Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008124.1 Hibiscus syriacus cultivar Beakdansim tig00110678_pilon, 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: 3296903
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 19
Found at i:981462 original size:21 final size:21
Alignment explanation
Indices: 981415--981468 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
981405 TATTCGGGGT
*
981415 AGTATCGATACTCTAATACTGG
1 AGTATCGATACTCTAATAC-AG
981437 AGTATCGATACTCTAATTA-AG
1 AGTATCGATACTCTAA-TACAG
*
981458 AGTATAGATAC
1 AGTATCGATAC
981469 CGAGTAGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
22 16 0.55
23 2 0.07
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (21 bp):
AGTATCGATACTCTAATACAG
Found at i:982796 original size:19 final size:19
Alignment explanation
Indices: 982772--982810 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
982762 GAAAATAATG
*
982772 GCCAAACGACCAATAATAT
1 GCCAAAAGACCAATAATAT
982791 GCCAAAAGACCAATAATAT
1 GCCAAAAGACCAATAATAT
982810 G
1 G
982811 TCATAAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.23, G:0.13, T:0.15
Consensus pattern (19 bp):
GCCAAAAGACCAATAATAT
Found at i:987443 original size:21 final size:21
Alignment explanation
Indices: 987417--987469 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
987407 AATGTCTTGG
*
987417 TATCGATACTTATATGGGGAT
1 TATCGATACTCATATGGGGAT
987438 TATCGATACTCATATGGGGAT
1 TATCGATACTCATATGGGGAT
987459 TATCGATACTC
1 TATCGATACTC
987470 TACCCTTGGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (21 bp):
TATCGATACTCATATGGGGAT
Found at i:989082 original size:21 final size:21
Alignment explanation
Indices: 989056--989100 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
989046 GATTTCTGGG
* *
989056 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
989077 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
989098 CAA
1 CAA
989101 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:990174 original size:32 final size:31
Alignment explanation
Indices: 990132--990259 Score: 152
Period size: 31 Copynumber: 4.1 Consensus size: 31
990122 AGAGTCGAGG
990132 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
990163 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
990195 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
990226 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
990257 GTT
1 GTT
990260 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
31 54 0.66
32 28 0.34
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:990279 original size:30 final size:30
Alignment explanation
Indices: 990218--990314 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
990208 CTAAGGAACA
* * ***
990218 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
990249 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
990279 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
990309 TCTGGA
1 TATGGA
990315 TAGGTCATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:990315 original size:30 final size:30
Alignment explanation
Indices: 990245--990317 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
990235 GGTTCTTCGG
* *
990245 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
990275 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
990305 GACCTCTGGATAG
1 GACCTCTGGATAG
990318 GTCATTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:993260 original size:21 final size:21
Alignment explanation
Indices: 993234--993278 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
993224 GATTTCTGGG
* *
993234 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
993255 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
993276 CAA
1 CAA
993279 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:994519 original size:31 final size:31
Alignment explanation
Indices: 994461--994587 Score: 159
Period size: 31 Copynumber: 4.1 Consensus size: 31
994451 AGAGTCGAGG
994461 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
994492 GTTTTACCTATG-TCTTC-GAGACATATGGACA
1 G-TTTACCTATGTTCTACGGA-ACATATGGACA
* *
994523 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
994554 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
994585 GTT
1 GTT
994588 ACCGAGGATC
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
30 11 0.13
31 59 0.72
32 12 0.15
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:994570 original size:62 final size:61
Alignment explanation
Indices: 994463--994590 Score: 195
Period size: 62 Copynumber: 2.1 Consensus size: 61
994453 AGTCGAGGGT
* *
994463 TTACCTATGTTCTACGGAACATATGGACAGTTTTACCTATGTCTTCGAGACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTCGAGACATATGGACAG
* *
994524 TATACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTCGGGACCTATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGG-TCTTCGAGACATATGGACAG
994586 TTACC
1 TTACC
994591 GAGGATCTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 14 0.23
62 47 0.77
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (61 bp):
TTACCTATGTTCTAAGGAACATATGGACAGTTTTACCTAGGTCTTCGAGACATATGGACAG
Found at i:994607 original size:30 final size:30
Alignment explanation
Indices: 994546--994642 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
994536 CTAAGGAACA
* * ***
994546 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
994577 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
994607 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
994637 TCTGGA
1 TATGGA
994643 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:994643 original size:30 final size:30
Alignment explanation
Indices: 994573--994645 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
994563 GGTTCTTCGG
* *
994573 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
994603 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
994633 GACCTCTGGATAG
1 GACCTCTGGATAG
994646 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:996473 original size:60 final size:60
Alignment explanation
Indices: 996340--996475 Score: 245
Period size: 60 Copynumber: 2.3 Consensus size: 60
996330 AATTAAAACG
* * *
996340 AAATAAAAGTGACAATATATTATGTTTTTTGAATCCAGTGATCATAAGTTTATAAAATTC
1 AAATGAAAGTGACCATATATTATGTTTTTTGAATCCAATGATCATAAGTTTATAAAATTC
996400 AAATGAAAGTGACCATATATTATGTTTTTTGAATCCAATGATCATAAGTTTATAAAATTC
1 AAATGAAAGTGACCATATATTATGTTTTTTGAATCCAATGATCATAAGTTTATAAAATTC
996460 AAATGAAAGTGACCAT
1 AAATGAAAGTGACCAT
996476 TTTTGTAGTT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (60 bp):
AAATGAAAGTGACCATATATTATGTTTTTTGAATCCAATGATCATAAGTTTATAAAATTC
Found at i:999478 original size:60 final size:60
Alignment explanation
Indices: 999350--999530 Score: 167
Period size: 60 Copynumber: 3.0 Consensus size: 60
999340 ATGAATTTGG
* * * * * * *
999350 GGATGAAATTGAAA-GATCTAAAAGTTTAGGGACCAA-TTATAATGAGA-TTCATAGTTTAG
1 GGATGAAATTAAAATGTTC-AAAAGTTTAAGGACTAATTTAGAATAAGAGTT-ATAGTTTAA
* *
999409 GGATAAAATTCAAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTTATAGTTTAA
1 GGATGAAATTAAAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTTATAGTTTAA
* * * *
999469 GGATGAAATTAAAATAATT-AAAAGTTTAAGGACTTATTT-GAAATAA-AGTCATAATTTAA
1 GGATGAAATTAAAAT-GTTCAAAAGTTTAAGGACTAATTTAG-AATAAGAGTTATAGTTTAA
999528 GGA
1 GGA
999531 CATATGATGC
Statistics
Matches: 103, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
59 42 0.41
60 57 0.55
61 4 0.04
ACGTcount: A:0.45, C:0.05, G:0.18, T:0.32
Consensus pattern (60 bp):
GGATGAAATTAAAATGTTCAAAAGTTTAAGGACTAATTTAGAATAAGAGTTATAGTTTAA
Found at i:1000423 original size:57 final size:58
Alignment explanation
Indices: 1000327--1000439 Score: 156
Period size: 57 Copynumber: 2.0 Consensus size: 58
1000317 AGTTGAAATG
* * ** *
1000327 ACCCGACCCGACTTATTATAGACCCAAATAAAACCGAAACTTGAAATGACTTAACCAT
1 ACCCAACCCGACTTACTATAGACCCAAATAAAACCGAAACCCGAAATGACATAACCAT
* *
1000385 ACCCAACCCGACTTACTATA-ACCCGAATAAAACTGAAACCCGAAATGACATAACC
1 ACCCAACCCGACTTACTATAGACCCAAATAAAACCGAAACCCGAAATGACATAACC
1000440 CGACTTACTA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 30 0.62
58 18 0.38
ACGTcount: A:0.42, C:0.30, G:0.10, T:0.18
Consensus pattern (58 bp):
ACCCAACCCGACTTACTATAGACCCAAATAAAACCGAAACCCGAAATGACATAACCAT
Found at i:1000440 original size:47 final size:48
Alignment explanation
Indices: 1000389--1000480 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
1000379 AACCATACCC
1000389 AACCCGACTTACTATA-ACCCGAATAAAACTGAAACCCGAAATGACAT
1 AACCCGACTTACTATATACCCGAATAAAACTGAAACCCGAAATGACAT
* *
1000436 AACCCGACTTACTATATATCCGAATAAAACTGAAACTCGAAATGA
1 AACCCGACTTACTATATACCCGAATAAAACTGAAACCCGAAATGA
1000481 TCCGACTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
47 16 0.38
48 26 0.62
ACGTcount: A:0.45, C:0.25, G:0.11, T:0.20
Consensus pattern (48 bp):
AACCCGACTTACTATATACCCGAATAAAACTGAAACCCGAAATGACAT
Found at i:1000536 original size:15 final size:15
Alignment explanation
Indices: 1000509--1000548 Score: 71
Period size: 15 Copynumber: 2.6 Consensus size: 15
1000499 TAATCTGAAT
1000509 TAATTCTAAACCAAAA
1 TAATTC-AAACCAAAA
1000525 TAATTCAAACCAAAA
1 TAATTCAAACCAAAA
1000540 TAATTCAAA
1 TAATTCAAA
1000549 TCCCATCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 18 0.75
16 6 0.25
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.25
Consensus pattern (15 bp):
TAATTCAAACCAAAA
Found at i:1010764 original size:18 final size:19
Alignment explanation
Indices: 1010741--1010779 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1010731 TTAGTTCATA
1010741 AATATTTCAAAATA-TATT
1 AATATTTCAAAATATTATT
* *
1010759 AATATTTTAATATATTATT
1 AATATTTCAAAATATTATT
1010778 AA
1 AA
1010780 AATAAGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AATATTTCAAAATATTATT
Found at i:1011282 original size:13 final size:15
Alignment explanation
Indices: 1011258--1011290 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1011248 GAAAAACTTC
1011258 AAAATCTAATAA-AA
1 AAAATCTAATAACAA
1011272 AAAATCT-ATAACAA
1 AAAATCTAATAACAA
1011286 AAAAT
1 AAAAT
1011291 AGATACGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATCTAATAACAA
Found at i:1011430 original size:40 final size:39
Alignment explanation
Indices: 1011320--1011461 Score: 144
Period size: 39 Copynumber: 3.6 Consensus size: 39
1011310 AAAATTGGCA
* *
1011320 AACGATTTATTTCCTTTTACAAAGCAAGAAAATAAATTC
1 AACGATTTATTTCCTTTTACAAAACATGAAAATAAATTC
* * *
1011359 TACGATTTATTTCCTTTTACAAAA-TTCGAAAATTAATAT-
1 AACGATTTATTTCCTTTTACAAAACAT-GAAAATAAAT-TC
* * *
1011398 AACGATTTTTTTTCTATTTACAAAACATGAAAAATAAATTT
1 AACGATTTATTTCCT-TTTACAAAACATG-AAAATAAATTC
* *
1011439 TATGATTTATTTCCTTTTACAAA
1 AACGATTTATTTCCTTTTACAAA
1011462 CCAGAATCAT
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
39 43 0.52
40 20 0.24
41 20 0.24
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (39 bp):
AACGATTTATTTCCTTTTACAAAACATGAAAATAAATTC
Found at i:1011545 original size:39 final size:38
Alignment explanation
Indices: 1011502--1011625 Score: 135
Period size: 39 Copynumber: 3.2 Consensus size: 38
1011492 AATTTAGTGG
*
1011502 TTTATTTCTTCTTACAAAATAGGAAAATAAATTCAACGA
1 TTTATTTCTT-TTACAAAATAAGAAAATAAATTCAACGA
* * * * *
1011541 TTTATATCTTTTTACAAAACATA-AAAAGAAATCCAATGA
1 TTTATTTC-TTTTACAAAATA-AGAAAATAAATTCAACGA
1011580 TTTATTTACTTTTACAAAATAAGAAAATAAA-TCAAACGA
1 TTTATTT-CTTTTACAAAATAAGAAAATAAATTC-AACGA
1011619 TTTATTT
1 TTTATTT
1011626 TCTTAATTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
38 2 0.03
39 64 0.93
40 3 0.04
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (38 bp):
TTTATTTCTTTTACAAAATAAGAAAATAAATTCAACGA
Found at i:1011662 original size:130 final size:131
Alignment explanation
Indices: 1011506--1011755 Score: 312
Period size: 130 Copynumber: 1.9 Consensus size: 131
1011496 TAGTGGTTTA
* **
1011506 TTTCTTCTTACAAAATAGGAAAATAAATTCA-ACGATTTATATCTTTTTACAAAACATA-AAAAG
1 TTTCTTCTTACAAAATAAGAAAATAAATT-ATACGATTTATATAATTTTACAAAACA-AGAAAAG
1011569 AAATCCA-ATGATTTATTTACTTTTACAAAAT-AAGAAAATAAATCAAACGATTTATTTTCTTAA
64 AAAT-CATATGATTTATTTACTTTTACAAAATCAA-AAAATAAATCAAACGATTTATTTTCTTAA
1011632 TTAAT
127 TTAAT
* * ** *
1011637 TTTCTT-TTACAAAGTAAGAAAATAAATTATACGATTTATTTAATTTTACAACGCAAGAAAATAA
1 TTTCTTCTTACAAAATAAGAAAATAAATTATACGATTTATATAATTTTACAAAACAAGAAAAGAA
* * * * *
1011701 ATTATATGGTTTATTTCCTTTTACAAAATCCAAAAATAAATCTAACGATTTATTT
66 ATCATATGATTTATTTACTTTTACAAAATCAAAAAATAAATCAAACGATTTATTT
1011756 CTTTCAACAA
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
129 3 0.03
130 92 0.90
131 7 0.07
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.38
Consensus pattern (131 bp):
TTTCTTCTTACAAAATAAGAAAATAAATTATACGATTTATATAATTTTACAAAACAAGAAAAGAA
ATCATATGATTTATTTACTTTTACAAAATCAAAAAATAAATCAAACGATTTATTTTCTTAATTAA
T
Found at i:1011695 original size:39 final size:39
Alignment explanation
Indices: 1011641--1011755 Score: 126
Period size: 39 Copynumber: 2.9 Consensus size: 39
1011631 ATTAATTTTC
*
1011641 TTTTACAAAGTAAGAAAATAAATTATACGATTTATTTAA
1 TTTTACAAAGCAAGAAAATAAATTATACGATTTATTTAA
* * * **
1011680 TTTTACAACGCAAGAAAATAAATTATATGGTTTATTTCC
1 TTTTACAAAGCAAGAAAATAAATTATACGATTTATTTAA
* *
1011719 TTTTACAAAATCCA-AAAATAAATCTA-ACGATTTATTT
1 TTTTAC-AAAGCAAGAAAATAAAT-TATACGATTTATTT
1011756 CTTTCAACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
39 57 0.90
40 6 0.10
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.38
Consensus pattern (39 bp):
TTTTACAAAGCAAGAAAATAAATTATACGATTTATTTAA
Found at i:1011756 original size:39 final size:38
Alignment explanation
Indices: 1011710--1011877 Score: 107
Period size: 39 Copynumber: 4.4 Consensus size: 38
1011700 AATTATATGG
* *
1011710 TTTATTTCCTTTTACAAAATCCAAAAATAAATCTAACGA
1 TTTATTTCC-TTTACAAAATACAAAAATAAATCCAACGA
*
1011749 TTTATTT-CTTT-C---A-ACAAAAACAAATCCAATTC-A
1 TTTATTTCCTTTACAAAATACAAAAATAAATCCAA--CGA
* * * *
1011782 TTTATTTCCTTTACACAATAAAAAAATTCAATCCAACAA
1 TTTATTTCCTTTACAAAATACAAAAA-TAAATCCAACGA
** ** * *
1011821 TTTATTTAAATTTACAAAATAGGAAAATAAATTCTACGA
1 TTTATTT-CCTTTACAAAATACAAAAATAAATCCAACGA
*
1011860 TTTATTTCATTTTACAAA
1 TTTATTTC-CTTTACAAA
1011878 CCAAAATCCT
Statistics
Matches: 100, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
32 13 0.13
33 9 0.09
34 5 0.05
35 1 0.01
36 1 0.01
37 3 0.03
38 3 0.03
39 44 0.44
40 21 0.21
ACGTcount: A:0.44, C:0.16, G:0.02, T:0.38
Consensus pattern (38 bp):
TTTATTTCCTTTACAAAATACAAAAATAAATCCAACGA
Found at i:1011956 original size:39 final size:39
Alignment explanation
Indices: 1011901--1012225 Score: 311
Period size: 39 Copynumber: 8.3 Consensus size: 39
1011891 AGATTCTCAG
* * *
1011901 GAAAATAAATTAAATGATTTATTTCTTTTTACAAAATAG
1 GAAAATAAATTCAATGATTTATTTCCTTTTACAAAATAA
* * *
1011940 GAAAATAAATTCAATGATTTATTTACTTTTACACAA-CA
1 GAAAATAAATTCAATGATTTATTTCCTTTTACAAAATAA
* **
1011978 GAAAAATAAATCCAGCGATTTATTTCCTTTTACAAAATAA
1 G-AAAATAAATTCAATGATTTATTTCCTTTTACAAAATAA
* *
1012018 GAAAATAAA-TCAAATGATTTATTTTCTTTTATAAAATCCAA
1 GAAAATAAATTC-AATGATTTATTTCCTTTTACAAAAT--AA
* * *
1012059 -AAAATAAA-TCTAACGATTTATTTCCTTCTACAAAATAC
1 GAAAATAAATTC-AATGATTTATTTCCTTTTACAAAATAA
* * * * *
1012097 GAAAATAAA-TCTAACGATTTATTTCATTATAAAAAATAT
1 GAAAATAAATTC-AATGATTTATTTCCTTTTACAAAATAA
* *
1012136 GAAAATAAATCCAATTGATTTATTTCCTTTTACACAATAA
1 GAAAATAAATTCAA-TGATTTATTTCCTTTTACAAAATAA
* * * *
1012176 GAAAATAAATTCAATAATTTATTT-TTATTTAGAAAACAA
1 GAAAATAAATTCAATGATTTATTTCCT-TTTACAAAATAA
1012215 GAAAATAAATT
1 GAAAATAAATT
1012226 GTAGAAAAAT
Statistics
Matches: 237, Mismatches: 40, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
38 4 0.02
39 165 0.70
40 66 0.28
41 2 0.01
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.37
Consensus pattern (39 bp):
GAAAATAAATTCAATGATTTATTTCCTTTTACAAAATAA
Found at i:1012083 original size:79 final size:78
Alignment explanation
Indices: 1011902--1012224 Score: 336
Period size: 79 Copynumber: 4.1 Consensus size: 78
1011892 GATTCTCAGG
** * * * *
1011902 AAAATAAATTAAATGATTTATTTCTTTTTACAAAATAGGAAAATAAATTCAATGATTTATTTACT
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAATGATTTATTTTCT
* *
1011967 TTTACACAACAGA
66 TTTAAAAAACAGA
*
1011980 AAAATAAATCCAGCGATTTATTTCCTTTTACAAAATAAGAAAATAAA-TCAAATGATTTATTTTC
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTC-AATGATTTATTTTC
*
1012044 TTTTATAAAATCCA-A
65 TTTTA-AAAA-ACAGA
* * * *
1012059 AAAATAAATCTAACGATTTATTTCCTTCTACAAAATACGAAAATAAA-TCTAACGATTTA-TTTC
1 AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTC-AATGATTTATTTTC
* *
1012122 ATTATAAAAAATATG-
65 -TTTTAAAAAACA-GA
* * *
1012137 AAAATAAATCCAATTGATTTATTTCCTTTTACACAATAAGAAAATAAATTCAATAATTTATTTT-
1 AAAATAAATCCAA-CGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAATGATTTATTTTC
*
1012201 TATTTAGAAAACA-A
65 T-TTTAAAAAACAGA
1012215 GAAAATAAAT
1 -AAAATAAAT
1012225 TGTAGAAAAA
Statistics
Matches: 204, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
77 3 0.01
78 80 0.39
79 114 0.56
80 7 0.03
ACGTcount: A:0.47, C:0.11, G:0.05, T:0.37
Consensus pattern (78 bp):
AAAATAAATCCAACGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAATGATTTATTTTCT
TTTAAAAAACAGA
Found at i:1012219 original size:118 final size:117
Alignment explanation
Indices: 1011901--1012224 Score: 368
Period size: 118 Copynumber: 2.8 Consensus size: 117
1011891 AGATTCTCAG
* * *
1011901 GAAAATAAATTAAATGATTTATTTCTTTTTACAAAATAGGAAAATAAATTCAATGATTTATTTAC
1 GAAAATAAATCAAATGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAATGATTTATTTAC
* * * * *
1011966 TTTTACACAAC-AGAAAAATAAATCCAGCGATTTATTTCCTTTTACAAAATAA
66 TTTTACAAAACAAG-AAAATAAATCCAACGATTTATTTCATTATAAAAAATAA
* * *
1012018 GAAAATAAATCAAATGATTTATTTTCTTTTATAAAATCCAA-AAAATAAA-TCTAACGATTTATT
1 GAAAATAAATCAAATGATTTATTTCCTTTTACAAAAT--AAGAAAATAAATTC-AATGATTTATT
* * * * * *
1012081 TCCTTCTACAAAATACGAAAATAAATCTAACGATTTATTTCATTATAAAAAATAT
63 TACTTTTACAAAACAAGAAAATAAATCCAACGATTTATTTCATTATAAAAAATAA
* * *
1012136 GAAAATAAATCCAATTGATTTATTTCCTTTTACACAATAAGAAAATAAATTCAATAATTTATTT-
1 GAAAATAAAT-CAAATGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAATGATTTATTTA
* *
1012200 TTATTTAGAAAACAAGAAAATAAAT
65 CT-TTTACAAAACAAGAAAATAAAT
1012225 TGTAGAAAAA
Statistics
Matches: 171, Mismatches: 28, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
117 38 0.22
118 106 0.62
119 27 0.16
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (117 bp):
GAAAATAAATCAAATGATTTATTTCCTTTTACAAAATAAGAAAATAAATTCAATGATTTATTTAC
TTTTACAAAACAAGAAAATAAATCCAACGATTTATTTCATTATAAAAAATAA
Found at i:1012289 original size:39 final size:38
Alignment explanation
Indices: 1012231--1012318 Score: 124
Period size: 39 Copynumber: 2.3 Consensus size: 38
1012221 AAATTGTAGA
*
1012231 AAAATAAATTCAATGATTTA-TTTCTTTTTACAAAATAGG
1 AAAATAAA-TCAATCATTTATTTTC-TTTTACAAAATAGG
*
1012270 AAAATAAATCAATCCATTTATTTTCTTTTACAAACTAGG
1 AAAATAAATCAAT-CATTTATTTTCTTTTACAAAATAGG
1012309 AAAATAAATC
1 AAAATAAATC
1012319 CTACGATTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 5 0.11
39 36 0.80
40 4 0.09
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (38 bp):
AAAATAAATCAATCATTTATTTTCTTTTACAAAATAGG
Found at i:1012471 original size:58 final size:58
Alignment explanation
Indices: 1012397--1012615 Score: 248
Period size: 58 Copynumber: 3.7 Consensus size: 58
1012387 ATAAAATGAG
* *
1012397 TTCAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAACTAGGATCA
1 TTCAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGCTAGAATCA
* * * *
1012455 TTCAAGATTCTTAAGGAAATAAATTTAA-TAATTTATTTTCCTTACAAAGTTAGAATAA
1 TTCAAGATTCTCAAGGAAATAAATTCAACT-ATTTATTTTCCTTACAAAGCTAGAATCA
* * *
1012513 TTTAGGATTCTCAAGGAAATAAA-TCTAACTATTTATTTTCCTTACGAAGCTAGAATCAA
1 TTCAAGATTCTCAAGGAAATAAATTC-AACTATTTATTTTCCTTACAAAGCTAGAATC-A
* **
1012572 TGCAAGATTCTAACAATTAAATAAATTCAA-TGATTTA-TTTCCTT
1 TTCAAGATTCT--CAAGGAAATAAATTCAACT-ATTTATTTTCCTT
1012616 TATATTTTAT
Statistics
Matches: 135, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
57 2 0.01
58 96 0.71
59 10 0.07
60 8 0.06
61 17 0.13
62 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (58 bp):
TTCAAGATTCTCAAGGAAATAAATTCAACTATTTATTTTCCTTACAAAGCTAGAATCA
Found at i:1013080 original size:2 final size:2
Alignment explanation
Indices: 1013073--1013105 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1013063 TAAAATAATG
1013073 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
1013106 AATGGGGATA
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:1040365 original size:15 final size:15
Alignment explanation
Indices: 1040345--1040413 Score: 129
Period size: 15 Copynumber: 4.6 Consensus size: 15
1040335 TCATATGGCA
1040345 GAAGAAGAGTCAGAT
1 GAAGAAGAGTCAGAT
1040360 GAAGAAGAGTCAGAT
1 GAAGAAGAGTCAGAT
1040375 GAAGAAGAGTCAGAT
1 GAAGAAGAGTCAGAT
*
1040390 GAAGAAGAATCAGAT
1 GAAGAAGAGTCAGAT
1040405 GAAGAAGAG
1 GAAGAAGAG
1040414 GTTCAGACCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 52 1.00
ACGTcount: A:0.49, C:0.06, G:0.33, T:0.12
Consensus pattern (15 bp):
GAAGAAGAGTCAGAT
Found at i:1044459 original size:15 final size:17
Alignment explanation
Indices: 1044429--1044461 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1044419 TTATATAATA
1044429 TTATGTAAATATAATTT
1 TTATGTAAATATAATTT
1044446 TTAT-TAAA-ATAATTT
1 TTATGTAAATATAATTT
1044461 T
1 T
1044462 ATATAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 4 0.25
17 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTATGTAAATATAATTT
Found at i:1044626 original size:28 final size:28
Alignment explanation
Indices: 1044591--1044649 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1044581 GATATGGTAA
* *
1044591 TATTTTTATAATTAATGTTATT-TTAATT
1 TATTTTTAT-ATTAAAGTTATTATGAATT
*
1044619 TATTTTTATTTTAAAGTTATTATGAATT
1 TATTTTTATATTAAAGTTATTATGAATT
1044647 TAT
1 TAT
1044650 ATTAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (28 bp):
TATTTTTATATTAAAGTTATTATGAATT
Found at i:1046210 original size:21 final size:21
Alignment explanation
Indices: 1046180--1046227 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1046170 GCAGGGGTAC
* *
1046180 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1046201 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1046222 ATGCCA
1 ATGCCA
1046228 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1046257 original size:21 final size:21
Alignment explanation
Indices: 1046231--1046324 Score: 145
Period size: 21 Copynumber: 4.5 Consensus size: 21
1046221 TATGCCATCT
1046231 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
1046252 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
1046273 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
1046294 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
1046315 CCGCAGGGTT
1 CCGCAGGGTT
1046325 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.34, G:0.28, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:1046905 original size:33 final size:34
Alignment explanation
Indices: 1046846--1046942 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
1046836 AAATGTTTTT
*
1046846 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
1046880 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
1046913 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
1046943 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:1046949 original size:34 final size:33
Alignment explanation
Indices: 1046844--1046949 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
1046834 ATAAATGTTT
*
1046844 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
1046878 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
1046910 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
1046945 TTAAA
1 TTAAA
1046950 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:1047490 original size:128 final size:128
Alignment explanation
Indices: 1047335--1048216 Score: 1513
Period size: 128 Copynumber: 6.9 Consensus size: 128
1047325 TTACCTGATT
* *
1047335 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATTGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *** *
1047400 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
1047463 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1047528 TGACGAAATAATGGAAAGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1047591 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTT
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1047656 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1047719 TACTGATATATCTAGTGTCCCCGA-GGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
1047783 TGACGAAATAATGGAAGGCGTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
1047846 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
1047911 TGAC-AAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
1047972 TACTGATGTATCTAGTGTCCCCGAGGGACATGAGTGATATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
1048037 TGATGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTAATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
1048100 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
1048165 TGACGAAATAATGGAATGCGCGCCCCCGGGAACACGCCTTCATGTTAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
1048217 ACTCCGATTA
Statistics
Matches: 714, Mismatches: 34, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
126 99 0.14
127 161 0.23
128 454 0.64
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:1048300 original size:8 final size:8
Alignment explanation
Indices: 1048287--1048327 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1048277 TCACAATCTT
1048287 TCAAATTC
1 TCAAATTC
1048295 TCAAATTC
1 TCAAATTC
* *
1048303 CCAAACTC
1 TCAAATTC
1048311 T-AAATTC
1 TCAAATTC
1048318 TCAAATTC
1 TCAAATTC
1048326 TC
1 TC
1048328 TAAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:1066666 original size:19 final size:20
Alignment explanation
Indices: 1066629--1066668 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1066619 AAACTAAAAT
**
1066629 AAAAATAAAAAAGTGTTATA
1 AAAAATAAAAAAGCATTATA
1066649 AAAAATAAAAAA-CATTATA
1 AAAAATAAAAAAGCATTATA
1066668 A
1 A
1066669 TGAACAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (20 bp):
AAAAATAAAAAAGCATTATA
Found at i:1068639 original size:20 final size:20
Alignment explanation
Indices: 1068610--1068647 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1068600 TTTCAAAGTG
1068610 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1068630 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1068648 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:1068716 original size:45 final size:46
Alignment explanation
Indices: 1068667--1068756 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 46
1068657 AAACATCGAA
* *
1068667 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
1068712 TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACTCA
1 TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACTCA
1068757 TATTTTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
45 21 0.50
46 21 0.50
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (46 bp):
TGCATTTAATGCATCGATGCACAAGACCATGCATCGATGCACTCAG
Found at i:1068817 original size:111 final size:109
Alignment explanation
Indices: 1068610--1068819 Score: 291
Period size: 111 Copynumber: 1.9 Consensus size: 109
1068600 TTTCAAAGTG
*
1068610 ATGCACCGATGCACCAATCCATGCATCGATGCACCAATTAATTTTTCAAACATCGAATGCATTTT
1 ATGCACCGATGCACCAAACCATGCATCGATGCACCAATT-ATTTTTCAAACATCGAATGCATTTT
* *
1068675 ATGCATCGATGCACATACCATGCATCGATGCACTCAGTGCATTTA
65 ATGCATCGATGCACATAACATGCACCGATGCACTCAGTGCATTTA
*
1068720 ATGCATCGATGCA-CAAGACCATGCATCGATGCACTCATATT-TTTTTCAAAACATCGAATGCAT
1 ATGCACCGATGCACCAA-ACCATGCATCGATGCAC-CA-ATTATTTTTC-AAACATCGAATGCAT
* *
1068783 TTTATGCATCGGTGCAC-TAAGAGTGCACCGATGCACT
62 TTTATGCATCGATGCACATAACA-TGCACCGATGCACT
1068820 GAGAGTCCAA
Statistics
Matches: 89, Mismatches: 6, Indels: 9
0.86 0.06 0.09
Matches are distributed among these distances:
109 3 0.03
110 37 0.42
111 46 0.52
112 3 0.03
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (109 bp):
ATGCACCGATGCACCAAACCATGCATCGATGCACCAATTATTTTTCAAACATCGAATGCATTTTA
TGCATCGATGCACATAACATGCACCGATGCACTCAGTGCATTTA
Found at i:1068833 original size:19 final size:19
Alignment explanation
Indices: 1068795--1068833 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1068785 TATGCATCGG
* *
1068795 TGCACTAAGAGTGCACCGA
1 TGCACTAAGAGTCCAACGA
*
1068814 TGCACTGAGAGTCCAACGA
1 TGCACTAAGAGTCCAACGA
1068833 T
1 T
1068834 CAAAATATTT
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:0.31, C:0.26, G:0.26, T:0.18
Consensus pattern (19 bp):
TGCACTAAGAGTCCAACGA
Found at i:1075342 original size:23 final size:23
Alignment explanation
Indices: 1075312--1075365 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
1075302 GTTGAGTCGT
1075312 TCTCGTTCAAACCAACCTCCTAA
1 TCTCGTTCAAACCAACCTCCTAA
1075335 TCTCGTTCAAACCAACCTCCTAA
1 TCTCGTTCAAACCAACCTCCTAA
1075358 TCTCGTTC
1 TCTCGTTC
1075366 CTCCTCCACC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.26, C:0.39, G:0.06, T:0.30
Consensus pattern (23 bp):
TCTCGTTCAAACCAACCTCCTAA
Found at i:1076208 original size:21 final size:21
Alignment explanation
Indices: 1076179--1076222 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1076169 ACCCCGGGAA
*
1076179 CTAGTTCTTCACGAGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
1076200 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
1076221 CT
1 CT
1076223 CCTCCTCCGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.41, G:0.14, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:1084163 original size:23 final size:23
Alignment explanation
Indices: 1084137--1084205 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1084127 CACCACAACT
*
1084137 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1084160 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
1084183 TGTAGAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1084206 TATAAGATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1094082 original size:168 final size:169
Alignment explanation
Indices: 1093793--1094116 Score: 431
Period size: 168 Copynumber: 1.9 Consensus size: 169
1093783 TTTCAATTCT
** * * *
1093793 CTCAGCACCATTGACTGTCACAACCGACGCCAATCGACCAAAAAATTTGAAGGTGCGCAACCACT
1 CTCAGCACCACCGACTGTCACAACCGACGCCAATAGACCAAAAAATTAGAAGGTGCGCAACAACT
* * * * * *
1093858 CGAACACCAAAAGACCAAACCCCCATGCTTCAAGCGATGATTGCATCAACTTATTGATT-TCGAC
66 CCAACACCAAAAGACCAAACCCCCATACTTAAAACGACGATTGCAACAACTTATTGATTCT-GAC
*
1093922 TAATGACGATGATTCCATCGATTCAAGTAATTTAAATCCC
130 TAACGACGATGATTCCATCGATTCAAGTAATTTAAATCCC
* *
1093962 CTCAGCACCACCGATTGTCACAACCGTCGCCAATTAG-CC-AAAAATTAGAAGGTGCGCAACAAC
1 CTCAGCACCACCGACTGTCACAACCGACGCCAA-TAGACCAAAAAATTAGAAGGTGCGCAACAAC
* * * *
1094025 TCCAACA-CATAAAGATCGAACCCCCATACTTAAAACGACGATTGGAACAATTTATTGATTCTGA
65 TCCAACACCA-AAAGACCAAACCCCCATACTTAAAACGACGATTGCAACAACTTATTGATTCTGA
1094089 CTAACGACGATGATTCCATCGATTCAAG
129 CTAACGACGATGATTCCATCGATTCAAG
1094117 CAACGACTCC
Statistics
Matches: 134, Mismatches: 18, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
167 2 0.01
168 98 0.73
169 32 0.24
170 2 0.01
ACGTcount: A:0.35, C:0.28, G:0.15, T:0.22
Consensus pattern (169 bp):
CTCAGCACCACCGACTGTCACAACCGACGCCAATAGACCAAAAAATTAGAAGGTGCGCAACAACT
CCAACACCAAAAGACCAAACCCCCATACTTAAAACGACGATTGCAACAACTTATTGATTCTGACT
AACGACGATGATTCCATCGATTCAAGTAATTTAAATCCC
Found at i:1096282 original size:22 final size:22
Alignment explanation
Indices: 1096257--1096307 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1096247 CGGATAAAAA
* *
1096257 TTCGGTTTGAGTTACTTTCGGT
1 TTCGGTTTGAGTTAATTTCGAT
*
1096279 TTCGGTTTGGGTTAATTTCGAT
1 TTCGGTTTGAGTTAATTTCGAT
1096301 TTCGGTT
1 TTCGGTT
1096308 CTGGTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.10, C:0.12, G:0.27, T:0.51
Consensus pattern (22 bp):
TTCGGTTTGAGTTAATTTCGAT
Found at i:1096313 original size:22 final size:21
Alignment explanation
Indices: 1096257--1096318 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
1096247 CGGATAAAAA
* *
1096257 TTCGGTTTGAGTTACTTTCGGT
1 TTCGGTTTG-GTTAATTTCGAT
1096279 TTCGGTTTGGGTTAATTTCGAT
1 TTCGGTTT-GGTTAATTTCGAT
*
1096301 TTCGGTTCTGGTTGATTT
1 TTCGGTT-TGGTTAATTT
1096319 TGGTTTTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 33 0.94
23 2 0.06
ACGTcount: A:0.10, C:0.11, G:0.27, T:0.52
Consensus pattern (21 bp):
TTCGGTTTGGTTAATTTCGAT
Found at i:1096776 original size:23 final size:25
Alignment explanation
Indices: 1096746--1096794 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
1096736 GAATTTAGAC
1096746 TTATCACAAG-TAAAG-TGTAATAT
1 TTATCACAAGCTAAAGTTGTAATAT
1096769 TTATCACAAGTCTAAAGTTGTAATAT
1 TTATCACAAG-CTAAAGTTGTAATAT
1096795 ACTATTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.43
25 5 0.22
26 8 0.35
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (25 bp):
TTATCACAAGCTAAAGTTGTAATAT
Found at i:1098094 original size:16 final size:16
Alignment explanation
Indices: 1098070--1098129 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
1098060 TCGAATGGGA
*
1098070 TCGGATCGGATTAAAT
1 TCGGTTCGGATTAAAT
***
1098086 TCGGTTCGGATTGCTT
1 TCGGTTCGGATTAAAT
**
1098102 TTAGTTCGGATTAAA-
1 TCGGTTCGGATTAAAT
1098117 TCAGGTTCGGATT
1 TC-GGTTCGGATT
1098130 GCTTTCGATT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
15 1 0.03
16 31 0.97
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (16 bp):
TCGGTTCGGATTAAAT
Found at i:1101512 original size:24 final size:24
Alignment explanation
Indices: 1101449--1101506 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
1101439 CGTTAAAACA
*
1101449 ATAAACGAACACAAATGAACGAAC
1 ATAAACGAACACAAACGAACGAAC
*
1101473 ATAAACGAATACAAACGAACGAAC
1 ATAAACGAACACAAACGAACGAAC
*
1101497 ATAAATGAAC
1 ATAAACGAAC
1101507 GTAAACAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.59, C:0.19, G:0.12, T:0.10
Consensus pattern (24 bp):
ATAAACGAACACAAACGAACGAAC
Found at i:1101512 original size:34 final size:34
Alignment explanation
Indices: 1101469--1101535 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1101459 ACAAATGAAC
*
1101469 GAACATAAACGAA-TACAAACGAACGAACATAAAT
1 GAACATAAAC-AAGCACAAACGAACGAACATAAAT
* *
1101503 GAACGTAAACAAGCATAAACGAACGAACATAAA
1 GAACATAAACAAGCACAAACGAACGAACATAAA
1101536 ATTTATTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.58, C:0.18, G:0.13, T:0.10
Consensus pattern (34 bp):
GAACATAAACAAGCACAAACGAACGAACATAAAT
Found at i:1101535 original size:14 final size:14
Alignment explanation
Indices: 1101452--1101535 Score: 50
Period size: 14 Copynumber: 5.9 Consensus size: 14
1101442 TAAAACAATA
* *
1101452 AACGAACACAAATG
1 AACGAACATAAACG
1101466 AACGAACATAAACG
1 AACGAACATAAACG
*
1101480 AA--TAC--AAACG
1 AACGAACATAAACG
*
1101490 AACGAACATAAATG
1 AACGAACATAAACG
1101504 AACGTAAACAAGCATAAACG
1 AACG-----AA-CATAAACG
1101524 AACGAACATAAA
1 AACGAACATAAA
1101536 ATTTATTGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
10 7 0.13
12 4 0.07
14 28 0.52
15 2 0.04
19 2 0.04
20 11 0.20
ACGTcount: A:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:1101739 original size:10 final size:10
Alignment explanation
Indices: 1101721--1101756 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
1101711 GAGATTGAAC
*
1101721 TGAATATAAA
1 TGAACATAAA
1101731 TGAACATAAA
1 TGAACATAAA
1101741 TGAACATAAA
1 TGAACATAAA
1101751 TGAACA
1 TGAACA
1101757 AACATAAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.58, C:0.08, G:0.11, T:0.22
Consensus pattern (10 bp):
TGAACATAAA
Found at i:1103427 original size:17 final size:18
Alignment explanation
Indices: 1103401--1103435 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1103391 AAAGAGCAAC
1103401 AAAGAGGAAAGAAGAAAG
1 AAAGAGGAAAGAAGAAAG
1103419 AAAGA-GAAAGAAGAAAG
1 AAAGAGGAAAGAAGAAAG
1103436 GAGGAGGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AAAGAGGAAAGAAGAAAG
Found at i:1114243 original size:31 final size:31
Alignment explanation
Indices: 1114203--1114358 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1114193 AGGGTCGAGG
1114203 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1114234 GCTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1114265 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1114296 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1114327 GTTTACCTAGGTTTTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1114358 G
1 G
1114359 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
31 116 0.99
32 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1116998 original size:55 final size:55
Alignment explanation
Indices: 1116912--1117064 Score: 198
Period size: 55 Copynumber: 2.8 Consensus size: 55
1116902 TGTCGCTCTG
* * * *
1116912 GATTGACCCAATTTCCTCAGAGAAAAAGAACAGTGTCAACACCAAATTATCTTTA
1 GATTGACCCGATTTCCTCAGAGAGAAGGAACAGTGTCAACACCAAATTATCTTCA
* * *
1116967 GATTGACCCGATTTCTTCATAGAGAAGGAACAGTGTCAACACTAAATTATCTTCA
1 GATTGACCCGATTTCCTCAGAGAGAAGGAACAGTGTCAACACCAAATTATCTTCA
** * * *
1117022 GATTGACCCGACGTCCTAAGAGAGAAGGAACAATGTCATCACC
1 GATTGACCCGATTTCCTCAGAGAGAAGGAACAGTGTCAACACC
1117065 CTAAAATGAC
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 83 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (55 bp):
GATTGACCCGATTTCCTCAGAGAGAAGGAACAGTGTCAACACCAAATTATCTTCA
Found at i:1117255 original size:200 final size:199
Alignment explanation
Indices: 1116877--1117264 Score: 503
Period size: 200 Copynumber: 1.9 Consensus size: 199
1116867 CAGGACGACT
* * * ** *
1116877 AGATCTCTTCAATATGGATGAGCATTGTCGCTCTGGATTGACCCAATTTCCTCAGAGAAAAAGAA
1 AGATCTCTTCAATATAGATGAGCAGTGTAGCTCCAGATTGACCCAATTTCCTCAAAGAAAAAGAA
* ** *
1116942 CAGTGTCAACACCAAATTATCTTTAGATTGACCCGATTTCTTCATAGAGAAGGAACAGTGTCAAC
66 CAATGTCAACACCAAATTATCTCCAGATTGACCCGATTTCTTCAGAGAGAAGGAACAGTGTCAAC
*
1117007 ACTAAATTATCTTCAGATTGACCCGACGTCCTAAGAGAGAAGGAACAATGTCATCACCCTAAAAT
131 ACTAAATTATCTTCAGATTGACCCGACGTCCTAAGAGAGAAGGAACAATGTCAACACCCTAAAAT
1117072 GACC
196 GACC
* * * * *
1117076 AGATCTCTTCAATGTAGATGAGGAGTGTAGTCTCCAGATTGACCCGATTTCCTTAAAGAAAATGA
1 AGATCTCTTCAATATAGATGAGCAGTGTAG-CTCCAGATTGACCCAATTTCCTCAAAGAAAAAGA
* * **
1117141 ACAATGTCAATACGAAATTATCTCCAGATTGACTTGATTT-TCTCAGAGAGAAGGAACAGTGTCA
65 ACAATGTCAACACCAAATTATCTCCAGATTGACCCGATTTCT-TCAGAGAGAAGGAACAGTGTCA
* ** *
1117205 ACA-TCAAATTATCTTCATATTGACCCGATTTCCTCAA-AGAGAATGAACAATGTCAACACC
129 ACACT-AAATTATCTTCAGATTGACCCGACGTCCT-AAGAGAGAAGGAACAATGTCAACACC
1117265 TAATTATCTC
Statistics
Matches: 161, Mismatches: 24, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
199 27 0.17
200 132 0.82
201 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (199 bp):
AGATCTCTTCAATATAGATGAGCAGTGTAGCTCCAGATTGACCCAATTTCCTCAAAGAAAAAGAA
CAATGTCAACACCAAATTATCTCCAGATTGACCCGATTTCTTCAGAGAGAAGGAACAGTGTCAAC
ACTAAATTATCTTCAGATTGACCCGACGTCCTAAGAGAGAAGGAACAATGTCAACACCCTAAAAT
GACC
Found at i:1117301 original size:55 final size:55
Alignment explanation
Indices: 1117106--1117308 Score: 226
Period size: 55 Copynumber: 3.7 Consensus size: 55
1117096 AGGAGTGTAG
* * * * *
1117106 TCTCCAGATTGACCCGATTTCCTTAAAGAAAATGAACAATGTCAATACGAAATTA
1 TCTCCAGATTGACCCGATTTCCTCAAAGAGAAGGAACAATGTCAACACCAAATTA
** * * * *
1117161 TCTCCAGATTGACTTGATTTTCTCAGAGAGAAGGAACAGTGTCAACATCAAATTA
1 TCTCCAGATTGACCCGATTTCCTCAAAGAGAAGGAACAATGTCAACACCAAATTA
* * * *
1117216 TCTTCATATTGACCCGATTTCCTCAAAGAGAATGAACAATGTCAACACCTAATTA
1 TCTCCAGATTGACCCGATTTCCTCAAAGAGAAGGAACAATGTCAACACCAAATTA
* ** * *
1117271 TCTCCAGATTGACCCAACATCCTTAGAGAGAAGGAACA
1 TCTCCAGATTGACCCGATTTCCTCAAAGAGAAGGAACA
1117309 GTGGCATCCC
Statistics
Matches: 119, Mismatches: 29, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
55 119 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (55 bp):
TCTCCAGATTGACCCGATTTCCTCAAAGAGAAGGAACAATGTCAACACCAAATTA
Found at i:1117306 original size:110 final size:110
Alignment explanation
Indices: 1117113--1117311 Score: 290
Period size: 110 Copynumber: 1.8 Consensus size: 110
1117103 TAGTCTCCAG
* * * ***
1117113 ATTGACCCGATTTCCTTAAAGAAAATGAACAATGTCAATACGAAATTATCTCCAGATTGACTTGA
1 ATTGACCCGATTTCCTCAAAGAAAATGAACAATGTCAACACCAAATTATCTCCAGATTGACCCAA
** *
1117178 TTTTCTCAGAGAGAAGGAACAGTGTCAACATCAAATTATCTTCAT
66 CATCCTCAGAGAGAAGGAACAGTGTCAACATCAAATTATCTTCAT
* *
1117223 ATTGACCCGATTTCCTCAAAGAGAATGAACAATGTCAACACCTAATTATCTCCAGATTGACCCAA
1 ATTGACCCGATTTCCTCAAAGAAAATGAACAATGTCAACACCAAATTATCTCCAGATTGACCCAA
*
1117288 CATCCTTAGAGAGAAGGAACAGTG
66 CATCCTCAGAGAGAAGGAACAGTG
1117312 GCATCCCCCA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
110 77 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (110 bp):
ATTGACCCGATTTCCTCAAAGAAAATGAACAATGTCAACACCAAATTATCTCCAGATTGACCCAA
CATCCTCAGAGAGAAGGAACAGTGTCAACATCAAATTATCTTCAT
Found at i:1117719 original size:99 final size:100
Alignment explanation
Indices: 1117332--1117736 Score: 400
Period size: 99 Copynumber: 4.1 Consensus size: 100
1117322 AAAAGCAGGA
* * *
1117332 AGATCTCTTCAATGCAGATGAGGAGTGTCA-TTTCCAAGATAGACC-CGACGTCCTCAGAGAGAA
1 AGATCTCTTCAATGCAGATGAGCAGTGT-AGTTTCCAAGATTGACCTCGACATCCTCAGAGAGAA
* * *
1117395 TGAGCAATGTCATCTTCAATTTAACCGAAAATGGCC
65 TGAACAATGTCATCTTCAATTTAACCGAAAGTGACC
* * * * * *
1117431 ATATCTCTTGAATGCATACGAGCAGTGTCGTTTCCAAGATTGA-CTCGACATCCTCATAGAGAAT
1 AGATCTCTTCAATGCAGATGAGCAGTGTAGTTTCCAAGATTGACCTCGACATCCTCAGAGAGAAT
** *
1117495 GAACAATGTCATCTTCAATTTAACTAAAAGCGGA-C
66 GAACAATGTCATCTTCAATTTAACCGAAAG-TGACC
* * * * * * * *
1117530 AGGTCGCTTTAATGCTGATGAGCAATGTCGTTTCCAAGATT-AACTCGACA---TCAGAGAGAAG
1 AGATCTCTTCAATGCAGATGAGCAGTGTAGTTTCCAAGATTGACCTCGACATCCTCAGAGAGAAT
* *
1117591 GAACATTGTCATCTTTAATTT-ACACGAAAGTGACC
66 GAACAATGTCATCTTCAATTTAAC-CGAAAGTGACC
* * *
1117626 AGATCTCTTCAAAGTAGATGAGCAGTGTAGTTTCCAAGATTGACCT-GACATCTTCAGAGAGAAT
1 AGATCTCTTCAATGCAGATGAGCAGTGTAGTTTCCAAGATTGACCTCGACATCCTCAGAGAGAAT
* * * *
1117690 GAACAATATCA-CATTCAATTTACCCGAAAGCGACA
66 GAACAATGTCATC-TTCAATTTAACCGAAAGTGACC
*
1117725 AGATCTATTCAA
1 AGATCTCTTCAA
1117737 AGCGAAAGAG
Statistics
Matches: 247, Mismatches: 47, Indels: 24
0.78 0.15 0.08
Matches are distributed among these distances:
95 4 0.02
96 70 0.28
97 3 0.01
98 3 0.01
99 165 0.67
100 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (100 bp):
AGATCTCTTCAATGCAGATGAGCAGTGTAGTTTCCAAGATTGACCTCGACATCCTCAGAGAGAAT
GAACAATGTCATCTTCAATTTAACCGAAAGTGACC
Found at i:1117866 original size:3 final size:3
Alignment explanation
Indices: 1117853--1117907 Score: 101
Period size: 3 Copynumber: 18.0 Consensus size: 3
1117843 CTGTGTTTTA
1117853 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1117899 ATT ATT ATT
1 ATT ATT ATT
1117908 TATTTTCTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 48 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1121630 original size:24 final size:24
Alignment explanation
Indices: 1121603--1121678 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
1121593 TATATCAAAA
* *
1121603 ATCAAAACATAAATCAGGTCAAGT
1 ATCAAAACAGAAATCAAGTCAAGT
* * *
1121627 ATCATATCAGAAATCAAGTCAAAT
1 ATCAAAACAGAAATCAAGTCAAGT
* * *
1121651 AACAGATCAG-AATCCAAGTCAAGT
1 ATCAAAACAGAAAT-CAAGTCAAGT
1121675 ATCA
1 ATCA
1121679 GATCAGAATC
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 3 0.07
24 39 0.93
ACGTcount: A:0.49, C:0.18, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCAAAACAGAAATCAAGTCAAGT
Found at i:1121672 original size:48 final size:48
Alignment explanation
Indices: 1121620--1121739 Score: 161
Period size: 48 Copynumber: 2.5 Consensus size: 48
1121610 CATAAATCAG
*
1121620 GTCAAGTATCATATCAGAAATCAAGTCAAATAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAAATCAAGTCAAATAACAGATCAGAATCCAA
* * * * *
1121668 GTCAAGTATCAGATCAG-AATCTATGTCAGATATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAAATC-AAGTCAAATAACAGATCAGAATCCAA
*
1121716 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAAATCAA
1121740 ATTGAAAATC
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
47 4 0.06
48 55 0.89
49 3 0.05
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAAATCAAGTCAAATAACAGATCAGAATCCAA
Found at i:1121680 original size:24 final size:24
Alignment explanation
Indices: 1121620--1121735 Score: 137
Period size: 24 Copynumber: 4.8 Consensus size: 24
1121610 CATAAATCAG
*
1121620 GTCAAGTATCATATCAGAAAT-CAA
1 GTCAAGTATCAGATCAG-AATCCAA
* *
1121644 GTCAAATAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
1121668 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
1121692 GTC-AGATATCATATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
1121716 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1121736 TCAAATTGAA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
23 5 0.06
24 72 0.91
25 2 0.03
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:1124286 original size:13 final size:13
Alignment explanation
Indices: 1124268--1124309 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
1124258 GCCGGTCAAC
1124268 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1124281 GGTCAACAGGTCG
1 GGTCAACGGGTCG
*
1124294 GGTAAACGGGTCG
1 GGTCAACGGGTCG
1124307 GGT
1 GGT
1124310 TCGGGTCGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.45, T:0.17
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1125891 original size:31 final size:31
Alignment explanation
Indices: 1125853--1125929 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
1125843 TCAAAATACA
1125853 TAAGATATGATCACCTTCGTTTTTATTTAAT
1 TAAGATATGATCACCTTCGTTTTTATTTAAT
* * * *
1125884 TAAGATATAATCACTTTTGTTTTTATTTATT
1 TAAGATATGATCACCTTCGTTTTTATTTAAT
* *
1125915 TAAGATGTGGTCACC
1 TAAGATATGATCACC
1125930 ACGGGTTAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (31 bp):
TAAGATATGATCACCTTCGTTTTTATTTAAT
Found at i:1127499 original size:14 final size:14
Alignment explanation
Indices: 1127480--1127560 Score: 55
Period size: 14 Copynumber: 6.1 Consensus size: 14
1127470 CGTTTGGTAA
1127480 TATGTTCGTTTATG
1 TATGTTCGTTTATG
*
1127494 TATGTTC----ATT
1 TATGTTCGTTTATG
*
1127504 TATGTTCATTTATG
1 TATGTTCGTTTATG
1127518 T-TCGTTCGTTTATG
1 TAT-GTTCGTTTATG
**
1127532 TGCGTTCGTTTATG
1 TATGTTCGTTTATG
** *
1127546 TGCGTTCATTTATG
1 TATGTTCGTTTATG
1127560 T
1 T
1127561 TTAGCCCAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
10 9 0.16
13 1 0.02
14 46 0.82
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.56
Consensus pattern (14 bp):
TATGTTCGTTTATG
Found at i:1127507 original size:10 final size:10
Alignment explanation
Indices: 1127494--1127520 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1127484 TTCGTTTATG
1127494 TATGTTCATT
1 TATGTTCATT
1127504 TATGTTCATT
1 TATGTTCATT
1127514 TATGTTC
1 TATGTTC
1127521 GTTCGTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.59
Consensus pattern (10 bp):
TATGTTCATT
Found at i:1127509 original size:24 final size:23
Alignment explanation
Indices: 1127480--1127561 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 23
1127470 CGTTTGGTAA
1127480 TATGTTCGTTTATGTATGTTCATT
1 TATGTTCGTTTATGT-TGTTCATT
* *
1127504 TATGTTCATTTATGTTCGTTCGTT
1 TATGTTCGTTTATGTT-GTTCATT
*
1127528 TATGTGCGTTCGTTTATGTGCGTTCATT
1 TA--T--GTTCGTTTATGT-TGTTCATT
1127556 TATGTT
1 TATGTT
1127562 TAGCCCAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
23 1 0.02
24 25 0.53
26 2 0.04
28 19 0.40
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (23 bp):
TATGTTCGTTTATGTTGTTCATT
Found at i:1127551 original size:28 final size:28
Alignment explanation
Indices: 1127507--1127560 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
1127497 GTTCATTTAT
* *
1127507 GTTCATTTATGTTCGTTCGTTTATGTGC
1 GTTCATTTATGTGCGTTCATTTATGTGC
*
1127535 GTTCGTTTATGTGCGTTCATTTATGT
1 GTTCATTTATGTGCGTTCATTTATGT
1127561 TTAGCCCAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.54
Consensus pattern (28 bp):
GTTCATTTATGTGCGTTCATTTATGTGC
Found at i:1127751 original size:10 final size:10
Alignment explanation
Indices: 1127729--1127767 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
1127719 TATATATATT
1127729 TTCATTTATG
1 TTCATTTATG
* *
1127739 TTCGTTTACG
1 TTCATTTATG
1127749 TTCATTTATG
1 TTCATTTATG
1127759 TTCATTTAT
1 TTCATTTAT
1127768 TGTGTTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.18, C:0.13, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:1127754 original size:20 final size:20
Alignment explanation
Indices: 1127729--1127766 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1127719 TATATATATT
*
1127729 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTTCATTTACG
1127749 TTCATTTATGTTCATTTA
1 TTCATTTATGTTCATTTA
1127767 TTGTGTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (20 bp):
TTCATTTATGTTCATTTACG
Found at i:1127778 original size:23 final size:24
Alignment explanation
Indices: 1127748--1127797 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1127738 GTTCGTTTAC
*
1127748 GTTCATTTATGTTCATTTA-TTGT
1 GTTCATTTACGTTCATTTATTTGT
**
1127771 GTTCATTTACGTTTGTTTATTTGT
1 GTTCATTTACGTTCATTTATTTGT
1127795 GTT
1 GTT
1127798 TGTTTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.14, C:0.08, G:0.16, T:0.62
Consensus pattern (24 bp):
GTTCATTTACGTTCATTTATTTGT
Found at i:1127807 original size:14 final size:14
Alignment explanation
Indices: 1127781--1127815 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1127771 GTTCATTTAC
1127781 GTTTGTTTATTTGT
1 GTTTGTTTATTTGT
1127795 GTTTGTTTATTTGT
1 GTTTGTTTATTTGT
1127809 GTTTGTT
1 GTTTGTT
1127816 CACGTTCGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.06, C:0.00, G:0.23, T:0.71
Consensus pattern (14 bp):
GTTTGTTTATTTGT
Found at i:1127835 original size:23 final size:24
Alignment explanation
Indices: 1127799--1127850 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
1127789 ATTTGTGTTT
1127799 GTTTATTTGTGTTTGTTCACGTTC
1 GTTTATTTGTGTTTGTTCACGTTC
* *
1127823 GTTTA-TTGTGTTTGTTTATGTTC
1 GTTTATTTGTGTTTGTTCACGTTC
1127846 GTTTA
1 GTTTA
1127851 CATCTGTTCG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.10, C:0.08, G:0.21, T:0.62
Consensus pattern (24 bp):
GTTTATTTGTGTTTGTTCACGTTC
Found at i:1127868 original size:61 final size:61
Alignment explanation
Indices: 1127758--1127876 Score: 139
Period size: 61 Copynumber: 2.0 Consensus size: 61
1127748 GTTCATTTAT
* ** * * * *
1127758 GTTCATTTATTGTGTTCATTTACGTTTGTTTATTTGTGTTTGTTTATTTGTGTTTGTTCAC
1 GTTCATTTATTGTGTTCATTTACGTTCGTTTACATCTGTTCGTTCATTTGTGTCTGTTCAC
* ** *
1127819 GTTCGTTTATTGTGTTTGTTTATGTTCGTTTACATCTGTTCGTTCATTTGTGTCTGTT
1 GTTCATTTATTGTGTTCATTTACGTTCGTTTACATCTGTTCGTTCATTTGTGTCTGTT
1127877 TATCATTTAA
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.10, C:0.10, G:0.19, T:0.61
Consensus pattern (61 bp):
GTTCATTTATTGTGTTCATTTACGTTCGTTTACATCTGTTCGTTCATTTGTGTCTGTTCAC
Found at i:1129001 original size:42 final size:42
Alignment explanation
Indices: 1128954--1129068 Score: 221
Period size: 42 Copynumber: 2.7 Consensus size: 42
1128944 CCAAATTTCA
*
1128954 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCC
1128996 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCC
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCC
1129038 GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 GTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1129069 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (42 bp):
GTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGTTTTCCC
Found at i:1129293 original size:23 final size:22
Alignment explanation
Indices: 1129263--1129312 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
1129253 TTAAAATATT
*
1129263 TAAAATATAT-TT-ATATTTTA
1 TAAAATATATATTAATATTATA
1129283 TAATAATATATATTAATATTATA
1 TAA-AATATATATTAATATTATA
1129306 TAAAATA
1 TAAAATA
1129313 ATCAATTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 3 0.12
21 7 0.27
22 6 0.23
23 10 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAAATATATATTAATATTATA
Found at i:1129660 original size:20 final size:20
Alignment explanation
Indices: 1129582--1129651 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
1129572 TTTCCAGATG
1129582 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1129602 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
1129622 TTTTACATAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
1129642 TTTTCCAGAA
1 TTTTCCAGAA
1129652 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:1129670 original size:15 final size:15
Alignment explanation
Indices: 1129634--1129715 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
1129624 TTACATAAAT
**
1129634 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1129649 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
1129663 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
1129678 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1129693 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
1129708 GTAATTCA
1 GTAATTCA
1129716 TTTTCTGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:1129686 original size:30 final size:30
Alignment explanation
Indices: 1129634--1129715 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
1129624 TTACATAAAT
1129634 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
1129663 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
1129693 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
1129716 TTTTCTGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:1129708 original size:45 final size:44
Alignment explanation
Indices: 1129634--1129720 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
1129624 TTACATAAAT
**
1129634 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1129678 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
1129721 TGAAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:1129775 original size:3 final size:3
Alignment explanation
Indices: 1129767--1129805 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
1129757 AACAAAAGAA
*
1129767 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1129806 TTTGTTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1130666 original size:23 final size:23
Alignment explanation
Indices: 1130594--1130658 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
1130584 AATAACATAT
1130594 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
1130617 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATGTAA
1130640 TAGGTAGCGCTTATATAAT
1 TAGGTAGCGCTTATATAAT
1130659 AAAATAGGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATGTAA
Found at i:1130750 original size:110 final size:110
Alignment explanation
Indices: 1130557--1130765 Score: 337
Period size: 110 Copynumber: 1.9 Consensus size: 110
1130547 TATGTTATAT
*
1130557 CATTTAACCAAAAATATTATCAAACACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAAAAATATTATCAAACACAATAACATATTAGGTAGCCCTTATATAATGTAATAGGT
* * *
1130622 AGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGG
66 AGCACTTATATAATGTAATAGATAGCACTTATATAATAAAATAGG
** ** *
1130667 CATTTAACCGGAAATATTATCAAGTACAATAATATATTAGGTAGCCCTTATATAATGTAATAGGT
1 CATTTAACCAAAAATATTATCAAACACAATAACATATTAGGTAGCCCTTATATAATGTAATAGGT
1130732 AGCACTTATATAATGTAATAGATAGCACTTATAT
66 AGCACTTATATAATGTAATAGATAGCACTTATAT
1130766 TGACCTATTT
Statistics
Matches: 90, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
110 90 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (110 bp):
CATTTAACCAAAAATATTATCAAACACAATAACATATTAGGTAGCCCTTATATAATGTAATAGGT
AGCACTTATATAATGTAATAGATAGCACTTATATAATAAAATAGG
Found at i:1130756 original size:27 final size:23
Alignment explanation
Indices: 1130594--1130765 Score: 124
Period size: 23 Copynumber: 7.7 Consensus size: 23
1130584 AATAACATAT
*
1130594 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCACTTATATAATGTAA
*
1130617 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCACTTATATAATGTAA
* **
1130640 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCACTTATATAATGTAA
** *
1130663 TA-G--GCA-TT-TA-ACCGGAAA
1 TAGGTAGCACTTATATA-ATGTAA
* * ** * * *
1130681 TA-TTATCAAGTACAATAATATAT
1 TAGGTAGCACTTA-TATAATGTAA
*
1130704 TAGGTAGCCCTTATATAATGTAA
1 TAGGTAGCACTTATATAATGTAA
1130727 TAGGTAGCACTTATATAATGTAA
1 TAGGTAGCACTTATATAATGTAA
*
1130750 TAGATAGCACTTATAT
1 TAGGTAGCACTTATAT
1130766 TGACCTATTT
Statistics
Matches: 116, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
17 1 0.01
18 7 0.06
19 2 0.02
20 4 0.03
21 1 0.01
22 1 0.01
23 94 0.81
24 6 0.05
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (23 bp):
TAGGTAGCACTTATATAATGTAA
Found at i:1130950 original size:21 final size:21
Alignment explanation
Indices: 1130926--1130983 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1130916 TTGGAAAAAA
* *
1130926 AGTATCGACACATATTTAAAG
1 AGTATCGATACATAATTAAAG
1130947 AGTATCGATACATAATTAAAG
1 AGTATCGATACATAATTAAAG
1130968 AGTATCGATACATAAT
1 AGTATCGATACATAAT
1130984 GTAGACATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (21 bp):
AGTATCGATACATAATTAAAG
Found at i:1131480 original size:182 final size:182
Alignment explanation
Indices: 1131169--1131845 Score: 1060
Period size: 182 Copynumber: 3.7 Consensus size: 182
1131159 TGTTGACCTA
* * * *
1131169 TTTTCTCATATTTTTAATTGTTATATTGTTATCGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
*
1131234 TTTA-ACGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * *
1131298 CACTTTCAACATATTCGGTATCCTTTTACCGGTTTTGTCATTTTGAGACCGG
131 CACTTGCAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGACCGG
*
1131350 TTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTTGA-AAAGTATCGACACT
1 TTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACA-TTTTCATAAAGTATCGACACT
1131414 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
65 TTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCG
* * *
1131479 ACACTTGCAACATATCCGGTAGCGTTTTACCGGTTTTGTTATTTTGAGATCGG
130 ACACTTGCAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * *
1131532 TTTTGTCATATTTTTACATGTTATATTGTTATAGATCGATACATTTTCATAAAGTGTCGACACTT
1 TTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
1131597 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
66 TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
* * * * *
1131662 CACTTGCAACAAATCCGATATCGTTTTACC-ATTTTTTCATTTTGAGACTGG
131 CACTTGCAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGACCGG
* * *
1131713 TTTTGTCATATTTTTACCTGTAATATTGTTATGGATCGATACATTTT-TTAAAGTATCGACACTT
1 TTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
* *
1131777 TTTAGGCGCTATAACTTCTTCTCTTATT-ATTTCCA-AAAGTGTCGATACTTATATTAAAGTATC
66 TTTAGGCGCTATAACTTCTTCTCTT-TTAAATT-CAGAAAGTGTCGATACTTATATTAAATTATC
1131840 GACACT
129 GACACT
1131846 GTTAATTTAC
Statistics
Matches: 460, Mismatches: 31, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
180 76 0.17
181 127 0.28
182 257 0.56
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (182 bp):
TTTTGTCATATTTTTACTTGTTATATTGTTATGGATCGATACATTTTCATAAAGTATCGACACTT
TTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGA
CACTTGCAACATATCCGGTATCGTTTTACCGGTTTTGTCATTTTGAGACCGG
Found at i:1135815 original size:198 final size:199
Alignment explanation
Indices: 1135526--1136308 Score: 1203
Period size: 199 Copynumber: 3.9 Consensus size: 199
1135516 GTAAAAAGTA
* * * * * * * *
1135526 TCGATACATTATGTATACCTATTTGCTCATAAAATCGGTATATTTAGACTGGTTACATTGTTAAT
1 TCGATACTTTTTGTACACCTGTTTTCTCA-AAAACCGGTATACTTAGACCGGTTACATTGTTAAT
* *
1135591 TTACCTATTAC-TTCATAATTATGGGTTTCGATGTTTTTGGGATCGACACGTATTATAAATGTAT
65 TTACCTAGTACATT-ATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTAT
* * *
1135655 CGACAC-ATTTAGTGCATTTGGTTTTGAAATACATTCTAGACCAAAAGTATCGACACTTGTTTTA
129 CGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTA
1135719 TTTGTG
194 TTTGTG
* *
1135725 TCGATACTTTTTGTACACCTGTTTTCTTAAAAACCGGTATACTTAGACCGGTTACATTGTTAGTT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATT
* *
1135790 TACCTAGTACATTATAATCATGGGTTTCGATGTTTTTGGGATCGACATTTATTATAAATGTATCG
66 TACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
* *
1135855 ACACTTTTTAGTGCACTTGGTTTTGAAATATATTCTGGACCAAAAGTATCGACACATGTTTTATT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
1135920 TGTG
196 TGTG
* *
1135924 TCGATACTTTTTGTACACCTGTTTTCTCAAAAGCCGGTATACTTAGACCAGTTACATTGTTAATT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATT
* *
1135989 TACCTAGTATATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTCTTATAAATGTATCG
66 TACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
1136054 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
131 ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
1136119 TGTG
196 TGTG
* ** *
1136123 TCGATACTTTTTGTACACTTGTTTTCTCAAAAATTGGTATACTTAGACCGGTTAAATTGTTAATT
1 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATT
* * *
1136188 TACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCAACACTTATTATAAATATATCG
66 TACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
* * * *
1136253 ACACTTTTTTCGTGCACTTGGTTTGGAAATACATTATGGA-CAACATGTATCGACAC
131 ACAC-TTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAA-AAGTATCGACAC
1136309 GAATGAATAA
Statistics
Matches: 536, Mismatches: 44, Indels: 7
0.91 0.07 0.01
Matches are distributed among these distances:
198 94 0.18
199 399 0.74
200 43 0.08
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (199 bp):
TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATACTTAGACCGGTTACATTGTTAATT
TACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTTATTATAAATGTATCG
ACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATT
TGTG
Found at i:1136520 original size:24 final size:24
Alignment explanation
Indices: 1136493--1136539 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1136483 ATTTACATTT
1136493 AAATTCAAACTCAAACTCAAATTG
1 AAATTCAAACTCAAACTCAAATTG
* * *
1136517 AAATTTAAATTCAAACTCTAATT
1 AAATTCAAACTCAAACTCAAATT
1136540 ATAAATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (24 bp):
AAATTCAAACTCAAACTCAAATTG
Found at i:1137173 original size:17 final size:17
Alignment explanation
Indices: 1137151--1137189 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1137141 TACCAGATTA
1137151 TGAATCATTTTTCGCGG
1 TGAATCATTTTTCGCGG
1137168 TGAATCATTTTTCGCGG
1 TGAATCATTTTTCGCGG
1137185 TGAAT
1 TGAAT
1137190 AATCGACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (17 bp):
TGAATCATTTTTCGCGG
Found at i:1137810 original size:12 final size:12
Alignment explanation
Indices: 1137793--1137836 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1137783 ACTTATTTGG
1137793 ATCATCATCGTC
1 ATCATCATCGTC
*
1137805 ATCATCATCTTC
1 ATCATCATCGTC
*
1137817 ATCTTCATCGTC
1 ATCATCATCGTC
*
1137829 ATCTTCAT
1 ATCATCAT
1137837 TGACCGCTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.23, C:0.32, G:0.05, T:0.41
Consensus pattern (12 bp):
ATCATCATCGTC
Found at i:1137812 original size:6 final size:6
Alignment explanation
Indices: 1137797--1137836 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
1137787 ATTTGGATCA
* * *
1137797 TCATCG TCATCA TCATCT TCATCT TCATCG TCATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
1137837 TGACCGCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.42
Consensus pattern (6 bp):
TCATCT
Found at i:1137824 original size:18 final size:18
Alignment explanation
Indices: 1137797--1137836 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1137787 ATTTGGATCA
1137797 TCATCGTCATCATCATCT
1 TCATCGTCATCATCATCT
* *
1137815 TCATCTTCATCGTCATCT
1 TCATCGTCATCATCATCT
1137833 TCAT
1 TCAT
1137837 TGACCGCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.33, G:0.05, T:0.42
Consensus pattern (18 bp):
TCATCGTCATCATCATCT
Found at i:1139019 original size:15 final size:15
Alignment explanation
Indices: 1138985--1139054 Score: 77
Period size: 15 Copynumber: 4.5 Consensus size: 15
1138975 GGGTGATTGT
1138985 TTGAGAAGAAGGTTGTGG
1 TTGAGAAG-AGG-TG-GG
**
1139003 TTGAGAAGAAATGGG
1 TTGAGAAGAGGTGGG
*
1139018 TTGGGAAGAGGTGGG
1 TTGAGAAGAGGTGGG
*
1139033 TTGGGAAGAGGTGGG
1 TTGAGAAGAGGTGGG
1139048 TTGAGAA
1 TTGAGAA
1139055 AAGCTTTGAG
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
15 35 0.76
16 2 0.04
17 1 0.02
18 8 0.17
ACGTcount: A:0.29, C:0.00, G:0.49, T:0.23
Consensus pattern (15 bp):
TTGAGAAGAGGTGGG
Found at i:1139747 original size:199 final size:199
Alignment explanation
Indices: 1139407--1141099 Score: 2717
Period size: 199 Copynumber: 8.5 Consensus size: 199
1139397 TTTTCAAATT
** * *
1139407 AAACTGGTATTTTTATACCAGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
1139472 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTTCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
*
1139537 CATTCTGGACCAACAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
1139602 TCAA
196 TCAA
*
1139606 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGGGTTTCGA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
1139671 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
*
1139736 CATTCTGGACCAAAAGTATCGACAATTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
1139801 T-ATA
196 TCA-A
* * * *
1139805 AAA-TCGGTATACTTAGACTGGTTAAATTGTTAATTTTCCTATTACATTATAATTATGAGTTTCG
1 AAACT-GGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCG
* * **
1139869 ATATTTTTAGGATCGACACTTATTATAAATGTATAAACACTTTTTAGTGCACTTGGTTTTGAAAT
65 ATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAAT
*
1139934 TCATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
1139999 CTCAA
195 CTCAA
* * * *
1140004 AAACCGGTATACTTAGACAGGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
1140069 TGTTTTTGGGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
** * *
1140134 CATTCTGGACCAAAAGTATAAACACTTGTTTTATTTGTGTTGATACTTTTTGTACACTTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
1140199 TCAA
196 TCAA
* ** * *
1140203 AAACTGGTATACTTAAATTGGTTACATTGTTAATTTACCTAGTACATTATAATTATGGGTTTCAA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* *
1140268 TGTTTTTGAGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGTACTTGGTATTTGAAAT
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGT-TTTGAAAT
* * *
1140333 ACATTCTGGACCAAAGGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACTCCTATTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
1140398 CTCAA
195 CTCAA
* * * *
1140403 AAA-TCAGTATACTTAGATCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGAGTTTCG
1 AAACT-GGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCG
* *
1140467 ATGTTTTTGTGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAAT
65 ATGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAAT
*
1140532 ACATTCTGGACCAAAAGTATCAACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
130 ACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTT
1140597 CTCAA
195 CTCAA
* * * * * * * *
1140602 AAACCGGTACACATAGATCGGTTAAATTGTTAATTTACCGATTATATCATAATTATGGGTTTCGA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
* * *
1140667 TATTTTTGGGATCAACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
*
1140732 CATTCTAGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
*
1140797 TTAA
196 TCAA
* * * *
1140801 AAACCGGTATACTTAGACCGGTTGCATTGTTAATTTACCTAGTACATTATAATTATTGGTTTCGA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
*
1140866 TATTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
* * *
1140931 CATTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGACACTTTTTGTACACATGTTTTC
131 CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
1140996 TCAA
196 TCAA
* * *
1141000 AAACCGGTATACTTAGACCGGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGA
1 AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
1141065 TGTTTTTGGGATCGACACTTATTATAAATGTATCG
66 TGTTTTTGGGATCGACACTTATTATAAATGTATCG
1141100 TTACATAAGT
Statistics
Matches: 1382, Mismatches: 105, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
198 2 0.00
199 1197 0.87
200 183 0.13
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (199 bp):
AAACTGGTATACTTAGACCGGTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGA
TGTTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATA
CATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTC
TCAA
Found at i:1140942 original size:797 final size:796
Alignment explanation
Indices: 1139427--1141099 Score: 2816
Period size: 797 Copynumber: 2.1 Consensus size: 796
1139417 TTTTATACCA
1139427 GTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
1139492 ATTATAAATGTATCGACACTTTTTAGTTCACTTGGTTTTGAAATACATTCTGGACCAACAGTATC
66 ATTATAAATGTATCGACACTTTTTAGTTCACTTGGTTTTGAAATACATTCTGGACCAACAGTATC
* *
1139557 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATACTTAG
131 GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACTAGTATACTTAG
*
1139622 ACCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGAC
196 ACCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGAC
1139687 ACTTATTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGAAATACATTCTGGACCAAAAG
261 ACTTATTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGAAATACATTCTGGACCAAAAG
* * *
1139752 TATCGACAATTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTATAAAATCGGTATAC
326 TATCAACAATTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTATAAAACCGGTACAC
* * * *
1139817 TTAGACTGGTTAAATTGTTAATTTTCCTATTACATTATAATTATGAGTTTCGATATTTTTAGGAT
391 ATAGACTGGTTAAATTGTTAATTTACCGATTACATCATAATTATGAGTTTCGATATTTTTAGGAT
* * *
1139882 CGACACTTATTATAAATGTATAAACACTTTTTAGTGCACTTGGTTTTGAAATTCATTCTGGACCA
456 CAACACTTATTATAAATGTATAAACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTAGACCA
1139947 AAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGT
521 AAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGT
* *
1140012 ATACTTAGACAGGTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTG
586 ATACTTAGACAGGTTAAATTGTTAATTTACCTAGTACATCATAATTATGGGTTTCGATATTTTTG
* *
1140077 GGATCGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGG
651 GGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTATGG
* * *
1140142 ACCAAAAGTATAAACACTTGTTTTATTTGTGTTGATACTTTTTGTACACTTGTTTTCTCAAAAAC
716 ACCAAAAGTATAAACACTTGTTTTATTTGTGTCGACACTTTTTGTACACATGTTTTCTCAAAAAC
* **
1140207 TGGTATACTTAAATTG
781 CGGTATACTTAAACCG
* * *
1140223 GTTACATTGTTAATTTACCTAGTACATTATAATTATGGGTTTCAATGTTTTTGAGATCGACACTT
1 GTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
1140288 ATTATAAATGTATCGACACTTTTTAGTGT-ACTTGGTATTTGAAATACATTCTGGACCAA-AGGT
66 ATTATAAATGTATCGACACTTTTTAGT-TCACTTGGT-TTTGAAATACATTCTGGACCAACA-GT
*
1140351 ATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACTCCTATTTTCTCAAAAA-TCAGTATAC
128 ATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACT-AGTATAC
* *
1140415 TTAGATCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGAGTTTCGATGTTTTTGTGAT
192 TTAGACCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGAGTTTCGATGTTTTTGGGAT
* *
1140480 CGACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTGGACCA
257 CGACACTTATTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGAAATACATTCTGGACCA
*
1140545 AAAGTATCAACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCA-AAAACCGG
322 AAAGTATCAACAATTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCT-ATAAAACCGG
* *
1140609 TACACATAGA-TCGGTTAAATTGTTAATTTACCGATTATATCATAATTATGGGTTTCGATATTTT
386 TACACATAGACT-GGTTAAATTGTTAATTTACCGATTACATCATAATTATGAGTTTCGATATTTT
* * **
1140673 TGGGATCAACACTTCTTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTCT
450 TAGGATCAACACTTATTATAAATGTATAAACACTTTTTAGTGCACTTGGTTTTGAAATACATTCT
*
1140738 AGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTTAAAA
515 AGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAA
* ** * *
1140803 ACCGGTATACTTAGACCGGTTGCATTGTTAATTTACCTAGTACATTATAATTATTGGTTTCGATA
580 ACCGGTATACTTAGACAGGTTAAATTGTTAATTTACCTAGTACATCATAATTATGGGTTTCGATA
1140868 TTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACA
645 TTTTTGGGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACA
**
1140933 TTATGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGACACTTTTTGTACACATGTTTTCTC
710 TTATGGACCAAAAGTATAAACACTTGTTTTATTTGTGTCGACACTTTTTGTACACATGTTTTCTC
*
1140998 AAAAACCGGTATACTTAGACCG
775 AAAAACCGGTATACTTAAACCG
* *
1141020 GTTAAATTGTTAATTTACCTATTACATCATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
1 GTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
1141085 ATTATAAATGTATCG
66 ATTATAAATGTATCG
1141100 TTACATAAGT
Statistics
Matches: 819, Mismatches: 52, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
796 99 0.12
797 719 0.88
798 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (796 bp):
GTTACATTGTTAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGACACTT
ATTATAAATGTATCGACACTTTTTAGTTCACTTGGTTTTGAAATACATTCTGGACCAACAGTATC
GACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTATTTTCTCAAAAACTAGTATACTTAG
ACCGGTTACATTGTTAATTTACCTAGTACATTATAATTATGAGTTTCGATGTTTTTGGGATCGAC
ACTTATTATAAATGTATCGACACTTTTTAGTGAACTTGGTTTTGAAATACATTCTGGACCAAAAG
TATCAACAATTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTATAAAACCGGTACAC
ATAGACTGGTTAAATTGTTAATTTACCGATTACATCATAATTATGAGTTTCGATATTTTTAGGAT
CAACACTTATTATAAATGTATAAACACTTTTTAGTGCACTTGGTTTTGAAATACATTCTAGACCA
AAAGTATCGACACTTGTTTTATTTGTGTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGT
ATACTTAGACAGGTTAAATTGTTAATTTACCTAGTACATCATAATTATGGGTTTCGATATTTTTG
GGATCGACACTTATTATAAATGTATCGACACTTTTTAGTGCACTTGGTTTTGAAATACATTATGG
ACCAAAAGTATAAACACTTGTTTTATTTGTGTCGACACTTTTTGTACACATGTTTTCTCAAAAAC
CGGTATACTTAAACCG
Found at i:1141503 original size:19 final size:19
Alignment explanation
Indices: 1141479--1141524 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1141469 ATTCACATAT
*
1141479 AAAATTATAAATCGTATAC
1 AAAATTAAAAATCGTATAC
*
1141498 AAAATTAAAAATCTTATAC
1 AAAATTAAAAATCGTATAC
1141517 AAAATTAA
1 AAAATTAA
1141525 CCATACATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATTAAAAATCGTATAC
Found at i:1142978 original size:21 final size:18
Alignment explanation
Indices: 1142940--1142978 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
1142930 TTCTCCCCAT
1142940 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
1142958 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
1142976 TTC
1 TTC
1142979 AAATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:1143645 original size:22 final size:21
Alignment explanation
Indices: 1143617--1143673 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 21
1143607 AACCTGTATT
*
1143617 TATAATAAAAGTTATCATTTTA
1 TATAATAAAA-CTATCATTTTA
1143639 TATAATAATTATACTATCATTTTA
1 TATAATAA--A-ACTATCATTTTA
*
1143663 TATAAAAAAAC
1 TATAATAAAAC
1143674 AAAAACATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
21 2 0.07
22 9 0.30
24 18 0.60
25 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (21 bp):
TATAATAAAACTATCATTTTA
Found at i:1144984 original size:20 final size:19
Alignment explanation
Indices: 1144929--1145016 Score: 131
Period size: 19 Copynumber: 4.6 Consensus size: 19
1144919 CATTTATACA
* *
1144929 ACCTAAAATATCATTTTCT
1 ACCTATAATATCATTTTTT
1144948 ACCTATAATATCATTTTTT
1 ACCTATAATATCATTTTTT
1144967 ACCTATAATATCATTTTTT
1 ACCTATAATATCATTTTTT
*
1144986 ACATATAATATCATTTTTTT
1 ACCTATAATATCA-TTTTTT
*
1145006 ACATATAATAT
1 ACCTATAATAT
1145017 TAAATAAAAG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
19 48 0.74
20 17 0.26
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.49
Consensus pattern (19 bp):
ACCTATAATATCATTTTTT
Found at i:1145896 original size:181 final size:179
Alignment explanation
Indices: 1145404--1146193 Score: 1007
Period size: 181 Copynumber: 4.3 Consensus size: 179
1145394 TACACGTACT
* ** * * *
1145404 TATTAAATTATCGACACTTTCAATATATTTGGTATCATTTTACCGGTTTTATCATTTTTTAGACC
1 TATTAAATTATCGACACTTTCAACATA-TCAGTAGCGTTTTACCGGTTTTGTCA-TTTTTAGACC
* * * * *
1145469 TGTTTTGTCCTATTTTTACCTGTTATATTATTATGGATCGATATATTTTTTTAAAGTATCGACAC
64 GGTTTTGTCATA-TTTTAGCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
* *
1145534 TTTATAGGCGCTATAACTTCTTCTCTTTTAAACTTCAAAAGTCTCTATACTTA
128 TTTATAGGCGCTATAACTTCTTCTCTTTTAAA-TTCAAAAGTGTCGATACTTA
* * * * *
1145587 TAATAAAGTATCGACACTTTCAACATATCATGTAG-TTATTTACCTGTTTTGTCATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATATCA-GTAGCGT-TTTACCGGTTTTGTCATTTTTAGACC
** *
1145651 GGTTTTGTCATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
64 GGTTTTGTCATATTTTA-GCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
*
1145716 GTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATATTTA
128 -TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCA-AAAGTGTCGATACTTA
* * *
1145769 TATTAAATTATTGATACTTTCAACATATCAGTAGCGTTTTACCGGTTTTGTCATTTTTAGACCGA
1 TATTAAATTATCGACACTTTCAACATATCAGTAGCGTTTTACCGGTTTTGTCATTTTTAGACCGG
*
1145834 TTTTGTCCTATTTTTA-CATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
66 TTTTGTCATA-TTTTAGC-TGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
* * *
1145898 TTGTAGGTGCTATAACTTCTTCTATTTTAAATTCCAAAAGTGTCGATACTTA
129 TTATAGGCGCTATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTA
* * * *
1145950 TATTAAAGTATCGACACTTTCAACATATCCAGTAG-TTATTTACCTGTTTTGTCATTTTGAGACC
1 TATTAAATTATCGACACTTTCAACATAT-CAGTAGCGT-TTTACCGGTTTTGTCATTTTTAGACC
* * *
1146014 GGTTTTGTCATATTTTAGGCTGTTATACTGTTATAGATCGATACA-TTTTTTAAAGTGTCGACAC
64 GGTTTTGTCATATTTTA-GCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACAC
*
1146078 GTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTA
128 -TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCA-AAAGTGTCGATACTTA
* * * *
1146131 TATTAAATTATCGACACTTTCAATATATCCGGTATCGTTTTACAGGTTTTGTCATTTTTAGAC
1 TATTAAATTATCGACACTTTCAACATAT-CAGTAGCGTTTTACCGGTTTTGTCATTTTTAGAC
1146194 TTGTTTTTAA
Statistics
Matches: 532, Mismatches: 58, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
180 6 0.01
181 277 0.52
182 204 0.38
183 45 0.08
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (179 bp):
TATTAAATTATCGACACTTTCAACATATCAGTAGCGTTTTACCGGTTTTGTCATTTTTAGACCGG
TTTTGTCATATTTTAGCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACTTT
ATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTA
Found at i:1146172 original size:363 final size:363
Alignment explanation
Indices: 1145404--1146200 Score: 1296
Period size: 363 Copynumber: 2.2 Consensus size: 363
1145394 TACACGTACT
* * *
1145404 TATTAAATTATCGACACTTTCAATATATTTGGTATCATTTTACCGGTTTTATCATTTTTTAGACC
1 TATTAAATTATCGACACTTTCAATATA-TCGGTATCGTTTTACCGGTTTTGTCA-TTTTTAGACC
* *
1145469 TGTTTTGTCCTATTTTTACCTGTTATATTATTATGGATCGATATATTTTTTTAAAGTATCGACAC
64 TGTTTTGTCCTATTTTTACATGTTATATTATTATGGATCGATACATTTTTTTAAAGTATCGACAC
* *
1145534 TTTATAGGCGCTATAACTTCTTCTCTTTTAAACTTCAAAAGTCTCTATACTTATAATAAAGTATC
129 TTTATAGGCGCTATAACTTCTTCTATTTTAAACTTCAAAAGTCTCGATACTTATAATAAAGTATC
1145599 GACACTTTCAACATATCATGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATAT
194 GACACTTTCAACATATCATGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATAT
* *
1145664 TTTAGGCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACGTTTTAGGCGCTA
259 TTTAGGCTGTTATACTGTTATAGATCGATACATTTTCATAAAGTGTCGACACGTTTTAGGCGCTA
* *
1145729 TAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATATTTA
324 TAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTA
* * * * *
1145769 TATTAAATTATTGATACTTTCAACATATCAGTAGCGTTTTACCGGTTTTGTCATTTTTAGACC-G
1 TATTAAATTATCGACACTTTCAATATATCGGTATCGTTTTACCGGTTTTGTCATTTTTAGACCTG
*
1145833 ATTTTGTCCTATTTTTACATGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCGACACT
66 -TTTTGTCCTATTTTTACATGTTATATTATTATGGATCGATACATTTTTTTAAAGTATCGACACT
* * * *
1145898 TTGTAGGTGCTATAACTTCTTCTATTTTAAA-TTCCAAAAGTGTCGATACTTATATTAAAGTATC
130 TTATAGGCGCTATAACTTCTTCTATTTTAAACTT-CAAAAGTCTCGATACTTATAATAAAGTATC
1145962 GACACTTTCAACATATCCA-GTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATA
194 GACACTTTCAACATAT-CATGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATA
*
1146026 TTTTAGGCTGTTATACTGTTATAGATCGATACATTTT-TTAAAGTGTCGACACGTTTTAGGCGCT
258 TTTTAGGCTGTTATACTGTTATAGATCGATACATTTTCATAAAGTGTCGACACGTTTTAGGCGCT
1146090 ATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTA
323 ATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTA
* *
1146131 TATTAAATTATCGACACTTTCAATATATCCGGTATCGTTTTACAGGTTTTGTCATTTTTAGACTT
1 TATTAAATTATCGACACTTTCAATATAT-CGGTATCGTTTTACCGGTTTTGTCATTTTTAGACCT
1146196 GTTTT
65 GTTTT
1146201 TAAAGTATCG
Statistics
Matches: 398, Mismatches: 29, Indels: 12
0.91 0.07 0.03
Matches are distributed among these distances:
362 93 0.23
363 257 0.65
364 24 0.06
365 24 0.06
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (363 bp):
TATTAAATTATCGACACTTTCAATATATCGGTATCGTTTTACCGGTTTTGTCATTTTTAGACCTG
TTTTGTCCTATTTTTACATGTTATATTATTATGGATCGATACATTTTTTTAAAGTATCGACACTT
TATAGGCGCTATAACTTCTTCTATTTTAAACTTCAAAAGTCTCGATACTTATAATAAAGTATCGA
CACTTTCAACATATCATGTAGTTATTTACCTGTTTTGTCATTTTGAGACCGGTTTTGTCATATTT
TAGGCTGTTATACTGTTATAGATCGATACATTTTCATAAAGTGTCGACACGTTTTAGGCGCTATA
ACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTA
Found at i:1146310 original size:137 final size:136
Alignment explanation
Indices: 1146060--1146330 Score: 395
Period size: 137 Copynumber: 2.0 Consensus size: 136
1146050 ATCGATACAT
*
1146060 TTTTTAAAGTGTCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAA
1 TTTTTAAAGTATCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAA
* * * * *
1146125 TACTTATATTAAATTATCGACACTTTCAATATATCCGGTATCGTTTTACAGGTTTTGTCATTTTT
66 TACTTATATTAAAGTATCGACACTTTCAACATATCCGATATC-TTTTACAGCTTTTGTCATTTTG
1146190 AGACTTG
130 AGACTTG
1146197 TTTTTAAAGTATCGACAC-TTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTC
1 TTTTTAAAGTATCGACACGTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTC
* **
1146260 GATACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGT-TATTTACCTCTTTTGTCATT
64 AATACTTATATTAAAGTATCGACACTTTCAACATATCCGATA-TCT-TTTACAGCTTTTGTCATT
1146324 TTGAGAC
127 TTGAGAC
1146331 CGGTTTTGTC
Statistics
Matches: 121, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
136 4 0.03
137 114 0.94
138 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (136 bp):
TTTTTAAAGTATCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAA
TACTTATATTAAAGTATCGACACTTTCAACATATCCGATATCTTTTACAGCTTTTGTCATTTTGA
GACTTG
Found at i:1146738 original size:183 final size:183
Alignment explanation
Indices: 1146197--1146930 Score: 1015
Period size: 182 Copynumber: 4.0 Consensus size: 183
1146187 TTTAGACTTG
1146197 TTTTTAAAGTATCGACAC-TTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCA-AAAGTGTC
1 TTTTTAAAGTATCGACACGTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGTC
* *
1146260 GATACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGTTATTTACCTCTTTTGTCA-TT
64 GATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTT
* * *
1146324 TTGAGACCGGTTTTGTCATA-TTTTAGGTTGTTGTATTGTTATGGATCGATACATT
129 TTGAGACCTGTTTTGTCATATTTTTA-GCTGTTATATTGTTATGGATCGATACATT
* *
1146379 TTTTTAAAGTGTCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAA
1 TTTTTAAAGTATCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGA
* * *
1146444 TACTTATATTAAATTATCGACACTTTCAATATATCCGGTA-TCGT-TTTACCGGTTTTGTCATTT
66 TACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGT--TATTTACCTGTTTTGTCATTT
* * *
1146507 TTTAGACCTGTTTTATCCTATTTTTA-CATGTTATATTGTTATGGATCGATACATT
129 TTGAGACCTGTTTTGTCATATTTTTAGC-TGTTATATTGTTATGGATCGATACATT
* *
1146562 TTTTTAAAAGTATCGATAC-TTTATAGGCGCTATAAATTCTTCTCTTTTAAATTCCA-AAAGTGT
1 TTTTT-AAAGTATCGACACGTTT-TAGGCGCTATAACTTCTTCTCTTTTAAATT-CAGAAAGTGT
* *
1146625 CGATACTTATATCAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACATGTTTTGTCA-T
63 CGATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATT
1146689 TTTGAGACC-GATTTTGTCATA-TTTTAGGCTGTTATATTGTTATGGATCGATACATT
128 TTTGAGACCTG-TTTTGTCATATTTTTA-GCTGTTATATTGTTATGGATCGATACATT
*** *
1146745 TGCATAAAGTGTCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGA
1 TTTTTAAAGTATCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGA
* ** ** *
1146810 TACTTATATTAAATTATCGACACTTTCAACATATTTGGTAGCAATTGACCTGTTTTGTCATTTTT
66 TACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTT
* * *
1146875 TAGACCTGTTTTGTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATT
131 GAGACCTGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATT
1146928 TTT
1 TTT
1146931 CATTTGTATC
Statistics
Matches: 488, Mismatches: 44, Indels: 39
0.85 0.08 0.07
Matches are distributed among these distances:
181 5 0.01
182 215 0.44
183 153 0.31
184 112 0.23
185 3 0.01
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (183 bp):
TTTTTAAAGTATCGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGA
TACTTATATTAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACCTGTTTTGTCATTTTT
GAGACCTGTTTTGTCATATTTTTAGCTGTTATATTGTTATGGATCGATACATT
Found at i:1146874 original size:366 final size:365
Alignment explanation
Indices: 1146197--1146930 Score: 1243
Period size: 366 Copynumber: 2.0 Consensus size: 365
1146187 TTTAGACTTG
* *
1146197 TTTTTAAAGTATCGACACTTTGTAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGA
1 TTTTTAAAGTATCGACACTTTATAGGCGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCGA
* *
1146262 TACTTATATTAAAGTATCGACACTTTCAACATATCCGATAGTTATTTACCTCTTTTGTCATTTTG
66 TACTTATATCAAAGTATCGACACTTTCAACATATCCGATAGTTATTTACATCTTTTGTCATTTTG
* * * ***
1146327 AGACCGGTTTTGTCATATTTTAGGTTGTTGTATTGTTATGGATCGATACATTTTTTTAAAGTGTC
131 AGACCGATTTTGTCATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTC
1146392 GACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTATATTAAA
196 GACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTATATTAAA
* * ** *
1146457 TTATCGACACTTTCAATATATCCGGTATCGTTTTACCGGTTTTGTCATTTTTTAGACCTGTTTTA
261 TTATCGACACTTTCAACATATCCGGTAGCAATTGACCGGTTTTGTCATTTTTTAGACCTGTTTTA
1146522 TCCTATTTTTACATGTTATATTGTTATGGATCGATACATT
326 TCCTATTTTTACATGTTATATTGTTATGGATCGATACATT
*
1146562 TTTTTAAAAGTATCGATACTTTATAGGCGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCG
1 TTTTT-AAAGTATCGACACTTTATAGGCGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCG
* *
1146627 ATACTTATATCAAAGTATCGACACTTTCAACATATCCGGTAGTTATTTACATGTTTTGTCATTTT
65 ATACTTATATCAAAGTATCGACACTTTCAACATATCCGATAGTTATTTACATCTTTTGTCATTTT
1146692 GAGACCGATTTTGTCATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGT
130 GAGACCGATTTTGTCATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGT
*
1146757 CGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAA
195 CGACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTATATTAA
** *
1146822 ATTATCGACACTTTCAACATATTTGGTAGCAATTGACCTGTTTTGTCATTTTTTAGACCTGTTTT
260 ATTATCGACACTTTCAACATATCCGGTAGCAATTGACCGGTTTTGTCATTTTTTAGACCTGTTTT
* *
1146887 GTCCTATTTTTACCTGTTATATTGTTATGGATCGATACATT
325 ATCCTATTTTTACATGTTATATTGTTATGGATCGATACATT
1146928 TTT
1 TTT
1146931 CATTTGTATC
Statistics
Matches: 344, Mismatches: 24, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
365 5 0.01
366 339 0.99
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (365 bp):
TTTTTAAAGTATCGACACTTTATAGGCGCTATAAATTCTTCTCTTTTAAATTCCAAAAGTGTCGA
TACTTATATCAAAGTATCGACACTTTCAACATATCCGATAGTTATTTACATCTTTTGTCATTTTG
AGACCGATTTTGTCATATTTTAGGCTGTTATATTGTTATGGATCGATACATTTGCATAAAGTGTC
GACACGTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTGTCAATACTTATATTAAA
TTATCGACACTTTCAACATATCCGGTAGCAATTGACCGGTTTTGTCATTTTTTAGACCTGTTTTA
TCCTATTTTTACATGTTATATTGTTATGGATCGATACATT
Found at i:1146880 original size:21 final size:22
Alignment explanation
Indices: 1146856--1146898 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1146846 GGTAGCAATT
1146856 GACCTGTTTTGTCAT-TTTTTA
1 GACCTGTTTTGTCATATTTTTA
*
1146877 GACCTGTTTTGTCCTATTTTTA
1 GACCTGTTTTGTCATATTTTTA
1146899 CCTGTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.56
Consensus pattern (22 bp):
GACCTGTTTTGTCATATTTTTA
Found at i:1146903 original size:20 final size:20
Alignment explanation
Indices: 1146857--1146904 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1146847 GTAGCAATTG
1146857 ACCTGTTTTGTCATTTTTTA
1 ACCTGTTTTGTCATTTTTTA
*
1146877 GACCTGTTTTGTCCTATTTTT-
1 -ACCTGTTTTGTCAT-TTTTTA
1146898 ACCTGTT
1 ACCTGTT
1146905 ATATTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 13 0.52
22 5 0.20
ACGTcount: A:0.12, C:0.19, G:0.12, T:0.56
Consensus pattern (20 bp):
ACCTGTTTTGTCATTTTTTA
Found at i:1149373 original size:16 final size:16
Alignment explanation
Indices: 1149330--1149373 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
1149320 TAATAAATAA
1149330 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
1149346 ACGTACAGAAACGAAC
1 ACGAACATAAACGAAC
1149362 ACGAACATAAAC
1 ACGAACATAAAC
1149374 AAACGAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.55, C:0.25, G:0.14, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1151382 original size:29 final size:29
Alignment explanation
Indices: 1151349--1151433 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
1151339 AGCAGGGGAT
* * **
1151349 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
1151378 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
1151407 GTCGCTGGGAGTGCATGGCGACCTACG
1 GTCGCCGGGAGTGCATGGCGACCTACG
1151434 GCCACTGTTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:1155047 original size:23 final size:23
Alignment explanation
Indices: 1155018--1155096 Score: 113
Period size: 23 Copynumber: 3.4 Consensus size: 23
1155008 GTGTTTGTGT
*
1155018 TGTTCGTTTATGTTCATTTATTG
1 TGTTCGTTTATGTTCATTTATTA
1155041 TGTTCGTTTATGTTCATTTATTA
1 TGTTCGTTTATGTTCATTTATTA
* * *
1155064 TGTTCGTTTATTTTCGTTTATTT
1 TGTTCGTTTATGTTCATTTATTA
1155087 TCGTTCGTTT
1 T-GTTCGTTT
1155097 GCGTTCGTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
23 43 0.84
24 8 0.16
ACGTcount: A:0.11, C:0.10, G:0.15, T:0.63
Consensus pattern (23 bp):
TGTTCGTTTATGTTCATTTATTA
Found at i:1155112 original size:10 final size:10
Alignment explanation
Indices: 1155018--1155091 Score: 58
Period size: 10 Copynumber: 6.8 Consensus size: 10
1155008 GTGTTTGTGT
1155018 TGTTCGTTTA
1 TGTTCGTTTA
*
1155028 TGTTCATTTA
1 TGTTCGTTTA
1155038 TTGTGTTCGTTTA
1 ---TGTTCGTTTA
*
1155051 TGTTCATTTATTA
1 TGTTC--GT-TTA
1155064 TGTTCGTTTA
1 TGTTCGTTTA
*
1155074 TTTTCGTTTA
1 TGTTCGTTTA
*
1155084 TTTTCGTT
1 TGTTCGTT
1155092 CGTTTGCGTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
10 34 0.64
11 1 0.02
12 1 0.02
13 17 0.32
ACGTcount: A:0.12, C:0.09, G:0.15, T:0.64
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:1163846 original size:2 final size:2
Alignment explanation
Indices: 1163839--1163886 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1163829 ATTTTATGAA
1163839 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1163881 AT AT AT
1 AT AT AT
1163887 TTGTTGTTGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1164727 original size:39 final size:38
Alignment explanation
Indices: 1164616--1164730 Score: 119
Period size: 37 Copynumber: 3.0 Consensus size: 38
1164606 TTTTTATTTA
* * * *
1164616 TAATTT-TCAAATTATTTCACGCTAACATTCTGAATTCT
1 TAATTTCTTAAATTATTTCAC-ATAACATTCTAAATTAT
* * *
1164654 GAATTTCTTAAA-T-TGTCACCATAACATTTTAAATTAT
1 TAATTTCTTAAATTATTTCA-CATAACATTCTAAATTAT
1164691 TAATTTCTTAAATTATTTCACATTAACATTCTAAATTAT
1 TAATTTCTTAAATTATTTCACA-TAACATTCTAAATTAT
1164730 T
1 T
1164731 TTTAAAATAT
Statistics
Matches: 62, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
37 28 0.45
38 10 0.16
39 24 0.39
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (38 bp):
TAATTTCTTAAATTATTTCACATAACATTCTAAATTAT
Found at i:1164891 original size:2 final size:2
Alignment explanation
Indices: 1164884--1164918 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1164874 TTTTAGAATT
1164884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1164919 TAAAAATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1173677 original size:21 final size:21
Alignment explanation
Indices: 1173648--1173691 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1173638 TTAATAAAAA
* * *
1173648 TTATTTAAAATATTATTATTT
1 TTATCTAAAATATCAATATTT
1173669 TTATCTAAAATATCAATATTT
1 TTATCTAAAATATCAATATTT
1173690 TT
1 TT
1173692 TAATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATCTAAAATATCAATATTT
Found at i:1173772 original size:15 final size:15
Alignment explanation
Indices: 1173737--1173775 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
1173727 TAATAGAAAA
*
1173737 AATAACAATATCAAT
1 AATAATAATATCAAT
*
1173752 AATAATAATATTAAT
1 AATAATAATATCAAT
1173767 AATAATAAT
1 AATAATAAT
1173776 CTTTTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAATAATATCAAT
Done.