTTTAAGAAAAATGATAAGCAAAAAAGCCTTTCTTGG
* * *
753211 AAACCAAAGAAATAATACTGTGTATCTTAATAAGGAAAATGTGTTTTTGTTGACAAATCATGAAA
66 AAACCAAAGAAATAATACTATGTATCTTAACAAGAAAAATGTGTTTTTGTTGACAAATCATGAAA
753276 AA
131 AA
753278 ACTAAAGATT
Statistics
Matches: 115, Mismatches: 13, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
156 1 0.01
157 98 0.85
158 16 0.14
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (157 bp):
TTTGTCTTATATGACAGACAAACTTTAATTTTAAGAAAAATGATAAGCAAAAAAGCCTTTCTTGG
AAACCAAAGAAATAATACTATGTATCTTAACAAGAAAAATGTGTTTTTGTTGACAAATCATGAAA
AATTGAATATTCTTATGGGAATCCGCT
Found at i:754704 original size:158 final size:158
Alignment explanation
Indices: 753556--754738 Score: 727
Period size: 158 Copynumber: 7.5 Consensus size: 158
753546 AAGAAATATA
** * * * *
753556 TGTTTGTCTTATATGATGGATGAACTTTGATTCTAAGGAAAATGAT-AGGAAGAAAAGCTTTTCC
1 TGTTTGTCTTATATGACAGACGAACTTTGATTCTAAAGAAAATGATGA-GAAAAAAAGCTTTT-T
*** * * **
753620 TA-GAAATTGAAGCATCAATATCAT-ATATCCTAATAAAAAGAATGTGTTTTTGTTGTCAAATCA
64 TAGGAAACCAAAGCATCAATATCATGCTAT-CTAATGAGGAGAATGTGTTTTTGTTGTCAAATCA
* *
753683 CAAAAAAATTGGAGATTACTATGAGAATCAG
128 CAAAAAAATTAGAGATTACTATGAGAATCCG
* * * * *
753714 TGTTTGTCTTATATGAC-GTATGAACGTTGATTCT-AAGAAAAATAATGGGAAGAAAAGCTTTTC
1 TGTTTGTCTTATATGACAG-ACGAACTTTGATTCTAAAG-AAAATGATGAGAAAAAAAGCTTTT-
* * * * * * * ** * *
753777 ATGGGAAACTAAATCATCGATATCAT-CTATTCTAAAGAAGAGAACAT-ATTTTGTT-ACAAATC
63 TTAGGAAACCAAAGCATCAATATCATGCTA-TCTAATGAGGAGAATGTGTTTTTGTTGTCAAATC
* * *
753839 ATAAAAAAAGTTAGAGATTATTATGAGAATCTG
127 ACAAAAAAA-TTAGAGATTACTATGAGAATCCG
* * * * * *
753872 AGTTTATTTTATATGATAGACGAACTTTGATTCTAAGGAAAATGATAGGGAAAAAAA-CTTTACT
1 TGTTTGTCTTATATGACAGACGAACTTTGATTCTAAAGAAAATGAT-GAGAAAAAAAGCTTT--T
* * ** * * * *
753936 TT-GGAAACCAATGCATCAAAATTGTG-TATCCTAACGAGAAGAATGTAG-TTTTATTGCCAAAT
63 TTAGGAAACCAAAGCATCAATATCATGCTAT-CTAATGAGGAGAATGT-GTTTTTGTTGTCAAAT
* * * *
753998 CATGAAAAACATGAAGATGATTAC-A--AGAATCCA
126 CA-CAAAAAAAT-TAGA-GATTACTATGAGAATCCG
* * * * * * *
754031 TATTTGTCTTATTTGA-AGTACGAACTTTAATTAT-AAGAAATATG-TTAGAAAGAAAAGATTTG
1 TGTTTGTCTTATATGACAG-ACGAACTTTGATTCTAAAGAAA-ATGATGAGAAA-AAAAGCTTTT
* * ** ** *
754093 TTAGGAAACCAAAACATCGATATTGTGC-ATCCTAATGAGGAGAACATGTTTTTGTT-TTAAATC
63 TTAGGAAACCAAAGCATCAATATCATGCTAT-CTAATGAGGAGAATGTGTTTTTGTTGTCAAATC
* ** **
754156 ACAAAAAAATTGGAGATTTTTATGAGAATCAT
127 ACAAAAAAATTAGAGATTACTATGAGAATCCG
* * ** * ** * * ** * *
754188 TGTTTGTCTCATATAAGGGACAAACTTTGATTCTAGGGAAAAAGTTGAGATGAAACGTTTTTTTA
1 TGTTTGTCTTATATGACAGACGAACTTTGATTCTAAAGAAAATGATGAGAAAAAAAGCTTTTTTA
* * * * *
754253 GAAAATCAAAGCATCAATATCAT-CTATCAAAATGAGGTA-AATGTGTTTTTATTG-CTAACTCA
66 GGAAACCAAAGCATCAATATCATGCTATC-TAATGAGG-AGAATGTGTTTTTGTTGTC-AAATCA
* * * * *
754315 CAAAAAGATTTA-AGATTATTAAGAAAATCCA
128 CAAAAA-AATTAGAGATTACTATGAGAATCCG
* * * *
754346 TGTTTATTTTATATGACAGATGAACTTTGATTCTATAA-AAAATGATGAGAAGAAAAA-TTTTTC
1 TGTTTGTCTTATATGACAGACGAACTTTGATTCTA-AAGAAAATGATGAGAA-AAAAAGCTTTT-
* * * * ** **
754409 TTAGGAAATCAAGGAATCAATATAATG-TATCCTAATGAGGAGAACATGTTTTTGTTACCAAATC
63 TTAGGAAACCAAAGCATCAATATCATGCTAT-CTAATGAGGAGAATGTGTTTTTGTTGTCAAATC
* * *
754473 AC-AAAAGATT-GA-ATATTCTTATGAGAATTCG
127 ACAAAAAAATTAGAGAT-TAC-TATGAGAATCCG
* * * * *
754504 TGTTTGTCTTATATGATAAACGAAATTTGATTCTAATGAAAATGATGGGAAAAAAAAGCTTTTTT
1 TGTTTGTCTTATATGACAGACGAACTTTGATTCTAAAGAAAATGATGAG-AAAAAAAGCTTTTTT
* * * *
754569 GGGAAACCATAGCATCAATATCATGCT-TCTAATGAGGAGAATGTGTTTTTGTTGTGAAATCACG
65 AGGAAACCAAAGCATCAATATCATGCTATCTAATGAGGAGAATGTGTTTTTGTTGTCAAATCACA
754633 AAAAAATTAGAGATTACTATGAGAATCCG
130 AAAAAATTAGAGATTACTATGAGAATCCG
* * * * * * *
754662 TGTTTGTCTTGTATGACATATGAACCTTGATTCTAAAGAAAATAATGAGAAATAAAGCTTTTCAT
1 TGTTTGTCTTATATGACAGACGAACTTTGATTCTAAAGAAAATGATGAGAAAAAAAGCTTTT-TT
*
754727 GGGAAACCAAAG
65 AGGAAACCAAAG
754739 TTTGTGTTGC
Statistics
Matches: 781, Mismatches: 188, Indels: 112
0.72 0.17 0.10
Matches are distributed among these distances:
154 4 0.01
155 3 0.00
156 11 0.01
157 157 0.20
158 425 0.54
159 152 0.19
160 14 0.02
161 10 0.01
162 5 0.01
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (158 bp):
TGTTTGTCTTATATGACAGACGAACTTTGATTCTAAAGAAAATGATGAGAAAAAAAGCTTTTTTA
GGAAACCAAAGCATCAATATCATGCTATCTAATGAGGAGAATGTGTTTTTGTTGTCAAATCACAA
AAAAATTAGAGATTACTATGAGAATCCG
Found at i:754909 original size:20 final size:20
Alignment explanation
Indices: 754876--754916 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
754866 AAAGCTTTTC
754876 TTTGGAAACCAATGCATCAA
1 TTTGGAAACCAATGCATCAA
* *
754896 TTTGGGAACTAATGCATCAA
1 TTTGGAAACCAATGCATCAA
754916 T
1 T
754917 ATCATGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (20 bp):
TTTGGAAACCAATGCATCAA
Found at i:756259 original size:156 final size:156
Alignment explanation
Indices: 755955--756300 Score: 388
Period size: 156 Copynumber: 2.2 Consensus size: 156
755945 TGTTGACAAG
*
755955 AAAAGCTTTTCTTGAAAAACCAAAGCATCAATATCATGTATCTCAATGGAAGAACATTTTTTTGT
1 AAAAGCTTTTCTTG-GAAACCAAAGCATCAATATCATGTATCTCAATGGAAGAACATTTTTTTGT
* * *
756020 TGCCAAATCATGAAAAATTGAATACTCTTATAAGAATCCATGTTTGTCTTATGTGATAGACAAAC
65 TGCCAAATCATGAAAAATTGAATA-TATTACAAGAATCCATGTTTGTCTTATATGATAGACAAAC
*
756085 TTTGATTCCAAGGAAAATGATGAGAAAA
129 TTTGATTCCAAGAAAAATGATGAGAAAA
* *
756113 AAAAGCTTTTCTTGGAAGCCAAAGCAAT-AATATCATGTATGCT-AA-GG-AGAATATGTTTTTT
1 AAAAGCTTTTCTTGGAAACCAAAGC-ATCAATATCATGTAT-CTCAATGGAAGAACAT-TTTTTT
* *
756174 -TTGCCAAATCATGAAAAAAATTAGAGAT-TATT-CAAGAATCTGA-GTTTGTTTTATATGACTA
63 GTTGCCAAATCATG--AAAAATT-GA-ATATATTACAAGAATC-CATGTTTGTCTTATATGA-TA
*** *
756235 G-CAAACTTTGATTTTGAGAAAAATGATGGGAAAA
122 GACAAACTTTGATTCCAAGAAAAATGATGAGAAAA
756269 AAAAGCTTTTCTTTGGAAA-CAAATGCATCAAT
1 AAAAGCTTTTC-TTGGAAACCAAA-GCATCAAT
756301 TACCTTATCC
Statistics
Matches: 162, Mismatches: 14, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
155 19 0.12
156 73 0.45
157 48 0.30
158 20 0.12
159 2 0.01
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (156 bp):
AAAAGCTTTTCTTGGAAACCAAAGCATCAATATCATGTATCTCAATGGAAGAACATTTTTTTGTT
GCCAAATCATGAAAAATTGAATATATTACAAGAATCCATGTTTGTCTTATATGATAGACAAACTT
TGATTCCAAGAAAAATGATGAGAAAA
Found at i:756871 original size:157 final size:152
Alignment explanation
Indices: 756566--757454 Score: 470
Period size: 157 Copynumber: 5.7 Consensus size: 152
756556 GAGAAAAGCT
* * * * *
756566 TTTCTTGGGAAACCAAAGCATCAGTATAATGTA-TCTCAATGAGTAGAACATG-TTTTTGTTGCC
1 TTTCTT-GGAAA-CAAATCATCAATATCATGTATTC-CAAT-A--AGAAAATGATTTTTGTTGTC
* ** * * * * * *
756629 AAATGACAAAAAAATTAAAGATTCCTATGAGAATCCATATTTGTCTTAAATGATAG-ATGAA-CT
60 AAATCATGAAAAAATTGAAGATTACTATGAAAATCCATGTTTGTCTTATATGAT-GTAAGAACCT
* * *
756692 TCAATTCTAAAGAAAATGATGGGAAGAGAAGCC
124 T-GATTCTTAAGAAAATAATGGGAAGA-AA--C
* * * *
756725 TTTCTTAGAAATCAAATCATCAATATCTTGTATTCCAACAAGGAAAATGGGTTTTTGTTGTCAAA
1 TTTCTTGGAAA-CAAATCATCAATATCATGTATTCCAATAA-GAAAAT-GATTTTTGTTGTCAAA
756790 TCATGAAAAAATTGAAGATTACTAT-AAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGAT
63 TCATGAAAAAATTGAAGATTACTATGAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGAT
*
756854 TCTTAAGAAAATAATGGGAAGAAAAAT
128 TCTTAAGAAAATAATGGGAAG--AAAC
* * * * * *
756881 TTTCCATGGGAAACCATATCTTCAATATCATGTATCCCATGATAAGAACAT-ATTTTTGTTGACA
1 TTT-C-TTGGAAA-CAAATCATCAATATCATGTATTCCA--ATAAGAAAATGATTTTTGTTGTCA
* * ** * * *
756945 AATCATG-AAAAATTGAAGATTATTATGAGAATTTGA-GTTTGTTTTAT-TGAT-TGACGAACTT
61 AATCATGAAAAAATTGAAGATTACTATGA-AAATCCATGTTTGTCTTATATGATGT-AAGAACCT
* * * *
757006 TGATTC-TAAGTAAAATGATAGAAAAACAAC
124 TGATTCTTAAG-AAAATAATGGGAAGA-AAC
* * * * * * *
757036 TTTTTTGGTAACTAATGCATCAATATCGTGTA-TCTTAATGATGAAAATGCAATTTTGTTGTCAA
1 TTTCTTGGAAACAAAT-CATCAATATCATGTATTC-CAAT-AAGAAAATG-ATTTTTGTTGTCAA
* *
757100 ATCATGAAAAAAATTGTAGATTACTATG-AATTCCATGTTTGTCTTATATGATGTAAGAACCTTG
62 ATCATG-AAAAAATTGAAGATTACTATGAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTG
*
757164 ATTCTTAAGAAAATAATGGGAAGAAAAAT
126 ATTCTTAAGAAAATAATGGGAAG--AAAC
* * * * * * *
757193 TTTCCATGGGAAACCATAGCTTCAATATCATGTATCCCATGATAAGAACAT-ATTTTTGTTGACA
1 TTT-C-TTGGAAA-CAAATCATCAATATCATGTATTCCA--ATAAGAAAATGATTTTTGTTGTCA
* * * ** *
757257 AATCAT-AAGAAATTGGAGATTATTAT-AAGAATTTGA-GTTTGTTTTATATGAT-TGACA-AAC
61 AATCATGAAAAAATTGAAGATTACTATGAA-AA-TCCATGTTTGTCTTATATGATGT-A-AGAAC
* * *
757317 TTTGATTC-TAAGTAAAATGATAGGAA-AACACC
122 CTTGATTCTTAAG-AAAATAATGGGAAGAA-A-C
* * * * * * * * **
757349 TCTTTTTAGTAACTAATTCATCAATATCGTGTATCCCAATGAAGAAAATGAAATTTTATTACCAA
1 T-TTCTTGGAAAC-AAATCATCAATATCATGTATTCCAAT-AAGAAAATG-ATTTTTGTTGTCAA
* * * * * *
757414 TTCATGAAAAACTTGGAGATAATTATGAGAATCCATGTTTG
62 ATCATGAAAAAATTGAAGATTACTATGAAAATCCATGTTTG
757455 CTTCAAGGAA
Statistics
Matches: 562, Mismatches: 116, Indels: 106
0.72 0.15 0.14
Matches are distributed among these distances:
151 2 0.00
152 10 0.02
153 21 0.04
154 34 0.06
155 45 0.08
156 137 0.24
157 153 0.27
158 113 0.20
159 33 0.06
160 12 0.02
161 2 0.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (152 bp):
TTTCTTGGAAACAAATCATCAATATCATGTATTCCAATAAGAAAATGATTTTTGTTGTCAAATCA
TGAAAAAATTGAAGATTACTATGAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGATTCT
TAAGAAAATAATGGGAAGAAAC
Found at i:757112 original size:156 final size:155
Alignment explanation
Indices: 756934--757445 Score: 494
Period size: 156 Copynumber: 3.3 Consensus size: 155
756924 AAGAACATAT
*
756934 TTTTGTTGACAAATCATG-AAAAATTGAAGATTATTATGAGAATTTGAGTTTGTTTTAT-TGATT
1 TTTTGTTGACAAATCATGAAAAAATTGGAGATTATTATGAGAATTTGAGTTTGTTTTATATGATT
756997 GACGAACTTTGATTCTAAGTAAAATGATAGAAAAACAACTTTTTTGGTAACTAATGCATCAATAT
66 GACGAACTTTGATTCTAAGTAAAATGATAGAAAAACAACTTTTTTGGTAACTAATGCATCAATAT
*
757062 CGTGTATCTTAATGATGAAAATGCAA
131 CGTGTATC-CAATGATGAAAATGCAA
* * * ** *
757088 TTTTGTTGTCAAATCATGAAAAAAATTGTAGATTACTAT--GAATTCCATGTTTGTCTTATATGA
1 TTTTGTTGACAAATCATG-AAAAAATTGGAGATTATTATGAGAATTTGA-GTTTGTTTTATATGA
* * * * * * *
757151 -TGTAAGAACCTTGATTCTTAAG-AAAATAATGGGAAGAAA-AA-TTTTCCATGGGAAAC-CATA
64 TTG-ACGAACTTTGATTC-TAAGTAAAATGAT-AGAA-AAACAACTTTT---TTGGTAACTAAT-
* * *
757211 GCTTCAATATCATGTATCCCATGAT-AAGAA--CATA
121 GCATCAATATCGTGTATCCAATGATGAA-AATGCA-A
* *
757245 TTTTTGTTGACAAATCAT-AAGAAATTGGAGATTATTATAAGAATTTGAGTTTGTTTTATATGAT
1 -TTTTGTTGACAAATCATGAAAAAATTGGAGATTATTATGAGAATTTGAGTTTGTTTTATATGAT
* * * * *
757309 TGACAAACTTTGATTCTAAGTAAAATGATAGGAAAACACCTCTTTTTAGTAACTAATTCATCAAT
65 TGACGAACTTTGATTCTAAGTAAAATGATAGAAAAACAACT-TTTTTGGTAACTAATGCATCAAT
* *
757374 ATCGTGTATCCCAATGAAGAAAATGAAA
129 ATCGTGTAT-CCAATGATGAAAATGCAA
* * * *
757402 TTTTATT-ACCAATTCATGAAAAACTTGGAGATAATTATGAGAAT
1 TTTTGTTGA-CAAATCATGAAAAAATTGGAGATTATTATGAGAAT
757446 CCATGTTTGC
Statistics
Matches: 282, Mismatches: 47, Indels: 55
0.73 0.12 0.14
Matches are distributed among these distances:
154 23 0.08
155 35 0.12
156 92 0.33
157 70 0.25
158 40 0.14
159 22 0.08
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (155 bp):
TTTTGTTGACAAATCATGAAAAAATTGGAGATTATTATGAGAATTTGAGTTTGTTTTATATGATT
GACGAACTTTGATTCTAAGTAAAATGATAGAAAAACAACTTTTTTGGTAACTAATGCATCAATAT
CGTGTATCCAATGATGAAAATGCAA
Found at i:757140 original size:312 final size:314
Alignment explanation
Indices: 756742--757424 Score: 1088
Period size: 312 Copynumber: 2.2 Consensus size: 314
756732 GAAATCAAAT
* * * ***
756742 CATCAATATCTTGTATTCCAA-CAAGGAAAATGGGTTTTTGTTGTCAAATCATG-AAAAAATTGA
1 CATCAATATCGTGTATCCCAATGAA-GAAAATGAAATTTTGTTGTCAAATCATGAAAAAAATTGA
756805 AGATTACTATAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGATTCTTAAGAAAATAATG
65 AGATTACTATAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGATTCTTAAGAAAATAATG
*
756870 GGAAGAAAAATTTTCCATGGGAAACCATATCTTCAATATCATGTATCCCATGATAAGAACATATT
130 GGAAGAAAAATTTTCCATGGGAAACCATAGCTTCAATATCATGTATCCCATGATAAGAACATATT
*
756935 TTTGTTGACAAATCATGAA-AAATTGAAGATTATTATGAGAATTTGAGTTTGTTTTAT-TGATTG
195 TTTGTTGACAAATCAT-AAGAAATTGAAGATTATTATAAGAATTTGAGTTTGTTTTATATGATTG
* *
756998 ACGAACTTTGATTCTAAGTAAAATGATAGAAAAACAACT-TTTTTGGTAACTAATG
259 ACAAACTTTGATTCTAAGTAAAATGATAGAAAAACAACTCTTTTTAGTAACTAATG
** * * *
757053 CATCAATATCGTGTATCTTAATGATGAAAATGCAATTTTGTTGTCAAATCATGAAAAAAATTGTA
1 CATCAATATCGTGTATCCCAATGAAGAAAATGAAATTTTGTTGTCAAATCATGAAAAAAATTGAA
* *
757118 GATTACTATGAATTCCATGTTTGTCTTATATGATGTAAGAACCTTGATTCTTAAGAAAATAATGG
66 GATTACTATAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGATTCTTAAGAAAATAATGG
757183 GAAGAAAAATTTTCCATGGGAAACCATAGCTTCAATATCATGTATCCCATGATAAGAACATATTT
131 GAAGAAAAATTTTCCATGGGAAACCATAGCTTCAATATCATGTATCCCATGATAAGAACATATTT
*
757248 TTGTTGACAAATCATAAGAAATTGGAGATTATTATAAGAATTTGAGTTTGTTTTATATGATTGAC
196 TTGTTGACAAATCATAAGAAATTGAAGATTATTATAAGAATTTGAGTTTGTTTTATATGATTGAC
* * *
757313 AAACTTTGATTCTAAGTAAAATGATAGGAAAACACCTCTTTTTAGTAACTAATT
261 AAACTTTGATTCTAAGTAAAATGATAGAAAAACAACTCTTTTTAGTAACTAATG
* ** *
757367 CATCAATATCGTGTATCCCAATGAAGAAAATGAAATTTTATTACCAATTCATGAAAAA
1 CATCAATATCGTGTATCCCAATGAAGAAAATGAAATTTTGTTGTCAAATCATGAAAAA
757425 CTTGGAGATA
Statistics
Matches: 339, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
311 44 0.13
312 189 0.56
313 42 0.12
314 64 0.19
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (314 bp):
CATCAATATCGTGTATCCCAATGAAGAAAATGAAATTTTGTTGTCAAATCATGAAAAAAATTGAA
GATTACTATAAAATCCATGTTTGTCTTATATGATGTAAGAACCTTGATTCTTAAGAAAATAATGG
GAAGAAAAATTTTCCATGGGAAACCATAGCTTCAATATCATGTATCCCATGATAAGAACATATTT
TTGTTGACAAATCATAAGAAATTGAAGATTATTATAAGAATTTGAGTTTGTTTTATATGATTGAC
AAACTTTGATTCTAAGTAAAATGATAGAAAAACAACTCTTTTTAGTAACTAATG
Found at i:758300 original size:14 final size:15
Alignment explanation
Indices: 758281--758309 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
758271 AAATGTATCA
758281 ATACAA-TTGCAATG
1 ATACAACTTGCAATG
758295 ATACAACTTGCAATG
1 ATACAACTTGCAATG
758310 TATCAATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (15 bp):
ATACAACTTGCAATG
Found at i:758412 original size:21 final size:21
Alignment explanation
Indices: 758386--758445 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
758376 TACGCACATA
758386 AGAATGTATTGATACAATTCC
1 AGAATGTATTGATACAATTCC
*
758407 AGAATG-ATTTGATAC-A-TCT
1 AGAATGTA-TTGATACAATTCC
*
758426 AGAATTGTATCGATACAATT
1 AGAA-TGTATTGATACAATT
758446 AGCCCAACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 6 0.19
20 10 0.31
21 15 0.47
22 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (21 bp):
AGAATGTATTGATACAATTCC
Found at i:760688 original size:13 final size:13
Alignment explanation
Indices: 760670--760695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
760660 TACACCAAAT
760670 ATGTATCGATACA
1 ATGTATCGATACA
760683 ATGTATCGATACA
1 ATGTATCGATACA
760696 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:760693 original size:32 final size:33
Alignment explanation
Indices: 760652--760715 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
760642 TAGCCAAACT
* *
760652 TGTATCGATACACCAAATA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
760684 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
760716 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.