Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001174.1 Hibiscus syriacus cultivar Beakdansim tig00002338_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: 2182627
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1896648 original size:30 final size:29
Alignment explanation
Indices: 1896608--1896666 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
1896598 ATATTTGATT
*
1896608 AAATAAAAATATATTATTTATGAATTTATA
1 AAATAAAAATATATTA-TTATAAATTTATA
*
1896638 AAATATAAATATATTATTATAAATTTATA
1 AAATAAAAATATATTATTATAAATTTATA
1896667 TTCGAGTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (29 bp):
AAATAAAAATATATTATTATAAATTTATA
Found at i:1897812 original size:20 final size:21
Alignment explanation
Indices: 1897787--1897831 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1897777 TTTTAAATAA
*
1897787 GAAAATCGGT-AAAAATGATT
1 GAAAATCGGTAAAAAATGATC
1897807 GAAAATCGGTAAAAAATGATC
1 GAAAATCGGTAAAAAATGATC
1897828 GAAA
1 GAAA
1897832 CCATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
GAAAATCGGTAAAAAATGATC
Found at i:1899212 original size:28 final size:28
Alignment explanation
Indices: 1899168--1899226 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1899158 CGATACACAG
* *
1899168 TTGTTGAATTGACCACTGAGTTGCTTAA
1 TTGTTGAATTGACCACTGAGGTGCTCAA
*
1899196 TTGTTG-ATTGCATCACTGAGGTGCTCAA
1 TTGTTGAATTG-ACCACTGAGGTGCTCAA
1899224 TTG
1 TTG
1899227 GTTGTCAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (28 bp):
TTGTTGAATTGACCACTGAGGTGCTCAA
Found at i:1899385 original size:54 final size:54
Alignment explanation
Indices: 1899327--1899556 Score: 165
Period size: 56 Copynumber: 4.2 Consensus size: 54
1899317 AAGTACATAT
* * * *
1899327 GTGCTCAATCATTACAACGCACAAATGTGTCAGATTCTAGACTGAAGCATAGAG
1 GTGCTCAATCATTACAACGCACAGAGGTGTCAGATTATAGACTGAAGCACAGAG
* ** * * ** * * *
1899381 GTGCTCATTCATTTTTAACTGCATAGAGGTGTTATTTTGTCGATTGAAGCACAGAG
1 GTGCTCAATCA-TTACAAC-GCACAGAGGTGTCAGATTATAGACTGAAGCACAGAG
* * *
1899437 GTACTCAATCATTACCAA-GCACAGAGGTGCCAGATTATAGGCTGAAGCACAGAG
1 GTGCTCAATCATTA-CAACGCACAGAGGTGTCAGATTATAGACTGAAGCACAGAG
* ** * * * * * * *
1899491 GTGCTCAGTCATTTTTAACTGTACAGGGGTGTTAGTTTATCGATTGAAGCACAAAG
1 GTGCTCAATCA-TTACAAC-GCACAGAGGTGTCAGATTATAGACTGAAGCACAGAG
1899547 GTGCTCAATC
1 GTGCTCAATC
1899557 GTTAATTCAA
Statistics
Matches: 130, Mismatches: 40, Indels: 10
0.72 0.22 0.06
Matches are distributed among these distances:
54 48 0.37
55 9 0.07
56 73 0.56
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (54 bp):
GTGCTCAATCATTACAACGCACAGAGGTGTCAGATTATAGACTGAAGCACAGAG
Found at i:1899437 original size:56 final size:56
Alignment explanation
Indices: 1899369--1899556 Score: 191
Period size: 56 Copynumber: 3.4 Consensus size: 56
1899359 GATTCTAGAC
* * * * *
1899369 TGAAGCATAGAGGTGCTCATTCATTTTTAACTGCATAGAGGTGTTATTTTGTCGAT
1 TGAAGCACAGAGGTGCTCAATCATTTTTAACTGCACAGAGGTGTTAGTTTATCGAT
* *** ** * * **
1899425 TGAAGCACAGAGGTACTCAATCATTACCAA--GCACAGAGGTGCCAGATTATAGGC
1 TGAAGCACAGAGGTGCTCAATCATTTTTAACTGCACAGAGGTGTTAGTTTATCGAT
* * *
1899479 TGAAGCACAGAGGTGCTCAGTCATTTTTAACTGTACAGGGGTGTTAGTTTATCGAT
1 TGAAGCACAGAGGTGCTCAATCATTTTTAACTGCACAGAGGTGTTAGTTTATCGAT
*
1899535 TGAAGCACAAAGGTGCTCAATC
1 TGAAGCACAGAGGTGCTCAATC
1899557 GTTAATTCAA
Statistics
Matches: 100, Mismatches: 30, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
54 40 0.40
56 60 0.60
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (56 bp):
TGAAGCACAGAGGTGCTCAATCATTTTTAACTGCACAGAGGTGTTAGTTTATCGAT
Found at i:1899459 original size:110 final size:110
Alignment explanation
Indices: 1899312--1899556 Score: 321
Period size: 110 Copynumber: 2.2 Consensus size: 110
1899302 TCAACCTTTA
* * * * * * *
1899312 GATTGAAGTACATATGTGCTCAATCATTACAACGCACAAATGTGTCAGATTCTAGACTGAAGCAT
1 GATTGAAGCACAAAGGTGCTCAATCATTACAACGCACAAAGGTGCCAGATTATAGACTGAAGCAC
* * * *
1899377 AGAGGTGCTCATTCATTTTTAACTGCATAGAGGTGTTATTTTGTC
66 AGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTTAGTTTATC
* * * *
1899422 GATTGAAGCACAGAGGTACTCAATCATTACCAA-GCACAGAGGTGCCAGATTATAGGCTGAAGCA
1 GATTGAAGCACAAAGGTGCTCAATCATTA-CAACGCACAAAGGTGCCAGATTATAGACTGAAGCA
* *
1899486 CAGAGGTGCTCAGTCATTTTTAACTGTACAGGGGTGTTAGTTTATC
65 CAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTTAGTTTATC
1899532 GATTGAAGCACAAAGGTGCTCAATC
1 GATTGAAGCACAAAGGTGCTCAATC
1899557 GTTAATTCAA
Statistics
Matches: 116, Mismatches: 18, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
110 113 0.97
111 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (110 bp):
GATTGAAGCACAAAGGTGCTCAATCATTACAACGCACAAAGGTGCCAGATTATAGACTGAAGCAC
AGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTTAGTTTATC
Found at i:1899568 original size:28 final size:28
Alignment explanation
Indices: 1899537--1899609 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 28
1899527 TTATCGATTG
1899537 AAGCACAAAGGTGCTCAATCGTTAATTC
1 AAGCACAAAGGTGCTCAATCGTTAATTC
* * *
1899565 AAGCATATAGGTGAT--AT-G--AATTC
1 AAGCACAAAGGTGCTCAATCGTTAATTC
*
1899588 -AGCACAATGGTGCTCAATCGTT
1 AAGCACAAAGGTGCTCAATCGTT
1899610 TTCCTGATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 11
0.65 0.14 0.22
Matches are distributed among these distances:
22 10 0.30
23 5 0.15
24 2 0.06
25 2 0.06
26 2 0.06
28 12 0.36
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (28 bp):
AAGCACAAAGGTGCTCAATCGTTAATTC
Found at i:1906535 original size:14 final size:15
Alignment explanation
Indices: 1906501--1906540 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1906491 GAATTATGAC
*
1906501 TATTAAAATATTTTT
1 TATTAAAATATTATT
*
1906516 TATTAAATTATTATT
1 TATTAAAATATTATT
1906531 T-TTAAAATAT
1 TATTAAAATAT
1906541 CTATCGAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTAAAATATTATT
Found at i:1907853 original size:194 final size:194
Alignment explanation
Indices: 1907421--1907957 Score: 1044
Period size: 194 Copynumber: 2.8 Consensus size: 194
1907411 GTAATTTTAG
1907421 AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
1 AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
1907486 ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTAT-AGTGAGTGG-AAATCCGTCAAAGAAATC
66 ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTATAAGTGAGTGGCAAATCCGTCAAAGAAATC
1907549 ACTACTAGT-ACCGGGAATGATAAAAATGGTACTAAAATGTAATTTTAGTTATGATTTTGAAAA
131 ACTACTAGTAACCGGGAATGATAAAAATGGTACTAAAATGTAATTTTAGTTATGATTTTGAAAA
1907612 AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
1 AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
1907677 ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTATAAGTGAGTGGCAAATCCGTCAAAGAAATC
66 ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTATAAGTGAGTGGCAAATCCGTCAAAGAAATC
1907742 ACTACTAGTAACCGGGAATGATAAAAATGGTACTAAAATGTAATTTTAGTTATGATTTTGAAAA
131 ACTACTAGTAACCGGGAATGATAAAAATGGTACTAAAATGTAATTTTAGTTATGATTTTGAAAA
1907806 AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
1 AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
1907871 ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTATAAGTGAGTGGCAAATCCGTCAAAGAAATC
66 ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTATAAGTGAGTGGCAAATCCGTCAAAGAAATC
*
1907936 ACTACTACTAACCGGGAATGAT
131 ACTACTAGTAACCGGGAATGAT
1907958 TTCGAGCTTG
Statistics
Matches: 342, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
191 101 0.30
192 9 0.03
193 27 0.08
194 205 0.60
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (194 bp):
AAAATATAATACCCAAGACCAAAACGAAATCAATGTGATTGTTGAGTGACTAAAGACGAGTTTAC
ATCAAATATAATTGGCGCTTTGGTAGTTTGGAGTATAAGTGAGTGGCAAATCCGTCAAAGAAATC
ACTACTAGTAACCGGGAATGATAAAAATGGTACTAAAATGTAATTTTAGTTATGATTTTGAAAA
Found at i:1909842 original size:2 final size:2
Alignment explanation
Indices: 1909835--1909861 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1909825 TCGAGAAAAT
1909835 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1909862 AATATACGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1915628 original size:34 final size:31
Alignment explanation
Indices: 1915553--1915618 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
1915543 AAAGACTAGG
*
1915553 CTTTGACTATTGGATGCTCAGTGGGTTCGTT
1 CTTTGACTATTGGACGCTCAGTGGGTTCGTT
1915584 CTTTGACTATTGGACGCTCAGTGGGTTCGTT
1 CTTTGACTATTGGACGCTCAGTGGGTTCGTT
1915615 CTTT
1 CTTT
1915619 TTTGACTATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.42
Consensus pattern (31 bp):
CTTTGACTATTGGACGCTCAGTGGGTTCGTT
Found at i:1923239 original size:55 final size:55
Alignment explanation
Indices: 1923155--1924008 Score: 1170
Period size: 55 Copynumber: 15.7 Consensus size: 55
1923145 CTCCATAGCC
* * *
1923155 CTTCAGAGAGTATAAGACTTGAACAATCTTTAACAATTGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
** * *
1923210 CTTCAGAGAGTATAAGACTCGAACAATCTTCAATGATCACGTCTG-CCCCAATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
*
1923264 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1923317 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTCTACCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1923372 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCACGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * * *
1923425 CTTCAAAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCTTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
** * *
1923480 CTTCAGAGAGTATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCCATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1923535 CTTCAGAGAGTATAAGACTC--ACAATCTTCATCAAGCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1923588 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTTTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* *
1923643 CTTCAGAGAGTATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
1923696 CATCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1923751 CTTCA-AGAGTATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
1923805 CTTCAGAGAGTATAAGACCCGAACAATCTTCAATAATCGTGTCCGCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * *
1923860 CCTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGCGTCTCCCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * **
1923915 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCCACCCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
* * * *
1923970 CTTCAGAGAGTATGAGACTTGAACAACCTTCAACGATCG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCG
1924009 TAGGGAACCT
Statistics
Matches: 702, Mismatches: 87, Indels: 20
0.87 0.11 0.02
Matches are distributed among these distances:
52 19 0.03
53 166 0.24
54 80 0.11
55 437 0.62
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGCGTCTGCCCCCTATTT
Found at i:1923423 original size:108 final size:109
Alignment explanation
Indices: 1923155--1924008 Score: 1139
Period size: 108 Copynumber: 7.9 Consensus size: 109
1923145 CTCCATAGCC
* * *
1923155 CTTCAGAGAGTATAAGACTTGAACAATCTTTAACAATTGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGAC-TCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
1923220 TATAAGACTCGAACAATCTTCAATGATCACGTCTG-CCCCAATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* *
1923264 CTTCAGAGAGTATAAGACTC-ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
*
1923328 ATAAGACTCGAACAATCTTCAACGATCGCGTCTACCCCCTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * * *
1923372 CTTCAGAGAGTATAAGAC-CCACAATCTTCATCAATCACGTCTGCCCCCTATTTCTTCAAAGAGT
1 CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
* * * * *
1923436 ATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCTTATTT
66 ATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
** * *
1923480 CTTCAGAGAGTATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCCATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
1923545 TATAAGACTC--ACAATCTTCATCAAGCGCGTCTGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * *
1923588 CGTCAGAGAGTATAAGACTCGAACAATCTTCAACGATCGCGTTTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
1923653 TATAAGAC-C-CACAATCTTCATCAATCGCGTCTGCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * * *
1923696 CATCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCA-AGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* *
1923760 TATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCTCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * * * *
1923805 CTTCAGAGAGTATAAGACCCGAACAATCTTCAATAATCGTGTCCGCCCCCTATTTCCTCAGAGAG
1 CTTCAGAGAGTATAAGACTC-AACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* *
1923870 TATAAGACTCGAACAATCTTCAACTATCGCGTCTCCCCCCTATTT
65 TATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
* * **
1923915 CTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCGCGTCCACCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGAC-TCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAG
* * *
1923980 TATGAGACTTGAACAACCTTCAACGATCG
65 TATAAGACTCGAACAATCTTCAACGATCG
1924009 TAGGGAACCT
Statistics
Matches: 671, Mismatches: 65, Indels: 17
0.89 0.09 0.02
Matches are distributed among these distances:
107 85 0.13
108 307 0.46
109 105 0.16
110 174 0.26
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (109 bp):
CTTCAGAGAGTATAAGACTCAACAATCTTCAACAATCGCGTCTGCCCCCTATTTCTTCAGAGAGT
ATAAGACTCGAACAATCTTCAACGATCGCGTCTGCCCCCTATTT
Found at i:1923643 original size:271 final size:271
Alignment explanation
Indices: 1923155--1924009 Score: 1320
Period size: 271 Copynumber: 3.1 Consensus size: 271
1923145 CTCCATAGCC
** * * * *
1923155 CTTCAGAGAGTATAAGACTTGAACAATCTTTAACAATTGCGTCTGCCCCCTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCAGAGAG
1923220 TATAAGACTCGAACAATCTTCAATGATCACGTCTG-CCCCAATTTCTTCAGAGAGTATAAGACTC
66 TATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCAATTTCTTCAGAGAGTATAAGACTC
1923284 ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGTATAAGACTCGAACAATCTTCA
131 ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGTATAAGACTCGAACAATCTTCA
*
1923349 ACGATCGCGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCACGTCT
196 ACGATCGCGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCT
1923414 GCCCCCTATTT
261 GCCCCCTATTT
* *
1923425 CTTCAAAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCTTATTTCTTCAGAGAG
1 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCAGAGAG
*
1923490 TATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCCATTTCTTCAGAGAGTATAAGACTC
66 TATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCAATTTCTTCAGAGAGTATAAGACTC
*
1923555 ACAATCTTCATCAAGCGCGTCTGCCCCCTATTTCGTCAGAGAGTATAAGACTCGAACAATCTTCA
131 ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGTATAAGACTCGAACAATCTTCA
* *
1923620 ACGATCGCGTTTGCCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCT
196 ACGATCGCGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCT
1923685 GCCCCCTATTT
261 GCCCCCTATTT
*
1923696 CATCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCA-AGAG
1 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCAGAGAG
* ** * * *
1923760 TATAAGACTCGAACAATCTTCAACGATTGCGTCTGCCCTCTATTTCTTCAGAGAGTATAAGACCC
66 TATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCAATTTCTTCAGAGAGTATAAGACTC
* * *
1923825 GAACAATCTTCAAT-AATCGTGTCCGCCCCCTATTTCCTCAGAGAGTATAAGACTCGAACAATCT
131 --ACAATCTTC-ATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGTATAAGACTCGAACAATCT
* * ** * *
1923889 TCAACTATCGCGTCTCCCCCCTATTTCTTCAGAGAGTATAAGACTTGAACAATCTTCAACGATCG
193 TCAACGATCGCGTCTACCCCCTATTTCTTCAGAGAGTATAAGAC--CCACAATCTTCATCAATCG
**
1923954 CGTCCACCCCCTATTT
256 CGTCTGCCCCCTATTT
* ** * *
1923970 CTTCAGAGAGTATGAGACTTGAACAACCTTCAACGATCGT
1 CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGT
1924010 AGGGAACCTG
Statistics
Matches: 538, Mismatches: 41, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
270 155 0.29
271 222 0.41
272 96 0.18
273 2 0.00
274 63 0.12
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.28
Consensus pattern (271 bp):
CTTCAGAGAGTATAAGACCCGAACAATCTTCAACAATCGTGTCCGCCCCCTATTTCTTCAGAGAG
TATAAGACTCGAACAATCTTCAATGATCACGTCTGCCCCCAATTTCTTCAGAGAGTATAAGACTC
ACAATCTTCATCAATCGCGTCTGCCCCCTATTTCGTCAGAGAGTATAAGACTCGAACAATCTTCA
ACGATCGCGTCTACCCCCTATTTCTTCAGAGAGTATAAGACCCACAATCTTCATCAATCGCGTCT
GCCCCCTATTT
Found at i:1925033 original size:18 final size:19
Alignment explanation
Indices: 1925008--1925053 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1924998 TCATCTTTTG
1925008 TTTC-TTTTTT-TTATT-T
1 TTTCATTTTTTATTATTCT
*
1925024 TTTTATTTTTTATTATTCT
1 TTTCATTTTTTATTATTCT
1925043 TTTCATTTTTT
1 TTTCATTTTTT
1925054 CCATTCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 6 0.24
18 5 0.20
19 11 0.44
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTCATTTTTTATTATTCT
Found at i:1928566 original size:2 final size:2
Alignment explanation
Indices: 1928559--1928586 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1928549 GGAAGAGAAG
1928559 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
1928587 GCATACCGGA
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:1934972 original size:16 final size:16
Alignment explanation
Indices: 1934951--1934981 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1934941 ACCTTATTCA
1934951 CATGATATCTACCCAG
1 CATGATATCTACCCAG
1934967 CATGATATCTACCCA
1 CATGATATCTACCCA
1934982 ATCATGCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.32, G:0.10, T:0.26
Consensus pattern (16 bp):
CATGATATCTACCCAG
Found at i:1945135 original size:20 final size:21
Alignment explanation
Indices: 1945110--1945487 Score: 173
Period size: 20 Copynumber: 16.5 Consensus size: 21
1945100 AATGAAATGT
1945110 ATGAAAGGATGCATT-AAGGC
1 ATGAAAGGATGCATTAAAGGC
*
1945130 ATGAAAGGATGCCATAATTGAAAATGC
1 ATGAAAGGATG-C---ATT--AAAGGC
1945157 ATGAAAGGATGCATT-AAGGC
1 ATGAAAGGATGCATTAAAGGC
*
1945177 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-CAT---T-AAAGGC
*
1945203 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-CAT---T-AAAGGC
*
1945229 ATGAAAGGATGCATT-AAGAC
1 ATGAAAGGATGCATTAAAGGC
*
1945249 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-CAT---T-AAAGGC
* *
1945275 ATGAAATGATACATT-AAGGC
1 ATGAAAGGATGCATTAAAGGC
*
1945295 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-CAT---T-AAAGGC
*
1945321 ATGAAACGATGCATT-AAGGC
1 ATGAAAGGATGCATTAAAGGC
* *
1945341 ATGAAA-GATTCCATAAATGAAATGC
1 ATGAAAGGA-TGCAT---T-AAAGGC
* *
1945366 ATGAAAGGATGTATT-AAGGA
1 ATGAAAGGATGCATTAAAGGC
*
1945386 ATGAAAGGATGCCATAAATGAAATGC
1 ATGAAAGGATG-CAT---T-AAAGGC
*
1945412 ATG-AACGATGCATT-AAGGC
1 ATGAAAGGATGCATTAAAGGC
*
1945431 ATGAAAGGATGTCATAAATGAAATGC
1 ATGAAAGGATG-CAT---T-AAAGGC
1945457 ATGAAAGGATGCATT-AAGGC
1 ATGAAAGGATGCATTAAAGGC
1945477 ATGAAAGGATG
1 ATGAAAGGATG
1945488 TCATAAATGA
Statistics
Matches: 284, Mismatches: 29, Indels: 90
0.70 0.07 0.22
Matches are distributed among these distances:
19 9 0.03
20 102 0.36
21 16 0.06
22 5 0.02
23 4 0.01
24 11 0.04
25 31 0.11
26 91 0.32
27 15 0.05
ACGTcount: A:0.44, C:0.10, G:0.25, T:0.21
Consensus pattern (21 bp):
ATGAAAGGATGCATTAAAGGC
Found at i:1945163 original size:47 final size:46
Alignment explanation
Indices: 1945095--1945214 Score: 213
Period size: 47 Copynumber: 2.6 Consensus size: 46
1945085 TAAAACGAAT
*
1945095 CCATAAATGAAATGTATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
*
1945141 CCATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1 CCATAAATG-AAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
1945188 CCATAAATGAAATGCATGAAAGGATGC
1 CCATAAATGAAATGCATGAAAGGATGC
1945215 CATAAATGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
46 26 0.37
47 44 0.63
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (46 bp):
CCATAAATGAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG
Found at i:1945170 original size:12 final size:12
Alignment explanation
Indices: 1945153--1945242 Score: 57
Period size: 12 Copynumber: 7.5 Consensus size: 12
1945143 ATAATTGAAA
1945153 ATGCATGAAAGG
1 ATGCATGAAAGG
*
1945165 ATGCAT-TAA-G
1 ATGCATGAAAGG
1945175 --GCATGAAAGG
1 ATGCATGAAAGG
*
1945185 ATGCCAT-AAATGAA
1 ATG-CATGAAA-G-G
1945199 ATGCATGAAAGG
1 ATGCATGAAAGG
*
1945211 ATGCCAT-AAATGAA
1 ATG-CATGAAA-G-G
1945225 ATGCATGAAAGG
1 ATGCATGAAAGG
1945237 ATGCAT
1 ATGCAT
1945243 TAAGACATGA
Statistics
Matches: 60, Mismatches: 6, Indels: 24
0.67 0.07 0.27
Matches are distributed among these distances:
8 4 0.07
9 2 0.03
10 2 0.03
11 2 0.03
12 22 0.37
13 16 0.27
14 12 0.20
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (12 bp):
ATGCATGAAAGG
Found at i:1945211 original size:26 final size:25
Alignment explanation
Indices: 1945096--1945526 Score: 316
Period size: 26 Copynumber: 18.5 Consensus size: 25
1945086 AAAACGAATC
*
1945096 CATAAATGAAATGTATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
*
1945121 CAT---T--AAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
*
1945141 CCATAATTGAAAATGCATGAAAGGATG
1 -CATAAATG-AAATGCATGAAAGGATG
*
1945168 CAT---T--AAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
1945188 CCATAAATGAAATGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAAGGATG
1945214 CCATAAATGAAATGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAAGGATG
*
1945240 CATTAA-G--A--CATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
1945260 CCATAAATGAAATGCATG-AA--ATG
1 -CATAAATGAAATGCATGAAAGGATG
* * *
1945283 -ATACAT-TAAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
*
1945306 CCATAAATGAAATGCATGAAACGATG
1 -CATAAATGAAATGCATGAAAGGATG
* *
1945332 CAT---T--AAGGCATGAAA-GATTC
1 CATAAATGAAATGCATGAAAGGA-TG
1945352 CATAAATGAAATGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
* * *
1945377 --T--AT-TAAGGAATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
*
1945397 CCATAAATGAAATGCATG-AACGATG
1 -CATAAATGAAATGCATGAAAGGATG
*
1945422 CAT---T--AAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
1945442 TCATAAATGAAATGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAAGGATG
*
1945468 CAT---T--AAGGCATGAAAGGATG
1 CATAAATGAAATGCATGAAAGGATG
1945488 TCATAAATGAAATGCATGAAAGGATG
1 -CATAAATGAAATGCATGAAAGGATG
1945514 ACATAAATGAAAT
1 -CATAAATGAAAT
1945527 TAACGAATAA
Statistics
Matches: 324, Mismatches: 31, Indels: 101
0.71 0.07 0.22
Matches are distributed among these distances:
19 9 0.03
20 97 0.30
21 27 0.08
22 5 0.02
23 10 0.03
24 9 0.03
25 40 0.12
26 112 0.35
27 15 0.05
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (25 bp):
CATAAATGAAATGCATGAAAGGATG
Found at i:1945252 original size:46 final size:46
Alignment explanation
Indices: 1945201--1945513 Score: 522
Period size: 46 Copynumber: 6.8 Consensus size: 46
1945191 TAAATGAAAT
1945201 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* * *
1945247 ACATGAAAGGATGCCATAAATGAAATGCATGAAATGATACATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
1945293 GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* *
1945339 GCATGAAA-GATTCCATAAATGAAATGCATGAAAGGATGTATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
* *
1945384 GAATGAAAGGATGCCATAAATGAAATGCATG-AACGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
1945429 GCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
*
1945475 GCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATG
1945514 ACATAAATGA
Statistics
Matches: 249, Mismatches: 16, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
45 82 0.33
46 167 0.67
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAG
Found at i:1945373 original size:137 final size:137
Alignment explanation
Indices: 1945201--1945513 Score: 524
Period size: 137 Copynumber: 2.3 Consensus size: 137
1945191 TAAATGAAAT
*
1945201 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAA-GACATGAAAGGATGCCATA
1 GCATGAAAGGATTCCATAAATGAAATGCATGAAAGGATGCATTAAGGA-ATGAAAGGATGCCATA
*
1945265 AATGAAATGCATGAAATGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAACGA
65 AATGAAATGCATG-AACGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAACGA
1945330 TGCATTAAG
129 TGCATTAAG
*
1945339 GCATGAAA-GATTCCATAAATGAAATGCATGAAAGGATGTATTAAGGAATGAAAGGATGCCATAA
1 GCATGAAAGGATTCCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAA
* * *
1945403 ATGAAATGCATGAACGATGCATTAAGGCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATG
66 ATGAAATGCATGAACGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAACGATG
1945468 CATTAAG
131 CATTAAG
1945475 GCATGAAAGGATGT-CATAAATGAAATGCATGAAAGGATG
1 GCATGAAAGGAT-TCCATAAATGAAATGCATGAAAGGATG
1945514 ACATAAATGA
Statistics
Matches: 166, Mismatches: 6, Indels: 7
0.93 0.03 0.04
Matches are distributed among these distances:
136 64 0.39
137 91 0.55
138 11 0.07
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.21
Consensus pattern (137 bp):
GCATGAAAGGATTCCATAAATGAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGCCATAA
ATGAAATGCATGAACGATACATTAAGGCATGAAAGGATGCCATAAATGAAATGCATGAAACGATG
CATTAAG
Found at i:1945410 original size:91 final size:92
Alignment explanation
Indices: 1945201--1945513 Score: 515
Period size: 91 Copynumber: 3.4 Consensus size: 92
1945191 TAAATGAAAT
* * *
1945201 GCATGAAAGGATGCCATAAATGAAATGCATGAAAGGATGCATTAAGACATGAAAGGATGCCATAA
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATGCATTAAGGCATGAAAGGATTCCATAA
* *
1945266 ATGAAATGCATGAAATGATACATTAAG
66 ATGAAATGCATGAAAGGATGCATTAAG
1945293 GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATGCATTAAGGCATGAAA-GATTCCATAA
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATGCATTAAGGCATGAAAGGATTCCATAA
*
1945357 ATGAAATGCATGAAAGGATGTATTAAG
66 ATGAAATGCATGAAAGGATGCATTAAG
*
1945384 GAATGAAAGGATGCCATAAATGAAATGCATG-AACGATGCATTAAGGCATGAAAGGATGT-CATA
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATGCATTAAGGCATGAAAGGAT-TCCATA
1945447 AATGAAATGCATGAAAGGATGCATTAAG
65 AATGAAATGCATGAAAGGATGCATTAAG
* *
1945475 GCATGAAAGGATGTCATAAATGAAATGCATGAAAGGATG
1 GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATG
1945514 ACATAAATGA
Statistics
Matches: 207, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
90 22 0.11
91 126 0.61
92 59 0.29
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.21
Consensus pattern (92 bp):
GCATGAAAGGATGCCATAAATGAAATGCATGAAACGATGCATTAAGGCATGAAAGGATTCCATAA
ATGAAATGCATGAAAGGATGCATTAAG
Found at i:1948161 original size:28 final size:28
Alignment explanation
Indices: 1948129--1948183 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1948119 TATTTTAAAT
1948129 TTAAAATACAATT-CAAAAAAATAAAAAA
1 TTAAAATA-AATTGCAAAAAAATAAAAAA
* * *
1948157 TTAAATTAAATTGCTAAAAATTAAAAA
1 TTAAAATAAATTGCAAAAAAATAAAAA
1948184 TATTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.27
Consensus pattern (28 bp):
TTAAAATAAATTGCAAAAAAATAAAAAA
Found at i:1948856 original size:21 final size:21
Alignment explanation
Indices: 1948813--1948876 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 21
1948803 TTACTCTAGT
1948813 TAATTTATATTTTTAATTTTTTAG
1 TAATTTA-ATTTTT-A-TTTTTAG
1948837 TAATTTAATTTTTATTTTTAG
1 TAATTTAATTTTTATTTTTAG
* * *
1948858 TATTTTTATATTTATTTTT
1 TAATTTAATTTTTATTTTT
1948877 TCTATATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.62
22 1 0.03
23 6 0.16
24 7 0.19
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TAATTTAATTTTTATTTTTAG
Found at i:1948877 original size:29 final size:29
Alignment explanation
Indices: 1948812--1948877 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1948802 ATTACTCTAG
*
1948812 TTAATTTATATTTTTAATTTTTTAGTAAT
1 TTAATTTTTATTTTTAATTTTTTAGTAAT
*
1948841 TTAATTTTTATTTTTAGTATTTTTA-T-AT
1 TTAATTTTTATTTTTAAT-TTTTTAGTAAT
*
1948869 TTATTTTTT
1 TTAATTTTT
1948878 CTATATTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 10 0.30
29 17 0.52
30 6 0.18
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (29 bp):
TTAATTTTTATTTTTAATTTTTTAGTAAT
Found at i:1948976 original size:28 final size:29
Alignment explanation
Indices: 1948945--1949001 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 29
1948935 AATCAAATAA
* *
1948945 GCCCTTTAACT-TAAAAAAATTAATTTGG
1 GCCCTTGAACTATAAAAAAATCAATTTGG
1948973 GCCCTTGAACTCAATAAAAAAATCAATTT
1 GCCCTTGAACT--ATAAAAAAATCAATTT
1949002 AGTCTATCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 10 0.42
31 14 0.58
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (29 bp):
GCCCTTGAACTATAAAAAAATCAATTTGG
Found at i:1952394 original size:2 final size:2
Alignment explanation
Indices: 1952387--1952412 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1952377 TTTTATTTTA
1952387 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
1952413 GATACTTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1954529 original size:20 final size:19
Alignment explanation
Indices: 1954500--1954548 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1954490 AATAACCAAG
*
1954500 GTATCAATACTAACATTTGA
1 GTATCGATACTAAC-TTTGA
**
1954520 GTATCGATACTCTCTTTGA
1 GTATCGATACTAACTTTGA
1954539 GTATCGATAC
1 GTATCGATAC
1954549 CAAATTCAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (19 bp):
GTATCGATACTAACTTTGA
Found at i:1955207 original size:3 final size:3
Alignment explanation
Indices: 1955201--1955259 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
1955191 TTATTTTTTT
*
1955201 TTA TTA TT- TTA TTTG TTAA TTA TTA TTA TTA TTA -TA TTA TTA TT-
1 TTA TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1955245 TTA TTT TTA TTA TTA
1 TTA TTA TTA TTA TTA
1955260 ATACATATTA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 6 0.13
3 37 0.79
4 4 0.09
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1955210 original size:11 final size:11
Alignment explanation
Indices: 1955187--1955255 Score: 52
Period size: 11 Copynumber: 6.1 Consensus size: 11
1955177 TTTCATTTTG
1955187 TTTTTTATT-T
1 TTTTTTATTAT
1955197 TTTTTTATTAT
1 TTTTTTATTAT
*
1955208 TTTATTTGTTAAT
1 TTT-TTTATT-AT
*
1955221 TATTATTATTAT
1 T-TTTTTATTAT
* *
1955233 TATATTATTAT
1 TTTTTTATTAT
1955244 TTTATTT-TTAT
1 TTT-TTTATTAT
1955255 T
1 T
1955256 ATTAATACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
10 9 0.19
11 20 0.42
12 10 0.21
13 7 0.15
14 2 0.04
ACGTcount: A:0.23, C:0.00, G:0.01, T:0.75
Consensus pattern (11 bp):
TTTTTTATTAT
Found at i:1955238 original size:14 final size:14
Alignment explanation
Indices: 1955221--1955259 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
1955211 ATTTGTTAAT
1955221 TATTATTATTATTA
1 TATTATTATTATTA
1955235 TATTATTATT-TTA
1 TATTATTATTATTA
1955248 T-TT-TTATTATTA
1 TATTATTATTATTA
1955260 ATACATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.21
12 5 0.21
13 4 0.17
14 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TATTATTATTATTA
Found at i:1955241 original size:28 final size:28
Alignment explanation
Indices: 1955201--1955259 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1955191 TTATTTTTTT
*
1955201 TTATTATTTTATT-TGTTAATTATTATTA
1 TTATTATATTATTAT-TTAATTATTATTA
* *
1955229 TTATTATATTATTATTTTATTTTTATTA
1 TTATTATATTATTATTTAATTATTATTA
1955257 TTA
1 TTA
1955260 ATACATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TTATTATATTATTATTTAATTATTATTA
Found at i:1955248 original size:25 final size:24
Alignment explanation
Indices: 1955190--1955259 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 24
1955180 CATTTTGTTT
*
1955190 TTTATT-TTTTTTTATTATT-TTA
1 TTTATTATTTTATTATTATTATTA
* *
1955212 TTTGTTA-ATTATTATTATTATTA
1 TTTATTATTTTATTATTATTATTA
*
1955235 TATTATTATTTTATTTTTATTATTA
1 T-TTATTATTTTATTATTATTATTA
1955260 ATACATATTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
22 15 0.39
23 4 0.11
24 5 0.13
25 14 0.37
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (24 bp):
TTTATTATTTTATTATTATTATTA
Found at i:1956285 original size:21 final size:21
Alignment explanation
Indices: 1956259--1956304 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1956249 GAGTTCTGGG
* *
1956259 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1956280 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1956301 CAAG
1 CAAG
1956305 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1957189 original size:31 final size:31
Alignment explanation
Indices: 1957126--1957311 Score: 304
Period size: 31 Copynumber: 6.0 Consensus size: 31
1957116 AGGGTCGAGG
1957126 GTTTACCTATGTTCTTCGGGACATA-GGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1957156 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1957187 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1957218 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1957249 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1957280 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1957311 G
1 G
1957312 GTCCTTCGGG
Statistics
Matches: 147, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
30 25 0.17
31 121 0.82
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1960604 original size:21 final size:21
Alignment explanation
Indices: 1960578--1960623 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1960568 GAGTTCTGGG
* *
1960578 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1960599 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1960620 CAAG
1 CAAG
1960624 CGACAGAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.15
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1961488 original size:31 final size:31
Alignment explanation
Indices: 1961450--1961636 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
1961440 AGGGTCGAGG
1961450 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1961481 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1961512 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1961543 GTTTACCTATGTTCTTCGGAACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1961574 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1961605 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1961636 G
1 G
1961637 GTCCTTCGGG
Statistics
Matches: 148, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1963307 original size:2 final size:2
Alignment explanation
Indices: 1963300--1963336 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1963290 CCGAATGTTT
*
1963300 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1963337 TAGGTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1963835 original size:31 final size:33
Alignment explanation
Indices: 1963781--1963851 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
1963771 AAAAATATCC
*
1963781 TATTTTTATAAATGATATATATT-AT-TTTAAT
1 TATTTTTATAAATAATATATATTAATATTTAAT
* *
1963812 TATTTTTATAAA-AATATTTTATTAATATTTATT
1 TATTTTTATAAATAATA-TATATTAATATTTAAT
1963845 TATTTTT
1 TATTTTT
1963852 TAATATTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 3 0.09
31 17 0.50
32 2 0.06
33 12 0.35
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (33 bp):
TATTTTTATAAATAATATATATTAATATTTAAT
Found at i:1963973 original size:24 final size:24
Alignment explanation
Indices: 1963946--1964009 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
1963936 TAAAGATATA
1963946 TATATATATATTAATATATTTTCT
1 TATATATATATTAATATATTTTCT
1963970 TATATATATATTAATATATTTTCT
1 TATATATATATTAATATATTTTCT
*
1963994 TA-AAATTATATTAATA
1 TATATA-TATATTAATA
1964010 AACAACATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 2 0.05
24 36 0.95
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATATATATTAATATATTTTCT
Found at i:1965068 original size:15 final size:17
Alignment explanation
Indices: 1965037--1965068 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1965027 TTTTCTGAAT
1965037 AAATGCATGCGAATTAG
1 AAATGCATGCGAATTAG
1965054 AAAT-CATGC-AATTAG
1 AAATGCATGCGAATTAG
1965069 GTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (17 bp):
AAATGCATGCGAATTAG
Found at i:1965454 original size:36 final size:36
Alignment explanation
Indices: 1965407--1965475 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
1965397 GAGCTATGCA
** *
1965407 CACAAAGATCCTGTTATATTAATACCAAAAGTATTC
1 CACAAAGATCCTGCCAGATTAATACCAAAAGTATTC
*
1965443 CACAAAGATCCTGCCAGATTGATACCAAAAGTA
1 CACAAAGATCCTGCCAGATTAATACCAAAAGTA
1965476 GTCTACGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.12, T:0.25
Consensus pattern (36 bp):
CACAAAGATCCTGCCAGATTAATACCAAAAGTATTC
Found at i:1966070 original size:6 final size:7
Alignment explanation
Indices: 1966029--1966069 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1966019 TTTTCGTACA
1966029 TGCA-TT
1 TGCATTT
1966035 TGCATTT
1 TGCATTT
1966042 TGCATCTT
1 TGCAT-TT
*
1966050 TGTATTT
1 TGCATTT
1966057 T-CATTT
1 TGCATTT
1966063 TGCATTT
1 TGCATTT
1966070 GTTGTTTGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
6 9 0.30
7 15 0.50
8 6 0.20
ACGTcount: A:0.15, C:0.15, G:0.12, T:0.59
Consensus pattern (7 bp):
TGCATTT
Found at i:1973555 original size:54 final size:55
Alignment explanation
Indices: 1973483--1973627 Score: 168
Period size: 54 Copynumber: 2.7 Consensus size: 55
1973473 CAGAAACCAT
***
1973483 AGAAAAGGATGAATGTGTTGTCAAATGCTTTACGAACATCTTTCCAGAAGCCAC-A
1 AGAAAA-GATGAATGTGTTGTCAAATGCTTTACGAACATCCGGCCAGAAGCCACGA
* * * *
1973538 AGAAAAGATGAATGTGTTATCAAAAGCTTTACGAAAATCCGGGCAGAAGCCACGA
1 AGAAAAGATGAATGTGTTGTCAAATGCTTTACGAACATCCGGCCAGAAGCCACGA
* * * *
1973593 A-AAAATATGAATGTATTGTCACATGTTTTACGAAC
1 AGAAAAGATGAATGTGTTGTCAAATGCTTTACGAAC
1973628 CAGTGATTAT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
54 67 0.89
55 8 0.11
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (55 bp):
AGAAAAGATGAATGTGTTGTCAAATGCTTTACGAACATCCGGCCAGAAGCCACGA
Found at i:1974507 original size:39 final size:40
Alignment explanation
Indices: 1974453--1974549 Score: 151
Period size: 40 Copynumber: 2.5 Consensus size: 40
1974443 CCAGGTAGAG
* *
1974453 TTCATAATGAGAAGAACTCATCTAAAG-AGGGAGAATAAA
1 TTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAA
* *
1974492 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
1 TTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAA
1974532 TTCATAATGAGAAGAACT
1 TTCATAATGAGAAGAACT
1974550 TGTTTAACAT
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 26 0.49
40 27 0.51
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.21
Consensus pattern (40 bp):
TTCATAATGAGAAGAACTCATCTAAAGAAGGAAGAAGAAA
Found at i:1974547 original size:40 final size:39
Alignment explanation
Indices: 1974451--1974549 Score: 153
Period size: 39 Copynumber: 2.5 Consensus size: 39
1974441 TGCCAGGTAG
* *
1974451 AGTTCATAATGAGAAGAACTCATCTAAAGAGGGAGAATA
1 AGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGA
* *
1974490 AATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 AGTTCATAATGAGAAGAACTCATCTAAAG-AGGAAGAAGA
1974530 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
1974550 TGTTTAACAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
39 27 0.50
40 27 0.50
ACGTcount: A:0.47, C:0.10, G:0.22, T:0.20
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTCATCTAAAGAGGAAGAAGA
Found at i:1974706 original size:112 final size:112
Alignment explanation
Indices: 1974492--1974909 Score: 451
Period size: 112 Copynumber: 3.6 Consensus size: 112
1974482 GGAGAATAAA
*
1974492 TTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAA
1 TTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA
* * * *
1974557 CATTTTACTCGAATTCATCACTTGATGGATCAACATTGCCAG-GTAGAG
65 CATTTTGCTCGAATTCATCACTAGATGAATCAACATTGCCAGAG-AAAG
* *
1974605 TTTATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* *
1974670 TTTTTGCTCGAATTCATCACTAGATGAATCAGCATTGCCAGAGAAAG
66 ATTTTGCTCGAATTCATCACTAGATGAATCAACATTGCCAGAGAAAG
* * * * *
1974717 TTCACAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGATCTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
* * ** ** * * *
1974782 CTTTTGCTCGACGCTATCGTAGAAGGAGATAGATCAGCATACACTTTTCCAGGGAAAG
66 ATTTTGCTCGA--AT-TC--ATCACTAGAT-GA--ATCA-ACA--TTGCCAGAGAAAG
* * * * *
1974840 TTCATAATGAGAAGAACTTATCTGAAGAGGAAAAAGAAGTTCATAATAAGAAGAGCTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
*
1974905 CTTTT
66 ATTTT
1974910 ACGTAACTCT
Statistics
Matches: 265, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
112 142 0.54
113 29 0.11
114 1 0.00
115 2 0.01
117 6 0.02
118 2 0.01
120 3 0.01
121 2 0.01
123 78 0.29
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (112 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
ATTTTGCTCGAATTCATCACTAGATGAATCAACATTGCCAGAGAAAG
Found at i:1974849 original size:123 final size:122
Alignment explanation
Indices: 1974697--1975029 Score: 422
Period size: 123 Copynumber: 2.7 Consensus size: 122
1974687 CACTAGATGA
* * *
1974697 ATCAGCATTGCCAGAGAAAGTTCACAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAG-GAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * * *
1974762 ATAAGAAGATCTTGTTCAACCTTTTGC-TCGACGCTATCGTAGAAGGAGATAGATCAGC
65 ATAAGAAGAACTTGTTCAACCTTTTACGT-AACGCTATCATAGAAGGAGATAGATCAGC
* *
1974820 AT-ACACTTTTCCAGGGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAAAAGAAGTTCAT
1 ATCA-ACATTTCCA-GGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCAT
* * *
1974884 AATAAGAAGAGCTTGTTCAACCTTTTACGTAACTCTATCATAGAAGGAGATAGGTCAGC
64 AATAAGAAGAACTTGTTCAACCTTTTACGTAACGCTATCATAGAAGGAGATAGATCAGC
* * * * *
1974943 ATCAACATTTCCA-GAAGCGTTCATAATAAGAAGAACTCATCCGAAGAAGG-AGAATAAGTTCAT
1 ATCAACATTTCCAGGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
*
1975006 AATGAGAAGAACTTGTTCAACCTT
64 AATAAGAAGAACTTGTTCAACCTT
1975030 GCCTTAATTC
Statistics
Matches: 184, Mismatches: 20, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
121 3 0.02
122 59 0.32
123 119 0.65
124 3 0.02
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (122 bp):
ATCAACATTTCCAGGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
TAAGAAGAACTTGTTCAACCTTTTACGTAACGCTATCATAGAAGGAGATAGATCAGC
Found at i:1975406 original size:3 final size:3
Alignment explanation
Indices: 1975386--1975470 Score: 70
Period size: 3 Copynumber: 29.0 Consensus size: 3
1975376 TTTTTTCATT
* * *
1975386 TTA TTT TTA TTT TTA TTA TTA TTA TT- TTA TTTG TTAA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A TTA TTA TTA
* * *
1975432 TTA TTA TT- TT- TTG TTT TTA TTA TTA AT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1975471 CATATTACAG
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
2 7 0.10
3 56 0.84
4 4 0.06
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:1975432 original size:25 final size:25
Alignment explanation
Indices: 1975398--1975469 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
1975388 ATTTTTATTT
1975398 TTATTATTATTATT-TTATTTGTTAA
1 TTATTATTATTATTATTATTTGTT-A
* *
1975423 TTATTATTATTATTATTTTTTGTTT
1 TTATTATTATTATTATTATTTGTTA
1975448 TTATTATTAATTTATTATTATT
1 TTATTATT-A-TTATTATTATT
1975470 ACATATTACA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
25 22 0.54
26 9 0.22
27 10 0.24
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (25 bp):
TTATTATTATTATTATTATTTGTTA
Found at i:1977272 original size:24 final size:24
Alignment explanation
Indices: 1977245--1977297 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 24
1977235 AAAAATAAAG
1977245 ATATA-TAT-ATATATATATATTA
1 ATATATTATCATATATATATATTA
* *
1977267 ATATATTTTCTTATATATATATTA
1 ATATATTATCATATATATATATTA
1977291 ATATATT
1 ATATATT
1977298 TTCTTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 5 0.19
23 2 0.07
24 20 0.74
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATATTATCATATATATATATTA
Found at i:1977298 original size:24 final size:24
Alignment explanation
Indices: 1977254--1977317 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
1977244 GATATATATA
1977254 TATATATATATTAATATATTTTCT
1 TATATATATATTAATATATTTTCT
1977278 TATATATATATTAATATATTTTCT
1 TATATATATATTAATATATTTTCT
*
1977302 TA-AAATTATATTAATA
1 TATATA-TATATTAATA
1977318 AACAACATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
23 2 0.05
24 36 0.95
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (24 bp):
TATATATATATTAATATATTTTCT
Found at i:1978167 original size:10 final size:10
Alignment explanation
Indices: 1978152--1978182 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1978142 TGTCTCTCAC
*
1978152 AAAGAACTTG
1 AAAGAACTTA
1978162 AAAGAACTTA
1 AAAGAACTTA
1978172 AAAGAACTTA
1 AAAGAACTTA
1978182 A
1 A
1978183 TGAAAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.10, G:0.13, T:0.19
Consensus pattern (10 bp):
AAAGAACTTA
Found at i:1987994 original size:18 final size:18
Alignment explanation
Indices: 1987967--1988053 Score: 102
Period size: 18 Copynumber: 4.8 Consensus size: 18
1987957 ATATGATATA
1987967 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
* * *
1987985 TGGTCATTCGGAACATAA
1 TGGTCCTTCGGGACATAG
* * *
1988003 TGGTTCTTCGAGATATAG
1 TGGTCCTTCGGGACATAG
*
1988021 TGCTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
1988039 TGGTCCTTCGAGACA
1 TGGTCCTTCGGGACA
1988054 AATTCTAAGT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:1988021 original size:36 final size:36
Alignment explanation
Indices: 1987966--1988053 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
1987956 TATATGATAT
* *
1987966 ATGGTCCTTCGGGACATAGTGGTCATTCGGAACATA
1 ATGGTCCTTCGAGACATAGTGCTCATTCGGAACATA
* * * *
1988002 ATGGTTCTTCGAGATATAGTGCTCCTTCGGGACATA
1 ATGGTCCTTCGAGACATAGTGCTCATTCGGAACATA
*
1988038 GTGGTCCTTCGAGACA
1 ATGGTCCTTCGAGACA
1988054 AATTCTAAGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (36 bp):
ATGGTCCTTCGAGACATAGTGCTCATTCGGAACATA
Found at i:1992503 original size:15 final size:14
Alignment explanation
Indices: 1992478--1992508 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
1992468 TCATATGATA
1992478 ATATGATATGAGAT
1 ATATGATATGAGAT
1992492 ATATGATAATGAGAT
1 ATATGAT-ATGAGAT
1992507 AT
1 AT
1992509 GAAATTCCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (14 bp):
ATATGATATGAGAT
Found at i:1992509 original size:22 final size:23
Alignment explanation
Indices: 1992455--1992510 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
1992445 ATTAAGTGAC
* *
1992455 ATGAGTTATGTGATCATATGATA
1 ATGAGATATGAGATCATATGATA
1992478 AT-ATGATATGAGAT-ATATGATA
1 ATGA-GATATGAGATCATATGATA
1992500 ATGAGATATGA
1 ATGAGATATGA
1992511 AATTCCATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.41, C:0.02, G:0.21, T:0.36
Consensus pattern (23 bp):
ATGAGATATGAGATCATATGATA
Found at i:1992836 original size:18 final size:18
Alignment explanation
Indices: 1992815--1992873 Score: 100
Period size: 18 Copynumber: 3.3 Consensus size: 18
1992805 TGGTCCTTTA
1992815 GGACATAGTGATCCTTCG
1 GGACATAGTGATCCTTCG
*
1992833 GGACATAGTGATCATTCG
1 GGACATAGTGATCCTTCG
*
1992851 GGACATAGTGGTCCTTCG
1 GGACATAGTGATCCTTCG
1992869 GGACA
1 GGACA
1992874 AATTCTAAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (18 bp):
GGACATAGTGATCCTTCG
Found at i:1996238 original size:42 final size:42
Alignment explanation
Indices: 1996191--1996298 Score: 155
Period size: 42 Copynumber: 2.6 Consensus size: 42
1996181 CCCGAATTTG
** *
1996191 TAAATCCTTCGGGTTTTCAGTAAGTCT-TACGAGCATGATGTT
1 TAAATCCTTCGGGTCATCAGTAAGT-TATACGAGCATGATGCT
*
1996233 TAAATCCTTCGGGTCATCAGTAAGTTATTCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTTATACGAGCATGATGCT
*
1996275 TAAATCCTTCGGGTCATCTGTAAG
1 TAAATCCTTCGGGTCATCAGTAAG
1996299 CCTTTCGAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 1 0.02
42 59 0.98
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTTATACGAGCATGATGCT
Found at i:1996508 original size:73 final size:73
Alignment explanation
Indices: 1996384--1996864 Score: 720
Period size: 73 Copynumber: 6.6 Consensus size: 73
1996374 ATCAGCGACA
* *
1996384 TCTCACTTGAGACAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1996449 AAACTTTT
66 AAACTTTT
1996457 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1996522 AAACTTTT
66 AAACTTTT
* * * * *
1996530 TCTTGCTTGAGAAAGTTTCACTTGAAATAGTAAATTATCTCACTTGAGATTTTCTTTTCTTAAAA
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGT-TTTTCTTAAAA
1996595 CAAAC--TT
65 CAAACTTTT
* *
1996602 TCTCGCTTGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGATATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
*
1996667 AAACTTTC
66 AAACTTTT
* * *
1996675 TCTCGCTTGAGACAGTTTCACTTGAAATAGTAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1996740 AAACTTTGT
66 AAACTTT-T
* *
1996749 T-TCGCTTGAGATAGTTTCACTCGAAACAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
*
1996813 AAGA-TTTA
66 AA-ACTTTT
* * *
1996821 TCTCGCTTGAGACAGTTTCACTAGAAATAGAAATTT-TCATCACT
1 TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATC-TCACT
1996865 CGATGGATCA
Statistics
Matches: 375, Mismatches: 26, Indels: 14
0.90 0.06 0.03
Matches are distributed among these distances:
71 16 0.04
72 53 0.14
73 288 0.77
74 18 0.05
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (73 bp):
TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAAC
AAACTTTT
Found at i:1996767 original size:218 final size:219
Alignment explanation
Indices: 1996383--1996864 Score: 747
Period size: 218 Copynumber: 2.2 Consensus size: 219
1996373 AATCAGCGAC
* *
1996383 ATCTCACTTGAGACAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 ATCTCGCTTGAGACAGTTTCACTAGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
*
1996448 CAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTT
66 CAAACTTTCTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTT
* * * *
1996513 TCTTAAAACAAACTTTTTCTTGCTTGAGAAAGTTTCACTTGAAATAGTAAATTATCTCACTTGAG
131 TCTTAAAACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAACAGCAAATTATCTCACTTGAG
*
1996578 ATTTTCTTTTCTTAAAACAA-ACTT
196 ATTGT-TTTTCTTAAAACAAGACTT
* * *
1996602 -TCTCGCTTGAGAAAGTTTCACTTGAAATAGCAATTTATCTCACTTGATATTGTTTTTCTTAAAA
1 ATCTCGCTTGAGACAGTTTCACTAGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
* * *
1996666 CAAACTTTCTCTCGCTTGAGACAGTTTCACTTGAAATAGTAATTTATCTCACTTGAGATTGTTTT
66 CAAACTTTCTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTT
* *
1996731 TCTTAAAACAAACTTTGTT-TCGCTTGAGATAGTTTCACTCGAAACAGCAATTTATCTCACTTGA
131 TCTTAAAACAAACTTT-TTCTCGCTTGAGAAAGTTTCACTCGAAACAGCAAATTATCTCACTTGA
*
1996795 GATTGTTTTTCTTAAAACAAGATTT
195 GATTGTTTTTCTTAAAACAAGACTT
*
1996820 ATCTCGCTTGAGACAGTTTCACTAGAAATAGAAATTT-TCATCACT
1 ATCTCGCTTGAGACAGTTTCACTAGAAATAGCAATTTATC-TCACT
1996865 CGATGGATCA
Statistics
Matches: 240, Mismatches: 19, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
217 14 0.06
218 186 0.77
219 40 0.17
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (219 bp):
ATCTCGCTTGAGACAGTTTCACTAGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
CAAACTTTCTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTT
TCTTAAAACAAACTTTTTCTCGCTTGAGAAAGTTTCACTCGAAACAGCAAATTATCTCACTTGAG
ATTGTTTTTCTTAAAACAAGACTT
Found at i:1997093 original size:123 final size:120
Alignment explanation
Indices: 1996885--1997106 Score: 327
Period size: 123 Copynumber: 1.8 Consensus size: 120
1996875 AAATTTCCAA
*
1996885 AAGGAGTTCGTAATAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTATTC
1 AAGGAGTTCGTAATAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTATTC
* * *
1996950 AATCTTTTGCTCGACTCTATCGCAGAAGAAGATAGAGCAGCTTCAACATTTCTAG
66 AACCTTTTGATCGACTCTATCACAGAAGAAGATAGAGCAGCTTCAACATTTCTAG
* * * *
1997005 AAGGAGTTCGTAATAAGAAGAATTCATCTAAAGATGAATAAGAAGTTCATAATCTGAAGAACTTA
1 AAGGAGTTCGTAAT---AAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTA
* *
1997070 TTCAACCTTTTGATCGATTCTATCACAGAAGGAGATA
63 TTCAACCTTTTGATCGACTCTATCACAGAAGAAGATA
1997107 AATCAACATC
Statistics
Matches: 89, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
120 14 0.16
123 75 0.84
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (120 bp):
AAGGAGTTCGTAATAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATCTGAAGAACTTATTC
AACCTTTTGATCGACTCTATCACAGAAGAAGATAGAGCAGCTTCAACATTTCTAG
Found at i:1997119 original size:123 final size:120
Alignment explanation
Indices: 1996871--1997122 Score: 324
Period size: 123 Copynumber: 2.1 Consensus size: 120
1996861 CACTCGATGG
* *
1996871 ATCAAAATTTCCAAAAGGAGTTCGTAATAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATC
1 ATCAACATTTCCAAAAGGAGTTCGTAATAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATC
* * * * *
1996936 TGAAGAACTTATTCAATCTTTTGCTCGACTCTATCGCAGAAGAAGATAGAGCAGC
66 TGAAGAACTTATTCAACCTTTTGATCGACTCTATCACAGAAGAAGATAAAGCAAC
* * * * * * *
1996991 TTCAACATTTCTAGAAGGAGTTCGTAATAAGAAGAATTCATCTAAAGATGAATAAGAAGTTCATA
1 ATCAACATTTCCAAAAGGAGTTCGTAAT---AAGAACTCATCTAAAGAGGAAGAAGAAATTCATA
* * *
1997056 ATCTGAAGAACTTATTCAACCTTTTGATCGATTCTATCACAGAAGGAGATAAATCAAC
63 ATCTGAAGAACTTATTCAACCTTTTGATCGACTCTATCACAGAAGAAGATAAAGCAAC
1997114 ATCAACATT
1 ATCAACATT
1997123 GTCATTCTTA
Statistics
Matches: 111, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
120 24 0.22
123 87 0.78
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (120 bp):
ATCAACATTTCCAAAAGGAGTTCGTAATAAGAACTCATCTAAAGAGGAAGAAGAAATTCATAATC
TGAAGAACTTATTCAACCTTTTGATCGACTCTATCACAGAAGAAGATAAAGCAAC
Found at i:1999457 original size:25 final size:22
Alignment explanation
Indices: 1999429--1999474 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1999419 GTTTTAACTC
1999429 AATCTTAATTCCTAATAAAATAATA
1 AATC-TAA-TCCTAA-AAAATAATA
*
1999454 AATCTAATCCTAAAAGATAAT
1 AATCTAATCCTAAAAAATAAT
1999475 GCATCATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 3 0.15
25 4 0.20
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.33
Consensus pattern (22 bp):
AATCTAATCCTAAAAAATAATA
Found at i:2000437 original size:20 final size:20
Alignment explanation
Indices: 2000395--2000435 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2000385 TTACATATGC
*
2000395 ATATGCATATACTCACTTAA
1 ATATGCATATACGCACTTAA
*
2000415 ATATGCATATAGGCACATTAA
1 ATATGCATATACGCAC-TTAA
2000436 TAGAACTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (20 bp):
ATATGCATATACGCACTTAA
Found at i:2001481 original size:20 final size:19
Alignment explanation
Indices: 2001392--2001481 Score: 56
Period size: 19 Copynumber: 4.5 Consensus size: 19
2001382 AACTTTTACA
2001392 TTTTAAATAGTTTTTTCATATT
1 TTTTAAA-A-TTTTTT-ATATT
* *
2001414 TTTTAAAATTTTTAATAAT
1 TTTTAAAATTTTTTATATT
* **
2001433 GTTTAATGTTTTTTA-ATT
1 TTTTAAAATTTTTTATATT
***
2001451 TGAAAATAATTTTTTATATT
1 TTTTAA-AATTTTTTATATT
2001471 TTTTAACAATT
1 TTTTAA-AATT
2001482 AATATTTTTA
Statistics
Matches: 49, Mismatches: 17, Indels: 6
0.68 0.24 0.08
Matches are distributed among these distances:
18 4 0.08
19 22 0.45
20 15 0.31
21 1 0.02
22 7 0.14
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
TTTTAAAATTTTTTATATT
Found at i:2001502 original size:17 final size:15
Alignment explanation
Indices: 2001470--2001545 Score: 71
Period size: 17 Copynumber: 4.7 Consensus size: 15
2001460 TTTTTTATAT
*
2001470 TTTTTAACAATTAATA
1 TTTTTAA-ATTTAATA
2001486 TTTTTAAATTTAAAATA
1 TTTTTAAATTT--AATA
*
2001503 CTTTTAATATTTAATA
1 TTTTTAA-ATTTAATA
2001519 TTTTTATAATGTTAATA
1 TTTTTA-AAT-TTAATA
*
2001536 TTTTTGAATT
1 TTTTTAAATT
2001546 ATTAAAAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
15 4 0.08
16 21 0.41
17 22 0.43
18 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTTTAAATTTAATA
Found at i:2003724 original size:20 final size:20
Alignment explanation
Indices: 2003699--2003739 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2003689 TTGAACCTTG
2003699 GATGTTAGTCCTATGAAAAA
1 GATGTTAGTCCTATGAAAAA
2003719 GATGTTAGTCCTATGAAAAA
1 GATGTTAGTCCTATGAAAAA
2003739 G
1 G
2003740 GGGCAACGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (20 bp):
GATGTTAGTCCTATGAAAAA
Found at i:2014320 original size:2 final size:2
Alignment explanation
Indices: 2014313--2014350 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2014303 TAATTACAGA
2014313 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
2014351 CAACCCTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2016156 original size:57 final size:57
Alignment explanation
Indices: 2016087--2016255 Score: 311
Period size: 57 Copynumber: 3.0 Consensus size: 57
2016077 TAATTCACGG
*
2016087 CTGCAGCAGAACGTCAGTCTGGTTTGATACACCAAACTGATTTCGCGAGAAAATCGA
1 CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAAACTGATTTCGCGAGAAAATCGA
*
2016144 CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAAATTGATTTCGCGAGAAAATCGA
1 CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAAACTGATTTCGCGAGAAAATCGA
*
2016201 CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAAACTAATTTCGCGAGAAAATC
1 CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAAACTGATTTCGCGAGAAAATC
2016256 AAGAATTGCC
Statistics
Matches: 108, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 108 1.00
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (57 bp):
CTGCAGCAGAACGTCAGTCTGGTTGGATACACCAAACTGATTTCGCGAGAAAATCGA
Found at i:2027396 original size:86 final size:87
Alignment explanation
Indices: 2027217--2027398 Score: 312
Period size: 86 Copynumber: 2.1 Consensus size: 87
2027207 AGTTTTAATT
*
2027217 GCCAACAACTCATATAAGGTAGGAGGACTAGACCCTATAGGTTCAAAAAAAGGACCCCAAGAGAT
1 GCCACCAACTCATATAAGGTAGGAGGACTAGACCCTATAGGTTCAAAAAAAGGACCCCAAGAGAT
2027282 TACAATCAAAGTCCCAAAGTAA
66 TACAATCAAAGTCCCAAAGTAA
* * *
2027304 GACACCAACTCATATAAGGTAGGAGGACTAGACCCTATAGGTTC-AGAAAAGGACCCCAAGCGAT
1 GCCACCAACTCATATAAGGTAGGAGGACTAGACCCTATAGGTTCAAAAAAAGGACCCCAAGAGAT
*
2027368 TACAATCAGAGTCCCAAAGTAA
66 TACAATCAAAGTCCCAAAGTAA
2027390 GCCACCAAC
1 GCCACCAAC
2027399 ACCACCACTT
Statistics
Matches: 89, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
86 47 0.53
87 42 0.47
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.15
Consensus pattern (87 bp):
GCCACCAACTCATATAAGGTAGGAGGACTAGACCCTATAGGTTCAAAAAAAGGACCCCAAGAGAT
TACAATCAAAGTCCCAAAGTAA
Found at i:2047927 original size:8 final size:8
Alignment explanation
Indices: 2047914--2048059 Score: 99
Period size: 8 Copynumber: 17.8 Consensus size: 8
2047904 TTCGCTTGAA
2047914 GAAAAAAT
1 GAAAAAAT
*
2047922 GAAAAAAGA
1 GAAAAAA-T
2047931 GAGAAAAAT
1 GA-AAAAAT
*
2047940 -TAAAAAT
1 GAAAAAAT
*
2047947 TAAAAAATT
1 GAAAAAA-T
*
2047956 AAAAAAAT
1 GAAAAAAT
2047964 G-AAAAAT
1 GAAAAAAT
2047971 GAAGAAAA-
1 GAA-AAAAT
*
2047979 GAGAAAAT
1 GAAAAAAT
2047987 G-AAAAAT
1 GAAAAAAT
2047994 GAAAAAAT
1 GAAAAAAT
2048002 GAAAAAAAAT
1 G--AAAAAAT
2048012 -AAGAAAAT
1 GAA-AAAAT
2048020 -AAGAAAAT
1 GAA-AAAAT
2048028 GAAAAAAAT
1 G-AAAAAAT
2048037 GAAAAATGAT
1 GAAAAA--AT
2048047 GAAAAAA-
1 GAAAAAAT
2048054 GAAAAA
1 GAAAAA
2048060 GAAATAAAAA
Statistics
Matches: 115, Mismatches: 8, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
7 31 0.27
8 43 0.37
9 19 0.17
10 22 0.19
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (8 bp):
GAAAAAAT
Found at i:2047968 original size:7 final size:7
Alignment explanation
Indices: 2047958--2048045 Score: 67
Period size: 7 Copynumber: 12.1 Consensus size: 7
2047948 AAAAAATTAA
2047958 AAAAATG
1 AAAAATG
2047965 AAAAATG
1 AAAAATG
*
2047972 AAGAAAAG
1 AA-AAATG
2047980 AGAAAATG
1 A-AAAATG
2047988 AAAAATG
1 AAAAATG
2047995 AAAAAATG
1 -AAAAATG
2048003 AAAAA--
1 AAAAATG
2048008 AAATAA-G
1 AAA-AATG
*
2048015 -AAAATA
1 AAAAATG
2048021 AGAAAATG
1 A-AAAATG
2048029 AAAAAAATG
1 --AAAAATG
2048038 AAAAATG
1 AAAAATG
2048045 A
1 A
2048046 TGAAAAAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
5 5 0.07
6 4 0.06
7 28 0.42
8 22 0.33
9 7 0.10
10 1 0.01
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:2048010 original size:41 final size:43
Alignment explanation
Indices: 2047965--2048063 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 43
2047955 TAAAAAAATG
*
2047965 AAAAATGAAGAAAA-GAGAAAATG-AAAAATGAAAAA-ATGAAA
1 AAAAAT-AAGAAAATAAGAAAATGAAAAAATGAAAAAGATGAAA
2048006 AAAAATAAGAAAATAAGAAAATGAAAAAAATGAAAAATGATGAAA
1 AAAAATAAGAAAATAAGAAAATG-AAAAAATGAAAAA-GATGAAA
*
2048051 AAAGAAAAAGAAA
1 AAA-AATAAGAAA
2048064 TAAAAAGGGG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
40 7 0.14
41 14 0.28
43 12 0.24
45 9 0.18
46 8 0.16
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (43 bp):
AAAAATAAGAAAATAAGAAAATGAAAAAATGAAAAAGATGAAA
Found at i:2048033 original size:73 final size:72
Alignment explanation
Indices: 2047916--2048063 Score: 201
Period size: 73 Copynumber: 2.0 Consensus size: 72
2047906 CGCTTGAAGA
* * * *
2047916 AAAAATGAAAAAAGAGAGAAAAATTAAAAATTAAAAAATTAAAAAAATGAAAAATGAAGAAAAGA
1 AAAAATGAAAAAAGAGAGAAAAAATAAAAAATAAAAAATGAAAAAAATGAAAAATGAAGAAAAAA
*
2047981 GAAAATG
66 GAAAAAG
*
2047988 AAAAATGAAAAAATGA-A-AAAAAATAAGAAAATAAGAAAATGAAAAAAATGAAAAATGATGAAA
1 AAAAATGAAAAAA-GAGAGAAAAAATAA-AAAATAA-AAAATGAAAAAAATGAAAAATGAAGAAA
2048051 AAAGAAAAAG
63 AAAGAAAAAG
2048061 AAA
1 AAA
2048064 TAAAAAGGGG
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
71 8 0.12
72 20 0.30
73 39 0.58
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (72 bp):
AAAAATGAAAAAAGAGAGAAAAAATAAAAAATAAAAAATGAAAAAAATGAAAAATGAAGAAAAAA
GAAAAAG
Found at i:2048057 original size:7 final size:7
Alignment explanation
Indices: 2047957--2048063 Score: 51
Period size: 7 Copynumber: 14.4 Consensus size: 7
2047947 TAAAAAATTA
2047957 AAAAAATG
1 AAAAAA-G
*
2047965 AAAAATG
1 AAAAAAG
2047972 AAGAAAAG
1 AA-AAAAG
*
2047980 AGAAAATG
1 A-AAAAAG
*
2047988 AAAAATG
1 AAAAAAG
2047995 AAAAAATG
1 AAAAAA-G
2048003 -AAAAA-
1 AAAAAAG
*
2048008 AAATAAG
1 AAAAAAG
2048015 AAAATAAG
1 AAAA-AAG
2048023 AAAATGAA-
1 AAAA--AAG
*
2048031 AAAAATG
1 AAAAAAG
2048038 AAAAATGATG
1 AAAAA--A-G
2048048 AAAAAAG
1 AAAAAAG
2048055 -AAAAAG
1 AAAAAAG
2048061 AAA
1 AAA
2048064 TAAAAAGGGG
Statistics
Matches: 78, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
6 11 0.14
7 30 0.38
8 28 0.36
9 3 0.04
10 6 0.08
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (7 bp):
AAAAAAG
Found at i:2049400 original size:37 final size:38
Alignment explanation
Indices: 2049350--2049421 Score: 128
Period size: 37 Copynumber: 1.9 Consensus size: 38
2049340 AATCTAATCT
*
2049350 TAAGCCTTCACGGAAGAGTAGTGAAGCAAA-TCATATA
1 TAAGCCTCCACGGAAGAGTAGTGAAGCAAACTCATATA
2049387 TAAGCCTCCACGGAAGAGTAGTGAAGCAAACTCAT
1 TAAGCCTCCACGGAAGAGTAGTGAAGCAAACTCAT
2049422 TTTATGAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 29 0.88
38 4 0.12
ACGTcount: A:0.39, C:0.19, G:0.22, T:0.19
Consensus pattern (38 bp):
TAAGCCTCCACGGAAGAGTAGTGAAGCAAACTCATATA
Found at i:2049506 original size:55 final size:54
Alignment explanation
Indices: 2049432--2049988 Score: 530
Period size: 55 Copynumber: 10.1 Consensus size: 54
2049422 TTTATGAAGA
* * * *
2049432 TCGAGTCTTATACTCTCTGATA-AAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGA-AGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGT
2049487 TCGAGTCCTATACTCTCTGATA-GAATAGGGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGA-AGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGT
* * *
2049542 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTCGTTTTATGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTT-TGAAGATTGT
* * *
2049597 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTT-TGAAGATTGT
* * * *
2049652 TTGAGTCCTATACTCTCTGAAGAAATAGAGAGCGGACACGTTTGTTGAAGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGT
* * * * *
2049707 TCAAGTCCTATACTCTCTGAAGGAATAGGGAGCGCACACATTTGTTGAAAATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGT
* * ** * *
2049762 TCGAGGT-CTATACTCCCTGAACGAATAGGGATTGAACCCATTTTTAGAAGATTGT
1 TCGA-GTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTT-GAAGATTGT
* * * * * ** * *
2049817 TCAAGTTCTATACTCTCTGAACGAATAAGGAGCGAACATGTTTTCAGAGGATTGT
1 TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTT-TGAAGATTGT
* * * * **
2049872 TCGAGTTCTATACTC-CTTTAAAGAATAGGGAGTGGACCCGTTTGCCGAAGATTGT
1 TCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGT
* * * * * *
2049927 TCAAGTCATATACT-TCTTGAAAGAATAGGGAGCAGACCCGTTTTTGAATATTTT
1 TCGAGTCCTATACTCTC-TGAAGGAATAGGGAGCGGACCCGTTTTTGAAGATTGT
*
2049981 TCAAGTCC
1 TCGAGTCC
2049989 AACCTATTAT
Statistics
Matches: 431, Mismatches: 61, Indels: 21
0.84 0.12 0.04
Matches are distributed among these distances:
54 21 0.05
55 407 0.94
56 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (54 bp):
TCGAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTTGAAGATTGT
Found at i:2051470 original size:28 final size:27
Alignment explanation
Indices: 2051435--2051493 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 27
2051425 CACAAGAAAG
*
2051435 GAGGAGAGAAAATAAAGAGTAAAGTGT
1 GAGGAGAGAAAATAAAGAGTAAAGCGT
*
2051462 GAGGCAGAGAAAGTAAAGAGTAAAGCGT
1 GAGG-AGAGAAAATAAAGAGTAAAGCGT
2051490 GAGG
1 GAGG
2051494 TTGGGTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 4 0.14
28 25 0.86
ACGTcount: A:0.47, C:0.03, G:0.37, T:0.12
Consensus pattern (27 bp):
GAGGAGAGAAAATAAAGAGTAAAGCGT
Found at i:2059912 original size:7 final size:7
Alignment explanation
Indices: 2059900--2059930 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
2059890 GGGGTAATTT
2059900 AATAGGA
1 AATAGGA
2059907 AATAGGA
1 AATAGGA
2059914 AATAGGA
1 AATAGGA
2059921 AATAGGA
1 AATAGGA
2059928 AAT
1 AAT
2059931 GGTAAATGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (7 bp):
AATAGGA
Found at i:2059937 original size:7 final size:7
Alignment explanation
Indices: 2059927--2059951 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2059917 AGGAAATAGG
2059927 AAATGGT
1 AAATGGT
2059934 AAATGGT
1 AAATGGT
2059941 AAATGGT
1 AAATGGT
2059948 AAAT
1 AAAT
2059952 ACTTATACGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (7 bp):
AAATGGT
Found at i:2059937 original size:14 final size:14
Alignment explanation
Indices: 2059906--2059952 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2059896 ATTTAATAGG
2059906 AAATAGGAAATAGG-
1 AAATAGGAAAT-GGT
2059920 AAATAGGAAATGGT
1 AAATAGGAAATGGT
2059934 AAAT-GGTAAATGGT
1 AAATAGG-AAATGGT
2059948 AAATA
1 AAATA
2059953 CTTATACGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.13
14 26 0.87
ACGTcount: A:0.53, C:0.00, G:0.26, T:0.21
Consensus pattern (14 bp):
AAATAGGAAATGGT
Found at i:2062439 original size:29 final size:29
Alignment explanation
Indices: 2062352--2062439 Score: 69
Period size: 29 Copynumber: 3.1 Consensus size: 29
2062342 ATAATTAGCT
2062352 AAATTTGTAGAAATAATATTTGTTCTCAA
1 AAATTTGTAGAAATAATATTTGTTCTCAA
* * *** *
2062381 AAA----TAAATAATAACATTT-AAATGAA
1 AAATTTGTAGA-AATAATATTTGTTCTCAA
2062406 TAAATTTGTAGAAATAATATTTGTTCTCAA
1 -AAATTTGTAGAAATAATATTTGTTCTCAA
2062436 AAAT
1 AAAT
2062440 AAATAATAAC
Statistics
Matches: 40, Mismatches: 12, Indels: 14
0.61 0.18 0.21
Matches are distributed among these distances:
25 6 0.15
26 12 0.30
29 16 0.40
30 6 0.15
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.38
Consensus pattern (29 bp):
AAATTTGTAGAAATAATATTTGTTCTCAA
Found at i:2062478 original size:55 final size:55
Alignment explanation
Indices: 2062360--2062532 Score: 226
Period size: 55 Copynumber: 3.2 Consensus size: 55
2062350 CTAAATTTGT
** **
2062360 AGAAATAATATTTGTTCTCAAAAATAAATAATAACATTTAAATGAATAAATTTGT
1 AGAAATAATATTTGTTCTCAAAAATAAATAATAACATTTAAATGAATTTATTTAA
*
2062415 AGAAATAATATTTGTTCTCAAAAATAAATAATAACATTTAAATGAATTTATATAA
1 AGAAATAATATTTGTTCTCAAAAATAAATAATAACATTTAAATGAATTTATTTAA
* * * * * *
2062470 AGATATAATA--T-TTATGAAAAATAGAGAATAACATTTAAATGAATTTGTTTAA
1 AGAAATAATATTTGTTCTCAAAAATAAATAATAACATTTAAATGAATTTATTTAA
2062522 AGAAATAATAT
1 AGAAATAATAT
2062533 CTATTTCAGT
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
52 44 0.42
53 1 0.01
55 59 0.57
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (55 bp):
AGAAATAATATTTGTTCTCAAAAATAAATAATAACATTTAAATGAATTTATTTAA
Found at i:2062482 original size:29 final size:28
Alignment explanation
Indices: 2062438--2062525 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
2062428 GTTCTCAAAA
*
2062438 ATAAATAATAACATTTAAATGAATTTAT
1 ATAAAGAATAACATTTAAATGAATTTAT
* *
2062466 ATAAAGATATAATATTT--ATGAA---AA
1 ATAAAGA-ATAACATTTAAATGAATTTAT
* *
2062490 ATAGAGAATAACATTTAAATGAATTTGT
1 ATAAAGAATAACATTTAAATGAATTTAT
*
2062518 TTAAAGAA
1 ATAAAGAA
2062526 ATAATATCTA
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
23 8 0.18
24 7 0.16
25 5 0.11
27 5 0.11
28 12 0.27
29 8 0.18
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.35
Consensus pattern (28 bp):
ATAAAGAATAACATTTAAATGAATTTAT
Found at i:2062512 original size:52 final size:52
Alignment explanation
Indices: 2062379--2062532 Score: 164
Period size: 52 Copynumber: 2.9 Consensus size: 52
2062369 ATTTGTTCTC
* ** * ** * *
2062379 AAAAATAAATAATAACATTTAAATGAATAAATTTGTAGAAATAATATTTGTTCTC
1 AAAAATAAAGAATAACATTTAAATGAATTTATATAAAGAAATAATA--T-TTATG
* *
2062434 AAAAATAAATAATAACATTTAAATGAATTTATATAAAGATATAATATTTATG
1 AAAAATAAAGAATAACATTTAAATGAATTTATATAAAGAAATAATATTTATG
* * *
2062486 AAAAATAGAGAATAACATTTAAATGAATTTGTTTAAAGAAATAATAT
1 AAAAATAAAGAATAACATTTAAATGAATTTATATAAAGAAATAATAT
2062533 CTATTTCAGT
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
52 45 0.52
53 1 0.01
55 40 0.47
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (52 bp):
AAAAATAAAGAATAACATTTAAATGAATTTATATAAAGAAATAATATTTATG
Found at i:2064311 original size:13 final size:13
Alignment explanation
Indices: 2064274--2064300 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2064264 ATTATTAACT
2064274 AATTATAATTTTA
1 AATTATAATTTTA
2064287 AATTATAATTTTA
1 AATTATAATTTTA
2064300 A
1 A
2064301 TGTTTAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATAATTTTA
Found at i:2075692 original size:2 final size:2
Alignment explanation
Indices: 2075687--2075716 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2075677 TCTAGAGTTA
*
2075687 AT AT AT TT 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
2075717 GCTTTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2077602 original size:31 final size:31
Alignment explanation
Indices: 2077567--2077636 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
2077557 GTGCTATAAG
* ** *
2077567 CTATGTGATAAGGATCTATGTGATTATATGT
1 CTATGTGATAAGGAACTACATGATTATATGA
*
2077598 CTATGTGATAATGAACTACATGATTATATGA
1 CTATGTGATAAGGAACTACATGATTATATGA
*
2077629 ATATGTGA
1 CTATGTGA
2077637 AATGTGAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (31 bp):
CTATGTGATAAGGAACTACATGATTATATGA
Found at i:2077604 original size:45 final size:45
Alignment explanation
Indices: 2077449--2077604 Score: 147
Period size: 45 Copynumber: 3.5 Consensus size: 45
2077439 ATACCTGAAA
* *
2077449 ATGTGA-TATATG-CTATGTGACCATAATCTATGTGTTATGTGATCT
1 ATGTGATTATATGACTATGTG-CTATAAGCTATGTGTTATG-GATCT
** * ** *
2077494 ATGTGATTATATGAGAATGTGATATAAGCTATGTGTTATTCACCT
1 ATGTGATTATATGACTATGTGCTATAAGCTATGTGTTATGGATCT
* * * *
2077539 AAGTGATTATAGGAAC-ATGTGCTATAAGCTATGTGATAAGGATCT
1 ATGTGATTATATG-ACTATGTGCTATAAGCTATGTGTTATGGATCT
*
2077584 ATGTGATTATATGTCTATGTG
1 ATGTGATTATATGACTATGTG
2077605 ATAATGAACT
Statistics
Matches: 87, Mismatches: 20, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
44 1 0.01
45 59 0.68
46 22 0.25
47 5 0.06
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (45 bp):
ATGTGATTATATGACTATGTGCTATAAGCTATGTGTTATGGATCT
Found at i:2077789 original size:22 final size:23
Alignment explanation
Indices: 2077764--2077818 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
2077754 AGTCGAATGT
2077764 TCTACGCGGTCCTTCAGGA-ATA
1 TCTACGCGGTCCTTCAGGACATA
* * * *
2077786 TCTACGTGGTTCTTCGGGACATT
1 TCTACGCGGTCCTTCAGGACATA
*
2077809 TCTACCCGGT
1 TCTACGCGGT
2077819 TCTTTGGGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (23 bp):
TCTACGCGGTCCTTCAGGACATA
Found at i:2077813 original size:23 final size:23
Alignment explanation
Indices: 2077763--2077931 Score: 75
Period size: 23 Copynumber: 7.7 Consensus size: 23
2077753 GAGTCGAATG
* * *
2077763 TTCTACGCGGTCCTTCAGGA-AT
1 TTCTACGTGGTTCTTCGGGACAT
*
2077785 ATCTACGTGGTTCTTCGGGACAT
1 TTCTACGTGGTTCTTCGGGACAT
** * * *
2077808 TTCTACCCGGTTCTTTGGGATAA
1 TTCTACGTGGTTCTTCGGGACAT
* * * * *
2077831 TACAATGTGGTTCTT-TGGACAC
1 TTCTACGTGGTTCTTCGGGACAT
* * *
2077853 ATCTATGTGGTCCTTCGGGACA-
1 TTCTACGTGGTTCTTCGGGACAT
* *
2077875 ---T--GTGGTTCTTTGGGACAC
1 TTCTACGTGGTTCTTCGGGACAT
* * *
2077893 ATCTATGTGGTCCTTCGGGACAT
1 TTCTACGTGGTTCTTCGGGACAT
*
2077916 TTCTACGTGGCTCTTC
1 TTCTACGTGGTTCTTC
2077932 AGTGTAATTT
Statistics
Matches: 107, Mismatches: 32, Indels: 15
0.69 0.21 0.10
Matches are distributed among these distances:
17 14 0.13
19 1 0.01
21 1 0.01
22 31 0.29
23 60 0.56
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTTCTTCGGGACAT
Found at i:2077879 original size:17 final size:17
Alignment explanation
Indices: 2077857--2077891 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2077847 GGACACATCT
2077857 ATGTGGTCCTTCGGGAC
1 ATGTGGTCCTTCGGGAC
* *
2077874 ATGTGGTTCTTTGGGAC
1 ATGTGGTCCTTCGGGAC
2077891 A
1 A
2077892 CATCTATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (17 bp):
ATGTGGTCCTTCGGGAC
Found at i:2077900 original size:40 final size:39
Alignment explanation
Indices: 2077835--2077915 Score: 153
Period size: 40 Copynumber: 2.1 Consensus size: 39
2077825 GGATAATACA
2077835 ATGTGGTTCTTTGGACACATCTATGTGGTCCTTCGGGAC
1 ATGTGGTTCTTTGGACACATCTATGTGGTCCTTCGGGAC
2077874 ATGTGGTTCTTTGGGACACATCTATGTGGTCCTTCGGGAC
1 ATGTGGTTCTTT-GGACACATCTATGTGGTCCTTCGGGAC
2077914 AT
1 AT
2077916 TTCTACGTGG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 12 0.29
40 29 0.71
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.36
Consensus pattern (39 bp):
ATGTGGTTCTTTGGACACATCTATGTGGTCCTTCGGGAC
Found at i:2078137 original size:6 final size:6
Alignment explanation
Indices: 2078056--2078134 Score: 68
Period size: 6 Copynumber: 13.0 Consensus size: 6
2078046 ATGAATAGTG
* * ** *
2078056 AATGAT AATGAT AATGAT GATGAG AACAAAT ATTGAT AATGAT AATGAT
1 AATGAT AATGAT AATGAT AATGAT AA-TGAT AATGAT AATGAT AATGAT
** * *
2078105 GTTGAT AATGAT AGTGAT AATGAT GATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT
2078135 GATATGTATA
Statistics
Matches: 55, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
6 53 0.96
7 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.22, T:0.33
Consensus pattern (6 bp):
AATGAT
Found at i:2081251 original size:18 final size:19
Alignment explanation
Indices: 2081228--2081265 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2081218 GTGAGTTCCG
*
2081228 GACAGTTCAA-ACTTATAA
1 GACAGTGCAACACTTATAA
*
2081246 GACAGTGCAACATTTATAA
1 GACAGTGCAACACTTATAA
2081265 G
1 G
2081266 TATTTTGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
GACAGTGCAACACTTATAA
Found at i:2081867 original size:23 final size:23
Alignment explanation
Indices: 2081840--2081909 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 23
2081830 GAGTCGAGGG
*
2081840 TTCTACGCGGTCCTTCGAGACAA
1 TTCTACGCGGTCATTCGAGACAA
* * * *
2081863 TTCTATGTGGTCATTTGAGACAT
1 TTCTACGCGGTCATTCGAGACAA
** * *
2081886 TTCTATACGGTCATTTGGGACAA
1 TTCTACGCGGTCATTCGAGACAA
2081909 T
1 T
2081910 ATTATGTGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (23 bp):
TTCTACGCGGTCATTCGAGACAA
Found at i:2081920 original size:23 final size:23
Alignment explanation
Indices: 2081858--2081936 Score: 79
Period size: 23 Copynumber: 3.4 Consensus size: 23
2081848 GGTCCTTCGA
*
2081858 GACAATTCTATGTGGTCATTTGA
1 GACAATTCTATGTGGTCATTTGG
* **
2081881 GACATTTCTATACGGTCATTTGG
1 GACAATTCTATGTGGTCATTTGG
* *
2081904 GACAATAT-TATGTGGTCCTTCGG
1 GACAAT-TCTATGTGGTCATTTGG
*
2081927 GACATTTCTA
1 GACAATTCTA
2081937 CGTGACACTT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
22 1 0.02
23 42 0.95
24 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (23 bp):
GACAATTCTATGTGGTCATTTGG
Found at i:2082145 original size:24 final size:24
Alignment explanation
Indices: 2082113--2082171 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
2082103 AGAACATATA
2082113 TTGATAATGATAATGATAATGATG
1 TTGATAATGATAATGATAATGATG
*
2082137 TTGATAATGATAGTGATAATGATG
1 TTGATAATGATAATGATAATGATG
* *
2082161 ATGATGATGAT
1 TTGATAATGAT
2082172 GTGTGTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (24 bp):
TTGATAATGATAATGATAATGATG
Found at i:2082172 original size:6 final size:6
Alignment explanation
Indices: 2082072--2082171 Score: 80
Period size: 6 Copynumber: 17.0 Consensus size: 6
2082062 ATGATCGGTG
* * * * *
2082072 AATGAT AATGAT AATAAT AATAAT GATGAT GA-GA- ACAT-AT ATTGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT A-ATGAT AATGAT
** * *
2082118 AATGAT AATGAT AATGAT GTTGAT AATGAT AGTGAT AATGAT GATGAT
1 AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT AATGAT
*
2082166 GATGAT
1 AATGAT
2082172 GTGTGTATAT
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
5 5 0.06
6 72 0.94
ACGTcount: A:0.45, C:0.01, G:0.20, T:0.34
Consensus pattern (6 bp):
AATGAT
Found at i:2087939 original size:20 final size:20
Alignment explanation
Indices: 2087914--2087959 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
2087904 TTAAAAATGT
2087914 ATGAAAAGATTCATTAAGGC
1 ATGAAAAGATTCATTAAGGC
*
2087934 ATGAAAGGATTCATTAAGGC
1 ATGAAAAGATTCATTAAGGC
2087954 ATGAAA
1 ATGAAA
2087960 CGATGTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.09, G:0.22, T:0.24
Consensus pattern (20 bp):
ATGAAAAGATTCATTAAGGC
Found at i:2087986 original size:47 final size:47
Alignment explanation
Indices: 2087932--2088171 Score: 347
Period size: 47 Copynumber: 5.1 Consensus size: 47
2087922 ATTCATTAAG
* *
2087932 GCATGAAAGGATTCATTAAGGCATGAAACGATGTCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAT
*
2087979 GCATGAAATGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAT
* * *
2088026 GCATGAAAGTATGCATTAAGTCATGAAAGGATGACATAATTGAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAT
**
2088073 TAATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTG-AAAAT
* * * *
2088121 ACATGAAATGATGCATTAATGCATGAAAGGATGCCATAAATT-AAAAT
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCAT-AATTGAAAAT
2088168 GCAT
1 GCAT
2088172 TATTGGATGT
Statistics
Matches: 173, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
47 132 0.76
48 37 0.21
49 4 0.02
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.25
Consensus pattern (47 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTGAAAAT
Found at i:2088004 original size:20 final size:20
Alignment explanation
Indices: 2087979--2088105 Score: 65
Period size: 20 Copynumber: 5.7 Consensus size: 20
2087969 AATTGAAAAT
*
2087979 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
*
2087999 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
2088026 GCATGAAAGTATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
2088046 TCATGAAAGGATGACATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
**
2088073 TAATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
2088093 GCATGAAAGGATG
1 GCATGAAAGGATG
2088106 TCATAATTGA
Statistics
Matches: 82, Mismatches: 11, Indels: 28
0.68 0.09 0.23
Matches are distributed among these distances:
20 38 0.46
21 2 0.02
23 6 0.07
24 6 0.07
26 2 0.02
27 28 0.34
ACGTcount: A:0.43, C:0.08, G:0.24, T:0.24
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:2094283 original size:20 final size:20
Alignment explanation
Indices: 2094256--2094309 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2094246 TTGATTCAAT
*
2094256 AGGTATCGATACCAAAGAGGG
1 AGGTATCGATACCAAAG-GGA
*
2094277 A-GTATCGATACCGAAGGGA
1 AGGTATCGATACCAAAGGGA
2094296 AGGTATCGATACCA
1 AGGTATCGATACCA
2094310 TTTCAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 25 0.86
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.30, T:0.17
Consensus pattern (20 bp):
AGGTATCGATACCAAAGGGA
Found at i:2094380 original size:22 final size:20
Alignment explanation
Indices: 2094332--2094403 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
2094322 ATGTAAAATT
*
2094332 AGTATCGATACCATAATAGG
1 AGTATCGATACCATAGTAGG
2094352 -GTATCGATACCATAGTATGG
1 AGTATCGATACCATAGTA-GG
* *
2094372 TAGTATCGATAGCATGGTAGG
1 -AGTATCGATACCATAGTAGG
*
2094393 GGTATCGATAC
1 AGTATCGATAC
2094404 TGAAGAGCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 16 0.36
20 11 0.25
21 2 0.05
22 15 0.34
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (20 bp):
AGTATCGATACCATAGTAGG
Found at i:2094399 original size:20 final size:21
Alignment explanation
Indices: 2094333--2094403 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 21
2094323 TGTAAAATTA
*
2094333 GTATCGATACCATA--ATAGG
1 GTATCGATACCATAGTATGGG
*
2094352 GTATCGATACCATAGTATGGTA
1 GTATCGATACCATAGTATGG-G
* *
2094374 GTATCGATAGCATGGTA-GGG
1 GTATCGATACCATAGTATGGG
2094394 GTATCGATAC
1 GTATCGATAC
2094404 TGAAGAGCTA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.33
20 9 0.21
21 5 0.12
22 15 0.35
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (21 bp):
GTATCGATACCATAGTATGGG
Found at i:2094871 original size:47 final size:47
Alignment explanation
Indices: 2094798--2095012 Score: 317
Period size: 47 Copynumber: 4.6 Consensus size: 47
2094788 AAATCGAATC
* *
2094798 CATAATTGAAAATGCATGAAAAGATGCATTAAGGTATGAAAGGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
* *
2094845 TATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAAGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
* *
2094892 CATAATTGAAAATGCATTAAAGGATGTATTAAGGCATGAAAGGATGT
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
* *
2094939 CATAATTGAAAATGCATGAAATGATGCATTAAGGCATGAAAGGATGAC
1 CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-T
2094987 CATAAATT-AAAATGCAT-AAATGGATG
1 CAT-AATTGAAAATGCATGAAA-GGATG
2095013 TGTTATATGT
Statistics
Matches: 152, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
47 132 0.87
48 16 0.11
49 4 0.03
ACGTcount: A:0.45, C:0.07, G:0.22, T:0.26
Consensus pattern (47 bp):
CATAATTGAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGT
Found at i:2094883 original size:20 final size:20
Alignment explanation
Indices: 2094858--2094984 Score: 74
Period size: 20 Copynumber: 5.7 Consensus size: 20
2094848 AATTGAAAAT
2094858 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* *
2094878 GCATGAAAAGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
* *
2094905 GCATTAAAGGATGTATTAAG
1 GCATGAAAGGATGCATTAAG
*
2094925 GCATGAAAGGATGTCATAATTGAAAAT
1 GCATGAAAGGATG-C---ATT---AAG
*
2094952 GCATGAAATGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
2094972 GCATGAAAGGATG
1 GCATGAAAGGATG
2094985 ACCATAAATT
Statistics
Matches: 81, Mismatches: 12, Indels: 28
0.67 0.10 0.23
Matches are distributed among these distances:
20 40 0.49
21 1 0.01
23 6 0.07
24 6 0.07
26 1 0.01
27 27 0.33
ACGTcount: A:0.43, C:0.08, G:0.25, T:0.24
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:2096729 original size:7 final size:7
Alignment explanation
Indices: 2096717--2096741 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2096707 ACGATCACAA
2096717 TTGTGTT
1 TTGTGTT
2096724 TTGTGTT
1 TTGTGTT
2096731 TTGTGTT
1 TTGTGTT
2096738 TTGT
1 TTGT
2096742 CTTAATAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.00, G:0.28, T:0.72
Consensus pattern (7 bp):
TTGTGTT
Found at i:2099553 original size:10 final size:10
Alignment explanation
Indices: 2099538--2099576 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
2099528 AATGAAAATG
2099538 AAAAAAAG-A
1 AAAAAAAGAA
2099547 AAAAAAAGAA
1 AAAAAAAGAA
*
2099557 AAAAAAGGAA
1 AAAAAAAGAA
*
2099567 AGAAAAAGAA
1 AAAAAAAGAA
2099577 TAGAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:2099561 original size:20 final size:20
Alignment explanation
Indices: 2099538--2099576 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2099528 AATGAAAATG
2099538 AAAAAAAGAAA-AAAAAGAA
1 AAAAAAAGAAAGAAAAAGAA
*
2099557 AAAAAAGGAAAGAAAAAGAA
1 AAAAAAAGAAAGAAAAAGAA
2099577 TAGAAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAAGAAAGAAAAAGAA
Found at i:2099583 original size:10 final size:9
Alignment explanation
Indices: 2099538--2099576 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
2099528 AATGAAAATG
2099538 AAAAAAAGA
1 AAAAAAAGA
2099547 AAAAAAAGA
1 AAAAAAAGA
2099556 AAAAAAAGGA
1 AAAAAAA-GA
2099566 AAGAAAAAGA
1 AA-AAAAAGA
2099576 A
1 A
2099577 TAGAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 16 0.57
10 7 0.25
11 5 0.18
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:2101057 original size:134 final size:134
Alignment explanation
Indices: 2100812--2101312 Score: 618
Period size: 134 Copynumber: 3.8 Consensus size: 134
2100802 ATCAAACTCG
* * * * *
2100812 ATTCAATCTTTCCTGAAGAATAGTGGAATGAATCAACATTTCCATATATGCTCTACCCTGAAGAA
1 ATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAA
* * * * * *
2100877 ACAGTGGAGCATATCCCTTTTTTCCATATCTGATCTTCTCTGAAGAAGCAGTGGAACAAGTCTGC
66 GCAGCGGAGCATATCCCCTTTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTCTGC
2100942 CTCA
131 CTCA
* * * *
2100946 ATTCAATATTCCTTAAAGAACAGTGGAATTAATCAACATTTCCATATATGATCTACCCTGAAGAA
1 ATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAA
* * ** *
2101011 GCAGCGGAGCATATCCCCTTTTTCCAGATTTGATCTTCCCTAAAGAAGCAATATAACAAGTCTAC
66 GCAGCGGAGCATATCCCCTTTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTCTGC
*
2101076 CTCG
131 CTCA
* * * * *
2101080 ATTCAATATTCCCTGAAGAACAGTGGGAT-ATATCAAAATTTACAGATGTGATATACCCTGAAGA
1 ATTCAATATTCCCTGAAGAACAGTGGAATGA-ATCAACATTTCCAGATATGATCTACCCTGAAGA
* * * * * *
2101144 AGCAGTGAAGAAGAT-CCCTTCTTTCCAGATTTGATCTTCCCTGAAGAAGTAGTGGAACAAGTAT
65 AGCAGCGGAGCATATCCCCTT-TTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTCT
2101208 GCCTCA
129 GCCTCA
* * *
2101214 ATTCAATCTTCCCTGAAGAACAGTTGAATGAATCAACATTTCCAGATATGATCTACCCTAAAG-A
1 ATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAA
*
2101278 GCAGCGGAGCATA-CCCC-TTTT-CAGATTCGATCTTC
66 GCAGCGGAGCATATCCCCTTTTTCCAGATTTGATCTTC
2101313 AAAAATCTCT
Statistics
Matches: 311, Mismatches: 52, Indels: 12
0.83 0.14 0.03
Matches are distributed among these distances:
130 13 0.04
131 3 0.01
132 1 0.00
133 19 0.06
134 274 0.88
135 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (134 bp):
ATTCAATATTCCCTGAAGAACAGTGGAATGAATCAACATTTCCAGATATGATCTACCCTGAAGAA
GCAGCGGAGCATATCCCCTTTTTCCAGATTTGATCTTCCCTGAAGAAGCAGTGGAACAAGTCTGC
CTCA
Found at i:2102391 original size:18 final size:18
Alignment explanation
Indices: 2102368--2102403 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2102358 GACCGACCGA
*
2102368 GAGAGAGAGGAGATAGGG
1 GAGAGAGAGGAGAGAGGG
*
2102386 GAGAGATAGGAGAGAGGG
1 GAGAGAGAGGAGAGAGGG
2102404 AGTAGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.56, T:0.06
Consensus pattern (18 bp):
GAGAGAGAGGAGAGAGGG
Found at i:2102867 original size:10 final size:10
Alignment explanation
Indices: 2102852--2102899 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
2102842 TCTGATATGT
2102852 TTTTATTTAA
1 TTTTATTTAA
2102862 TTTTATTTAA
1 TTTTATTTAA
*
2102872 TTTAATAATGTAA
1 TTT--T-ATTTAA
*
2102885 TTTTATTTTA
1 TTTTATTTAA
2102895 TTTTA
1 TTTTA
2102900 ATTTGGTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
10 22 0.69
11 1 0.03
12 1 0.03
13 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (10 bp):
TTTTATTTAA
Found at i:2104626 original size:2 final size:2
Alignment explanation
Indices: 2104621--2104670 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
2104611 ACATAAAGAA
2104621 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
2104663 AT AT -T AT A
1 AT AT AT AT A
2104671 CTGTTATAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2112334 original size:18 final size:17
Alignment explanation
Indices: 2112311--2112371 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 17
2112301 TTACTTTTTA
2112311 TTTTATTAAATTTTAAGT
1 TTTTATT-AATTTTAAGT
2112329 TTTTATTTAATGTTATAAGAGT
1 TTTTA-TTAAT-TT-T-A-AGT
* *
2112351 TTTTATTTATTTTAAAT
1 TTTTATTAATTTTAAGT
2112368 TTTT
1 TTTT
2112372 TATTTCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
17 6 0.17
18 9 0.25
19 5 0.14
20 3 0.08
21 5 0.14
22 8 0.22
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (17 bp):
TTTTATTAATTTTAAGT
Found at i:2112970 original size:2 final size:2
Alignment explanation
Indices: 2112965--2113000 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2112955 ACCATATACA
2112965 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
2113001 TCGTATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.