Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000251.1 Hibiscus syriacus cultivar Beakdansim tig00000453_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: 648719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:485463 original size:25 final size:23
Alignment explanation
Indices: 485432--485487 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
485422 TTGAACCTGA
485432 ATAATATAATATAAGTAATATAAAT
1 ATAATATAATAT-AGTAA-ATAAAT
* *
485457 ATAATATAATATATTAAATTAAT
1 ATAATATAATATAGTAAATAAAT
485480 ATAATATA
1 ATAATATA
485488 TACGATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 13 0.45
24 4 0.14
25 12 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
ATAATATAATATAGTAAATAAAT
Found at i:485479 original size:18 final size:20
Alignment explanation
Indices: 485434--485489 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
485424 GAACCTGAAT
485434 AATATAATATAAGTA-ATATA
1 AATATAATATAA-TATATATA
485454 AATATAATATAATATAT-TA
1 AATATAATATAATATATATA
485473 AAT-TAATATAATATATA
1 AATATAATATAATATATA
485490 CGATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 13 0.38
19 7 0.21
20 14 0.41
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
AATATAATATAATATATATA
Found at i:485671 original size:16 final size:16
Alignment explanation
Indices: 485640--485672 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
485630 TATACATTTT
485640 TAAAAGACTATATATA
1 TAAAAGACTATATATA
485656 TAAAA-ACTATAT-TA
1 TAAAAGACTATATATA
485670 TAA
1 TAA
485673 TATGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 7 0.41
16 5 0.29
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (16 bp):
TAAAAGACTATATATA
Found at i:487176 original size:30 final size:28
Alignment explanation
Indices: 487126--487181 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
487116 ATTTCTTAAA
487126 ATTTTTTTCTAATATATATAATTAATATT
1 ATTTTTTTCTAATATATATAA-TAATATT
* *
487155 ATTTTTATTTTAATTTATATAATAATA
1 ATTTTT-TTCTAATATATATAATAATA
487182 AAATTATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.46
30 13 0.54
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTTTTTCTAATATATATAATAATATT
Found at i:487188 original size:32 final size:29
Alignment explanation
Indices: 487126--487188 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
487116 ATTTCTTAAA
*
487126 ATTTTTTTCTAATATATATAATTAATATT
1 ATTTTTTTCTAATATATATAATTAAAATT
* *
487155 ATTTTTATTTTAATTTATATAATAATAAAATT
1 ATTTTT-TTCTAATATATATAAT--TAAAATT
487187 AT
1 AT
487189 AATTTATATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 14 0.50
32 8 0.29
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
ATTTTTTTCTAATATATATAATTAAAATT
Found at i:487989 original size:17 final size:19
Alignment explanation
Indices: 487939--487979 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
487929 TCAATTTAAA
*
487939 ATATAA-TAAAATAAAAAT
1 ATATAATTACAATAAAAAT
487957 ATATAATTACAATAAAAAT
1 ATATAATTACAATAAAAAT
487976 ATAT
1 ATAT
487980 TTTATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (19 bp):
ATATAATTACAATAAAAAT
Found at i:488052 original size:19 final size:20
Alignment explanation
Indices: 488007--488053 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
487997 TTTTATTTAC
488007 TTTTAAGTAATTAAAATAAAT
1 TTTTAAGTAA-TAAAATAAAT
* * *
488028 TATTAAGTAA-AAAATTATT
1 TTTTAAGTAATAAAATAAAT
488047 TTTTAAG
1 TTTTAAG
488054 GATGTTAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (20 bp):
TTTTAAGTAATAAAATAAAT
Found at i:490440 original size:20 final size:20
Alignment explanation
Indices: 490404--490441 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
490394 ATCATATTCC
**
490404 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
490424 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
490442 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:491011 original size:16 final size:16
Alignment explanation
Indices: 490990--491024 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
490980 AACCAAACAA
490990 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
491006 ATAAACTAACACGAAC
1 ATAAACGAACACGAAC
491022 ATA
1 ATA
491025 TTCTTGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.57, C:0.23, G:0.09, T:0.11
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:491127 original size:14 final size:14
Alignment explanation
Indices: 491097--491169 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
491087 TTAAATGATA
* *
491097 AACGAACACAAATG
1 AACGAACATAAACG
491111 AACGAACATAAACG
1 AACGAACATAAACG
* **
491125 AACTAATGTAAACG
1 AACGAACATAAACG
491139 AAC--ACAATAAACG
1 AACGAAC-ATAAACG
* * *
491152 AACAAAAATGAACG
1 AACGAACATAAACG
491166 AACG
1 AACG
491170 TAAACGAACA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
12 1 0.02
13 9 0.20
14 35 0.76
15 1 0.02
ACGTcount: A:0.58, C:0.19, G:0.14, T:0.10
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:491173 original size:37 final size:37
Alignment explanation
Indices: 491095--491201 Score: 151
Period size: 37 Copynumber: 2.9 Consensus size: 37
491085 ATTTAAATGA
* * * *
491095 TAAACGAACACAAATGAACGAACATAAACGAACTAATG
1 TAAACGAACAC-AATAAACGAACATAAATGAACGAACG
*
491133 TAAACGAACACAATAAACGAACAAAAATGAACGAACG
1 TAAACGAACACAATAAACGAACATAAATGAACGAACG
*
491170 TAAACGAACACAATAAATGAACATAAATGAAC
1 TAAACGAACACAATAAACGAACATAAATGAAC
491202 ATAAACGAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
37 51 0.82
38 11 0.18
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.12
Consensus pattern (37 bp):
TAAACGAACACAATAAACGAACATAAATGAACGAACG
Found at i:491195 original size:10 final size:10
Alignment explanation
Indices: 491182--491227 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
491172 AACGAACACA
491182 ATAAATGAAC
1 ATAAATGAAC
491192 ATAAATGAAC
1 ATAAATGAAC
*
491202 ATAAACGAAC
1 ATAAATGAAC
*
491212 ATAAATGAAA
1 ATAAATGAAC
491222 ATAAAT
1 ATAAAT
491228 TTTTTCTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.20
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:491408 original size:14 final size:14
Alignment explanation
Indices: 491402--491488 Score: 111
Period size: 14 Copynumber: 6.2 Consensus size: 14
491392 AACGCACATA
* *
491402 AACGAACACAAATG
1 AACGAACATAAACG
* *
491416 AACAAATATAAACG
1 AACGAACATAAACG
491430 AACGAACATAAACG
1 AACGAACATAAACG
*
491444 AACGAATATAAACG
1 AACGAACATAAACG
* *
491458 AACGAATATAAATG
1 AACGAACATAAACG
491472 AACGAACATAAACG
1 AACGAACATAAACG
491486 AAC
1 AAC
491489 ATATTACTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 63 1.00
ACGTcount: A:0.59, C:0.17, G:0.13, T:0.11
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:491414 original size:28 final size:27
Alignment explanation
Indices: 491383--491488 Score: 119
Period size: 28 Copynumber: 4.0 Consensus size: 27
491373 ATTGAGCTAA
*
491383 AAATAAATGAACGCACATAAACGAAC-
1 AAATAAATGAACGAACATAAACGAACG
* * *
491409 --ACAAATGAACAAATATAAACGAACG
1 AAATAAATGAACGAACATAAACGAACG
* *
491434 AACATAAACGAACGAATATAAACGAACG
1 AA-ATAAATGAACGAACATAAACGAACG
491462 AATATAAATGAACGAACATAAACGAAC
1 AA-ATAAATGAACGAACATAAACGAAC
491489 ATATTACTGA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
24 20 0.30
28 46 0.70
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.12
Consensus pattern (27 bp):
AAATAAATGAACGAACATAAACGAACG
Found at i:493656 original size:32 final size:32
Alignment explanation
Indices: 493569--493656 Score: 74
Period size: 32 Copynumber: 2.8 Consensus size: 32
493559 TATCATACTT
* * *
493569 AAAAAAACCCGACCCGA-ACTC-AAATTTTTTA
1 AAAAAAATCCGACCCTATAC-CAAAAATTTTTA
* *
493600 AAAAGAATCCGACCCTATCCCAAAAATTTTTA
1 AAAAAAATCCGACCCTATACCAAAAATTTTTA
* *
493632 AAAAAAAT-TGACCCTAATAGCAAAA
1 AAAAAAATCCGACCCT-ATACCAAAA
493657 GATTGATGAG
Statistics
Matches: 45, Mismatches: 9, Indels: 5
0.76 0.15 0.08
Matches are distributed among these distances:
31 21 0.47
32 24 0.53
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.22
Consensus pattern (32 bp):
AAAAAAATCCGACCCTATACCAAAAATTTTTA
Found at i:500960 original size:20 final size:20
Alignment explanation
Indices: 500937--500979 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
500927 GTTTCCAAAT
500937 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
*
500957 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATATGTAAA
500977 TCG
1 TCG
500980 AAACACTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:500992 original size:21 final size:20
Alignment explanation
Indices: 500945--500992 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
500935 ATTCGCAACG
* * *
500945 CGAATATGTAAATCGCAACG
1 CGAATTTGTAAATCGAAACA
500965 CGAATTTGTAAATCGAAACA
1 CGAATTTGTAAATCGAAACA
500985 CTGAATTT
1 C-GAATTT
500993 CAAATTCGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (20 bp):
CGAATTTGTAAATCGAAACA
Found at i:501063 original size:20 final size:20
Alignment explanation
Indices: 500995--501064 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
500985 CTGAATTTCA
*
500995 AATTCGCAACTCGATTTCTG
1 AATTCGCAACTCGATTTTTG
* * *
501015 AATTCACAA-TGTGAATTTTG
1 AATTCGCAACT-CGATTTTTG
* *
501035 -TTGTAGCAACTCGATTTTTG
1 AAT-TCGCAACTCGATTTTTG
501055 AATTCGCAAC
1 AATTCGCAAC
501065 AAGAATTTTA
Statistics
Matches: 35, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
19 2 0.06
20 31 0.89
21 2 0.06
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (20 bp):
AATTCGCAACTCGATTTTTG
Found at i:501084 original size:40 final size:40
Alignment explanation
Indices: 500987--501084 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 40
500977 TCGAAACACT
* * ***
500987 GAATTTCAAATTCGCAACTCGATTTCTGAATTCACAATGT
1 GAATTTTAATTTCGCAACTCGATTTCTGAATTCACAACAA
* * * *
501027 GAATTTT-GTTGTAGCAACTCGATTTTTGAATTCGCAACAA
1 GAATTTTAATT-TCGCAACTCGATTTCTGAATTCACAACAA
501067 GAATTTTAATTTCGCAAC
1 GAATTTTAATTTCGCAAC
501085 AGGTTTTAGT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
39 1 0.02
40 42 0.93
41 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (40 bp):
GAATTTTAATTTCGCAACTCGATTTCTGAATTCACAACAA
Found at i:502046 original size:24 final size:24
Alignment explanation
Indices: 502019--502072 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
502009 GTATTTGAAA
502019 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
502043 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
502067 TTTGAT
1 TTTGAT
502073 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:502268 original size:15 final size:16
Alignment explanation
Indices: 502247--502286 Score: 73
Period size: 15 Copynumber: 2.6 Consensus size: 16
502237 TTATAATCCT
502247 AAAGAAGAAAAAAAAG
1 AAAGAAGAAAAAAAAG
502263 -AAGAAGAAAAAAAAG
1 AAAGAAGAAAAAAAAG
502278 AAAGAAGAA
1 AAAGAAGAA
502287 GAAGTCACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAGAAGAAAAAAAAG
Found at i:502281 original size:19 final size:18
Alignment explanation
Indices: 502248--502289 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
502238 TATAATCCTA
*
502248 AAGAAGAAAAAAAAGAAG
1 AAGAAAAAAAAAAAGAAG
502266 AAGAAAAAAAAGAAAGAAG
1 AAGAAAAAAAA-AAAGAAG
502285 AAGAA
1 AAGAA
502290 GTCACCGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAAAAAAGAAG
Found at i:504617 original size:62 final size:63
Alignment explanation
Indices: 504493--504628 Score: 177
Period size: 62 Copynumber: 2.2 Consensus size: 63
504483 ATTTAAAACA
* *
504493 ACAAATCAACTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAATAAATCAACTTTT
1 ACAAATCAACTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAACAAAACAAC-TTT
* *** * *
504557 ACAAATCAATTAAACAAGC-AAAAA-AATTCTTATTTCCTCATCAATTAAACAAAACAACTTT
1 ACAAATCAACTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAACAAAACAACTTT
504618 ACAAATCAACT
1 ACAAATCAACT
504629 TTTACAAATA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 13 0.21
62 27 0.43
63 5 0.08
64 18 0.29
ACGTcount: A:0.53, C:0.18, G:0.02, T:0.26
Consensus pattern (63 bp):
ACAAATCAACTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTAAACAAAACAACTTT
Found at i:504627 original size:13 final size:14
Alignment explanation
Indices: 504605--504637 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
504595 CATCAATTAA
*
504605 ACAAAACAAC-TTT
1 ACAAATCAACTTTT
504618 ACAAATCAACTTTT
1 ACAAATCAACTTTT
504632 ACAAAT
1 ACAAAT
504638 ACATCAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:505975 original size:21 final size:21
Alignment explanation
Indices: 505951--506038 Score: 72
Period size: 21 Copynumber: 4.2 Consensus size: 21
505941 CAGATTCTCT
505951 AACGGTGAGAGGGACCTCTTG
1 AACGGTGAGAGGGACCTCTTG
* * *
505972 AACGATAACAAGGG-CCTCTTG
1 AACGGTGA-GAGGGACCTCTTG
* *
505993 AACGGTGGGAGGGGCCTCTTG
1 AACGGTGAGAGGGACCTCTTG
* * *
506014 AA-GGATGATAGAGACTTCTTG
1 AACGG-TGAGAGGGACCTCTTG
506035 AACG
1 AACG
506039 ATAGGAGAGT
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
20 6 0.12
21 40 0.78
22 5 0.10
ACGTcount: A:0.27, C:0.18, G:0.34, T:0.20
Consensus pattern (21 bp):
AACGGTGAGAGGGACCTCTTG
Found at i:506445 original size:21 final size:22
Alignment explanation
Indices: 506358--506448 Score: 59
Period size: 21 Copynumber: 4.3 Consensus size: 22
506348 GTAGAGCGGC
* * *
506358 TACCTCAACACGTAAAGTA-GA
1 TACCTCACCACGTAAAGCACCA
506379 TACCTCACCACGTAAAGCACC-
1 TACCTCACCACGTAAAGCACCA
* * * *
506400 -ACTGTCATCGCGTAAA--ACCTC
1 TAC-CTCACCACGTAAAGCACC-A
506421 TACCTCACCACGTAAAG-ACCA
1 TACCTCACCACGTAAAGCACCA
506442 TACCTCA
1 TACCTCA
506449 TCATGCCATG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
19 3 0.06
20 2 0.04
21 44 0.81
22 5 0.09
ACGTcount: A:0.35, C:0.35, G:0.11, T:0.19
Consensus pattern (22 bp):
TACCTCACCACGTAAAGCACCA
Found at i:521616 original size:25 final size:26
Alignment explanation
Indices: 521588--521636 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
521578 AATATAAACA
* *
521588 TATGCACATGATATGTAAC-ATAATG
1 TATGCACATCATATCTAACTATAATG
*
521613 TATGCATATCATATCTAACTATAA
1 TATGCACATCATATCTAACTATAA
521637 ACATAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (26 bp):
TATGCACATCATATCTAACTATAATG
Found at i:524701 original size:18 final size:18
Alignment explanation
Indices: 524678--524751 Score: 112
Period size: 18 Copynumber: 3.9 Consensus size: 18
524668 GTTCTTGCGG
524678 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
524696 AGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGGGAC--AT
*
524716 CAGTGGTCTTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
524735 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
524752 AATATAAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 32 0.63
19 2 0.04
20 2 0.04
21 15 0.29
ACGTcount: A:0.19, C:0.22, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:524732 original size:39 final size:39
Alignment explanation
Indices: 524678--524754 Score: 145
Period size: 39 Copynumber: 2.0 Consensus size: 39
524668 GTTCTTGCGG
524678 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAATC
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAATC
*
524717 AGTGGTCTTTCGGGACATAGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAAT
524755 ATAAAATACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (39 bp):
AGTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAATC
Found at i:529946 original size:21 final size:18
Alignment explanation
Indices: 529901--529974 Score: 103
Period size: 18 Copynumber: 3.9 Consensus size: 18
529891 GTTCTTAAGG
529901 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
529919 AGTGGTCCTTCGGGACAAATT
1 AGTGGTCCTTCGGGAC--A-T
*
529940 GGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
529958 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTCGGGACA
529975 AATATACAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 32 0.64
19 1 0.02
20 1 0.02
21 16 0.32
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:529956 original size:39 final size:39
Alignment explanation
Indices: 529902--529977 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
529892 TTCTTAAGGA
529902 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAATTG
1 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAATTG
*
529941 GTGGTCCTTCGGGACATAGTGGTCCTTTGGGACAAAT
1 GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAAT
529978 ATACAGTGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.18, C:0.20, G:0.33, T:0.29
Consensus pattern (39 bp):
GTGGTCCTTCGGGACATAGTGGTCCTTCGGGACAAATTG
Found at i:532182 original size:9 final size:9
Alignment explanation
Indices: 532158--532193 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
532148 ATTGTAAGTG
532158 AAAAAT-AA
1 AAAAATGAA
*
532166 AGAAATGAA
1 AAAAATGAA
532175 AAAAATGAA
1 AAAAATGAA
532184 AAAAATGAA
1 AAAAATGAA
532193 A
1 A
532194 GCACCTTACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 5 0.20
9 20 0.80
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAATGAA
Found at i:540693 original size:15 final size:15
Alignment explanation
Indices: 540673--540784 Score: 151
Period size: 15 Copynumber: 7.5 Consensus size: 15
540663 TAATAAGGTT
540673 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
540688 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
540703 ATTTA---TAAAATA
1 ATTTATTTTAAAATA
540715 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
540730 ATTTATTATAAAATAA
1 ATTTATTTTAAAAT-A
540746 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
540764 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
540778 ATTTATT
1 ATTTATT
540785 AGTATAGATT
Statistics
Matches: 88, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
12 12 0.14
14 12 0.14
15 49 0.56
16 1 0.01
18 1 0.01
19 13 0.15
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:540715 original size:27 final size:27
Alignment explanation
Indices: 540677--540784 Score: 119
Period size: 27 Copynumber: 3.7 Consensus size: 27
540667 AAGGTTATTT
540677 ATTT-TAAAATAATTTATTTTAAAATA
1 ATTTATAAAATAATTTATTTTAAAATA
540703 ATTTATAAAATAATTTATTTTAAAATA
1 ATTTATAAAATAATTTATTTTAAAATA
540730 ATTTATTATAAAATAATTGATTTATTTTAAAATA
1 A--T-TTATAAAAT-A---ATTTATTTTAAAATA
*
540764 ATTTATTTTAAATAATTTATT
1 ATTTA--TAAAATAATTTATT
540785 AGTATAGATT
Statistics
Matches: 71, Mismatches: 1, Indels: 17
0.80 0.01 0.19
Matches are distributed among these distances:
26 4 0.06
27 23 0.32
29 8 0.11
30 9 0.13
31 4 0.06
32 2 0.03
33 5 0.07
34 16 0.23
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
ATTTATAAAATAATTTATTTTAAAATA
Found at i:540721 original size:42 final size:45
Alignment explanation
Indices: 540673--540785 Score: 153
Period size: 42 Copynumber: 2.5 Consensus size: 45
540663 TAATAAGGTT
*
540673 ATTTATTTTAAAATAATTTATTTTAAAAT-A-ATTTA-TAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAATATTTATTAAAATA
540715 ATTTATTTTAAAATAATTTATTATAAAATAATTGATTTATTTTAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATAA-T-ATTTA--TTAAAATA
540764 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
540786 GTATAGATTG
Statistics
Matches: 63, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
42 28 0.44
43 1 0.02
46 5 0.08
48 13 0.21
49 16 0.25
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (45 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATATTTATTAAAATA
Found at i:540760 original size:61 final size:64
Alignment explanation
Indices: 540688--540837 Score: 182
Period size: 61 Copynumber: 2.3 Consensus size: 64
540678 TTTTAAAATA
540688 ATTTATTTTAAAATAATTTATAAAATAATTTATT-T-TAAAATAATTTATTATAAAATA-ATTG
1 ATTTATTTTAAAATAATTTATAAAATAATTTATTATATAAAATAATTTATTATAAAATAGATTG
* * * * *
540749 ATTTATTTTAAAATAATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGG
1 ATTTATTTTAAAATAATTTA--TAAAATAATTTATTA-TATAAAATAATTTATTATAAAATA--G
540814 ATTG
61 ATTG
540818 ATTTATTTT-AAATAATTTAT
1 ATTTATTTTAAAATAATTTAT
540838 TAGTATCATT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
61 20 0.26
63 13 0.17
65 1 0.01
66 19 0.25
68 10 0.13
69 13 0.17
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (64 bp):
ATTTATTTTAAAATAATTTATAAAATAATTTATTATATAAAATAATTTATTATAAAATAGATTG
Found at i:540770 original size:76 final size:78
Alignment explanation
Indices: 540625--540783 Score: 229
Period size: 76 Copynumber: 2.1 Consensus size: 78
540615 TCAAGAACAA
540625 TTATAAAATATAATTATTTATTAAAATAATTTAAATAATAATAAGGTTATTTATTTTAAAATAAT
1 TTATAAAATATAATTATTTATTAAAATAATTTAAATAATAATAA-GTTATTTATTTTAAAATAAT
540690 TTATTTTAAAATAAT
65 TTATTTT-AAATAAT
* *
540705 TTATAAAATA-ATTTA-TT-TTAAAATAATTTATTATAA-AATAA-TTGATTTATTTTAAAATAA
1 TTATAAAATATAATTATTTATTAAAATAATTTA-AATAATAATAAGTT-ATTTATTTTAAAATAA
540765 TTTATTTTAAATAAT
64 TTTATTTTAAATAAT
540780 TTAT
1 TTAT
540784 TAGTATAGAT
Statistics
Matches: 75, Mismatches: 2, Indels: 9
0.87 0.02 0.10
Matches are distributed among these distances:
75 13 0.17
76 24 0.32
77 18 0.24
78 6 0.08
79 4 0.05
80 10 0.13
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (78 bp):
TTATAAAATATAATTATTTATTAAAATAATTTAAATAATAATAAGTTATTTATTTTAAAATAATT
TATTTTAAATAAT
Found at i:540803 original size:22 final size:22
Alignment explanation
Indices: 540787--540829 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
540777 AATTTATTAG
540787 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
*
540809 TATGGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
540830 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:540870 original size:53 final size:54
Alignment explanation
Indices: 540764--541406 Score: 647
Period size: 53 Copynumber: 12.1 Consensus size: 54
540754 TTTTAAAATA
*
540764 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
540818 ATTTATTTTAAATAATTTATTAGTAT-CATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
540871 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAT-GATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
540924 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATA--GATTTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGA-TTG
**
540977 ATTTA-TTTAAATAATTTATTTCTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
541030 ATTTA--TT--AT--TGTAGTT-GTATTGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * * ***
541074 ATTAGTATGGATTGATTTATTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATT--TAT--TTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* *
541135 ATTTATTTTAAATAATTTATTAG--TGAATTGATTTATTTTAAAATAT-AATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
541186 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGA-TTTATTTTAAAATATGGATTG
*
541241 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * ****
541291 ATTTGTATGGATT-GATTATTT-TTAAATATGGA-TGATTTATTATTGTTTTGTATGGATTG
1 A-TT-TAT--TTTAAATAATTTATT-AGTATGGATTGATTTA-T-TT-TAAAATATGGATTG
* *
541350 ATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
541404 ATT
1 ATT
541407 ATTGTAGTTG
Statistics
Matches: 494, Mismatches: 51, Indels: 88
0.78 0.08 0.14
Matches are distributed among these distances:
44 6 0.01
46 2 0.00
47 5 0.01
48 20 0.04
49 2 0.00
50 8 0.02
51 29 0.06
52 60 0.12
53 159 0.32
54 94 0.19
55 44 0.09
56 26 0.05
57 21 0.04
58 5 0.01
59 7 0.01
61 6 0.01
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:541070 original size:132 final size:132
Alignment explanation
Indices: 540862--541284 Score: 501
Period size: 132 Copynumber: 3.2 Consensus size: 132
540852 TATTTTAAAA
*
540862 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGATTGATT
1 TATGGATTGATTTATTTT-AA-AA-TTATTAG--TGAATTGATTTATTTTAAAATATGATTGATT
*
540927 TATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATA-GATTTGATTTATTTAAATAA
61 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAGGA-TTGATTTATTTAAATAA
*
540991 TTTATTTC
125 TTTATTTG
***
540999 TATGGATTGATTTATTTTAAAA-TA-T-G-G-ATTGATTTATTATTGTAGTTGTATTGATTGATT
1 TATGGATTGATTTATTTTAAAATTATTAGTGAATTGATTTA-T-TT-TA-AAATA-TGATTGATT
541059 TATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTAAAATATGGATTGATTTA-TT--AT--
61 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATA-GGATTGATTTATTTAAATAA
* *
541118 TGTAGTTG
125 TTTATTTG
*
541126 TATGGATTGATTTATTTTAAATAATTTATTAGTGAATTGATTTATTTTAAAATATAATTGATTTA
1 TATGGATTGATTTATTTT-AA-AA-TTATTAGTGAATTGATTTATTTTAAAATATGATTGATTTA
*
541191 TTTTAAATAATTTATTAGTATAGATTGATTTTATTTTAAAATATGGATTGATTTATTTTAAATAA
63 TTTTAAATAATTTATTAGTATGGATTGA-TTTATTTTAAAATA-GGATTGATTTA-TTTAAATAA
*
541256 TTTATTAG
125 TTTATTTG
541264 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
541285 TAATTTATTT
Statistics
Matches: 248, Mismatches: 15, Indels: 47
0.80 0.05 0.15
Matches are distributed among these distances:
127 32 0.13
128 4 0.02
129 6 0.02
130 39 0.16
131 22 0.09
132 75 0.30
133 7 0.03
134 4 0.02
135 11 0.04
136 5 0.02
137 20 0.08
138 23 0.09
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (132 bp):
TATGGATTGATTTATTTTAAAATTATTAGTGAATTGATTTATTTTAAAATATGATTGATTTATTT
TAAATAATTTATTAGTATGGATTGATTTATTTTAAAATAGGATTGATTTATTTAAATAATTTATT
TG
Found at i:541109 original size:79 final size:80
Alignment explanation
Indices: 540809--541192 Score: 388
Period size: 79 Copynumber: 4.9 Consensus size: 80
540799 TATTTTAAAA
*
540809 TATGGATTGATTTATTTTAAATAATTTATTAGTAT-CATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
*
540873 TTATTTTAAATAATTTA-TTAG
66 TTA--TT--AT--TGTAGTT-G
* * * * * *
540894 TATGGATTGATTTATTTTAAAATATGATTGATTTA-TTTTAAATAATTTA-TTT---GTATGGAT
1 TATGGATTGATTTATTTT-AAATA--ATTTA-TTAGTATGAATTGATTTATTTTAAAATATGGAT
** * *
540954 TGATTTATT-TTAAAATAG
62 TGATTTATTATTGTAGTTG
** *
540972 -AT---TTGATTTA-TTTAAATAATTTATTTCTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
541032 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
* *
541047 TATTGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
541111 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
*
541126 TATGGATTGATTTATTTTAAATAATTTATTAG--TGAATTGATTTATTTTAAAATAT-AATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
541188 TTATT
66 TTATT
541193 TTAAATAATT
Statistics
Matches: 255, Mismatches: 26, Indels: 44
0.78 0.08 0.14
Matches are distributed among these distances:
69 2 0.01
70 13 0.05
71 3 0.01
72 5 0.02
73 3 0.01
74 24 0.09
75 5 0.02
76 2 0.01
77 24 0.09
78 13 0.05
79 73 0.29
80 30 0.12
83 2 0.01
85 32 0.13
86 5 0.02
88 9 0.04
89 10 0.04
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:541174 original size:21 final size:19
Alignment explanation
Indices: 541160--541202 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 19
541150 TTTATTAGTG
541160 AATTGATTTATTTTAAAATAT
1 AATTGATTTATTTT--AATAT
541181 AATTGATTTATTTTAA-AT
1 AATTGATTTATTTTAATAT
541199 AATT
1 AATT
541203 TATTAGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 2 0.09
21 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
AATTGATTTATTTTAATAT
Found at i:541176 original size:109 final size:107
Alignment explanation
Indices: 541052--541393 Score: 392
Period size: 109 Copynumber: 3.1 Consensus size: 107
541042 AGTTGTATTG
541052 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAAATATGGATTGATTTATTA
1 ATTGATTTATTTTAAATAATTTATT-GTATGGATTGA-TTATTTAAAATATGGATTGATTTATTA
541117 TTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG-TGA
64 TTGTA-TTGTATGGATTGATTTATTTTAAATAATTTATTAGATGA
* * * * * * *
541161 ATTGATTTATTTTAAAATATAATTGATT-TAT--TTTAAATAATTTATTAGTATAGATTGA-TT-
1 ATTGATTTATTTT--AA-ATAATTTATTGTATGGATT-GATTATTTA-AAATATGGATTGATTTA
* *** *
541221 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGG
61 TTATTGTATTGTATGGATTGATTTATTTTAAATAATTTATTAG-ATGA
*
541269 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTATTTTTAAATATGGA-TGATTTATTA
1 ATTGATTTATTTTAAATAATTTA-TTGTATGGATTGATTA-TTTAAAATATGGATTGATTTATTA
* *
541333 TTGTTTTGTATGGATTGATTTATTTTAAATAATTTATTTGTATGA
64 TTGTATTGTATGGATTGATTTATTTTAAATAATTTATTAG-ATGA
541378 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
541394 ATATGGATTG
Statistics
Matches: 192, Mismatches: 27, Indels: 28
0.78 0.11 0.11
Matches are distributed among these distances:
105 7 0.04
106 36 0.19
107 13 0.07
108 36 0.19
109 86 0.45
110 3 0.02
111 2 0.01
112 9 0.05
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (107 bp):
ATTGATTTATTTTAAATAATTTATTGTATGGATTGATTATTTAAAATATGGATTGATTTATTATT
GTATTGTATGGATTGATTTATTTTAAATAATTTATTAGATGA
Found at i:541220 original size:32 final size:32
Alignment explanation
Indices: 541178--541318 Score: 153
Period size: 32 Copynumber: 4.7 Consensus size: 32
541168 TATTTTAAAA
541178 TATA-ATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
541209 TATAGATTGATTTTATTTT-AA-AA--TA-T-G
1 TATAGATTGA-TTTATTTTAAATAATTTATTAG
541236 ----GATTGATTTATTTTAAATAATTTATTAG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
* *
541264 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATAGATTGATTTATTTTAAATAATTTATTAG
*
541296 TATGGATTGA-TTATTTTTAAATA
1 TATAGATTGATTTA-TTTTAAATA
541319 TGGATGATTT
Statistics
Matches: 96, Mismatches: 1, Indels: 25
0.79 0.01 0.20
Matches are distributed among these distances:
22 8 0.08
23 8 0.08
24 2 0.02
26 2 0.02
27 2 0.02
28 2 0.02
29 2 0.02
31 9 0.09
32 53 0.55
33 8 0.08
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (32 bp):
TATAGATTGATTTATTTTAAATAATTTATTAG
Found at i:541222 original size:79 final size:78
Alignment explanation
Indices: 540974--541483 Score: 421
Period size: 79 Copynumber: 6.8 Consensus size: 78
540964 TAAAATAGAT
540974 TTGATTTA-TTTAAATAATTTATTTCTA-TGGATTGATTTATTTTAAAATATGGATTGATTTATT
1 TTGATTTATTTTAAATAATTTA--T-TAGTGGATTGATTTATTTTAAAATATGGATTGATTTATT
541037 ATTGTAGTTGTATTGA
63 ATTGTAGTTGTATTGA
541053 TTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTAAAATATGGATTGATTTATTA
1 TTGATTTATTTTAAATAATTTATTAG--TGGATTGATTTATTTTAAAATATGGATTGATTTATTA
*
541117 TTGTAGTTGTATGGA
64 TTGTAGTTGTATTGA
* *
541132 TTGATTTATTTTAAATAATTTATTAGTGAATTGATTTATTTTAAAATAT-AATTGATTTATT-TT
1 TTGATTTATTTTAAATAATTTATTAGTGGATTGATTTATTTTAAAATATGGATTGATTTATTATT
* *
541195 AAATAATT-TATTAGTA
66 --GTAGTTGTATT-G-A
* * *
541211 TAGATTGATTTT--AT--TTTAAAATA-TGGATTGATTTATTTT--AA-AT--A---ATTTATTA
1 TTGATTTATTTTAAATAATTT--ATTAGTGGATTGATTTATTTTAAAATATGGATTGATTTATTA
*
541263 --GTA--TGGATTGA
64 TTGTAGTTGTATTGA
* ** * * *
541274 TTTATTTTA-AATAATTTATTT-GTA-TGGATTGATTAT-TTTT-AAATATGGA-TGATTTATTA
1 TTGA-TTTATTTTAAATAATTTATTAGTGGATTGATT-TATTTTAAAATATGGATTGATTTATTA
* *
541333 TTGT-TTTGTATGGA
64 TTGTAGTTGTATTGA
* *
541347 TTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAAATATGGATTG----ATTA
1 TTGATTTATTTTAAATAATTTATTAG--TGGATTGATTTATTTTAAAATATGGATTGATTTATTA
541408 TTGTAGTTGTA-TGAA
64 TTGTAGTTGTATTG-A
541423 TTGATTTATTTTAAATAATTTA-TAGTATGGATTGATTTATTTTAAAATA--GATTGATTTATT
1 TTGATTTATTTTAAATAATTTATTAG--TGGATTGATTTATTTTAAAATATGGATTGATTTATT
541484 TAAATTGATT
Statistics
Matches: 355, Mismatches: 33, Indels: 88
0.75 0.07 0.18
Matches are distributed among these distances:
63 4 0.01
64 21 0.06
65 7 0.02
66 4 0.01
67 3 0.01
68 1 0.00
69 7 0.02
70 8 0.02
72 7 0.02
73 24 0.07
74 3 0.01
75 37 0.10
76 46 0.13
77 48 0.14
78 25 0.07
79 85 0.24
80 25 0.07
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (78 bp):
TTGATTTATTTTAAATAATTTATTAGTGGATTGATTTATTTTAAAATATGGATTGATTTATTATT
GTAGTTGTATTGA
Found at i:541242 original size:185 final size:186
Alignment explanation
Indices: 540764--541286 Score: 639
Period size: 185 Copynumber: 2.8 Consensus size: 186
540754 TTTTAAAATA
540764 ATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGT-TA-ATTGATTTATTTTAAAATAT-GATTGATTTATTTTAA
540829 ATAATTTATTAGTATCATTGA-TTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
63 ATAATTTATTAGTATCATTGATTTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
* *
540893 GTATGGATTGATTTATTTTAAAATATGATTGATTTATTTTAAATAATTTATTTGTATGGATTG
128 GTATGGATTGATTTA-TTTAAAATATGATTGATTTA-TTT-AAT-ATGTAGTTGTATGGATTG
* * * *
540956 ATTTATTTTAAAATAGATTTGATTTATTTAAATAATTTATTTCT---AT-GGATTGATTTATTTT
1 ATTTATTTT-AAATA-ATTT-A-TTAGTTAATTGATTTATTT-TAAAATATGATTGATTTATTTT
** * * *
541017 AAA-ATATGGATT-G-ATTTATT-ATTGTAGTTGT---AT-T-GATTGATTTATTTTAAATAATT
61 AAATA-ATTTATTAGTA-TCATTGATTTTA-TTTTAAAATATGGATTGATTTATTTTAAATAATT
541073 TATTAGTATGGATTGATTTATTTAAAATATGGATTGATTTA-TT-AT-TGTAGTTGTATGGATTG
123 TATTAGTATGGATTGATTTATTTAAAATAT-GATTGATTTATTTAATATGTAGTTGTATGGATTG
* *
541135 ATTTATTTTAAATAATTTATTAGTGAATTGATTTATTTTAAAATATAATTGATTTATTTTAAATA
1 ATTTATTTTAAATAATTTATTAGTTAATTGATTTATTTTAAAATATGATTGATTTATTTTAAATA
*
541200 ATTTATTAGTATAGATTGATTTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGT
66 ATTTATTAGTAT-CATTGATTTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGT
*
541265 ATGGATTGATTTATTTTAAATA
130 ATGGATTGATTTATTTAAAATA
541287 ATTTATTTGT
Statistics
Matches: 284, Mismatches: 23, Indels: 55
0.78 0.06 0.15
Matches are distributed among these distances:
174 1 0.00
175 15 0.05
176 1 0.00
177 6 0.02
178 26 0.09
179 27 0.10
180 7 0.02
181 7 0.02
183 4 0.01
184 11 0.04
185 102 0.36
186 1 0.00
187 2 0.01
188 2 0.01
189 9 0.03
190 25 0.09
192 11 0.04
193 5 0.02
194 14 0.05
195 4 0.01
196 4 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (186 bp):
ATTTATTTTAAATAATTTATTAGTTAATTGATTTATTTTAAAATATGATTGATTTATTTTAAATA
ATTTATTAGTATCATTGATTTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTA
TGGATTGATTTATTTAAAATATGATTGATTTATTTAATATGTAGTTGTATGGATTG
Found at i:541332 original size:24 final size:25
Alignment explanation
Indices: 541300--541356 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
541290 TATTTGTATG
*
541300 GATTGATTATT-TTTAAATATGGA-T
1 GATTTATTATTGTTT-AATATGGATT
**
541324 GATTTATTATTGTTTTGTATGGATT
1 GATTTATTATTGTTTAATATGGATT
541349 GATTTATT
1 GATTTATT
541357 TTAAATAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 16 0.57
25 12 0.43
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (25 bp):
GATTTATTATTGTTTAATATGGATT
Found at i:541373 original size:32 final size:32
Alignment explanation
Indices: 541337--541511 Score: 111
Period size: 32 Copynumber: 5.1 Consensus size: 32
541327 TTATTATTGT
541337 TTTGTATGGATTGATTTATTTTAAATAATTTA
1 TTTGTATGGATTGATTTATTTTAAATAATTTA
* *
541369 TTTGTATGAATTGATTTATTTTAAAATATGGATTGA
1 TTTGTATGGATTGATTTATTTT-AAATA---ATTTA
* *
541405 TTATTGTAGTTG-TATGAATTGATTTATTTTAAATAATTTA
1 -T-TTGTA-TGGAT-TG-ATT--TAT--TTTAAATAATTTA
* *
541445 -TAGTATGGATTGATTTATTTTAAAATAGATTGA
1 TTTGTATGGATTGATTTATTTT-AAATA-ATTTA
* * **
541478 TTTATTTAAATTGATTTATTTTAAATAATTTA
1 TTTGTATGGATTGATTTATTTTAAATAATTTA
541510 TT
1 TT
541512 GTAGTTGTAT
Statistics
Matches: 110, Mismatches: 16, Indels: 34
0.69 0.10 0.21
Matches are distributed among these distances:
31 3 0.03
32 32 0.29
33 16 0.15
34 16 0.15
35 3 0.03
36 8 0.07
37 6 0.05
38 6 0.05
39 3 0.03
40 7 0.06
42 2 0.02
43 5 0.05
44 3 0.03
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (32 bp):
TTTGTATGGATTGATTTATTTTAAATAATTTA
Found at i:541385 original size:18 final size:18
Alignment explanation
Indices: 541337--541389 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
541327 TTATTATTGT
*
541337 TTTGTATGGATTGATTTA
1 TTTGTATGAATTGATTTA
*
541355 TTT-TA--AA-TAATTTA
1 TTTGTATGAATTGATTTA
541369 TTTGTATGAATTGATTTA
1 TTTGTATGAATTGATTTA
541387 TTT
1 TTT
541390 TAAAATATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
14 9 0.32
15 3 0.11
17 4 0.14
18 12 0.43
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TTTGTATGAATTGATTTA
Found at i:541391 original size:77 final size:77
Alignment explanation
Indices: 541182--541483 Score: 339
Period size: 77 Copynumber: 3.8 Consensus size: 77
541172 TTAAAATATA
541182 ATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTTATTTTAAAATATGGATTGATTTA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGA-TTTATTTT-AAA-ATGGATTGATTTA
541246 TTTTAAATAAT-TTATTAGTATGG
62 --TT--AT--TGTT-TT-GTATGG
* *
541269 ATTGATTTATTTTAAATAATTTATTTGTATGGATTGA-TTATTTTTAAATATGGA-TGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTA-TTTTAAA-ATGGATTGATTTATT
541332 ATTGTTTTGTATGG
64 ATTGTTTTGTATGG
* * *
541346 ATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTTTAAAAT--ATGGATTGATTAT
1 ATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATGGATTGATTTATTAT
* *
541409 TGTAGTTGTATGA
66 TGT-TTTGTATGG
* *
541422 ATTGATTTATTTTAAATAATTTA-TAGTATGGATTGATTTATTTTAAAATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATGGATTGATTTATT
541484 TAAATTGATT
Statistics
Matches: 196, Mismatches: 11, Indels: 26
0.84 0.05 0.11
Matches are distributed among these distances:
74 1 0.01
75 36 0.18
76 32 0.16
77 58 0.30
78 6 0.03
79 2 0.01
80 2 0.01
82 2 0.01
84 7 0.04
85 12 0.06
86 4 0.02
87 34 0.17
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (77 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATGGATTGATTTATTAT
TGTTTTGTATGG
Found at i:541398 original size:22 final size:22
Alignment explanation
Indices: 541373--541437 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
541363 AATTTATTTG
541373 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
* * ***
541395 TATGGATTGA-TTATTGTAGTTG
1 TATGAATTGATTTATTTTA-AAA
541417 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
541438 TAATTTATAG
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
21 7 0.22
22 18 0.56
23 7 0.22
ACGTcount: A:0.34, C:0.00, G:0.15, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:541492 original size:14 final size:15
Alignment explanation
Indices: 541473--541503 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
541463 TTTAAAATAG
541473 ATTGATTTA-TTTAA
1 ATTGATTTATTTTAA
541487 ATTGATTTATTTTAA
1 ATTGATTTATTTTAA
541502 AT
1 AT
541504 AATTTATTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTGATTTATTTTAA
Found at i:541559 original size:30 final size:30
Alignment explanation
Indices: 541523--541579 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
541513 TAGTTGTATG
* *
541523 AATTATTTAAATTTCAGTATTGTAAAATAA
1 AATTATTTAAATCTCAGTATTGCAAAATAA
541553 AATTATTTAAATCTCAGTATTGCAAAA
1 AATTATTTAAATCTCAGTATTGCAAAA
541580 CTCTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTATTTAAATCTCAGTATTGCAAAATAA
Found at i:542620 original size:42 final size:42
Alignment explanation
Indices: 542572--542706 Score: 131
Period size: 42 Copynumber: 3.2 Consensus size: 42
542562 TACTTAAGTC
542572 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGAT
1 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGAT
* * *
542614 ATGAATATGCAT--GATTGCA-A-AAT-AAG-ATGA-TCAAAGCACAAT
1 ATGAATATGAATGGGA-TGCATAGCATAAAGTAT-ACT-AATG----AT
542656 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGAT
1 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGAT
542698 ATGAATATG
1 ATGAATATG
542707 CATGATTGCA
Statistics
Matches: 73, Mismatches: 6, Indels: 28
0.68 0.06 0.26
Matches are distributed among these distances:
37 3 0.04
38 7 0.10
39 2 0.03
40 3 0.04
41 4 0.05
42 35 0.48
43 4 0.05
44 3 0.04
45 2 0.03
46 7 0.10
47 3 0.04
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.27
Consensus pattern (42 bp):
ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGAT
Found at i:542668 original size:84 final size:84
Alignment explanation
Indices: 542572--542743 Score: 344
Period size: 84 Copynumber: 2.0 Consensus size: 84
542562 TACTTAAGTC
542572 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGATATGAATATGCATGATTGCAAAAT
1 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGATATGAATATGCATGATTGCAAAAT
542637 AAGATGATCAAAGCACAAT
66 AAGATGATCAAAGCACAAT
542656 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGATATGAATATGCATGATTGCAAAAT
1 ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGATATGAATATGCATGATTGCAAAAT
542721 AAGATGATCAAAGCACAAT
66 AAGATGATCAAAGCACAAT
542740 ATGA
1 ATGA
542744 CACGTATGAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.26
Consensus pattern (84 bp):
ATGAATATGAATGGGATGCATAGCATAAAGTATACTAATGATATGAATATGCATGATTGCAAAAT
AAGATGATCAAAGCACAAT
Found at i:546221 original size:19 final size:18
Alignment explanation
Indices: 546196--546246 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
546186 AACATATTTA
546196 TATTTATAGAAATCTTAT
1 TATTTATAGAAATCTTAT
*
546214 TAATTTATAGATACATTTTAT
1 T-ATTTATAGA-A-ATCTTAT
546235 T-TTTATAGAAAT
1 TATTTATAGAAAT
546247 ATATATTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 2 0.07
19 17 0.59
20 1 0.03
21 7 0.24
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (18 bp):
TATTTATAGAAATCTTAT
Found at i:549076 original size:18 final size:18
Alignment explanation
Indices: 549053--549124 Score: 135
Period size: 18 Copynumber: 4.0 Consensus size: 18
549043 ACTGAATATT
549053 TGTCCTGAAGGACCACTA
1 TGTCCTGAAGGACCACTA
549071 TGTCCTGAAGGACCACTA
1 TGTCCTGAAGGACCACTA
549089 TGTCCTGAAGGACCACTA
1 TGTCCTGAAGGACCACTA
*
549107 TGTCCAGAAGGACCACTA
1 TGTCCTGAAGGACCACTA
549125 ATAATCCCTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (18 bp):
TGTCCTGAAGGACCACTA
Found at i:550321 original size:7 final size:7
Alignment explanation
Indices: 550309--550334 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
550299 CTTCATGTAT
550309 GAAGAAG
1 GAAGAAG
550316 GAAGAAG
1 GAAGAAG
550323 GAAGAAG
1 GAAGAAG
550330 GAAGA
1 GAAGA
550335 GGAGAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (7 bp):
GAAGAAG
Found at i:555939 original size:18 final size:18
Alignment explanation
Indices: 555918--555955 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
555908 GAATGACGAT
555918 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
555936 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
555954 TA
1 TA
555956 ATAATCCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.32, G:0.21, T:0.18
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:559692 original size:38 final size:38
Alignment explanation
Indices: 559650--559788 Score: 154
Period size: 38 Copynumber: 3.7 Consensus size: 38
559640 ATTTCAGATT
* *
559650 AACAGATTGTTGTAG-AGATGGTTATCCATAAATGCATG
1 AACAGATTGTTGT-GCAGATGATTATCCATATATGCATG
* * * * *
559688 AACAGATAGTTGTGTAGATGATTATCTATATGTGCAAG
1 AACAGATTGTTGTGCAGATGATTATCCATATATGCATG
* * *
559726 AACATATTGTTGTGCAGATGATTATCCATGTATACATG
1 AACAGATTGTTGTGCAGATGATTATCCATATATGCATG
* *
559764 AACCGATTGTTGTGTAGATGATTAT
1 AACAGATTGTTGTGCAGATGATTAT
559789 ATATATACAC
Statistics
Matches: 83, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
37 1 0.01
38 82 0.99
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.35
Consensus pattern (38 bp):
AACAGATTGTTGTGCAGATGATTATCCATATATGCATG
Found at i:559751 original size:76 final size:76
Alignment explanation
Indices: 559650--559794 Score: 202
Period size: 76 Copynumber: 1.9 Consensus size: 76
559640 ATTTCAGATT
* * *
559650 AACAGATTGTTGTAGAGATGGTTATCCATAAATGCATGAACAGATAGTTGTGTAGATGATTATCT
1 AACAGATTGTTGTAGAGATGATTATCCATAAATACATGAACAGATAGTTGTGTAGATGATTATAT
559715 ATATGTGCAAG
66 ATATGTGCAAG
* ** * *
559726 AACATATTGTTGT-GCAGATGATTATCCATGTATACATGAACCGATTGTTGTGTAGATGATTATA
1 AACAGATTGTTGTAG-AGATGATTATCCATAAATACATGAACAGATAGTTGTGTAGATGATTATA
559790 TATAT
65 TATAT
559795 ACACACACAC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 1 0.02
76 59 0.98
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (76 bp):
AACAGATTGTTGTAGAGATGATTATCCATAAATACATGAACAGATAGTTGTGTAGATGATTATAT
ATATGTGCAAG
Found at i:562675 original size:19 final size:20
Alignment explanation
Indices: 562633--562675 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
562623 AAATAAGATG
*
562633 TTAAAAGAAAATAATAATAA
1 TTAAAAGAAAATAACAATAA
562653 -TAAAAGAAAATAACAA-AA
1 TTAAAAGAAAATAACAATAA
562671 TTAAA
1 TTAAA
562676 GAGTAAACCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (20 bp):
TTAAAAGAAAATAACAATAA
Found at i:563059 original size:13 final size:13
Alignment explanation
Indices: 563041--563067 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
563031 ATAACGTTAG
563041 AAAAATATAGTAA
1 AAAAATATAGTAA
563054 AAAAATATAGTAA
1 AAAAATATAGTAA
563067 A
1 A
563068 TAAGTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (13 bp):
AAAAATATAGTAA
Found at i:564750 original size:106 final size:106
Alignment explanation
Indices: 564432--565170 Score: 974
Period size: 106 Copynumber: 7.0 Consensus size: 106
564422 GCATTGTTCC
* * ***
564432 GAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCAGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * * *
564496 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* *
564538 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-TGAG-AA---TTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * * *
564597 TCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * * *
564638 GGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* *
564703 CCAACGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * *
564744 GAGTCCAATATCCTACGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
564809 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* * * * *
564850 GAGTCCAATATCCTTCGTTGTGAAGCTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
* * * *
564915 CCAGCGGTCCCTTCGTCATAAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
** * *
564956 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
*
565021 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
* *
565062 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTAGGAAAATT-ATTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATT-GGGAAATTGTTTGTTGACA
* * *
565126 ACCAGCTGT-CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
565167 GAGT
1 GAGT
565171 GGCACGATAT
Statistics
Matches: 557, Mismatches: 68, Indels: 17
0.87 0.11 0.03
Matches are distributed among these distances:
100 82 0.15
101 2 0.00
102 3 0.01
103 3 0.01
104 1 0.00
105 36 0.06
106 422 0.76
107 8 0.01
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
Found at i:566742 original size:171 final size:173
Alignment explanation
Indices: 566422--566767 Score: 592
Period size: 171 Copynumber: 2.0 Consensus size: 173
566412 TAAATAGGCC
*
566422 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
566487 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
64 CTCAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
566552 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
* * *
566597 CAAACAAGTGTTTCAGGGTGTTGAACCAATGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
566659 CAAAATGTTTCTCTCTCTTGATGCTCTATGATCTTC-AGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
566723 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
566768 TTTAGGGAAT
Statistics
Matches: 165, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
170 14 0.08
171 73 0.44
172 28 0.17
174 1 0.01
175 49 0.30
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (173 bp):
CAAACAAGTATTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATGAT
TGTGCTTGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:566834 original size:16 final size:16
Alignment explanation
Indices: 566815--566885 Score: 67
Period size: 16 Copynumber: 4.4 Consensus size: 16
566805 CTTTTTGATT
*
566815 TTTTTTCTTGTTTCTC
1 TTTTTTCTTGTTTTTC
566831 TTTTTTCTTTGTTTTTC
1 TTTTTTC-TTGTTTTTC
566848 TTTGTTT-TT-TTTTTGC
1 TTT-TTTCTTGTTTTT-C
*
566864 TTTTTTGCTT-CTTTTC
1 TTTTTT-CTTGTTTTTC
566880 TTTTTT
1 TTTTTT
566886 GTTCTTGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
15 8 0.17
16 20 0.42
17 17 0.35
18 3 0.06
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTGTTTTTC
Found at i:566846 original size:42 final size:41
Alignment explanation
Indices: 566800--566891 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 41
566790 TTTTTGTCCC
566800 TTTTTCTTT-TTGATTTTTTTT-CTTGTTTCT-CTT-TTTTCTTT
1 TTTTTCTTTGTT--TTTTTTTTGCTT-TTT-TGCTTCTTTTCTTT
566841 GTTTTTCTTTGTTTTTTTTTTGCTTTTTTGCTTCTTTTCTTT
1 -TTTTTCTTTGTTTTTTTTTTGCTTTTTTGCTTCTTTTCTTT
566883 TTTGTTCTT
1 TTT-TTCTT
566892 GATTGGATCT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
40 1 0.02
41 17 0.38
42 25 0.56
43 2 0.04
ACGTcount: A:0.01, C:0.12, G:0.08, T:0.79
Consensus pattern (41 bp):
TTTTTCTTTGTTTTTTTTTTGCTTTTTTGCTTCTTTTCTTT
Found at i:566856 original size:11 final size:11
Alignment explanation
Indices: 566831--566869 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
566821 CTTGTTTCTC
566831 TTTTTTCTTTG
1 TTTTTTCTTTG
566842 -TTTTTCTTTG
1 TTTTTTCTTTG
*
566852 TTTTTTTTTTG
1 TTTTTTCTTTG
566863 CTTTTTT
1 -TTTTTT
566870 GCTTCTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 10 0.40
11 9 0.36
12 6 0.24
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:566886 original size:16 final size:16
Alignment explanation
Indices: 566858--566891 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
566848 TTTGTTTTTT
566858 TTTTGCTTTTTTGCTTC
1 TTTTGCTTTTTTG-TTC
566875 TTTT-CTTTTTTGTTC
1 TTTTGCTTTTTTGTTC
566890 TT
1 TT
566892 GATTGGATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.76
Consensus pattern (16 bp):
TTTTGCTTTTTTGTTC
Found at i:571408 original size:18 final size:16
Alignment explanation
Indices: 571385--571432 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
571375 GGATGAAACA
571385 AATAAAAAAATGAAATTG
1 AATAAAAAAAT-AAA-TG
571403 AATAAAATAAAATAAATG
1 AAT-AAA-AAAATAAATG
*
571421 AAGAAAAAAATA
1 AATAAAAAAATA
571433 TATATACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 6 0.22
17 3 0.11
18 7 0.26
19 6 0.22
20 5 0.19
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (16 bp):
AATAAAAAAATAAATG
Found at i:571801 original size:10 final size:10
Alignment explanation
Indices: 571757--571887 Score: 58
Period size: 12 Copynumber: 12.8 Consensus size: 10
571747 ATAAAAAATA
571757 ATAATAT-AT
1 ATAATATAAT
571766 ATATATATATAT
1 ATA-ATATA-AT
* *
571778 ATAATAGAAA
1 ATAATATAAT
571788 ATAATATAAT
1 ATAATATAAT
***
571798 ATAACGCAA-
1 ATAATATAAT
* * *
571807 AAAAAATGAAA
1 ATAATAT-AAT
*
571818 AAAATTATAAT
1 ATAA-TATAAT
571829 A-AATA-AAT
1 ATAATATAAT
571837 A-AATA-AAT
1 ATAATATAAT
571845 ATAATATAAT
1 ATAATATAAT
571855 ATATATATATAT
1 ATA-ATATA-AT
571867 ATATATATATAT
1 ATA-ATATA-AT
571879 ATATATATA
1 ATA-ATATA
571888 TAGAAATAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
8 12 0.12
9 12 0.12
10 29 0.29
11 16 0.16
12 30 0.30
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (10 bp):
ATAATATAAT
Found at i:571848 original size:18 final size:20
Alignment explanation
Indices: 571827--571889 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 20
571817 AAAAATTATA
571827 ATAA-ATAA-ATAAATAAAT
1 ATAATATAATATAAATAAAT
* *
571845 ATAATATAATATATATATAT
1 ATAATATAATATAAATAAAT
* *
571865 ATATATATATATATATATATAT
1 ATA-ATATA-ATATAAATAAAT
571887 ATA
1 ATA
571890 GAAATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.10
19 4 0.10
20 11 0.28
21 5 0.13
22 15 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATAATATAATATAAATAAAT
Found at i:571858 original size:12 final size:12
Alignment explanation
Indices: 571823--571887 Score: 64
Period size: 14 Copynumber: 5.3 Consensus size: 12
571813 TGAAAAAAAT
571823 TATAATA-AATA
1 TATAATATAATA
*
571834 AATAA-ATAA-A
1 TATAATATAATA
571844 TATAATATAATA
1 TATAATATAATA
571856 TATATATATATATA
1 TATA-ATATA-ATA
571870 TATATATATATATA
1 TATA-ATATA-ATA
571884 TATA
1 TATA
571888 TAGAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
10 6 0.13
11 10 0.21
12 5 0.11
13 5 0.11
14 21 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TATAATATAATA
Found at i:571860 original size:2 final size:2
Alignment explanation
Indices: 571843--571889 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
571833 AAATAAATAA
571843 AT AT A- AT AT A- 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
571883 AT AT AT A
1 AT AT AT A
571890 GAAATAATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:579726 original size:21 final size:21
Alignment explanation
Indices: 579679--579726 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
579669 ACGTATAACT
579679 ATAAATTAGTTAAAATTTAAAG
1 ATAAATTAGTTAAAA-TTAAAG
*
579701 ATAAATTATTTAAAA-TAAAGG
1 ATAAATTAGTTAAAATTAAA-G
579722 ATAAA
1 ATAAA
579727 CTATATTAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 6 0.25
22 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (21 bp):
ATAAATTAGTTAAAATTAAAG
Found at i:581906 original size:323 final size:323
Alignment explanation
Indices: 581285--581936 Score: 1279
Period size: 323 Copynumber: 2.0 Consensus size: 323
581275 GTAACTTGAA
581285 ACTCGTCACTGAATATGAAGGGTTCTAATAAATATATATTTATTTATTGTAACTTGTTATTACAA
1 ACTC-TCACTGAATATGAAGGGTTCTAATAAATATATATTTATTTATTGTAACTTGTTATTACAA
581350 CGTGACAAAATCTAATAAAAGTTATATTTTAAAACTCATCACTTCGACAGGAAGAGTTTGAATAA
65 CGTGACAAAATCTAATAAAAGTTATATTTTAAAACTCATCACTTCGACAGGAAGAGTTTGAATAA
581415 AAAATATTATTGAGAAATTCATCATGGTATGACGAGTTTGATATATACACTAACATTTCGTAGAT
130 AAAATATTATTGAGAAATTCATCATGGTATGACGAGTTTGATATATACACTAACATTTCGTAGAT
581480 TACAAATTAATATTTAAGATGGTCTGATAAACTAATTTTTTTACATGATCTATTGGATCAATTTT
195 TACAAATTAATATTTAAGATGGTCTGATAAACTAATTTTTTTACATGATCTATTGGATCAATTTT
581545 ACCAAAAAATTCTGTGCCTTGTCCAATCAAATTAAATCACCAAAATTTCCTTTTGAAATTCTGG
260 ACCAAAAAATTCTGTGCCTTGTCCAATCAAATTAAATCACCAAAATTTCCTTTTGAAATTCTGG
581609 ACTCTCACATGAATATGAAGGGTTCTAATAAA-ATATATTTATTTATTGTAACTTGTTATTACAA
1 ACTCTCAC-TGAATATGAAGGGTTCTAATAAATATATATTTATTTATTGTAACTTGTTATTACAA
581673 CGTGACAAAATCTAATAAAAGTTATATTTTAAAACTCATCACTTCGACAGGAAGAGTTTGAATAA
65 CGTGACAAAATCTAATAAAAGTTATATTTTAAAACTCATCACTTCGACAGGAAGAGTTTGAATAA
581738 AAAATATTATTGAGAAATTCATCATGGTATGACGAGTTTGATATATACACTAACATTTCGTAGAT
130 AAAATATTATTGAGAAATTCATCATGGTATGACGAGTTTGATATATACACTAACATTTCGTAGAT
581803 TACAAATTAATATTTAAGATGGTCTGATAAACTAATTTTTTTACATGATCTATTGGATCAATTTT
195 TACAAATTAATATTTAAGATGGTCTGATAAACTAATTTTTTTACATGATCTATTGGATCAATTTT
581868 ACCAAAAAATTCTGTGCCTTGTCCAATCAAATTAAATCACCAAAATTTCCTTTTGAAATTCTGG
260 ACCAAAAAATTCTGTGCCTTGTCCAATCAAATTAAATCACCAAAATTTCCTTTTGAAATTCTGG
581932 ACTCT
1 ACTCT
581937 GCTGTAATTT
Statistics
Matches: 327, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
323 300 0.92
324 27 0.08
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (323 bp):
ACTCTCACTGAATATGAAGGGTTCTAATAAATATATATTTATTTATTGTAACTTGTTATTACAAC
GTGACAAAATCTAATAAAAGTTATATTTTAAAACTCATCACTTCGACAGGAAGAGTTTGAATAAA
AAATATTATTGAGAAATTCATCATGGTATGACGAGTTTGATATATACACTAACATTTCGTAGATT
ACAAATTAATATTTAAGATGGTCTGATAAACTAATTTTTTTACATGATCTATTGGATCAATTTTA
CCAAAAAATTCTGTGCCTTGTCCAATCAAATTAAATCACCAAAATTTCCTTTTGAAATTCTGG
Found at i:582162 original size:13 final size:13
Alignment explanation
Indices: 582144--582169 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
582134 AATACATTAT
582144 AAATATTTTAATG
1 AAATATTTTAATG
582157 AAATATTTTAATG
1 AAATATTTTAATG
582170 GGAGTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AAATATTTTAATG
Found at i:583018 original size:2 final size:2
Alignment explanation
Indices: 583011--583035 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
583001 TGAAACATAA
583011 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 A
583036 AAACATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:586463 original size:181 final size:184
Alignment explanation
Indices: 586256--586625 Score: 694
Period size: 181 Copynumber: 2.0 Consensus size: 184
586246 CTCCTCCAAG
586256 TTTTGTTTTTTTTATTATGGTCCTTGGAATTATCAAATGCTCTAGTTTTTGTCCATTGTATTTTG
1 TTTTGTTTTTTTTATTATGGTCCTTGGAATTATCAAATGCTCTAG-TTTTGTCCATTGTATTTTG
586321 GTTTATAATATTCATTTG-TTTTATTTCAATACCTTATTTATATACATATTGGTATTATTGCTTC
65 GTTTATAATATTCATTTGTTTTTATTTCAATACCTTATTTATATACATATTGGTATTATTGCTTC
586385 CATTTTA-TTTTA-ATTTCATTGTG-TTTCTAAAATATGTAAATGGAAAATTTCA
130 CATTTTATTTTTATATTTCATTGTGTTTTCTAAAATATGTAAATGGAAAATTTCA
586437 TTTTGTTTTTTTTATTATGGTCCTTGGAATTATCAAATGCTCTAGTTTTGTCCATTGTATTTTGG
1 TTTTGTTTTTTTTATTATGGTCCTTGGAATTATCAAATGCTCTAGTTTTGTCCATTGTATTTTGG
586502 TTTATAATATTCATTTGTTTTTATTTCAATACCTTATTTATATACATATTGGTATTATTGCTTCC
66 TTTATAATATTCATTTGTTTTTATTTCAATACCTTATTTATATACATATTGGTATTATTGCTTCC
*
586567 ATTTTATTTTTATATTTCATTTTGTTTTCTAAAATATGTAAATGGAAAATTTCA
131 ATTTTATTTTTATATTTCATTGTGTTTTCTAAAATATGTAAATGGAAAATTTCA
586621 TTTTG
1 TTTTG
586626 AGGGAAATCT
Statistics
Matches: 184, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
180 37 0.20
181 98 0.53
182 5 0.03
183 10 0.05
184 34 0.18
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.55
Consensus pattern (184 bp):
TTTTGTTTTTTTTATTATGGTCCTTGGAATTATCAAATGCTCTAGTTTTGTCCATTGTATTTTGG
TTTATAATATTCATTTGTTTTTATTTCAATACCTTATTTATATACATATTGGTATTATTGCTTCC
ATTTTATTTTTATATTTCATTGTGTTTTCTAAAATATGTAAATGGAAAATTTCA
Found at i:587706 original size:30 final size:32
Alignment explanation
Indices: 587670--587739 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
587660 TAAGGACCTA
587670 TCCATATGTTCCAG-AGAACATA-G-ATAACTG
1 TCCATATGTTCCAGAAGAACATATGTA-AACTG
* *
587700 TCCATATG-TCCTGAAGGACATATGTAAACTG
1 TCCATATGTTCCAGAAGAACATATGTAAACTG
587731 TCCATATGT
1 TCCATATGT
587740 CTCGAAAGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 4 0.12
30 15 0.44
31 14 0.41
32 1 0.03
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (32 bp):
TCCATATGTTCCAGAAGAACATATGTAAACTG
Found at i:587733 original size:31 final size:31
Alignment explanation
Indices: 587670--587757 Score: 92
Period size: 31 Copynumber: 2.9 Consensus size: 31
587660 TAAGGACCTA
* * *
587670 TCCATATGT-TCCAGAGAACATAGAT-AACTG
1 TCCATATGTCTCGAAAG-ACATAGGTAAACTG
* *
587700 TCCATATGTC-CTGAAGGACATATGTAAACTG
1 TCCATATGTCTC-GAAAGACATAGGTAAACTG
587731 TCCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCTCGAAAGACATAGGTAA
587758 CCCTCGACTC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
30 16 0.34
31 30 0.64
32 1 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.27
Consensus pattern (31 bp):
TCCATATGTCTCGAAAGACATAGGTAAACTG
Found at i:593486 original size:27 final size:27
Alignment explanation
Indices: 593456--593508 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
593446 AAGATTTTAG
*
593456 AGAACTGAAATATAAGTGTTCTAAAAT
1 AGAACTGAAATAGAAGTGTTCTAAAAT
*
593483 AGAAGTGAAATAGAAGTGTTCTAAAA
1 AGAACTGAAATAGAAGTGTTCTAAAA
593509 AGGCTAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (27 bp):
AGAACTGAAATAGAAGTGTTCTAAAAT
Found at i:594749 original size:66 final size:66
Alignment explanation
Indices: 594636--594840 Score: 177
Period size: 66 Copynumber: 3.1 Consensus size: 66
594626 TATGTTTCTT
* * *
594636 TTGAAACAAATTTTATCTCCCTCGAGACAGTTTCTCGTGAAACACC-AACATTTGAGATCATTTC
1 TTGAAACAAATTTTATCTCCCTCGAGACAGATTCTCATAAAACACCAAAC-TTTGAGATCATTTC
594700 CC
65 CC
* * * * **
594702 TTGAAA-ATAATTTTATCTCCCTTGAGATAGATTCTTATAAAATACCAAACTTTGAGATTGTTTC
1 TTGAAACA-AATTTTATCTCCCTCGAGACAGATTCTCATAAAACACCAAACTTTGAGATCATTTC
594766 CC
65 CC
** * * * * * * *
594768 TTGAAACAACCTTTGTCTCCCTTGAGACA-ACTTCTCTTGAAGCATC-ATCTTTGAGTAT-ATTT
1 TTGAAACAAATTTTATCTCCCTCGAGACAGA-TTCTCATAAAACACCAAACTTTGAG-ATCATTT
594830 CCC
64 CCC
594833 TTGAAACA
1 TTGAAACA
594841 TTATCCCTAA
Statistics
Matches: 113, Mismatches: 21, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
65 24 0.21
66 85 0.75
67 4 0.04
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (66 bp):
TTGAAACAAATTTTATCTCCCTCGAGACAGATTCTCATAAAACACCAAACTTTGAGATCATTTCC
C
Found at i:594783 original size:21 final size:21
Alignment explanation
Indices: 594759--594798 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
594749 AACTTTGAGA
*
594759 TTGTTTCCCTTGAAACAACCT
1 TTGTCTCCCTTGAAACAACCT
*
594780 TTGTCTCCCTTGAGACAAC
1 TTGTCTCCCTTGAAACAAC
594799 TTCTCTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.35
Consensus pattern (21 bp):
TTGTCTCCCTTGAAACAACCT
Found at i:596098 original size:2 final size:2
Alignment explanation
Indices: 596091--596143 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
596081 TGGTTTAAGG
596091 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
596133 AT AT AT CAT AT
1 AT AT AT -AT AT
596144 TCGAAACAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:597892 original size:49 final size:49
Alignment explanation
Indices: 597835--597930 Score: 192
Period size: 49 Copynumber: 2.0 Consensus size: 49
597825 GACCAACCAC
597835 GGTGGTCGGAGATGGTCCTAGAGTCTCAAAAGACTCGTCTCATTCCCCA
1 GGTGGTCGGAGATGGTCCTAGAGTCTCAAAAGACTCGTCTCATTCCCCA
597884 GGTGGTCGGAGATGGTCCTAGAGTCTCAAAAGACTCGTCTCATTCCC
1 GGTGGTCGGAGATGGTCCTAGAGTCTCAAAAGACTCGTCTCATTCCC
597931 TAAAACTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.25
Consensus pattern (49 bp):
GGTGGTCGGAGATGGTCCTAGAGTCTCAAAAGACTCGTCTCATTCCCCA
Found at i:600471 original size:86 final size:85
Alignment explanation
Indices: 600124--600795 Score: 805
Period size: 85 Copynumber: 7.8 Consensus size: 85
600114 ATGTGTCATC
* * ** * *
600124 GAGCTGAATGGAATC-AGACTCGACAGTTTTTTGTTGACAGATAGTCATTCTCGCCTTGAGCTAT
1 GAGCTGAATGTAATCGA-ACTCGA-AGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTAT
* * *
600188 GCTATAAATTTGACATGCCCTT
64 GCTGTAAATTTGATATGTCCTT
* * * ** * *
600210 GAGCTGATTGGT-ATCAAACTCGAAGGTATTCATTGACAAATAACCCTTATCGCCTTGAGTTATG
1 GAGCTGAAT-GTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
* *
600274 CTATAAATTTGATATCTCCTT
65 CTGTAAATTTGATATGTCCTT
* * * *
600295 AAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA-CCTTCTCGCCTTGAGCTATAC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
* *
600359 TGTAGATTTGATATGCCCTT
66 TGTAAATTTGATATGTCCTT
* *
600379 GAGCTGAATAG-AATCGAACTCGAAGGTATTTGTTGACAGATAACCCTTCTCTCCCTTGAGTTAT
1 GAGCTGAAT-GTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTC-GCCTTGAGTTAT
600443 GCTGTAAATTTGATATGTCCTT
64 GCTGTAAATTTGATATGTCCTT
* * * *
600465 GAGCTGAATGTAATCGAACTTGAAGGTCTTTGTTGACAGGTAACCCTTCTTGCCTTGAGTTATGC
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
600530 TGTAGATTTGATATG-CCATT
66 TGTAAATTTGATATGTCC-TT
* * * *
600550 GAGCTGAATGTAATCGAACTCAAAGGTTTTTATTGATAGATAACCCTTCTCGCCTTGAGTTATGT
1 GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
*
600615 TGTAAATTTGATATGTCCAT
66 TGTAAATTTGATATGTCCTT
* *
600635 GAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGACATATAACCCTTCTCGCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGG-TTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATG
*
600700 CTGTAAATTTGATATATCCTT
65 CTGTAAATTTGATATGTCCTT
* * * * * *
600721 GAGCTGAGTGTAATTGAACTCAGAAGGTTTTTTTTCTAGCAGATAACCCTTTTCGCCTTGAGCTA
1 GAGCTGAATGTAATCGAACTC-GAAGGTTTTTGTT-GA-CAGATAACCCTTCTCGCCTTGAGTTA
*
600786 TGCTGCAAAT
63 TGCTGTAAAT
600796 AGTTCCTTTA
Statistics
Matches: 504, Mismatches: 69, Indels: 24
0.84 0.12 0.04
Matches are distributed among these distances:
84 77 0.15
85 217 0.43
86 170 0.34
87 8 0.02
88 32 0.06
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (85 bp):
GAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGTTATGC
TGTAAATTTGATATGTCCTT
Found at i:600682 original size:171 final size:171
Alignment explanation
Indices: 600111--600795 Score: 808
Period size: 171 Copynumber: 4.0 Consensus size: 171
600101 TACCATGTGG
* * * * ** *
600111 TTGATGTGT-CATCGAGCTGAATGGAATC-AGACTCGACAGTTTTTTGTTGACAGATAGTCATTC
1 TTGATATGTCCAT-GAGCTGAATGTAATCGA-ACTCGA-AGGTCTTTGTTGACAGATAACCCTTC
* * * * * *
600174 TCGCCTTGAGCTATGCTATAAATTTGACATGCCCTTGAGCTGATTGGT-ATCAAACTCGAAGGTA
63 TCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATAGTAATCGAACTCAAAGGTA
* * * *
600238 TTCATTGACAAATAACCCTTATCGCCTTGAGTTATGCTATAAAT
128 TTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
* * *
600282 TTGATATCTCCTTAAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAA-CCTTCTCG
1 TTGATATGTCCATGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
* * *
600346 CCTTGAGCTATACTGTAGATTTGATATGCCCTTGAGCTGAATAG-AATCGAACTCGAAGGTATTT
66 CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATAGTAATCGAACTCAAAGGTATTT
* *
600410 GTTGACAGATAACCCTTCTCTCCCTTGAGTTATGCTGTAAAT
131 ATTGACAGATAACCCTTCTC-GCCTTGAGTTATGCTGTAAAT
* * * *
600452 TTGATATGTCCTTGAGCTGAATGTAATCGAACTTGAAGGTCTTTGTTGACAGGTAACCCTTCTTG
1 TTGATATGTCCATGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
* * * *
600517 CCTTGAGTTATGCTGTAGATTTGATATGCCATTGAGCTGAAT-GTAATCGAACTCAAAGGTTTTT
66 CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATAGTAATCGAACTCAAAGGTATTT
* *
600581 ATTGATAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAAT
131 ATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
* * *
600622 TTGATATGTCCATGAGCTGAATGTAATCGAACTCGAAGGTTTTTTGCTGACATATAACCCTTCTC
1 TTGATATGTCCATGAGCTGAATGTAATCGAACTCGAAGG-TCTTTGTTGACAGATAACCCTTCTC
* ** * * *
600687 GCCTTGAGTTATGCTGTAAATTTGATATATCCTTGAGCTGAGT-GTAATTGAACTCAGAAGGTTT
65 GCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATAGTAATCGAACTCA-AAGGTAT
* * * * *
600751 TTTTTCTAGCAGATAACCCTTTTCGCCTTGAGCTATGCTGCAAAT
129 TTATT-GA-CAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
600796 AGTTCCTTTA
Statistics
Matches: 448, Mismatches: 56, Indels: 17
0.86 0.11 0.03
Matches are distributed among these distances:
169 79 0.18
170 145 0.32
171 178 0.40
172 14 0.03
173 1 0.00
174 31 0.07
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (171 bp):
TTGATATGTCCATGAGCTGAATGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
CCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATAGTAATCGAACTCAAAGGTATTT
ATTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAAT
Found at i:606278 original size:15 final size:16
Alignment explanation
Indices: 606244--606291 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
606234 ATGAATAAAT
*
606244 AATAAAAAACAATAATA
1 AATAATAAA-AATAATA
*
606261 AATAATACAAATAA-A
1 AATAATAAAAATAATA
606276 AATAATAAAAATAATA
1 AATAATAAAAATAATA
606292 TTATTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 14 0.52
16 6 0.22
17 7 0.26
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (16 bp):
AATAATAAAAATAATA
Found at i:606307 original size:2 final size:2
Alignment explanation
Indices: 606300--606341 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
606290 TATTATTTAA
606300 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
606342 TTATTTTCCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:606372 original size:36 final size:35
Alignment explanation
Indices: 606331--606690 Score: 304
Period size: 36 Copynumber: 10.3 Consensus size: 35
606321 TATATATATA
*
606331 TATATATATATTTATTTTCCAAAAT-TTTTCTAAAAC
1 TATATATATATTTATTTT-CAAAATGTTTT-AAAAAC
* * *
606367 CATATAT-TATATATTTTCAAAATATTTTAAAAAC
1 TATATATATATTTATTTTCAAAATGTTTTAAAAAC
606401 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATA-TATAT-T-TATTTTCAAAATGTTTTAAAAAC
*
606439 TATATATTATATATATTTTTTCAAAATGTTTTAAAAAC
1 TATATA-TATAT-T-TATTTTCAAAATGTTTTAAAAAC
*
606477 TATATAT-TATATAAGTTTTCAAAATGTTTTAAAAAC
1 TATATATATAT-TTA-TTTTCAAAATGTTTTAAAAAC
* * * *
606513 TATATATATA--TA---T----AT-ATATATATA-
1 TATATATATATTTATTTTCAAAATGTTTTAAAAAC
* * *
606537 TATATATATATATATATTCAAAATGTTTTGAAAAC
1 TATATATATATTTATTTTCAAAATGTTTTAAAAAC
*
606572 TATATAT-TATATAAGTTTTCAAAATGTTTTAAAAAC
1 TATATATATAT-TTA-TTTTCAAAATGTTTTAAAAAC
* *
606608 TATATATTATATATATATTCAAAATGTTTTAAAAAC
1 TATATA-TATATTTATTTTCAAAATGTTTTAAAAAC
* *
606644 TATATAT-TATATAAGTTTTCAAAATGTTGTAAAAAC
1 TATATATATAT-TTA-TTTTCAAAATGTTTTAAAAAC
606680 TATAT-TATATT
1 TATATATATATT
606691 ATATATATAT
Statistics
Matches: 269, Mismatches: 30, Indels: 51
0.77 0.09 0.15
Matches are distributed among these distances:
24 10 0.04
25 5 0.02
26 4 0.01
29 1 0.00
30 1 0.00
33 2 0.01
34 27 0.10
35 26 0.10
36 120 0.45
37 5 0.02
38 68 0.25
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (35 bp):
TATATATATATTTATTTTCAAAATGTTTTAAAAAC
Found at i:606425 original size:38 final size:38
Alignment explanation
Indices: 606327--606531 Score: 271
Period size: 38 Copynumber: 5.5 Consensus size: 38
606317 TATATATATA
* *
606327 TATATATATATATATTTATTTTCCAAAAT-TTTTCTAAAAC
1 TATATAT-TATATATATATTTT-CAAAATGTTTT-AAAAAC
* *
606367 --CATA-TAT-TATATATTTTCAAAATATTTTAAAAAC
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
606401 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
*
606439 TATATATTATATATATTTTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
*
606477 TATATATTATATA-A-GTTTTCAAAATGTTTTAAAAAC
1 TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
606513 TATATATATATATATATAT
1 TATATAT-TATATATATAT
606532 ATATATATAT
Statistics
Matches: 149, Mismatches: 8, Indels: 17
0.86 0.05 0.10
Matches are distributed among these distances:
34 11 0.07
35 13 0.09
36 34 0.23
37 10 0.07
38 80 0.54
39 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (38 bp):
TATATATTATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:606520 original size:2 final size:2
Alignment explanation
Indices: 606513--606553 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
606503 TTTTAAAAAC
606513 TA TA TA 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 TA TA TA T
606554 TCAAAATGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:606562 original size:95 final size:93
Alignment explanation
Indices: 606439--606625 Score: 329
Period size: 95 Copynumber: 2.0 Consensus size: 93
606429 TTTTAAAAAC
* *
606439 TATATATTATATATATTTTTTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGT
1 TATATATTATATATATATATTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGT
606504 TTTAAAAACTATATATATATATATATATA
66 TTTAAAAACTATATAT-TATATATATATA
*
606533 TATATATATATATATATATATTCAAAATGTTTTGAAAACTATATATTATATAAGTTTTCAAAATG
1 TATATAT-TATATATATATATTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATG
606598 TTTTAAAAACTATATATTATATATATAT
65 TTTTAAAAACTATATATTATATATATAT
606626 TCAAAATGTT
Statistics
Matches: 89, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
94 18 0.20
95 71 0.80
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (93 bp):
TATATATTATATATATATATTCAAAATGTTTTAAAAACTATATATTATATAAGTTTTCAAAATGT
TTTAAAAACTATATATTATATATATATA
Found at i:606629 original size:131 final size:131
Alignment explanation
Indices: 606401--606656 Score: 428
Period size: 131 Copynumber: 2.0 Consensus size: 131
606391 TTTTAAAAAC
* *
606401 TATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATATATATTTTTTCAAAAT
1 TATATATTATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATGTTTTCAAAAT
*
606466 GTTTTAAAAACTATATATTATATAAGTTTTCAAAATGTTTTAAAAACTATATATATATATATATA
66 GTTTTAAAAACTATATATTATATAAGTATTCAAAATGTTTTAAAAACTATATAT-TATATATATA
606531 TA
130 TA
*
606533 TATATATATATATATATATATTCAAAATGTTTTGAAAACTATATATTATATA-A-GTTTTCAAAA
1 TATATAT-TATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATGTTTTCAAAA
606596 TGTTTTAAAAACTATATATTATATATA-TATTCAAAATGTTTTAAAAACTATATATTATATA
65 TGTTTTAAAAACTATATATTATATA-AGTATTCAAAATGTTTTAAAAACTATATATTATATA
606657 AGTTTTCAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
130 6 0.05
131 61 0.52
132 9 0.08
133 42 0.36
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (131 bp):
TATATATTATATATATATATTCAAAATGTTTTAAAAACTATATATTATATATATGTTTTCAAAAT
GTTTTAAAAACTATATATTATATAAGTATTCAAAATGTTTTAAAAACTATATATTATATATATAT
A
Found at i:608215 original size:30 final size:31
Alignment explanation
Indices: 608176--608234 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
608166 ATCATTGTTC
608176 AATATTAAAACAAAACAAA-ATTAAATTAAGA
1 AATATTAAAACAAAA-AAACATTAAATTAAGA
* *
608207 AATA-TAAAATAAAAAAACTTTAAATTAA
1 AATATTAAAACAAAAAAACATTAAATTAA
608235 AAGGATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.72
31 4 0.16
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (31 bp):
AATATTAAAACAAAAAAACATTAAATTAAGA
Found at i:609420 original size:4 final size:4
Alignment explanation
Indices: 609401--609451 Score: 57
Period size: 4 Copynumber: 11.5 Consensus size: 4
609391 GAAATATTAA
609401 AAAT GAAAT GAAAT AAAT AAAT AAAT AAAAT AAAAT AAAT AATAT AAAT
1 AAAT -AAAT -AAAT AAAT AAAT AAAT -AAAT -AAAT AAAT AA-AT AAAT
609450 AA
1 AA
609452 TAATATATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
4 22 0.50
5 22 0.50
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:609422 original size:27 final size:27
Alignment explanation
Indices: 609400--609451 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
609390 TGAAATATTA
*
609400 AAAATGAAATGAAATAA-ATAAATAAAT
1 AAAATAAAAT-AAATAATATAAATAAAT
609427 AAAATAAAATAAATAATATAAATAA
1 AAAATAAAATAAATAATATAAATAA
609452 TAATATATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
AAAATAAAATAAATAATATAAATAAAT
Found at i:609453 original size:9 final size:8
Alignment explanation
Indices: 609401--609451 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 8
609391 GAAATATTAA
609401 AAATGAAAT
1 AAAT-AAAT
609410 GAAATAAAT
1 -AAATAAAT
609419 AAATAAAT
1 AAATAAAT
609427 AAAATAAAAT
1 -AAAT-AAAT
609437 AAATAATAT
1 AAATAA-AT
609446 AAATAA
1 AAATAA
609452 TAATATATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
8 10 0.26
9 20 0.53
10 8 0.21
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (8 bp):
AAATAAAT
Found at i:609453 original size:12 final size:13
Alignment explanation
Indices: 609406--609458 Score: 65
Period size: 12 Copynumber: 4.1 Consensus size: 13
609396 ATTAAAAATG
609406 AAATGAAATAA-AT
1 AAAT-AAATAATAT
*
609419 AAATAAATAAAAT
1 AAATAAATAATAT
609432 AAAATAAATAATAT
1 -AAATAAATAATAT
609446 AAAT-AATAATAT
1 AAATAAATAATAT
609458 A
1 A
609459 TGCTAAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
12 15 0.41
13 10 0.27
14 12 0.32
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:609467 original size:35 final size:35
Alignment explanation
Indices: 609428--609495 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
609418 TAAATAAATA
609428 AAATAAAATAAATAA-TATA-AATAATAATATATGCT
1 AAATAAAATAAA-AACTATATAAT-ATAATATATGCT
* *
609463 AAATATAATAAAAACTATATAATATATTATATG
1 AAATAAAATAAAAACTATATAATATAATATATG
609496 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 2 0.07
35 24 0.83
36 3 0.10
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (35 bp):
AAATAAAATAAAAACTATATAATATAATATATGCT
Found at i:609794 original size:36 final size:35
Alignment explanation
Indices: 609484--609794 Score: 241
Period size: 36 Copynumber: 8.5 Consensus size: 35
609474 AAACTATATA
* * *
609484 ATATATTATATGTTTTCAAAAAACATTTTTTAAAGAAAT
1 ATATATTATACGTTTTC--AAAAC-TATTTTAAA-AACT
* * * *
609523 ATATATTATAAGTTTTTAAAACCATTTTTTTTAAAAACC
1 ATATATTATACGTTTTCAAAA-C---TATTTTAAAAACT
* * *
609562 ATATACTATACATTTTCAAAA-TCATTTTTTAAAACT
1 ATATATTATACGTTTTCAAAACT-A-TTTTAAAAACT
* *
609598 ATATATTATACATTTTCAAAA-TCATTTTAAAAAGCC
1 ATATATTATACGTTTTCAAAACT-ATTTTAAAAA-CT
* ** *
609634 ATATTATATAAATATTTTGAAAACCGT-TTTTAAAAACT
1 ATA-TAT-TATACGTTTTCAAAA-C-TATTTTAAAAACT
* **
609672 ATATATCATACGTTTTTGAAACTATTTTTAAAAACT
1 ATATATTATACGTTTTCAAAACTA-TTTTAAAAACT
609708 ATATATTATACGTTTTCAAAACTATTTTAAAAACT
1 ATATATTATACGTTTTCAAAACTATTTTAAAAACT
*
609743 ATATATTATACGTTTTCAAAACTATTTCAAAAAACT
1 ATATATTATACGTTTTCAAAACTATTT-TAAAAACT
* *
609779 ATATTTTATATGTTTT
1 ATATATTATACGTTTT
609795 TTTCCAAAAA
Statistics
Matches: 227, Mismatches: 31, Indels: 31
0.79 0.11 0.11
Matches are distributed among these distances:
34 2 0.01
35 47 0.21
36 98 0.43
37 10 0.04
38 17 0.07
39 43 0.19
40 9 0.04
41 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (35 bp):
ATATATTATACGTTTTCAAAACTATTTTAAAAACT
Found at i:629854 original size:20 final size:20
Alignment explanation
Indices: 629829--629889 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
629819 ATCAAGCTTG
629829 AAAATGAATCTACAACCTCA
1 AAAATGAATCTACAACCTCA
*
629849 AAAATGAATCTACAACCTCG
1 AAAATGAATCTACAACCTCA
629869 AAAATGAATCTACAACCTCA
1 AAAATGAATCTACAACCTCA
629889 A
1 A
629890 TAACCTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.49, C:0.25, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAATGAATCTACAACCTCA
Found at i:647923 original size:19 final size:20
Alignment explanation
Indices: 647899--647943 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
647889 CAAAATGACC
*
647899 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
647918 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
647938 AAATTT
1 CAATTT
647944 ACACCATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Done.