Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168481.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_8, 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: 25818110
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 67000 characters in sequence are not A, C, G, or T
File 5 of 127
Found at i:923126 original size:2 final size:2
Alignment explanation
Indices: 923121--923147 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
923111 TACCATTCAA
923121 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
923148 ATGTTTATGC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:933325 original size:14 final size:15
Alignment explanation
Indices: 933298--933341 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
933288 CAATCAAATT
933298 TTAAAAAATATATAA
1 TTAAAAAATATATAA
*
933313 TTAAAACAT-TATAA
1 TTAAAAAATATATAA
*
933327 TTATATAAATATATA
1 TTA-AAAAATATATA
933342 TGTGAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 12 0.50
16 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAAAATATATAA
Found at i:940182 original size:40 final size:41
Alignment explanation
Indices: 940127--940209 Score: 159
Period size: 40 Copynumber: 2.0 Consensus size: 41
940117 TTACTATGAG
940127 ATAAGATGTTTATTGTTTTATTTGTTAAAAATAC-AAAAGA
1 ATAAGATGTTTATTGTTTTATTTGTTAAAAATACAAAAAGA
940167 ATAAGATGTTTATTGTTTTATTTGTTAAAAATACAAAAAGA
1 ATAAGATGTTTATTGTTTTATTTGTTAAAAATACAAAAAGA
940208 AT
1 AT
940210 TTAGTTCAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 34 0.81
41 8 0.19
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (41 bp):
ATAAGATGTTTATTGTTTTATTTGTTAAAAATACAAAAAGA
Found at i:941129 original size:3 final size:3
Alignment explanation
Indices: 941121--941174 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
941111 TGAAAATCTT
* *
941121 TAA TAA TAA TAA TAA TAC TAA TAA TAA TAC TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
941169 TAA TAA
1 TAA TAA
941175 GATGAATTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:943508 original size:12 final size:12
Alignment explanation
Indices: 943491--943517 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
943481 TCTTACCCTT
943491 AATCTCTTCTTG
1 AATCTCTTCTTG
943503 AATCTCTTCTTG
1 AATCTCTTCTTG
943515 AAT
1 AAT
943518 AAGATCAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.48
Consensus pattern (12 bp):
AATCTCTTCTTG
Found at i:951719 original size:30 final size:31
Alignment explanation
Indices: 951683--951742 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
951673 TAAACTAAAT
*
951683 CTAAGGCTCTAAGTTAAGCCGCAGC-AAAAG
1 CTAAGGCTCTAAGCTAAGCCGCAGCTAAAAG
951713 CTAAGGCTCTAAGCTAAGCCGCAGCTAAAA
1 CTAAGGCTCTAAGCTAAGCCGCAGCTAAAA
951743 CTATTGCGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 24 0.86
31 4 0.14
ACGTcount: A:0.37, C:0.25, G:0.22, T:0.17
Consensus pattern (31 bp):
CTAAGGCTCTAAGCTAAGCCGCAGCTAAAAG
Found at i:952845 original size:10 final size:10
Alignment explanation
Indices: 952830--952880 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
952820 TTGAGTAAAT
952830 TTTATAATTA
1 TTTATAATTA
*
952840 TTTATAA-AA
1 TTTATAATTA
952849 TTTTATAATTA
1 -TTTATAATTA
*
952860 TTTATAA-AA
1 TTTATAATTA
952869 TTTTATAATTA
1 -TTTATAATTA
952880 T
1 T
952881 ATAGCTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
9 2 0.06
10 29 0.88
11 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTATAATTA
Found at i:952851 original size:20 final size:20
Alignment explanation
Indices: 952826--952880 Score: 110
Period size: 20 Copynumber: 2.8 Consensus size: 20
952816 GTTGTTGAGT
952826 AAATTTTATAATTATTTATA
1 AAATTTTATAATTATTTATA
952846 AAATTTTATAATTATTTATA
1 AAATTTTATAATTATTTATA
952866 AAATTTTATAATTAT
1 AAATTTTATAATTAT
952881 ATAGCTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AAATTTTATAATTATTTATA
Found at i:958418 original size:16 final size:16
Alignment explanation
Indices: 958394--958425 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
958384 TTATGATTAG
*
958394 AGTTTAAAAAAAAATC
1 AGTTAAAAAAAAAATC
958410 AGTTAAAAAAAAAATC
1 AGTTAAAAAAAAAATC
958426 TCATATCCTA
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:0.66, C:0.06, G:0.06, T:0.22
Consensus pattern (16 bp):
AGTTAAAAAAAAAATC
Found at i:958635 original size:2 final size:2
Alignment explanation
Indices: 958628--958671 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
958618 AAAGATAATT
* *
958628 TA TA TA TA TA TA TA TA TC TA TA TA AA 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
958670 TA
1 TA
958672 AAGATATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:958678 original size:10 final size:10
Alignment explanation
Indices: 958628--958683 Score: 58
Period size: 10 Copynumber: 5.6 Consensus size: 10
958618 AAAGATAATT
*
958628 TATATATATA
1 TATAAATATA
* *
958638 TATATATCTA
1 TATAAATATA
958648 TATAAATATA
1 TATAAATATA
*
958658 TATATATATA
1 TATAAATATA
*
958668 TATAAAGATA
1 TATAAATATA
*
958678 TTTAAA
1 TATAAA
958684 CCCTTAAGTA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 39 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (10 bp):
TATAAATATA
Found at i:958968 original size:23 final size:25
Alignment explanation
Indices: 958928--958976 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
958918 TTTTATATAG
* *
958928 ATATAAATTATGACATATAATTTTT
1 ATATAAAATATGACATATAAATTTT
958953 ATATAAAATAT-A-ATATAAATTTT
1 ATATAAAATATGACATATAAATTTT
958976 A
1 A
958977 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 1 0.05
25 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATATAAAATATGACATATAAATTTT
Found at i:966460 original size:13 final size:11
Alignment explanation
Indices: 966424--966455 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
966414 TAAATCATGC
966424 TATTTTTATA-
1 TATTTTTATAT
966434 T-TTTTTATAT
1 TATTTTTATAT
966444 TATTTTTATAT
1 TATTTTTATAT
966455 T
1 T
966456 GTATTACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 8 0.40
10 2 0.10
11 10 0.50
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (11 bp):
TATTTTTATAT
Found at i:967161 original size:16 final size:17
Alignment explanation
Indices: 967137--967169 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
967127 TTATTGAAAC
*
967137 AAATGAAAAT-TTTAAA
1 AAATAAAAATATTTAAA
967153 AAATAAAAATATTTAAA
1 AAATAAAAATATTTAAA
967170 TATGTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (17 bp):
AAATAAAAATATTTAAA
Found at i:968524 original size:2 final size:2
Alignment explanation
Indices: 968517--968544 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
968507 AAACCTCAGC
968517 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
968545 CTCAGTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:969374 original size:16 final size:17
Alignment explanation
Indices: 969353--969385 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
969343 AGTCTGTTTA
969353 AAAAAATAAAA-ATTTT
1 AAAAAATAAAATATTTT
969369 AAAAAATAAAATATTTT
1 AAAAAATAAAATATTTT
969386 TCTTTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAAATAAAATATTTT
Found at i:978002 original size:21 final size:21
Alignment explanation
Indices: 977976--978055 Score: 63
Period size: 21 Copynumber: 3.8 Consensus size: 21
977966 GGCCCATATG
977976 ACCCATTTGACCCATATTATA
1 ACCCATTTGACCCATATTATA
* ** *
977997 ACCCATCTGACCACCCATT-TG
1 ACCCATTTGACC-CATATTATA
* * * **
978018 ACCCATATGACCCATCTGACC
1 ACCCATTTGACCCATATTATA
978039 ACCCATTTGACCCATAT
1 ACCCATTTGACCCATAT
978056 GACTCATCTG
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.86
22 4 0.09
ACGTcount: A:0.29, C:0.38, G:0.07, T:0.26
Consensus pattern (21 bp):
ACCCATTTGACCCATATTATA
Found at i:978031 original size:30 final size:30
Alignment explanation
Indices: 977976--978077 Score: 159
Period size: 30 Copynumber: 3.3 Consensus size: 30
977966 GGCCCATATG
*
977976 ACCCATTTGACCCATATTATAACCCATCTGACC
1 ACCCATTTGACCC--A-TATGACCCATCTGACC
978009 ACCCATTTGACCCATATGACCCATCTGACC
1 ACCCATTTGACCCATATGACCCATCTGACC
*
978039 ACCCATTTGACCCATATGACTCATCTGACC
1 ACCCATTTGACCCATATGACCCATCTGACC
978069 ACCCATTTG
1 ACCCATTTG
978078 GCCTATCTGC
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
30 53 0.79
31 1 0.01
33 13 0.19
ACGTcount: A:0.27, C:0.37, G:0.09, T:0.26
Consensus pattern (30 bp):
ACCCATTTGACCCATATGACCCATCTGACC
Found at i:978043 original size:42 final size:42
Alignment explanation
Indices: 977968--978050 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
977958 TCCCATTTGG
* * *
977968 CCCATATGACCCATTTGACCCATATTATAACCCATCTGACCA
1 CCCATATGACCCATATGACCCATATGACAACCCATCTGACCA
* * * *
978010 CCCATTTGACCCATATGACCCATCTGACCACCCATTTGACC
1 CCCATATGACCCATATGACCCATATGACAACCCATCTGACC
978051 CATATGACTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.28, C:0.39, G:0.08, T:0.25
Consensus pattern (42 bp):
CCCATATGACCCATATGACCCATATGACAACCCATCTGACCA
Found at i:978052 original size:51 final size:51
Alignment explanation
Indices: 977959--978058 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
977949 TGGATAATTT
* * * *
977959 CCCATTTGGCCCATATGACCCATTTGACCCATATTATAACCCATCTGACCA
1 CCCATTTGACCCATATGACCCATCTGACCCACATTATAACCCATATGACCA
* *
978010 CCCATTTGACCCATATGACCCATCTGACCACCCATT-TGACCCATATGAC
1 CCCATTTGACCCATATGACCCATCTGACC-CACATTATAACCCATATGAC
978059 TCATCTGACC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 38 0.90
52 4 0.10
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.26
Consensus pattern (51 bp):
CCCATTTGACCCATATGACCCATCTGACCCACATTATAACCCATATGACCA
Found at i:978058 original size:21 final size:21
Alignment explanation
Indices: 978018--978058 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
978008 CACCCATTTG
*
978018 ACCCATATGACCCATCTGACC
1 ACCCATATGACCCATATGACC
*
978039 ACCCATTTGACCCATATGAC
1 ACCCATATGACCCATATGAC
978059 TCATCTGACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.39, G:0.10, T:0.22
Consensus pattern (21 bp):
ACCCATATGACCCATATGACC
Found at i:978680 original size:12 final size:11
Alignment explanation
Indices: 978663--978738 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
978653 CAAATTCCTC
978663 ATCATCATCATA
1 ATCATCATCA-A
978675 ATCATC--CAA
1 ATCATCATCAA
*
978684 CTCATCATCAA
1 ATCATCATCAA
978695 ATTCATCATCCAA
1 A-TCATCAT-CAA
* * *
978708 CTCATCACCGA
1 ATCATCATCAA
978719 A-C-TCATCATA
1 ATCATCATCA-A
978729 ATCATCATCA
1 ATCATCATCA
978739 GTTTCATCTA
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
9 10 0.20
10 5 0.10
11 6 0.12
12 25 0.51
13 3 0.06
ACGTcount: A:0.38, C:0.33, G:0.01, T:0.28
Consensus pattern (11 bp):
ATCATCATCAA
Found at i:978692 original size:24 final size:24
Alignment explanation
Indices: 978660--978714 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
978650 GGCCAAATTC
*
978660 CTCATCATCATCA-TAATCATCCAA
1 CTCATCATCA-AATTAATCATCCAA
*
978684 CTCATCATCAAATTCATCATCCAA
1 CTCATCATCAAATTAATCATCCAA
978708 CTCATCA
1 CTCATCA
978715 CCGAACTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.36, C:0.35, G:0.00, T:0.29
Consensus pattern (24 bp):
CTCATCATCAAATTAATCATCCAA
Found at i:978724 original size:24 final size:24
Alignment explanation
Indices: 978675--978727 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
978665 CATCATCATA
* *
978675 ATCATCCAACTCATCATCAAATTC
1 ATCATCCAACTCATCACCAAACTC
*
978699 ATCATCCAACTCATCACCGAACTC
1 ATCATCCAACTCATCACCAAACTC
978723 ATCAT
1 ATCAT
978728 AATCATCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATCATCCAACTCATCACCAAACTC
Found at i:981255 original size:27 final size:25
Alignment explanation
Indices: 981210--981260 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
981200 TCTTTTGTCT
*
981210 AAAAAACCAAAATTAAAATAATAATA
1 AAAAAACAAAAATTAAAAT-ATAATA
*
981236 AAAATAACAAAAATTGAAATATAAT
1 AAAA-AACAAAAATTAAAATATAAT
981261 GACGAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.22
Consensus pattern (25 bp):
AAAAAACAAAAATTAAAATATAATA
Found at i:983364 original size:6 final size:6
Alignment explanation
Indices: 983353--983381 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
983343 GTGTTGAACC
983353 CCATGA CCATGA CCATGA CCATGA CCATG
1 CCATGA CCATGA CCATGA CCATGA CCATG
983382 CGCCATGCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.34, G:0.17, T:0.17
Consensus pattern (6 bp):
CCATGA
Found at i:990162 original size:21 final size:20
Alignment explanation
Indices: 990136--990174 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
990126 CATATCAAAT
* *
990136 AAAAATTATTTTTAAAAGTA
1 AAAAAATATATTTAAAAGTA
990156 AAAAAATATATTTAAAAGT
1 AAAAAATATATTTAAAAGT
990175 TTTTTTAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAAAATATATTTAAAAGTA
Found at i:990510 original size:7 final size:7
Alignment explanation
Indices: 990491--990522 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
990481 AATATGAAAA
990491 TAAAATAT
1 TAAAAT-T
990499 TAAAATT
1 TAAAATT
990506 TAAAATT
1 TAAAATT
990513 TAAAATT
1 TAAAATT
990520 TAA
1 TAA
990523 TAATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAAATT
Found at i:990517 original size:14 final size:15
Alignment explanation
Indices: 990491--990527 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
990481 AATATGAAAA
990491 TAAAATATTAAAATT
1 TAAAATATTAAAATT
990506 TAAAAT-TTAAAATT
1 TAAAATATTAAAATT
990520 TAATAATA
1 TAA-AATA
990528 ATTATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATATTAAAATT
Found at i:990626 original size:32 final size:32
Alignment explanation
Indices: 990580--990656 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
990570 CTATATAAAT
*
990580 TATAAA-ATATAATTTTTTAATA-AAATATGA
1 TATAAATATATAAATTTTTAATATAAATATGA
**
990610 TATAAATATATAAA-TTTTAATATTTTATATGA
1 TATAAATATATAAATTTTTAATA-TAAATATGA
990642 TATAAATATATAAAT
1 TATAAATATATAAAT
990657 CATTAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 14 0.35
31 6 0.15
32 20 0.50
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
TATAAATATATAAATTTTTAATATAAATATGA
Found at i:990668 original size:3 final size:3
Alignment explanation
Indices: 990660--990696 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
990650 TATAAATCAT
*
990660 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
990697 TGTAGGCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:992090 original size:16 final size:17
Alignment explanation
Indices: 992062--992093 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
992052 TAATATTATA
992062 AAATTTAAAATTAATTC
1 AAATTTAAAATTAATTC
992079 AAATTT-AAATTAATT
1 AAATTTAAAATTAATT
992094 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTTAAAATTAATTC
Found at i:992253 original size:9 final size:10
Alignment explanation
Indices: 992234--992273 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
992224 AATTTTTTAT
992234 TTTATAAAAA
1 TTTATAAAAA
992244 TTTA-AAAAA
1 TTTATAAAAA
*
992253 TATATAAAAA
1 TTTATAAAAA
*
992263 TTAATAAAAA
1 TTTATAAAAA
992273 T
1 T
992274 ACATATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TTTATAAAAA
Found at i:992260 original size:19 final size:20
Alignment explanation
Indices: 992236--992274 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
992226 TTTTTTATTT
*
992236 TATAAAAATTTA-AAAAATA
1 TATAAAAATTAATAAAAATA
992255 TATAAAAATTAATAAAAATA
1 TATAAAAATTAATAAAAATA
992275 CATATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
TATAAAAATTAATAAAAATA
Found at i:998182 original size:3 final size:3
Alignment explanation
Indices: 998174--998200 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
998164 CCAAAAGTTT
998174 CAG CAG CAG CAG CAG CAG CAG CAG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG
998201 ATGAGAGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.33, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:1002601 original size:22 final size:22
Alignment explanation
Indices: 1002576--1002618 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
1002566 ATTATTAATA
1002576 TCAAATATAACTTGACCTAAAT
1 TCAAATATAACTTGACCTAAAT
* *
1002598 TCAAATATAATTTGATCTAAA
1 TCAAATATAACTTGACCTAAA
1002619 CCCAACCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.35
Consensus pattern (22 bp):
TCAAATATAACTTGACCTAAAT
Found at i:1002901 original size:2 final size:2
Alignment explanation
Indices: 1002888--1002941 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
1002878 CTACTCAAAT
* * * * *
1002888 TA TA TA TC TA TA TA TA TA TA TA TA CA CA TA TA TT TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1002930 TA TT TA TA TA TA
1 TA TA TA TA TA TA
1002942 CACACCACTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1003601 original size:5 final size:5
Alignment explanation
Indices: 1003593--1003639 Score: 58
Period size: 5 Copynumber: 8.8 Consensus size: 5
1003583 TCGCATGTTT
*
1003593 TTTTA TTTTA TTTTA TTTTTA ATTTA TATTTA TATTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA -TTTTA TTTTA T-TTTA T-TTTA TTTTA TTTT
1003640 TTTATAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
5 22 0.58
6 16 0.42
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1003617 original size:17 final size:16
Alignment explanation
Indices: 1003592--1003639 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
1003582 ATCGCATGTT
1003592 TTTTTATTTTATTTTA
1 TTTTTATTTTATTTTA
*
1003608 TTTTTAATTTATATTTA
1 TTTTTATTTTAT-TTTA
*
1003625 TATTTATTTTATTTT
1 TTTTTATTTTATTTT
1003640 TTTATAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 14 0.50
17 14 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTATTTTATTTTA
Found at i:1004535 original size:8 final size:8
Alignment explanation
Indices: 1004522--1004567 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
1004512 TTATAACATA
1004522 TATATTTT
1 TATATTTT
1004530 TATA-TTT
1 TATATTTT
1004537 TATATTTT
1 TATATTTT
1004545 TAAATATTTT
1 T--ATATTTT
*
1004555 TAAATTTT
1 TATATTTT
1004563 T-TATT
1 TATATT
1004568 ATATAAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 10 0.30
8 15 0.45
10 8 0.24
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (8 bp):
TATATTTT
Found at i:1004916 original size:61 final size:61
Alignment explanation
Indices: 1004843--1004965 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
1004833 AACTTTCTTG
* * * *
1004843 GGATCATATCATTAAAAAGTTCTTCCCCTATGGTTTCAAAATCTAGCTGCCTATGGCTTCA
1 GGATCATATCATTAAAAAATTCTCCCCCTATGGTTTCAAAATCCAGCTACCTATGGCTTCA
*
1004904 GGATCATATCATTAAAAAATTCTCCCCCTATGGTTTCAAAATCCAGCTACCTTTGGCTTCA
1 GGATCATATCATTAAAAAATTCTCCCCCTATGGTTTCAAAATCCAGCTACCTATGGCTTCA
1004965 G
1 G
1004966 TCCATACTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.33
Consensus pattern (61 bp):
GGATCATATCATTAAAAAATTCTCCCCCTATGGTTTCAAAATCCAGCTACCTATGGCTTCA
Found at i:1005297 original size:2 final size:2
Alignment explanation
Indices: 1005290--1005322 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1005280 AAGTTAAGTA
1005290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1005323 ACAATAGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1007283 original size:23 final size:23
Alignment explanation
Indices: 1007256--1007305 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
1007246 CCATGAAACA
*
1007256 AAAAACTTGTTCTGATCCATAGG
1 AAAAACTTGTTCTGATCCACAGG
1007279 AAAAACTTGTTCTGATCCACAGG
1 AAAAACTTGTTCTGATCCACAGG
1007302 AAAA
1 AAAA
1007306 TTTTTTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (23 bp):
AAAAACTTGTTCTGATCCACAGG
Found at i:1007348 original size:12 final size:12
Alignment explanation
Indices: 1007314--1007356 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
1007304 AATTTTTTTT
1007314 TATATAACTATG
1 TATATAACTATG
*
1007326 TATATTTACTATG
1 TATA-TAACTATG
*
1007339 TATATAACTATA
1 TATATAACTATG
1007351 TATATA
1 TATATA
1007357 TATTTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
12 16 0.59
13 11 0.41
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (12 bp):
TATATAACTATG
Found at i:1010288 original size:33 final size:32
Alignment explanation
Indices: 1010234--1010297 Score: 74
Period size: 33 Copynumber: 2.0 Consensus size: 32
1010224 ATTTTTAAGT
* * * *
1010234 AAATTTAATAATTCGTGTATTTTTATTATATA
1 AAATTTAATAATTCATATATTTATATAATATA
*
1010266 AAATATTAATAATTTATATATTTATATAATAT
1 AAAT-TTAATAATTCATATATTTATATAATAT
1010298 TTTATACGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
AAATTTAATAATTCATATATTTATATAATATA
Found at i:1015629 original size:121 final size:122
Alignment explanation
Indices: 1015451--1015678 Score: 368
Period size: 121 Copynumber: 1.9 Consensus size: 122
1015441 TAATGTTCGA
*
1015451 TTATCAACAGATGTTAGCTCTAAGTGACAAAGAGAATTTGTTTATTTTTTGGTTGTTTGAGTTCG
1 TTATCAACAGATGTTAGCTCTAAATGACAAAGAGAATTTGTTTATTTTTTGGTTGTTTGAGTTCG
*
1015516 AATTCATTGATAGGCTACAAGAAATTCATTTTTTATGAATTTAATGTTCAATAAATC
66 AATTCATTGATAGGCTACAAGAAATTAATTTTTTATGAATTTAATGTTCAATAAATC
** * *
1015573 TTATCAACAGATGTTAGCTC-AAATGATGAAGAGAATTTGTTTGTTTTTTTGTTGTTTGAGTTCG
1 TTATCAACAGATGTTAGCTCTAAATGACAAAGAGAATTTGTTTATTTTTTGGTTGTTTGAGTTCG
* * *
1015637 ACTTCATTGGTAGGTTACAAGAAATTAATTTTTTATGAATTT
66 AATTCATTGATAGGCTACAAGAAATTAATTTTTTATGAATTT
1015679 GTTAAGTCCA
Statistics
Matches: 97, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
121 77 0.79
122 20 0.21
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (122 bp):
TTATCAACAGATGTTAGCTCTAAATGACAAAGAGAATTTGTTTATTTTTTGGTTGTTTGAGTTCG
AATTCATTGATAGGCTACAAGAAATTAATTTTTTATGAATTTAATGTTCAATAAATC
Found at i:1020201 original size:3 final size:3
Alignment explanation
Indices: 1020193--1020221 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1020183 TGTATTTCTT
1020193 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1020222 TTTTGAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1043144 original size:14 final size:14
Alignment explanation
Indices: 1043125--1043152 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1043115 TATAATCTAT
1043125 CCATTTTGATAGAC
1 CCATTTTGATAGAC
1043139 CCATTTTGATAGAC
1 CCATTTTGATAGAC
1043153 TCAATTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
CCATTTTGATAGAC
Found at i:1048140 original size:23 final size:22
Alignment explanation
Indices: 1048104--1048163 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1048094 ATACAATTTG
* *
1048104 ATTTAAAATTAATAAAATATTAT
1 ATTTAATATAAATAAAA-ATTAT
*
1048127 TTTTAATATAAATATAAAATTAT
1 ATTTAATATAAATA-AAAATTAT
*
1048150 ATATAAT-TAAATAA
1 ATTTAATATAAATAA
1048164 TTAATTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 6 0.19
23 21 0.68
24 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAATATAAATAAAAATTAT
Found at i:1048450 original size:32 final size:30
Alignment explanation
Indices: 1048413--1048512 Score: 89
Period size: 32 Copynumber: 3.3 Consensus size: 30
1048403 CAAATCAAAT
1048413 ATTAAAATACTTAAATTTTATTTATTCAATAA
1 ATTAAAATA-TTAAATTTTATTTATT-AATAA
* * *
1048445 ATTAAATTATTTAAATTTGATTTAATAAT-A
1 ATTAAAATA-TTAAATTTTATTTATTAATAA
* **
1048475 ATTAAATTTATTTTATTTTA-TT-TTAATAA
1 ATTAAA-ATATTAAATTTTATTTATTAATAA
1048504 ATTAAAATA
1 ATTAAAATA
1048513 ATTTATTAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
28 6 0.11
29 9 0.16
30 14 0.25
31 6 0.11
32 22 0.39
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (30 bp):
ATTAAAATATTAAATTTTATTTATTAATAA
Found at i:1048486 original size:31 final size:32
Alignment explanation
Indices: 1048405--1048487 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
1048395 AAATTACTCA
* * * *
1048405 AATCAA-ATATTAAAATACTTAAATTTTATTT
1 AATCAATAAATTAAATTATTTAAATTTGATTT
*
1048436 ATTCAATAAATTAAATTATTTAAATTTGATTT
1 AATCAATAAATTAAATTATTTAAATTTGATTT
1048468 AAT-AAT-AATTAAATTTATTT
1 AATCAATAAATTAAA-TTATTT
1048488 TATTTTATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
30 7 0.16
31 14 0.32
32 23 0.52
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (32 bp):
AATCAATAAATTAAATTATTTAAATTTGATTT
Found at i:1055711 original size:2 final size:2
Alignment explanation
Indices: 1055704--1055737 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1055694 TATTTTGGAG
*
1055704 AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1055738 CAAACTCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1069612 original size:16 final size:16
Alignment explanation
Indices: 1069591--1069630 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
1069581 AATATTCTCT
1069591 ACCCAAACAAACACAA
1 ACCCAAACAAACACAA
1069607 ACCCAAACAAACACAA
1 ACCCAAACAAACACAA
1069623 ACCCAAAC
1 ACCCAAAC
1069631 TCTTGTGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.60, C:0.40, G:0.00, T:0.00
Consensus pattern (16 bp):
ACCCAAACAAACACAA
Found at i:1069751 original size:59 final size:59
Alignment explanation
Indices: 1069685--1069805 Score: 242
Period size: 59 Copynumber: 2.1 Consensus size: 59
1069675 CCCATACATT
1069685 ATACCTATGTGGACCCTCTCAGTCTCCTCTAGTCCACTCACAAACAAACATACACACCC
1 ATACCTATGTGGACCCTCTCAGTCTCCTCTAGTCCACTCACAAACAAACATACACACCC
1069744 ATACCTATGTGGACCCTCTCAGTCTCCTCTAGTCCACTCACAAACAAACATACACACCC
1 ATACCTATGTGGACCCTCTCAGTCTCCTCTAGTCCACTCACAAACAAACATACACACCC
1069803 ATA
1 ATA
1069806 AGATGTAGAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.31, C:0.38, G:0.08, T:0.22
Consensus pattern (59 bp):
ATACCTATGTGGACCCTCTCAGTCTCCTCTAGTCCACTCACAAACAAACATACACACCC
Found at i:1069998 original size:52 final size:52
Alignment explanation
Indices: 1069919--1070075 Score: 201
Period size: 52 Copynumber: 3.0 Consensus size: 52
1069909 TATAACCATA
* * *
1069919 CAAACTTGCCCATTAAGAATC-CTTTTCCTCTTAGAATTCTTTTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTC-TTTCCTCTTAGAATTCTTCTCCTGCAAGT
* * *
1069971 CAAACTTGCCTATTAAAAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
* **
1070023 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAAT-CTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
1070075 C
1 C
1070076 TTCTTGTTCA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 86 0.92
53 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTGCAAGT
Found at i:1074380 original size:23 final size:23
Alignment explanation
Indices: 1074345--1074388 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
1074335 CTTAATTTAA
*
1074345 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
1074368 TTTAATATAAATATAAAATTA
1 TTTAAAATAAATATAAAATTA
1074389 AATAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:1074389 original size:17 final size:18
Alignment explanation
Indices: 1074346--1074396 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 18
1074336 TTAATTTAAT
1074346 TTAAAATTAATA-AAATA
1 TTAAAATTAATATAAATA
***
1074363 TTATTTTTAATATAAATA
1 TTAAAATTAATATAAATA
1074381 -TAAAATTAA-ATAAATA
1 TTAAAATTAATATAAATA
1074397 AATAATAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
16 7 0.26
17 15 0.56
18 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAAATTAATATAAATA
Found at i:1082811 original size:29 final size:30
Alignment explanation
Indices: 1082761--1082819 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1082751 AAATATAAAA
**
1082761 TATATATTTTTAATTTTATTAAATT-TATT
1 TATATATTTTTAAAATTATTAAATTATATT
1082790 TATATATTTTTAAAAATT-TTAAATTATATT
1 TATATATTTTT-AAAATTATTAAATTATATT
1082820 ATTTTTATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATATATTTTTAAAATTATTAAATTATATT
Found at i:1084773 original size:3 final size:3
Alignment explanation
Indices: 1084767--1084824 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
1084757 CAAAGGCTCC
*
1084767 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
1084813 CAT AAT AAT AAT
1 AAT AAT AAT AAT
1084825 GGTTTTTTGC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1106050 original size:15 final size:15
Alignment explanation
Indices: 1106030--1106071 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
1106020 TAGAGTAGAT
1106030 ATTTAAAAATTATAA
1 ATTTAAAAATTATAA
*
1106045 ATTTAAAAAATTTTAA
1 ATTT-AAAAATTATAA
*
1106061 ATATAAAAATT
1 ATTTAAAAATT
1106072 TTTTATAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTTAAAAATTATAA
Found at i:1108608 original size:23 final size:23
Alignment explanation
Indices: 1108588--1108635 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1108578 ATTTATATAT
1108588 AATTCACATATATATAAATATCA
1 AATTCACATATATATAAATATCA
* *
1108611 AATTTATATATATATAAAT-TCA
1 AATTCACATATATATAAATATCA
1108633 AAT
1 AAT
1108636 CATTTAGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTCACATATATATAAATATCA
Found at i:1108625 original size:17 final size:17
Alignment explanation
Indices: 1108577--1108630 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1108567 GTTTATTTTT
1108577 AATTTATATATA-ATTCA
1 AATTTATATATATA-TCA
* * *
1108594 CATATATATAAATATCA
1 AATTTATATATATATCA
1108611 AATTTATATATATAT-A
1 AATTTATATATATATCA
1108627 AATT
1 AATT
1108631 CAAATCATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 5 0.17
17 24 0.80
18 1 0.03
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTTATATATATATCA
Found at i:1109338 original size:19 final size:18
Alignment explanation
Indices: 1109299--1109341 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
1109289 TTCAATTAAA
1109299 TTATATATTTTTATTAATT
1 TTATATATTTTTA-TAATT
1109318 TTATATATATTTTA-AATT
1 TTATATAT-TTTTATAATT
1109336 TT-TATA
1 TTATATA
1109342 AAATAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 8 0.35
20 5 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATATTTTTATAATT
Found at i:1119622 original size:45 final size:45
Alignment explanation
Indices: 1119572--1119662 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
1119562 AAGTTGAACA
1119572 ATAAGAGCAACATTCAGAACTTGGAGAATCAAGCTGAAGCTGCTG
1 ATAAGAGCAACATTCAGAACTTGGAGAATCAAGCTGAAGCTGCTG
*
1119617 ATAAGAGCAACGTTCAGAACTTGGAGAATCAAGCTGAAGCTGCTG
1 ATAAGAGCAACATTCAGAACTTGGAGAATCAAGCTGAAGCTGCTG
1119662 A
1 A
1119663 GAACAGAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (45 bp):
ATAAGAGCAACATTCAGAACTTGGAGAATCAAGCTGAAGCTGCTG
Found at i:1121697 original size:11 final size:11
Alignment explanation
Indices: 1121681--1121705 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1121671 TTTGAAATCG
1121681 GGGGTCGGGTC
1 GGGGTCGGGTC
1121692 GGGGTCGGGTC
1 GGGGTCGGGTC
1121703 GGG
1 GGG
1121706 TTTTAGGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.68, T:0.16
Consensus pattern (11 bp):
GGGGTCGGGTC
Found at i:1121836 original size:30 final size:30
Alignment explanation
Indices: 1121774--1121837 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
1121764 ATTTTTTAAT
* * *
1121774 TTTTTAATTATATATATTTATATAATGATA
1 TTTTTAAATATATATATTTAAAAAATGATA
*
1121804 TTTTTAAATATTTATATTTAAAAAAT-ACTA
1 TTTTTAAATATATATATTTAAAAAATGA-TA
1121834 TTTT
1 TTTT
1121838 ATTAATTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (30 bp):
TTTTTAAATATATATATTTAAAAAATGATA
Found at i:1130067 original size:24 final size:25
Alignment explanation
Indices: 1130032--1130078 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1130022 CATTGTACTC
*
1130032 CTTTAAATTTTCAGACTC-CTTCAT
1 CTTTAAATTTTCAAACTCTCTTCAT
1130056 CTTTAAGA-TTTCAAACTCTCTTC
1 CTTTAA-ATTTTCAAACTCTCTTC
1130079 TAAGATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.26, C:0.26, G:0.04, T:0.45
Consensus pattern (25 bp):
CTTTAAATTTTCAAACTCTCTTCAT
Found at i:1131601 original size:30 final size:30
Alignment explanation
Indices: 1131557--1131617 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1131547 CATTGAAGAG
*
1131557 ATTGCTGTTCAAAAGAGAGAGAAAGGTGCT
1 ATTGCTGTTCAAAAGAGAGAGAAAAGTGCT
* *
1131587 ATTGTTGTTGAAAAGAGAGAGAAAAGTGCT
1 ATTGCTGTTCAAAAGAGAGAGAAAAGTGCT
1131617 A
1 A
1131618 GTATAGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.07, G:0.30, T:0.25
Consensus pattern (30 bp):
ATTGCTGTTCAAAAGAGAGAGAAAAGTGCT
Found at i:1139687 original size:15 final size:15
Alignment explanation
Indices: 1139667--1139695 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1139657 ATTACGTCAA
1139667 AGAGTTGGAATTTCT
1 AGAGTTGGAATTTCT
1139682 AGAGTTGGAATTTC
1 AGAGTTGGAATTTC
1139696 CCGAATGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (15 bp):
AGAGTTGGAATTTCT
Found at i:1145465 original size:18 final size:19
Alignment explanation
Indices: 1145442--1145478 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1145432 TTAAAAAATT
1145442 CTCAAATAAA-TTAATATC
1 CTCAAATAAATTTAATATC
1145460 CTCAAATAAATTTAATATC
1 CTCAAATAAATTTAATATC
1145479 TATAAACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (19 bp):
CTCAAATAAATTTAATATC
Found at i:1147371 original size:2 final size:2
Alignment explanation
Indices: 1147364--1147400 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1147354 GGCAAAAGAA
1147364 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1147401 GATAGATAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1162065 original size:62 final size:62
Alignment explanation
Indices: 1161989--1162113 Score: 250
Period size: 62 Copynumber: 2.0 Consensus size: 62
1161979 GGTGTGAACC
1161989 CTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGT
1 CTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGT
1162051 CTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGT
1 CTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGT
1162113 C
1 C
1162114 CGTGACATTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.18, C:0.28, G:0.21, T:0.34
Consensus pattern (62 bp):
CTTTTATACCCCAGGGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGT
Found at i:1171494 original size:17 final size:17
Alignment explanation
Indices: 1171474--1171507 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1171464 ATTTTTATGT
1171474 AAAA-TAAATAAATATTA
1 AAAATTAAA-AAATATTA
1171491 AAAATTAAAAAATATTA
1 AAAATTAAAAAATATTA
1171508 TTAGTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATTAAAAAATATTA
Found at i:1175320 original size:114 final size:114
Alignment explanation
Indices: 1175120--1175349 Score: 406
Period size: 114 Copynumber: 2.0 Consensus size: 114
1175110 AACATTTCCC
*
1175120 ATATGAATTTTCATCTCTGAACTTTTATATTATACTCATATCTATATTTATATCTAATAAATATT
1 ATATGAATTTTCATCTCTGAACTTTTATATTATACTCATATCGATATTTATATCTAATAAATATT
1175185 TTAAATTTATCTTTATTCTTATCTCATATATATTTAATGGGTACGAACA
66 TTAAATTTATCTTTATTCTTATCTCATATATATTTAATGGGTACGAACA
* * *
1175234 ATATGAATTTTTATCTCTGAACTTTTATATTATACTTATATCGATATTTATATTTAATAAATATT
1 ATATGAATTTTCATCTCTGAACTTTTATATTATACTCATATCGATATTTATATCTAATAAATATT
* *
1175299 TTAAATTTATCTTTATTCTTATCTCATATGTATTTAATGGGTATGAACA
66 TTAAATTTATCTTTATTCTTATCTCATATATATTTAATGGGTACGAACA
1175348 AT
1 AT
1175350 TTTCATACCT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 110 1.00
ACGTcount: A:0.34, C:0.10, G:0.06, T:0.50
Consensus pattern (114 bp):
ATATGAATTTTCATCTCTGAACTTTTATATTATACTCATATCGATATTTATATCTAATAAATATT
TTAAATTTATCTTTATTCTTATCTCATATATATTTAATGGGTACGAACA
Found at i:1175436 original size:19 final size:19
Alignment explanation
Indices: 1175399--1175437 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1175389 AGTATATTTA
* * *
1175399 AATTTTTTTATCAATATAT
1 AATTTTTTAATAAAAATAT
1175418 AATTTTTTAATAAAAATAT
1 AATTTTTTAATAAAAATAT
1175437 A
1 A
1175438 TTAATTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTTTAATAAAAATAT
Found at i:1176664 original size:18 final size:20
Alignment explanation
Indices: 1176633--1176670 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1176623 ATTTAATGAA
1176633 TTAATTTAAAATT-AATTTT
1 TTAATTTAAAATTAAATTTT
1176652 TTAATTT-AAATTAAATTTT
1 TTAATTTAAAATTAAATTTT
1176671 AAAAAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAATTTAAAATTAAATTTT
Found at i:1177875 original size:177 final size:172
Alignment explanation
Indices: 1177579--1177900 Score: 464
Period size: 177 Copynumber: 1.8 Consensus size: 172
1177569 TTATCTTTGG
* * *
1177579 ATCTTTGCCGTTGAGATTTTTATTTGATTTTTAGATGGGTTTTAGTGGGGTTCACTGAATTTTTT
1 ATCTTTGCCGTTGAGATTTTTATTTGATTTTTAGATAGGTTCTAGTAGGGTTCACTGAATTTTTT
* * *
1177644 TTTAATAATTGGTTCATGCTTAATTTGTATACTTTTAGGCAAAAACTTTAATCTTTTTTATAGAT
66 TTTAATAATTGGTTCATGCTTAATTTGTATACTGTTAGACAAAAACTTTAATCTTTTTAATAGAT
1177709 TTGGGTATGATGGTTTTTTTGAGTTCATGAATTTGATTTTTT
131 TTGGGTATGATGGTTTTTTTGAGTTCATGAATTTGATTTTTT
* *
1177751 ATCTTTGCTGTTGAGATTTTTATTTGATTTTTAGATAGGTTCTAGTAGGGTTTACTGAAATGGTT
1 ATCTTTGCCGTTGAGATTTTTATTTGATTTTTAGATAGGTTCTAGTAGGGTTCACTG-AA----T
* * * * *
1177816 TTTTTTTTTATAATTGGTTTATGTTTAATTTGTATACTGTTAGACCAAAATTTTAATCTTTTTAA
61 TTTTTTTTAATAATTGGTTCATGCTTAATTTGTATACTGTTAGACAAAAACTTTAATCTTTTTAA
* *
1177881 TAGATTTTGGTTTGATGGTT
126 TAGATTTGGGTATGATGGTT
1177901 CTGGAACCTA
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
172 52 0.40
173 2 0.02
177 76 0.58
ACGTcount: A:0.23, C:0.06, G:0.18, T:0.53
Consensus pattern (172 bp):
ATCTTTGCCGTTGAGATTTTTATTTGATTTTTAGATAGGTTCTAGTAGGGTTCACTGAATTTTTT
TTTAATAATTGGTTCATGCTTAATTTGTATACTGTTAGACAAAAACTTTAATCTTTTTAATAGAT
TTGGGTATGATGGTTTTTTTGAGTTCATGAATTTGATTTTTT
Found at i:1181832 original size:13 final size:13
Alignment explanation
Indices: 1181814--1181838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1181804 GTTAATTTAA
1181814 AATATGATATAAT
1 AATATGATATAAT
1181827 AATATGATATAA
1 AATATGATATAA
1181839 ATACAATACG
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AATATGATATAAT
Found at i:1182676 original size:12 final size:12
Alignment explanation
Indices: 1182643--1182681 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1182633 TAATGCCGCA
1182643 TTTGCTTTAATG
1 TTTGCTTTAATG
1182655 CTTTGCTTTAATG
1 -TTTGCTTTAATG
* *
1182668 TTTGATTTACTG
1 TTTGCTTTAATG
1182680 TT
1 TT
1182682 CCTTAGGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.59
Consensus pattern (12 bp):
TTTGCTTTAATG
Found at i:1184179 original size:15 final size:15
Alignment explanation
Indices: 1184145--1184195 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1184135 TAACTTAATA
*
1184145 TAATTTTTATATTTTT
1 TAATTTTT-TAATTTT
*
1184161 TAATTTTTTAATTTG
1 TAATTTTTTAATTTT
* *
1184176 TAATTTATTCATTTT
1 TAATTTTTTAATTTT
1184191 TAATT
1 TAATT
1184196 CATAAATACA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 22 0.73
16 8 0.27
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (15 bp):
TAATTTTTTAATTTT
Found at i:1192859 original size:20 final size:22
Alignment explanation
Indices: 1192834--1192874 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
1192824 AGATTTTATT
*
1192834 AACAATC-TAGCA-TATGCTTC
1 AACAATCAGAGCATTATGCTTC
1192854 AACAATCAGAGCATTATGCTT
1 AACAATCAGAGCATTATGCTT
1192875 TGCTAAAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (22 bp):
AACAATCAGAGCATTATGCTTC
Found at i:1207856 original size:19 final size:19
Alignment explanation
Indices: 1207819--1207857 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1207809 CAACAAATGG
*
1207819 TTTTCCTTTTCTTTTTTTT
1 TTTTCCTTTTCTTTCTTTT
1207838 TTTTCCTTGTT-TTTCTTTT
1 TTTTCCTT-TTCTTTCTTTT
1207857 T
1 T
1207858 CCATTTTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (19 bp):
TTTTCCTTTTCTTTCTTTT
Found at i:1221234 original size:12 final size:12
Alignment explanation
Indices: 1221217--1221243 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1221207 TTGTTTCCTT
1221217 TCTTCTTCTTCA
1 TCTTCTTCTTCA
1221229 TCTTCTTCTTCA
1 TCTTCTTCTTCA
1221241 TCT
1 TCT
1221244 CTTTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.59
Consensus pattern (12 bp):
TCTTCTTCTTCA
Found at i:1224028 original size:15 final size:14
Alignment explanation
Indices: 1223999--1224038 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
1223989 AATTCATTTA
*
1223999 TATTTATTTTAAATT
1 TATTTATTAT-AATT
1224014 TATTTGATTATAATT
1 TATTT-ATTATAATT
1224029 TATTTATTAT
1 TATTTATTAT
1224039 TTATAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 14 0.61
16 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (14 bp):
TATTTATTATAATT
Found at i:1230240 original size:17 final size:18
Alignment explanation
Indices: 1230211--1230247 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1230201 TTTGTCGAGG
1230211 AATAATAAATTAT-ATTT
1 AATAATAAATTATGATTT
1230228 AATAA-AAATTTATGATTT
1 AATAATAAA-TTATGATTT
1230246 AA
1 AA
1230248 CAGTTAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 3 0.17
17 9 0.50
18 6 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (18 bp):
AATAATAAATTATGATTT
Found at i:1232556 original size:13 final size:12
Alignment explanation
Indices: 1232525--1232582 Score: 50
Period size: 11 Copynumber: 4.9 Consensus size: 12
1232515 ATATGATTTG
*
1232525 ATAATTTAAAAT
1 ATAATATAAAAT
1232537 A-AATATAATAAT
1 ATAATATAA-AAT
1232549 ATAATATAAAAAT
1 ATAATAT-AAAAT
**
1232562 ATACGA-AAAAT
1 ATAATATAAAAT
1232573 AT-ATATAAAA
1 ATAATATAAAA
1232583 GTAATACTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
10 1 0.03
11 17 0.46
12 5 0.14
13 12 0.32
14 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:1232706 original size:18 final size:18
Alignment explanation
Indices: 1232685--1232740 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
1232675 CATAATTTTT
1232685 ATATAAAATATAATATAA
1 ATATAAAATATAATATAA
*
1232703 ATATAAAA-AT--TATTA
1 ATATAAAATATAATATAA
**
1232718 ATATATTATATAATATAA
1 ATATAAAATATAATATAA
1232736 ATATA
1 ATATA
1232741 CGAATTATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 10 0.32
16 2 0.06
17 2 0.06
18 17 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAAATATAATATAA
Found at i:1235056 original size:2 final size:2
Alignment explanation
Indices: 1235049--1235076 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1235039 TCCCATACCT
1235049 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
1235077 AACTCAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1249462 original size:17 final size:18
Alignment explanation
Indices: 1249440--1249473 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1249430 GAGCCAAGTA
1249440 AAAGAGT-AAAATTGATG
1 AAAGAGTGAAAATTGATG
*
1249457 AAAGAGTGAAACTTGAT
1 AAAGAGTGAAAATTGAT
1249474 AGGTTTTAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.03, G:0.24, T:0.24
Consensus pattern (18 bp):
AAAGAGTGAAAATTGATG
Found at i:1251444 original size:21 final size:21
Alignment explanation
Indices: 1251413--1251452 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
1251403 AATTAACATT
1251413 TAATTTAATTAATTTTAAAAAA
1 TAATTTAATT-ATTTTAAAAAA
1251435 TAATTT-ATTATTTTAAAA
1 TAATTTAATTATTTTAAAA
1251453 TGAGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 3 0.17
22 6 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATTTAATTATTTTAAAAAA
Found at i:1254090 original size:12 final size:12
Alignment explanation
Indices: 1254073--1254107 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1254063 CCTGATCAGC
1254073 TTTCTTCTTCTT
1 TTTCTTCTTCTT
*
1254085 TTTCTTCTTCTC
1 TTTCTTCTTCTT
1254097 TTTCTT-TTCTT
1 TTTCTTCTTCTT
1254108 CAATAGCAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCTTCTTCTT
Found at i:1267529 original size:24 final size:24
Alignment explanation
Indices: 1267492--1267544 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
1267482 TGTGACGGGG
*
1267492 CCACCTCCTAGGGTATAACCACCT
1 CCACCTACTAGGGTATAACCACCT
*
1267516 CCACCTACTGGGGTATAACCACCT
1 CCACCTACTAGGGTATAACCACCT
1267540 CCACC
1 CCACC
1267545 ACCTCCACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.25, C:0.43, G:0.13, T:0.19
Consensus pattern (24 bp):
CCACCTACTAGGGTATAACCACCT
Found at i:1281421 original size:36 final size:36
Alignment explanation
Indices: 1281368--1281482 Score: 117
Period size: 41 Copynumber: 3.1 Consensus size: 36
1281358 ATGCCGTAAA
*
1281368 AGTTT-TTATATACTAATAAATTTTATTTATTTATT
1 AGTTTATTATATAATAATAAATTTTATTTATTTATT
1281403 AGTTTATTATATAATAATAAAGTTAGTTCATTTATTTATTT
1 AGTTTATTATATAATAATAAA-TT--TT-ATTTATTTA-TT
* * *
1281444 AATTTATTATATAATAGT-ATTATTTATTTATTATATT
1 AGTTTATTATATAATAATAAAT-TTTATTTATT-TATT
1281481 AG
1 AG
1281483 ATAATAACAA
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
35 5 0.07
36 14 0.21
37 12 0.18
38 4 0.06
39 3 0.04
40 11 0.16
41 18 0.27
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (36 bp):
AGTTTATTATATAATAATAAATTTTATTTATTTATT
Found at i:1282188 original size:46 final size:46
Alignment explanation
Indices: 1282135--1282226 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 46
1282125 TTGTGTCCTT
1282135 TGATCGTTGTACGATGAATTGTTTGAAAGCAAATTGTAACTCACCC
1 TGATCGTTGTACGATGAATTGTTTGAAAGCAAATTGTAACTCACCC
*
1282181 TGATCGTTGTATGATGAATTGTTTGAAAGCAAATTGTAACTCACCC
1 TGATCGTTGTACGATGAATTGTTTGAAAGCAAATTGTAACTCACCC
1282227 CCCTATGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (46 bp):
TGATCGTTGTACGATGAATTGTTTGAAAGCAAATTGTAACTCACCC
Found at i:1282499 original size:16 final size:16
Alignment explanation
Indices: 1282478--1282525 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1282468 TTAGAATATA
1282478 AAATATTATTATTTTT
1 AAATATTATTATTTTT
* * *
1282494 AAATATAAGTA-TTTA
1 AAATATTATTATTTTT
1282509 AAATATTATT-TTTTT
1 AAATATTATTATTTTT
1282524 AA
1 AA
1282526 TATAAATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 3
0.74 0.18 0.09
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AAATATTATTATTTTT
Found at i:1282530 original size:29 final size:31
Alignment explanation
Indices: 1282476--1282550 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 31
1282466 TTTTAGAATA
*
1282476 TAAAATATTATTATTTTTAAATATAAGTATT
1 TAAAATATTATTATTTTTAAATATAAATATT
1282507 TAAAATATTATT-TTTTT-AATATAAATATT
1 TAAAATATTATTATTTTTAAATATAAATATT
*
1282536 TAAAAATATCATTAT
1 T-AAAATATTATTAT
1282551 ATAAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 12 0.30
30 15 0.38
31 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TAAAATATTATTATTTTTAAATATAAATATT
Found at i:1282558 original size:30 final size:30
Alignment explanation
Indices: 1282493--1282568 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
1282483 TTATTATTTT
* * * *
1282493 TAAATATAAGTATTT-AAAATATTATTTTT
1 TAAATATAAATATTTAAAAATATCATTATA
*
1282522 TTAATATAAATATTTAAAAATATCATTATA
1 TAAATATAAATATTTAAAAATATCATTATA
**
1282552 TAAATATATTTATTTAA
1 TAAATATAAATATTTAA
1282569 TTAATTAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 13 0.34
30 25 0.66
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (30 bp):
TAAATATAAATATTTAAAAATATCATTATA
Found at i:1285867 original size:187 final size:182
Alignment explanation
Indices: 1285553--1285887 Score: 517
Period size: 187 Copynumber: 1.8 Consensus size: 182
1285543 CTAAAGTACA
* *
1285553 GAGAAAAAAAATATCTATGAAGCATTCGTCTCAATAACAAGACACCATGTCTAGGTTTAAGTTTC
1 GAGAAAAAAAATATCTATAAAGCATTCGTCTCAATAACAAGACACAATGTCTAGGTTTAAGTTTC
*
1285618 CTTCAACTTTTTATTAGATTCTTTCATCGATTTGGGTTTTTTAATTCCATAACTAATTTTTTATC
66 ATTCAACTTTTTATTAGATTCTTTCATCGATTTGGGTTTTTTAATTCCATAACTAATTTTTTATC
*
1285683 GATTAATTAATAAATATATATCGAGAATTATATCAATCAAACTACGTGTAAT
131 GATTAATAAATAAATATATATCGAGAATTATATCAATCAAACTACGTGTAAT
* * *
1285735 GAGAAAAAAAATTTTCTATAAAGCATTTGTCTCAATAACAAGAAAGACATAATGTCTAGGTTTAA
1 GAGAAAAAAAA-TATCTATAAAGCATTCGTCTCAATAAC----AAGACACAATGTCTAGGTTTAA
* * * *
1285800 GTTTCATTCAATTTTTTATTAGATTCTTTCATCGATTTGGTTTTTTTAATTTCATAATTAATTTT
61 GTTTCATTCAACTTTTTATTAGATTCTTTCATCGATTTGGGTTTTTTAATTCCATAACTAATTTT
*
1285865 TTATCGATTAATAAATATATATA
126 TTATCGATTAATAAATAAATATA
1285888 GAGAATTGTA
Statistics
Matches: 136, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
182 11 0.08
183 24 0.18
187 101 0.74
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.41
Consensus pattern (182 bp):
GAGAAAAAAAATATCTATAAAGCATTCGTCTCAATAACAAGACACAATGTCTAGGTTTAAGTTTC
ATTCAACTTTTTATTAGATTCTTTCATCGATTTGGGTTTTTTAATTCCATAACTAATTTTTTATC
GATTAATAAATAAATATATATCGAGAATTATATCAATCAAACTACGTGTAAT
Found at i:1293628 original size:20 final size:20
Alignment explanation
Indices: 1293603--1293651 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1293593 CCCATCTTGT
* *
1293603 TCGCTTTTTCTCAGTTTCCC
1 TCGCTTTCTCGCAGTTTCCC
*
1293623 TCGCTTTCTCGCAGTTTCTC
1 TCGCTTTCTCGCAGTTTCCC
*
1293643 TCACTTTCT
1 TCGCTTTCT
1293652 TTTCTTTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.06, C:0.35, G:0.10, T:0.49
Consensus pattern (20 bp):
TCGCTTTCTCGCAGTTTCCC
Found at i:1309798 original size:109 final size:108
Alignment explanation
Indices: 1309597--1309809 Score: 354
Period size: 109 Copynumber: 2.0 Consensus size: 108
1309587 GATGCCTCCG
* *
1309597 GTCAACAAGATGATTGGTTAGGAGCTAATGCTTGAAAATTTAGTTCTCAATGATGCAATCATCAA
1 GTCAACAAGATGATTGGTTAGGAGCTAATGCTTGAAAATTTAGTTCACAATGATGCAATCAGCAA
1309662 TCCGACCTGTTTGCAAAGAGAGTTTTCAATGGAAAACATAAAA
66 TCCGACCTGTTTGCAAAGAGAGTTTTCAATGGAAAACATAAAA
* * *
1309705 GTCAACAAAGCTGATTGGTTAGGGGCTGATGCTTGAAAATTTAGTTCACAATGATGCAATCAGCA
1 GTCAAC-AAGATGATTGGTTAGGAGCTAATGCTTGAAAATTTAGTTCACAATGATGCAATCAGCA
* *
1309770 ATCCGAGCTGTTTTCAAAGAGAGTTTTCAATGGAAAACAT
65 ATCCGACCTGTTTGCAAAGAGAGTTTTCAATGGAAAACAT
1309810 CAAATTTTAT
Statistics
Matches: 97, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
108 6 0.06
109 91 0.94
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (108 bp):
GTCAACAAGATGATTGGTTAGGAGCTAATGCTTGAAAATTTAGTTCACAATGATGCAATCAGCAA
TCCGACCTGTTTGCAAAGAGAGTTTTCAATGGAAAACATAAAA
Found at i:1316972 original size:38 final size:38
Alignment explanation
Indices: 1316924--1317005 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
1316914 AATTATCAAA
*
1316924 TCGAGTTCGGATATTATTTATATAAAATTGAATTGAAT
1 TCGAGATCGGATATTATTTATATAAAATTGAATTGAAT
1316962 TCGAGATCGGATATTATTTATATAAAATTGAATTGAAT
1 TCGAGATCGGATATTATTTATATAAAATTGAATTGAAT
1317000 TCGAGA
1 TCGAGA
1317006 CGAACAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (38 bp):
TCGAGATCGGATATTATTTATATAAAATTGAATTGAAT
Found at i:1320134 original size:34 final size:35
Alignment explanation
Indices: 1320096--1320195 Score: 109
Period size: 34 Copynumber: 2.9 Consensus size: 35
1320086 ATGTAATCCT
*
1320096 AATTTTTAAAAATTATATTAT-ATTTCTAAAACAA
1 AATTTTTAAAAATTATATTATAATTTCGAAAACAA
* *
1320130 AA-TTTTAAAAA-TATAATATAATTCTCGAAAA-TA
1 AATTTTTAAAAATTATATTATAATT-TCGAAAACAA
* * *
1320163 AATTTTTGATAATTATATTGTAATTTCGAAAAC
1 AATTTTTAAAAATTATATTATAATTTCGAAAAC
1320196 GAATTTTATG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
32 7 0.13
33 15 0.28
34 22 0.41
35 10 0.19
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (35 bp):
AATTTTTAAAAATTATATTATAATTTCGAAAACAA
Found at i:1329365 original size:23 final size:23
Alignment explanation
Indices: 1329339--1329384 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1329329 TCCTAAGGGG
* *
1329339 TTTTCTGCTTTTGTCTTATGATA
1 TTTTCTGCTTTTATATTATGATA
1329362 TTTTCTGCTTTTATATTATGATA
1 TTTTCTGCTTTTATATTATGATA
1329385 AACATGGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (23 bp):
TTTTCTGCTTTTATATTATGATA
Found at i:1336176 original size:53 final size:53
Alignment explanation
Indices: 1336119--1336226 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1336109 GCAGTCATTT
1336119 AGAAAGAAAGAAAATATTGATGGCAAATAAAAATAGGAACTGATTTCCTAAGG
1 AGAAAGAAAGAAAATATTGATGGCAAATAAAAATAGGAACTGATTTCCTAAGG
1336172 AGAAAGAAAGAAAATATTGATGGCAAATAAAAATAGGAACTGATTTCCTAAGG
1 AGAAAGAAAGAAAATATTGATGGCAAATAAAAATAGGAACTGATTTCCTAAGG
1336225 AG
1 AG
1336227 CATAGCGAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.51, C:0.07, G:0.21, T:0.20
Consensus pattern (53 bp):
AGAAAGAAAGAAAATATTGATGGCAAATAAAAATAGGAACTGATTTCCTAAGG
Found at i:1354251 original size:1 final size:1
Alignment explanation
Indices: 1354245--1354272 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
1354235 GCATGCGTCG
1354245 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1354273 GAAGTAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1358258 original size:2 final size:2
Alignment explanation
Indices: 1358251--1358278 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1358241 CATAAATGGA
1358251 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
1358279 TGGAGTTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1365226 original size:19 final size:19
Alignment explanation
Indices: 1365202--1365252 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
1365192 GATATTTTAG
*
1365202 TGTTAATTGTGTTTAATCA
1 TGTTAATTATGTTTAATCA
* *
1365221 TGTTAATAATGTATAATCA
1 TGTTAATTATGTTTAATCA
*
1365240 TATTAATTATGTT
1 TGTTAATTATGTT
1365253 GTGTCATGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (19 bp):
TGTTAATTATGTTTAATCA
Found at i:1367716 original size:12 final size:12
Alignment explanation
Indices: 1367699--1367725 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1367689 TTTATATATT
1367699 AAAAAAATTAAA
1 AAAAAAATTAAA
1367711 AAAAAAATTAAA
1 AAAAAAATTAAA
1367723 AAA
1 AAA
1367726 GTGAATGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAAAATTAAA
Found at i:1368413 original size:13 final size:14
Alignment explanation
Indices: 1368388--1368416 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1368378 TACACTTATA
1368388 TAATTATTATATTT
1 TAATTATTATATTT
1368402 TAATTA-TATATTT
1 TAATTATTATATTT
1368415 TA
1 TA
1368417 TTCAAAGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTATTATATTT
Found at i:1370593 original size:24 final size:23
Alignment explanation
Indices: 1370502--1370594 Score: 71
Period size: 24 Copynumber: 3.8 Consensus size: 23
1370492 AATATTATAA
*
1370502 AATTTCAAATTTT-AATTTAAATTT
1 AATTT-AATTTTTAAATTT-AATTT
*
1370526 AATTTCATATTTTTAAAATTAATTT
1 AATTT-A-ATTTTTAAATTTAATTT
* * *
1370551 GAATTAAATTTTATCAATTTGATTT
1 -AATTTAATTTT-TAAATTTAATTT
1370576 AATTTAATTTATTAAATTT
1 AATTTAATTT-TTAAATTT
1370595 TAAATTTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
24 27 0.48
25 21 0.38
26 8 0.14
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (23 bp):
AATTTAATTTTTAAATTTAATTT
Found at i:1370648 original size:22 final size:24
Alignment explanation
Indices: 1370607--1370660 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
1370597 AATTTTAATA
*
1370607 TTTTATATATTATTTTAATAAAGT
1 TTTTATATATTATTTAAATAAAGT
1370631 TTTTA-ATA-TATTTAAATAAA-T
1 TTTTATATATTATTTAAATAAAGT
*
1370652 TTATATATA
1 TTTTATATA
1370661 AAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.19
22 14 0.52
23 3 0.11
24 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTATATATTATTTAAATAAAGT
Found at i:1371066 original size:2 final size:2
Alignment explanation
Indices: 1371059--1371091 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1371049 ACTCGGTCCA
*
1371059 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1371092 GATAGATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1371104 original size:2 final size:2
Alignment explanation
Indices: 1371099--1371124 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1371089 ATAGATAGAT
1371099 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1371125 TGGGGATAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1373252 original size:33 final size:33
Alignment explanation
Indices: 1373210--1373276 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
1373200 AGTTTAAGGC
*
1373210 AGTAGATAAAGTGCATTAATCTCGCGTCAGATA
1 AGTAGATAAAGTGCATTAATCTCACGTCAGATA
*
1373243 AGTAGATAAAGTGCATTAATCTCATGTCAGATA
1 AGTAGATAAAGTGCATTAATCTCACGTCAGATA
1373276 A
1 A
1373277 AAAAAGAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (33 bp):
AGTAGATAAAGTGCATTAATCTCACGTCAGATA
Found at i:1374344 original size:22 final size:22
Alignment explanation
Indices: 1374318--1374361 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1374308 TTGATGGCAT
1374318 TGTTAAACACTCTAATCATTAC
1 TGTTAAACACTCTAATCATTAC
1374340 TGTTAAACACTCTAATCATTAC
1 TGTTAAACACTCTAATCATTAC
1374362 AGATTCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (22 bp):
TGTTAAACACTCTAATCATTAC
Found at i:1377833 original size:6 final size:6
Alignment explanation
Indices: 1377822--1377846 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1377812 TGGACCAACC
1377822 AACCAA AACCAA AACCAA AACCAA A
1 AACCAA AACCAA AACCAA AACCAA A
1377847 TTTTTATCTT
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:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AACCAA
Found at i:1381164 original size:14 final size:14
Alignment explanation
Indices: 1381147--1381176 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1381137 GAAAATGATG
1381147 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
*
1381161 AAAAAAAAGAAGAA
1 AAAAAAAAAAAGAA
1381175 AA
1 AA
1381177 GCTAGCAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:1382097 original size:14 final size:15
Alignment explanation
Indices: 1382073--1382101 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1382063 AGATTTGAAT
1382073 TATTAATTTATTAAA
1 TATTAATTTATTAAA
1382088 TATT-ATTTATTAAA
1 TATTAATTTATTAAA
1382102 AATAATTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATTAATTTATTAAA
Found at i:1384412 original size:14 final size:13
Alignment explanation
Indices: 1384387--1384416 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1384377 ATTGATTAAA
1384387 ATTAAATAATTTG
1 ATTAAATAATTTG
1384400 ATTAAATTAATTTG
1 ATTAAA-TAATTTG
1384414 ATT
1 ATT
1384417 TATTCGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (13 bp):
ATTAAATAATTTG
Found at i:1407995 original size:23 final size:21
Alignment explanation
Indices: 1407947--1407998 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 21
1407937 TTTTTATCAT
1407947 TTTTAATTAAAAATTTAACAA
1 TTTTAATTAAAAATTTAACAA
* *
1407968 ATTTAATCTAAAAAATTTAATAA
1 TTTTAAT-T-AAAAATTTAACAA
1407991 TTTTAATT
1 TTTTAATT
1407999 TTTATCATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.23
22 2 0.08
23 18 0.69
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTTAATTAAAAATTTAACAA
Done.