Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008653.1 Hibiscus syriacus cultivar Beakdansim tig00111644_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: 1778368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1662499 original size:103 final size:103
Alignment explanation
Indices: 1662374--1662585 Score: 361
Period size: 103 Copynumber: 2.1 Consensus size: 103
1662364 GCTACTGTTG
*
1662374 ATTTGTTTCCTCTATAGTCCTTGTTTGTGTTGTTGGTTGTTCATTCAGATTGCTTGTATAAGGTT
1 ATTTGTTTCCTCTATAGTCCTTGTTTGTGTTGTTGGTTGTTCATTCAGATTGCTTGTATAAGATT
* *
1662439 GTTAGCTGCCTTTATTTAGGATTTAAATAAACTGTTTA
66 GTTAGCTACCTTTATTTAGGATTTAAATAAAATGTTTA
* * *
1662477 ATTTGTTTCCTCTGTAGTCCTTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCTTGTATGAGATT
1 ATTTGTTTCCTCTATAGTCCTTGTTTGTGTTGTTGGTTGTTCATTCAGATTGCTTGTATAAGATT
*
1662542 GTTAGCTACCTTTATTTAGGATTTGAATAAAATGTTTA
66 GTTAGCTACCTTTATTTAGGATTTAAATAAAATGTTTA
1662580 ATTTGT
1 ATTTGT
1662586 AGCTACTGTT
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.19, C:0.11, G:0.20, T:0.50
Consensus pattern (103 bp):
ATTTGTTTCCTCTATAGTCCTTGTTTGTGTTGTTGGTTGTTCATTCAGATTGCTTGTATAAGATT
GTTAGCTACCTTTATTTAGGATTTAAATAAAATGTTTA
Found at i:1665126 original size:14 final size:14
Alignment explanation
Indices: 1665107--1665153 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
1665097 TATTTTTCTT
1665107 TATATAAATTAAAC
1 TATATAAATTAAAC
1665121 TATAT-AATT----
1 TATATAAATTAAAC
1665130 TATATAAATTAAAC
1 TATATAAATTAAAC
*
1665144 TATATTAATT
1 TATATAAATT
1665154 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:1665132 original size:23 final size:24
Alignment explanation
Indices: 1665105--1665154 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
1665095 ATTATTTTTC
1665105 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
1665128 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
1665152 TTT
1 TTT
1665155 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:1665448 original size:16 final size:16
Alignment explanation
Indices: 1665424--1665479 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
1665414 TCATTTACAG
*
1665424 GTCATGTTAAAAACAT
1 GTCAGGTTAAAAACAT
* *
1665440 GTCAGGTTAAAAATAG
1 GTCAGGTTAAAAACAT
* *
1665456 GTCAGGTTCATAACAT
1 GTCAGGTTAAAAACAT
*
1665472 GTTAGGTT
1 GTCAGGTT
1665480 GGAAACAGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (16 bp):
GTCAGGTTAAAAACAT
Found at i:1665490 original size:32 final size:32
Alignment explanation
Indices: 1665420--1665490 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
1665410 TCGATCATTT
*
1665420 ACAGGTCATGTTAAAAACATGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAAACATGTCAGGTTAAAA
* * * * **
1665452 ATAGGTCAGGTTCATAACATGTTAGGTTGGAA
1 ACAGGTCAGGTTAAAAACATGTCAGGTTAAAA
1665484 ACAGGTC
1 ACAGGTC
1665491 GGGTAATGCC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.27
Consensus pattern (32 bp):
ACAGGTCAGGTTAAAAACATGTCAGGTTAAAA
Found at i:1666079 original size:17 final size:15
Alignment explanation
Indices: 1666059--1666093 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
1666049 ATGAACTGAT
1666059 TTTTTTAATAAAAAACA
1 TTTTTT-ATAAAAAA-A
1666076 TTTTTTATAAAAAAA
1 TTTTTTATAAAAAAA
1666091 TTT
1 TTT
1666094 AAAATAACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 8 0.44
17 6 0.33
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTTTATAAAAAAA
Found at i:1668511 original size:16 final size:16
Alignment explanation
Indices: 1668490--1668522 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1668480 ACATGATTTT
*
1668490 TTTAATTTAATATAAA
1 TTTAATTTAAAATAAA
1668506 TTTAATTTAAAATAAA
1 TTTAATTTAAAATAAA
1668522 T
1 T
1668523 AATAAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAATTTAAAATAAA
Found at i:1680260 original size:18 final size:18
Alignment explanation
Indices: 1680214--1680262 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
1680204 TCTATTGGGG
*
1680214 GTATCGATACTACCCCTTGA
1 GTATCGATAC--CACCTTGA
*
1680234 -TATCAATACCACCTTGA
1 GTATCGATACCACCTTGA
1680251 GTATCGATACCA
1 GTATCGATACCA
1680263 AAATTGCACA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 7 0.28
18 10 0.40
19 8 0.32
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (18 bp):
GTATCGATACCACCTTGA
Found at i:1687408 original size:107 final size:106
Alignment explanation
Indices: 1687204--1687432 Score: 343
Period size: 107 Copynumber: 2.2 Consensus size: 106
1687194 TCAAAAAATA
* *
1687204 CCCTAGTATCGATACCCCTATGGGGAGTATCAATACTACCCCTTGAGTATATGTACCAAAATTGC
1 CCCTAATATCGATACCCCTATGGGGAGTATCAATACTACCCCTTGAGTATATGTACCAAAATTGA
* * * *
1687269 ACACTAAAATCCTAAATAAAACCTCGAGTATCGATACTCAC
66 ACACTAAAATCCAAAATAAAACCCCAAATATCGATACTCAC
* *
1687310 CCGTAATATTGATACCCCTATGGGGAGTATCAATACTACCCCCTTGAGTATCA-GTACCAAAATT
1 CCCTAATATCGATACCCCTATGGGGAGTATCAATACTA-CCCCTTGAGTAT-ATGTACCAAAATT
*
1687374 GAACACTAAAATCCAAAATAGAACCCCAAATATCGATACTCAC
64 GAACACTAAAATCCAAAATAAAACCCCAAATATCGATACTCAC
*
1687417 CCCTGATATCGATACC
1 CCCTAATATCGATACC
1687433 ATACGAACAG
Statistics
Matches: 109, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
106 35 0.32
107 73 0.67
108 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (106 bp):
CCCTAATATCGATACCCCTATGGGGAGTATCAATACTACCCCTTGAGTATATGTACCAAAATTGA
ACACTAAAATCCAAAATAAAACCCCAAATATCGATACTCAC
Found at i:1694371 original size:23 final size:23
Alignment explanation
Indices: 1694344--1694404 Score: 106
Period size: 22 Copynumber: 2.7 Consensus size: 23
1694334 AATTAATTTT
1694344 AAAAAATTATAATTTTTTAATAG
1 AAAAAATTATAATTTTTTAATAG
1694367 -AAAAATTATAATTTTTTAATAG
1 AAAAAATTATAATTTTTTAATAG
*
1694389 AAAAAAATATAATTTT
1 AAAAAATTATAATTTT
1694405 GATAGAAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 22 0.61
23 14 0.39
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
AAAAAATTATAATTTTTTAATAG
Found at i:1694409 original size:21 final size:22
Alignment explanation
Indices: 1694344--1694412 Score: 88
Period size: 22 Copynumber: 3.1 Consensus size: 22
1694334 AATTAATTTT
1694344 AAAAAATTATAATTTTTTAATAG
1 AAAAAATTATAA-TTTTTAATAG
1694367 -AAAAATTATAATTTTTTAATAG
1 AAAAAATTATAA-TTTTTAATAG
* *
1694389 AAAAAAATATAA-TTTTGATAG
1 AAAAAATTATAATTTTTAATAG
1694410 AAA
1 AAA
1694413 TAGCTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.26
22 22 0.51
23 10 0.23
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (22 bp):
AAAAAATTATAATTTTTAATAG
Found at i:1696493 original size:16 final size:16
Alignment explanation
Indices: 1696470--1696524 Score: 92
Period size: 16 Copynumber: 3.4 Consensus size: 16
1696460 GGGTCTCCAA
1696470 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
1696486 CATTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
*
1696502 TGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
1696518 CGTTTAT
1 CGTTTAT
1696525 TTATTAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:1697740 original size:33 final size:33
Alignment explanation
Indices: 1697696--1697761 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1697686 AAGAAAAAGA
1697696 GAAATCAAAATTTTAGTCCTCT-ACATTGGAAAT
1 GAAATCAAAATTTTAGTCCTCTGACA-TGGAAAT
* *
1697729 GAAATCTAAATTTTAGTTCTCTGACATGGAAAT
1 GAAATCAAAATTTTAGTCCTCTGACATGGAAAT
1697762 AGTTAGCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (33 bp):
GAAATCAAAATTTTAGTCCTCTGACATGGAAAT
Found at i:1699432 original size:2 final size:2
Alignment explanation
Indices: 1699419--1699453 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
1699409 ATAGTTGACG
1699419 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1699454 AATTAAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1699711 original size:24 final size:24
Alignment explanation
Indices: 1699678--1699731 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1699668 TCGTTCAATT
*
1699678 GAAGTTCTTCGTGGTGAAGGAACG
1 GAAGTACTTCGTGGTGAAGGAACG
1699702 GAAGTACTTCGTGGTGAAGGAACG
1 GAAGTACTTCGTGGTGAAGGAACG
1699726 GAAGTA
1 GAAGTA
1699732 TATACGACTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.37, T:0.22
Consensus pattern (24 bp):
GAAGTACTTCGTGGTGAAGGAACG
Found at i:1702579 original size:4 final size:4
Alignment explanation
Indices: 1702570--1702674 Score: 156
Period size: 4 Copynumber: 25.5 Consensus size: 4
1702560 TGTTCAGTGA
1702570 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
1702618 ATAC ATAC ATAC ATAC ATAC ATAC ATAC GGACAC AGTAC GTAC GTAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC --ATAC A-TAC ATAC ATAC ATAC
1702669 ATAC AT
1 ATAC AT
1702675 TATTTATAAC
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
4 89 0.95
5 2 0.02
6 3 0.03
ACGTcount: A:0.47, C:0.25, G:0.05, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1706125 original size:30 final size:30
Alignment explanation
Indices: 1706089--1706160 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
1706079 AAGTTAATTT
* *
1706089 TTAATTTTACCCTGAACTTTAGATATAATA
1 TTAATTTAACCCTGAACTTTAGATAAAATA
* * *
1706119 TTAATTTAATCCTTAATTTTAGATAAAATA
1 TTAATTTAACCCTGAACTTTAGATAAAATA
* *
1706149 TCAAATTAACCC
1 TTAATTTAACCC
1706161 CTAAATTCGA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (30 bp):
TTAATTTAACCCTGAACTTTAGATAAAATA
Found at i:1706543 original size:31 final size:32
Alignment explanation
Indices: 1706508--1706570 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
1706498 TGTTACATCT
*
1706508 TTAATACT-TACAAATAGTAAGAAAAA-TATAA
1 TTAATACTATACAAATAATAA-AAAAATTATAA
* *
1706539 TTAATATTATACATATAATAAAAAAATTATAA
1 TTAATACTATACAAATAATAAAAAAATTATAA
1706571 CATAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 12 0.44
32 15 0.56
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (32 bp):
TTAATACTATACAAATAATAAAAAAATTATAA
Found at i:1707789 original size:21 final size:21
Alignment explanation
Indices: 1707760--1707812 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1707750 ATTCTGACTA
1707760 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
1707781 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
1707802 TCGCAATGCGA
1 TCGCATTGCGA
1707813 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1707827 original size:20 final size:20
Alignment explanation
Indices: 1707802--1707956 Score: 211
Period size: 20 Copynumber: 7.7 Consensus size: 20
1707792 TTTTCCTAAT
1707802 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1707822 TCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
1707842 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
1707863 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1707883 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
1707903 TCGCAATGCAAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
1707924 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1707944 TCGCAATGCGAAT
1 TCGCAATGCGAAT
1707957 CTGACTATCG
Statistics
Matches: 115, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
20 81 0.70
21 34 0.30
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1707833 original size:41 final size:40
Alignment explanation
Indices: 1707802--1707954 Score: 207
Period size: 41 Copynumber: 3.8 Consensus size: 40
1707792 TTTTCCTAAT
*
1707802 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
* * *
1707842 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAA-TACGTAAATCGCAATGCGATTACGTAAA
* * * *
1707883 TCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGC-GATTACGTAAA
*
1707924 TCGCAATACGAATACGTAAATCGCAATGCGA
1 TCGCAATGCGAATACGTAAATCGCAATGCGA
1707955 ATCTGACTAT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
40 28 0.29
41 69 0.71
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAA
Found at i:1707869 original size:61 final size:61
Alignment explanation
Indices: 1707802--1707954 Score: 279
Period size: 61 Copynumber: 2.5 Consensus size: 61
1707792 TTTTCCTAAT
* *
1707802 TCGCAATGCGAATACGTAAATCGCAACGCGATTACGTAAATCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAA
1707863 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAA
*
1707924 TCGCAATACGAATACGTAAATCGCAATGCGA
1 TCGCAATGCGAATACGTAAATCGCAATGCGA
1707955 ATCTGACTAT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (61 bp):
TCGCAATGCGAATACGTAAATCGCAATGCGATTACGTAAATCGCAATGCAAATTAGGAAAA
Found at i:1707966 original size:20 final size:20
Alignment explanation
Indices: 1707943--1707994 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
1707933 GAATACGTAA
1707943 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
1707963 ATCGCAATGCGAATCTGACT
1 ATCGCAATGCGAATCTGACT
1707983 ATCGCAATGCGA
1 ATCGCAATGCGA
1707995 TTTACATAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATCTGACT
Found at i:1708553 original size:20 final size:19
Alignment explanation
Indices: 1708528--1708598 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 19
1708518 TTCTAAACTT
1708528 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
1708548 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
1708568 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
1708589 AAAATCGCAA
1 AAAATCGCAA
1708599 TGAGAGAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
20 30 0.68
21 14 0.32
ACGTcount: A:0.52, C:0.18, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:1708589 original size:21 final size:21
Alignment explanation
Indices: 1708528--1708606 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
1708518 TTCTAAACTT
1708528 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
1708548 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
1708568 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
*
1708589 AAAATCGCAATGAGAGAA
1 AAAATCGCAACGAGAGAA
1708607 TCGCAACGCG
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:1708644 original size:19 final size:19
Alignment explanation
Indices: 1708609--1708645 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1708599 TGAGAGAATC
**
1708609 GCAACGCGAAATGAAAATT
1 GCAACGCGAAACCAAAATT
1708628 GCAACGCGAAACCAAAAT
1 GCAACGCGAAACCAAAAT
1708646 CGCATTGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.11
Consensus pattern (19 bp):
GCAACGCGAAACCAAAATT
Found at i:1708686 original size:14 final size:14
Alignment explanation
Indices: 1708667--1708753 Score: 57
Period size: 14 Copynumber: 5.6 Consensus size: 14
1708657 TTTCATTTCG
1708667 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1708681 CGTTGCGATTAATTTCG
1 CGTTGCGA-T--TCTCT
*
1708698 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
*
1708712 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
1708731 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
1708745 CGTTGCGAT
1 CGTTGCGAT
1708754 AGTCATTTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 28 0.51
15 1 0.02
16 4 0.07
17 13 0.24
19 9 0.16
ACGTcount: A:0.10, C:0.22, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1708734 original size:33 final size:33
Alignment explanation
Indices: 1708650--1708802 Score: 184
Period size: 33 Copynumber: 4.5 Consensus size: 33
1708640 CAAAATCGCA
*
1708650 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
*
1708683 TTGCGA--TTAATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1708714 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
** *
1708747 TTGCGATAGTCATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTT--G----TGATTCTCTCG
1708787 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1708803 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
31 29 0.28
33 43 0.42
34 6 0.06
36 1 0.01
39 1 0.01
40 23 0.22
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
Found at i:1708779 original size:20 final size:21
Alignment explanation
Indices: 1708739--1708802 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 21
1708729 CGCGTTGTGA
* **
1708739 TTCTCTCGTTGCGATAGTCAT
1 TTCTCGCGTTGCGATTTTCAT
1708760 TTC-CGCGTTGCGATTTTCA-
1 TTCTCGCGTTGCGATTTTCAT
*
1708779 TTCTCTCGTTGCGATTTTCAT
1 TTCTCGCGTTGCGATTTTCAT
1708800 TTC
1 TTC
1708803 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 3 0.08
20 28 0.76
21 6 0.16
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCGCGTTGCGATTTTCAT
Found at i:1710659 original size:94 final size:94
Alignment explanation
Indices: 1710449--1710799 Score: 570
Period size: 94 Copynumber: 3.8 Consensus size: 94
1710439 TAGATTGCTT
* * *
1710449 AGTAAATTTATTCGGTTGCTGCCAATACTGATAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
1710510 ATTTGTCTTT-TGTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1710537 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1710602 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1710631 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1710696 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
1710725 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1710790 ATTTGTCTTT
66 ATTTGTCTTT
1710800 TGGTTGAAGT
Statistics
Matches: 248, Mismatches: 9, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
88 34 0.14
90 3 0.01
91 2 0.01
92 29 0.12
93 15 0.06
94 165 0.67
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1710986 original size:19 final size:19
Alignment explanation
Indices: 1710902--1710976 Score: 97
Period size: 19 Copynumber: 4.2 Consensus size: 19
1710892 TCTTTTGGTT
1710902 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1710921 GAAACGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1710938 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1710954 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1710973 GAAA
1 GAAA
1710977 CTATAATCGC
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
14 10 0.21
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 32 0.67
ACGTcount: A:0.48, C:0.21, G:0.23, T:0.08
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1711005 original size:19 final size:19
Alignment explanation
Indices: 1710983--1711046 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
1710973 GAAACTATAA
1710983 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1711002 TCGCATTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1711016 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1711035 TTGCGTTGCGAT
1 TCGCGTTGCGAT
1711047 AGTCATTTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
14 8 0.24
16 3 0.09
17 3 0.09
19 19 0.58
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1711052 original size:19 final size:19
Alignment explanation
Indices: 1711019--1711055 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1711009 ACGATTCTCT
**
1711019 CGTTGCGATTTTCATTTTG
1 CGTTGCGATAGTCATTTTG
1711038 CGTTGCGATAGTCATTTT
1 CGTTGCGATAGTCATTTT
1711056 TAACGTTGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.16, G:0.22, T:0.49
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTTG
Found at i:1711588 original size:21 final size:21
Alignment explanation
Indices: 1711529--1711589 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
1711519 CTCGAGAGTC
1711529 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
1711550 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
1711571 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
1711590 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:1712953 original size:14 final size:14
Alignment explanation
Indices: 1712934--1712969 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1712924 ATTGTTTAAT
1712934 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1712948 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1712962 TGATTTGT
1 TGATTTGT
1712970 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1713129 original size:33 final size:33
Alignment explanation
Indices: 1713087--1713169 Score: 123
Period size: 33 Copynumber: 2.5 Consensus size: 33
1713077 TCATAATGCA
* * *
1713087 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGACAAAAGCGCAACGCG
1713120 AAATGAAAATCGCAACGACAAAAGCGCAACGCG
1 AAATGAAAATCGCAACGACAAAAGCGCAACGCG
1713153 AAACT-AAAATCGCAACG
1 AAA-TGAAAATCGCAACG
1713170 CGAAACTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.20, T:0.08
Consensus pattern (33 bp):
AAATGAAAATCGCAACGACAAAAGCGCAACGCG
Found at i:1713191 original size:19 final size:19
Alignment explanation
Indices: 1713108--1713184 Score: 85
Period size: 19 Copynumber: 4.3 Consensus size: 19
1713098 GCAACGAGAG
1713108 AATCGCAACGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
1713127 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
1713141 AAGCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
1713160 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
1713179 ATTCGC
1 AATCGC
1713185 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 33 0.67
ACGTcount: A:0.45, C:0.26, G:0.18, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:1713202 original size:19 final size:19
Alignment explanation
Indices: 1713180--1713297 Score: 85
Period size: 19 Copynumber: 6.7 Consensus size: 19
1713170 CGAAACTAAA
1713180 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1713199 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1713214 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1713232 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
1713247 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* **
1713265 TTCGCATTGCGATAGTCAT
1 TTCGCGTTGCGATTTTCAT
1713284 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1713298 AGACATTAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 21
0.68 0.13 0.19
Matches are distributed among these distances:
14 17 0.23
16 6 0.08
17 6 0.08
19 35 0.47
20 10 0.14
ACGTcount: A:0.12, C:0.25, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1713226 original size:33 final size:33
Alignment explanation
Indices: 1713184--1713277 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1713174 ACTAAATTCG
*
1713184 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1713217 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1713250 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1713278 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1713296 original size:20 final size:19
Alignment explanation
Indices: 1713250--1713304 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
1713240 GCGATTCTCT
**
1713250 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
1713269 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
*
1713289 CGTTGCGATAGACATT
1 CGTTGCGATAGTCATT
1713305 AAGATGATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:1715779 original size:24 final size:24
Alignment explanation
Indices: 1715752--1715798 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
1715742 ATCATAAAAA
1715752 TCTGAGTATTGACCAAGATCAAAG
1 TCTGAGTATTGACCAAGATCAAAG
*
1715776 TCTGGGTATTGACCAAGATCAAA
1 TCTGAGTATTGACCAAGATCAAA
1715799 TTTCGAATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (24 bp):
TCTGAGTATTGACCAAGATCAAAG
Found at i:1716676 original size:20 final size:20
Alignment explanation
Indices: 1716660--1716709 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1716650 TAGAATCTCG
1716660 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
1716680 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
1716700 TTGCGATTTA
1 TTGCGATTTA
1716710 GGAAAATCGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:1716735 original size:22 final size:21
Alignment explanation
Indices: 1716705--1716747 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1716695 TCGCATTGCG
1716705 ATTTAGGAAAATCGCAACGCGA
1 ATTTAGG-AAATCGCAACGCGA
* *
1716727 ATTTGGGAAATCGCAATGCGA
1 ATTTAGGAAATCGCAACGCGA
1716748 TAGTCAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (21 bp):
ATTTAGGAAATCGCAACGCGA
Found at i:1717527 original size:24 final size:24
Alignment explanation
Indices: 1717495--1717546 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1717485 TTTATCACAT
*
1717495 CTCAGTCAATAGGTTAACATCCAG
1 CTCAATCAATAGGTTAACATCCAG
1717519 CTCAATCAATAGGTTAACATCCAG
1 CTCAATCAATAGGTTAACATCCAG
1717543 CTCA
1 CTCA
1717547 GACAAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (24 bp):
CTCAATCAATAGGTTAACATCCAG
Found at i:1720681 original size:21 final size:22
Alignment explanation
Indices: 1720656--1720707 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
1720646 ACAAGGCGTT
*
1720656 TCGATACTCTATCA-AAGGGTA
1 TCGATACTCTATCATAAGAGTA
*
1720677 TCGATA--CTGTCATAAGAGTA
1 TCGATACTCTATCATAAGAGTA
1720697 TCGATACTCTA
1 TCGATACTCTA
1720708 GGGGGAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 5 0.20
20 12 0.48
21 6 0.24
22 2 0.08
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (22 bp):
TCGATACTCTATCATAAGAGTA
Found at i:1725870 original size:21 final size:19
Alignment explanation
Indices: 1725846--1725900 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
1725836 TTTTTCGTCT
1725846 ATAAAAAATTTAACATATTAA
1 ATAAAAAATTTAACATA--AA
* *
1725867 ATAAATAATTTAAGATAAA
1 ATAAAAAATTTAACATAAA
1725886 ATAACAAAAATTTAA
1 AT-A-AAAAATTTAA
1725901 ACAAATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
20 1 0.03
21 24 0.83
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
ATAAAAAATTTAACATAAA
Found at i:1735561 original size:2 final size:2
Alignment explanation
Indices: 1735554--1735581 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1735544 AAAAACACTA
1735554 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
1735582 GTCGAATAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1736338 original size:17 final size:16
Alignment explanation
Indices: 1736285--1736340 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
1736275 TTTTTAGTAC
*
1736285 TTTAAT-TTTAGTCCT
1 TTTAATATTTAATCCT
*
1736300 TTTATATATTTAATCAT
1 TTTA-ATATTTAATCCT
*
1736317 CTTTAATATTTGTATCCT
1 -TTTAATATTT-AATCCT
1736335 TTTAAT
1 TTTAAT
1736341 TTAGTCCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 4 0.12
16 2 0.06
17 19 0.58
18 8 0.24
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.59
Consensus pattern (16 bp):
TTTAATATTTAATCCT
Found at i:1737787 original size:28 final size:28
Alignment explanation
Indices: 1737728--1737787 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
1737718 TATTTTGTTT
* * *
1737728 ATTTATTTCGATTTTGACATCCTATTGA
1 ATTTATTTCAATTTGGACATCATATTGA
* * *
1737756 ATTTATTTCAATTTGGTCATCATTTTGG
1 ATTTATTTCAATTTGGACATCATATTGA
1737784 ATTT
1 ATTT
1737788 TGTTATTTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (28 bp):
ATTTATTTCAATTTGGACATCATATTGA
Found at i:1740052 original size:69 final size:69
Alignment explanation
Indices: 1739914--1740053 Score: 239
Period size: 68 Copynumber: 2.0 Consensus size: 69
1739904 TTGATTTGAG
* *
1739914 TTATTCGAGTTTCTATGCTAATTTTATATAATTATTTATAGTATTATGATAAGGATTGGTTCCAA
1 TTATTCGAGTTTCTATACTAATTTTATATAATTATTTATAGTATTATGATAAGGATTGGTTCAAA
1739979 TTTT
66 TTTT
1739983 TTATTCGAGTTTCTATACTAATTTTATTATAATTA-TT-TAGTATTATGATAAGGATTGGTTCAA
1 TTATTCGAGTTTCTATACTAATTTTA-TATAATTATTTATAGTATTATGATAAGGATTGGTTCAA
1740046 ATTTT
65 ATTTT
1740051 TTA
1 TTA
1740054 ACTTTCTCTA
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
68 33 0.49
69 27 0.40
70 8 0.12
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.51
Consensus pattern (69 bp):
TTATTCGAGTTTCTATACTAATTTTATATAATTATTTATAGTATTATGATAAGGATTGGTTCAAA
TTTT
Found at i:1740235 original size:111 final size:113
Alignment explanation
Indices: 1739992--1740301 Score: 472
Period size: 111 Copynumber: 2.8 Consensus size: 113
1739982 TTTATTCGAG
*
1739992 TTTCTATA-CTAATTTTATTATAATTA-TT-TAGTATTATGATAAGGATTGGTTCAAATTTTTTA
1 TTTCTA-ACCTAATTTTATTATAATTATTTATAGTATTATGATAA-GATTGGTTCCAATTTTTTA
1740054 ACTTTCTCTAACCATATAAGATATATATATATTCATATTCTTTTTATTATCAT
64 ACTTTCTCTAACCATA-AAG--ATATATATATTCATATTCTTTTTATTATCAT
1740107 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGATTGGTTCCAATTTTTTAAC
1 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGATTGGTTCCAATTTTTTAAC
* *
1740172 CTTCTCTAACCATAAAGATATATAT-TTCATATTC-TTTTATTGTCAT
66 TTTCTCTAACCATAAAGATATATATATTCATATTCTTTTTATTATCAT
* *
1740218 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTTTGATAAAGATTGGTTCCAA-ATTTTAA
1 TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGAT-AAGATTGGTTCCAATTTTTTAA
1740282 CTTTCTCTAACCAT-AAGATA
65 CTTTCTCTAACCATAAAGATA
1740302 AGATTCATGC
Statistics
Matches: 185, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
110 6 0.03
111 71 0.38
112 23 0.12
113 8 0.04
114 1 0.01
115 27 0.15
116 35 0.19
117 14 0.08
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.49
Consensus pattern (113 bp):
TTTCTAACCTAATTTTATTATAATTATTTATAGTATTATGATAAGATTGGTTCCAATTTTTTAAC
TTTCTCTAACCATAAAGATATATATATTCATATTCTTTTTATTATCAT
Found at i:1740558 original size:60 final size:60
Alignment explanation
Indices: 1740463--1740718 Score: 304
Period size: 59 Copynumber: 4.3 Consensus size: 60
1740453 GCGATCATAA
* * *
1740463 AATCGCAACGCGATCTTCCA-AGAATCGCAACGCGATTCAGAAAATCGCAACGCGGTT-CAGAA
1 AATCGCAACGCGA--TT-CAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCA-AG
* *
1740525 AATCGCAACGCGGTTCAGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
* *
1740585 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTC-CAAGATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
***** *** *
1740644 AATCGCAACGCGATTTTCTTAATCGCGTTGCGATTCA-AGAATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
1740703 AATCGCAACGCGATTC
1 AATCGCAACGCGATTC
1740719 CAAGAATCTT
Statistics
Matches: 171, Mismatches: 20, Indels: 9
0.86 0.10 0.05
Matches are distributed among these distances:
59 86 0.50
60 71 0.42
61 2 0.01
62 12 0.07
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (60 bp):
AATCGCAACGCGATTCAGAAAATCGCAACGCGATTCAGAAAATCGCAACGCGATTCCAAG
Found at i:1740656 original size:59 final size:59
Alignment explanation
Indices: 1740418--1740718 Score: 279
Period size: 59 Copynumber: 5.0 Consensus size: 59
1740408 AACGTTGAAA
* * * *
1740418 AGAAGATCGCAACACGATCTTCCAAGAATCGCAATGCGA-T-CATAAAATCGCAACGCGATCTTC
1 AGAAAATCGCAACGCGA--TTCCAAG-ATCGCAACGCGATTCCA-AGAATCGCAACGCGA--TT-
1740481 C
59 C
* * * * * *
1740482 A-AGAATCGCAACGCGATTCAGAAAATCGCAACGCGGTT-CAGAAAATCGCAACGCGGTTC
1 AGAAAATCGCAACGCGATTC-CAAGATCGCAACGCGATTCCA-AGAATCGCAACGCGATTC
** *
1740541 AGAAAATCGCAACGCGATTAAGAAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATT-CCAAGATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
*
1740601 AGAAAATCGCAACGCGATTCCAAGATCGCAACGCGATTCCAAGAATCGCAACGCGATTT
1 AGAAAATCGCAACGCGATTCCAAGATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
**** ***
1740660 TCTTAATCGCGTTGCGATT-CAAGAATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1 AGAAAATCGCAACGCGATTCCAAG-ATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
1740719 CAAGAATCTT
Statistics
Matches: 205, Mismatches: 26, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
58 4 0.02
59 84 0.41
60 70 0.34
61 15 0.07
62 19 0.09
63 12 0.06
64 1 0.00
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (59 bp):
AGAAAATCGCAACGCGATTCCAAGATCGCAACGCGATTCCAAGAATCGCAACGCGATTC
Found at i:1740719 original size:20 final size:19
Alignment explanation
Indices: 1740440--1740726 Score: 276
Period size: 20 Copynumber: 14.4 Consensus size: 19
1740430 CACGATCTTC
*
1740440 CAAGAATCGCAATGCGA-T
1 CAAGAATCGCAACGCGATT
*
1740458 CATAAAATCGCAACGCGATCTT
1 CA-AGAATCGCAACGCGA--TT
1740480 CCAAGAATCGCAACGCGATT
1 -CAAGAATCGCAACGCGATT
* *
1740500 CAGAAAATCGCAACGCGGTT
1 CA-AGAATCGCAACGCGATT
* *
1740520 CAGAAAATCGCAACGCGGTT
1 CA-AGAATCGCAACGCGATT
*
1740540 CAGAAAATCGCAACGCGATT
1 CA-AGAATCGCAACGCGATT
1740560 -AAGAAAATCGCAACGCGATT
1 CAAG--AATCGCAACGCGATT
1740580 CCAAGAATCGCAACGCGATT
1 -CAAGAATCGCAACGCGATT
*
1740600 CAGAAAATCGCAACGCGATT
1 CA-AGAATCGCAACGCGATT
1740620 CCAAG-ATCGCAACGCGATT
1 -CAAGAATCGCAACGCGATT
1740639 CCAAGAATCGCAACGCGATTTT
1 -CAAGAATCGCAACGCGA--TT
** ***
1740661 C-TTAATCGCGTTGCGATT
1 CAAGAATCGCAACGCGATT
1740679 CAAGAATCGCAACGCGATT
1 CAAGAATCGCAACGCGATT
1740698 CCAAGAATCGCAACGCGATT
1 -CAAGAATCGCAACGCGATT
1740718 CCAAGAATC
1 -CAAGAATC
1740727 TTAATAGTAA
Statistics
Matches: 233, Mismatches: 19, Indels: 32
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.03
19 49 0.21
20 153 0.66
21 3 0.01
22 20 0.09
23 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (19 bp):
CAAGAATCGCAACGCGATT
Found at i:1744740 original size:34 final size:32
Alignment explanation
Indices: 1744674--1744744 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
1744664 ACCTTACAAA
* *
1744674 TTCCCTAGTTTTTCCGGGATAAACTAGTACCT
1 TTCCCTAGTTTTACCGGGATAAACTAGAACCT
* *
1744706 TTCCCTAGGTTTTACACGGGATTAGCTAGAACCT
1 TTCCCTA-GTTTTAC-CGGGATAAACTAGAACCT
1744740 TTCCC
1 TTCCC
1744745 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 7 0.21
33 6 0.18
34 20 0.61
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (32 bp):
TTCCCTAGTTTTACCGGGATAAACTAGAACCT
Found at i:1745053 original size:21 final size:21
Alignment explanation
Indices: 1745027--1745068 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1745017 CCAGAATGGG
*
1745027 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1745048 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
1745069 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:1745224 original size:19 final size:19
Alignment explanation
Indices: 1745175--1745225 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
1745165 AGCCTCGGGT
* * *
1745175 TACTGTTCAAACAGTGATT
1 TACTGTTCAAATAGTAATG
1745194 TACTGTTCAAATAGTAATG
1 TACTGTTCAAATAGTAATG
1745213 TACTGTTCAAATA
1 TACTGTTCAAATA
1745226 ATAAATTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (19 bp):
TACTGTTCAAATAGTAATG
Found at i:1745235 original size:19 final size:18
Alignment explanation
Indices: 1745174--1745240 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 18
1745164 GAGCCTCGGG
* *
1745174 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAATAGT-AA
1745193 TTACTGTTCAAATAGTAA
1 TTACTGTTCAAATAGTAA
*
1745211 TGTACTGTTCAAATAATAAA
1 T-TACTGTTCAAATAGT-AA
*
1745231 TTACTATTCA
1 TTACTGTTCA
1745241 TAAAAACATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.05
19 37 0.88
20 3 0.07
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.39
Consensus pattern (18 bp):
TTACTGTTCAAATAGTAA
Found at i:1745337 original size:29 final size:31
Alignment explanation
Indices: 1745305--1745364 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1745295 AAATTTTGAA
*
1745305 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1745334 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1745365 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:1749190 original size:181 final size:181
Alignment explanation
Indices: 1748928--1749303 Score: 580
Period size: 181 Copynumber: 2.1 Consensus size: 181
1748918 TATAAAACTA
* *
1748928 AATATTTTTTAATTAAAAATATAGTTTATAATTAATTTAATAATATATAATTATAAATAAAAAAT
1 AATA-TTTTTAATTAAAAAAATAGTTTACAATTAATTTAATAATATATAATTATAAATAAAAAAT
* *
1748993 TTATATAATTTTTTTAATTAA-TAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATT
65 TTATATAATATTTTTAATCAATTAATA-TGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATT
* *
1749057 AATTGGGTTTTAAATGGTTTGGGCTGAGCCCA-ATGTTATATATAATATATTT
129 AATTGAGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATTT
1749109 AATATTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAA-ATAAAA
1 AATATTTTTAATT-AAAAAAATAGTTTACAATTAATTT-AATAATATATAATTATAAATA-AAAA
*
1749173 TTTTATATAA-ATTTTTAATCAATTAATATGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
63 ATTTATATAATATTTTTAATCAATTAATATGATTTAGGTTTAAAAGTTATTGGATCTTAAATTAT
* *
1749237 TAATTGAGTTTTAAATGGTTTGAGTTGAGCTCATATGTTATATATAATATATTT
128 TAATTGAGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATTT
* *
1749291 AAAATTTTAAATT
1 AATATTTTTAATT
1749304 TAATTTCGGT
Statistics
Matches: 179, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
180 9 0.05
181 102 0.57
182 68 0.38
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (181 bp):
AATATTTTTAATTAAAAAAATAGTTTACAATTAATTTAATAATATATAATTATAAATAAAAAATT
TATATAATATTTTTAATCAATTAATATGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
TTGAGTTTTAAATGGTTTGAGCTGAGCCCATATGTTATATATAATATATTT
Found at i:1749724 original size:20 final size:20
Alignment explanation
Indices: 1749699--1749737 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1749689 AATCATCTTA
*
1749699 GTTCATCTAGTATTGATACC
1 GTTCATCTAGTATCGATACC
1749719 GTTCATCTAGTATCGATAC
1 GTTCATCTAGTATCGATAC
1749738 ACAAACTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (20 bp):
GTTCATCTAGTATCGATACC
Found at i:1750567 original size:21 final size:22
Alignment explanation
Indices: 1750533--1750574 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1750523 TACTAACGTG
1750533 GAATTTATGGTGTTACATACAA
1 GAATTTATGGTGTTACATACAA
1750555 GAATTTA-GGTGTTACATACA
1 GAATTTATGGTGTTACATACA
1750575 GGATGCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.36
Consensus pattern (22 bp):
GAATTTATGGTGTTACATACAA
Found at i:1751884 original size:29 final size:28
Alignment explanation
Indices: 1751833--1751888 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
1751823 TCGTCCCTAT
1751833 AAGTTTATTTTTTAAAATAAAATTTTGC
1 AAGTTTATTTTTTAAAATAAAATTTTGC
*
1751861 AAGTTTATTTCTTTAAAATTAAATTTTG
1 AAGTTTATTT-TTTAAAATAAAATTTTG
1751889 GGTACGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.52
Consensus pattern (28 bp):
AAGTTTATTTTTTAAAATAAAATTTTGC
Found at i:1754386 original size:21 final size:21
Alignment explanation
Indices: 1754347--1754387 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1754337 GTAAAAAAAT
* *
1754347 TACCTAAAACATTATTATTTC
1 TACCTAAAACATCAATATTTC
*
1754368 TACCTAAAATATCAATATTT
1 TACCTAAAACATCAATATTT
1754388 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:1754754 original size:2 final size:2
Alignment explanation
Indices: 1754747--1754779 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1754737 ATTAATGCAG
*
1754747 TA TA TA TA CA 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 T
1754780 TAATCTATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1758145 original size:16 final size:15
Alignment explanation
Indices: 1758124--1758153 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
1758114 TATCTATAAT
1758124 ATTATAATATTTAAAA
1 ATTATAA-ATTTAAAA
1758140 ATTATAAATTTAAA
1 ATTATAAATTTAAA
1758154 TGCGTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATAAATTTAAAA
Found at i:1761521 original size:55 final size:55
Alignment explanation
Indices: 1761465--1761947 Score: 679
Period size: 55 Copynumber: 8.9 Consensus size: 55
1761455 CGGGTTCGCT
* * * * * * *
1761465 CCCTCTTTCTTTAGAGAGTAT-AGAACTCGGACAATCTTTAATAATCGTGTCTGCT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
1761520 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1761573 CCCTATTTCTTCAGAGGGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
1761628 CCCTATTTCTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1761681 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCACCAATCGTGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1761736 CCCTATTTCTTCAGAGAGTATAAGTCTCGAACAATCTTCAACAATCACGTCTGTC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* **
1761791 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAATGATCGCGTCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * *
1761846 CCCTATTTCTTCAGGGAGTATAAGACTCGAACAATCTTCAACGATCGCATCTGCC
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1761901 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCG
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
1761948 TTGGGAAACC
Statistics
Matches: 384, Mismatches: 39, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
53 93 0.24
54 4 0.01
55 285 0.74
56 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (55 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:1761619 original size:108 final size:110
Alignment explanation
Indices: 1761465--1761948 Score: 692
Period size: 108 Copynumber: 4.4 Consensus size: 110
1761455 CGGGTTCGCT
* * * * *
1761465 CCCTCTTTCTTTAGAGAGTAT-AGAACTCG-GACAATCTTTAATAATCGTGTCTGCTCCCTATTT
1 CCCTATTTCTTCAGAGAGTATAAG-ACTCGAG-CAATCTTCAACAATCGTGTCTGCCCCCTATTT
* *
1761528 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
64 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1761573 CCCTATTTCTTCAGAGGGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* *
1761638 TCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCC
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
*
1761681 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCACCAATCGTGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* * *
1761746 TCAGAGAGTATAAGTCTCGAACAATCTTCAACAATCACGTCTGTC
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* * ** *
1761791 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATTTTCAATGATCGCGTCTGCCCCCTATTTCT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
* * *
1761856 TCAGGGAGTATAAGACTCGAACAATCTTCAACGATCGCATCTGCC
66 TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
* *
1761901 CCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGT
1 CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGT
1761949 TGGGAAACCT
Statistics
Matches: 344, Mismatches: 28, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
108 175 0.51
109 4 0.01
110 165 0.48
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (110 bp):
CCCTATTTCTTCAGAGAGTATAAGACTCGAGCAATCTTCAACAATCGTGTCTGCCCCCTATTTCT
TCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCC
Found at i:1762959 original size:8 final size:8
Alignment explanation
Indices: 1762946--1763001 Score: 55
Period size: 8 Copynumber: 6.9 Consensus size: 8
1762936 TCTTGAACCC
1762946 TCATTTTT
1 TCATTTTT
1762954 TCATTTTTTT
1 TCA--TTTTT
1762964 TCATTCATTT
1 TCATT--TTT
1762974 T-ATTTTT
1 TCATTTTT
1762981 T-A-TTTT
1 TCATTTTT
1762987 TCATTTTT
1 TCATTTTT
1762995 TCATTTT
1 TCATTTT
1763002 CACTCATTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
6 5 0.12
7 6 0.14
8 16 0.38
9 3 0.07
10 12 0.29
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (8 bp):
TCATTTTT
Found at i:1763002 original size:14 final size:14
Alignment explanation
Indices: 1762946--1763003 Score: 61
Period size: 14 Copynumber: 4.2 Consensus size: 14
1762936 TCTTGAACCC
1762946 TCATTTTTTCATTT
1 TCATTTTTTCATTT
1762960 T--TTTTCATTCATTT
1 TCATTTT--TTCATTT
1762974 T-ATTTTTT-ATTTT
1 TCATTTTTTCA-TTT
1762987 TCATTTTTTCATTT
1 TCATTTTTTCATTT
1763001 TCA
1 TCA
1763004 CTCATTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
12 5 0.13
13 6 0.16
14 22 0.58
15 5 0.13
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (14 bp):
TCATTTTTTCATTT
Found at i:1766522 original size:8 final size:8
Alignment explanation
Indices: 1766509--1766536 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
1766499 AAAAGAAGAT
1766509 ATATATAC
1 ATATATAC
1766517 ATATATAC
1 ATATATAC
1766525 ATATATAC
1 ATATATAC
1766533 ATAT
1 ATAT
1766537 GGGAGAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:1776767 original size:12 final size:13
Alignment explanation
Indices: 1776742--1776770 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1776732 GAATCATAAA
1776742 AAATTATCAAAAT
1 AAATTATCAAAAT
1776755 AAATTAT-AAAAT
1 AAATTATCAAAAT
1776767 AAAT
1 AAAT
1776771 AGGCTAAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATTATCAAAAT
Done.