Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 8 of 444
Found at i:2385134 original size:4 final size:4
Alignment explanation
Indices: 2385125--2385174 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
2385115 CATACATGTA
* * *
2385125 TATG TATG TATG TATG CATG CATG CATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2385173 TA
1 TA
2385175 CCTACCTTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 44 1.00
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (4 bp):
TATG
Found at i:2387001 original size:30 final size:30
Alignment explanation
Indices: 2386924--2387002 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
2386914 TAGTTAAACT
2386924 TAAATTTTATAATTTA-AAAAATAGAATAAC
1 TAAATTTTA-AATTTATAAAAATAGAATAAC
* ** *
2386954 TAAATTTTTAAA--AATAAAAATTTAATGAC
1 TAAA-TTTTAAATTTATAAAAATAGAATAAC
2386983 TAAATTTTAAATTTATAAAA
1 TAAATTTTAAATTTATAAAA
2387003 GAAATACAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
28 8 0.20
29 15 0.38
30 12 0.30
31 5 0.12
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (30 bp):
TAAATTTTAAATTTATAAAAATAGAATAAC
Found at i:2388336 original size:11 final size:11
Alignment explanation
Indices: 2388320--2388352 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2388310 ATTTACTTAA
2388320 TTTTAATATAT
1 TTTTAATATAT
2388331 TTTTAAT-TAT
1 TTTTAATATAT
*
2388341 TTATAATATAT
1 TTTTAATATAT
2388352 T
1 T
2388353 AAAGATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTAATATAT
Found at i:2396827 original size:145 final size:144
Alignment explanation
Indices: 2396540--2397132 Score: 518
Period size: 145 Copynumber: 4.1 Consensus size: 144
2396530 TTTAGTTAAT
* * **
2396540 AGTTTTCGGGTTAGTTCATTAGCTCTTGGTTAGACTCTGTAATCAAATGTTTCTCAAAGCAGTAA
1 AGTTTTCGGGTTAGTTCAGTAGCTCTTGGTTAGACTGTGTAATCAAATG--T-T----GCTTTAA
** * *** * ** * * * *
2396605 CTCAAACACGATCATTCTAGGTTCT-TCGAACGTGACTTGTTTACGTAATATATTCAATTAATGA
59 CTCAAACACGATTGTTCTAGGCTCTAT-GAAAAAGAGTTGTTCGCGTGATACATCCAGTT-ATGA
*
2396669 ACTTCGTTTGGTGTATGTAATGA
122 ACTTTGTTTGGTGTATGTAATGA
* * ** *
2396692 AGTTTCCGGGTTAGCTCAGTAGCTCTTGGTTAGACTGTAAAATCAAATGTTGCTTTAACTCGAAC
1 AGTTTTCGGGTTAGTTCAGTAGCTCTTGGTTAGACTGTGTAATCAAATGTTGCTTTAACTCAAAC
* * *
2396757 ACAATTGTTCTAGGCTGTATGAAAAAGAGTTGTTTGCGTGATACATCCAGTTGATGAACTTTGTT
66 ACGATTGTTCTAGGCTCTATGAAAAAGAGTTGTTCGCGTGATACATCCAGTT-ATGAACTTTGTT
2396822 TGGTGTATGTAATGA
130 TGGTGTATGTAATGA
* * *
2396837 AGTTTTCGGGTTAGTTAAGTAGCTTTTGGTTAGACTGTGTAATCAAATGTTTCTTTAACTCAAAC
1 AGTTTTCGGGTTAGTTCAGTAGCTCTTGGTTAGACTGTGTAATCAAATGTTGCTTTAACTCAAAC
* * ** * * * * *** *
2396902 ATGGTCATTCTAGGTTCTTTGAACAAGAGTTGTTCGCGTGATAGATTTGGTTATGAACTCTGTTT
66 ACGATTGTTCTAGGCTCTATGAAAAAGAGTTGTTCGCGTGATACATCCAGTTATGAACTTTGTTT
*
2396967 GGTTTATGTAATGA
131 GGTGTATGTAATGA
* * *
2396981 AGTTTTTGGGTTAGTTCAATAGCTC----TTAGACTGTGTAATCAAATGTTGCTTTAACCCAAAC
1 AGTTTTCGGGTTAGTTCAGTAGCTCTTGGTTAGACTGTGTAATCAAATGTTGCTTTAACTCAAAC
* * * * * * * ***
2397042 ACGATTGTTCTAGGCTCTGTGAACACGAGTTTTTCACATGATAGATTTGGTTGATGAACTTT-TT
66 ACGATTGTTCTAGGCTCTATGAAAAAGAGTTGTTCGCGTGATACATCCAGTT-ATGAACTTTGTT
2397106 CT--TGTATGTAATGA
130 -TGGTGTATGTAATGA
2397120 AGTTTTTCGGGTT
1 AG-TTTTCGGGTT
2397133 CTAATGTAAC
Statistics
Matches: 369, Mismatches: 68, Indels: 20
0.81 0.15 0.04
Matches are distributed among these distances:
139 13 0.04
140 87 0.24
141 9 0.02
144 46 0.12
145 168 0.46
146 1 0.00
149 1 0.00
150 1 0.00
152 43 0.12
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (144 bp):
AGTTTTCGGGTTAGTTCAGTAGCTCTTGGTTAGACTGTGTAATCAAATGTTGCTTTAACTCAAAC
ACGATTGTTCTAGGCTCTATGAAAAAGAGTTGTTCGCGTGATACATCCAGTTATGAACTTTGTTT
GGTGTATGTAATGA
Found at i:2397097 original size:285 final size:286
Alignment explanation
Indices: 2396540--2397132 Score: 667
Period size: 285 Copynumber: 2.0 Consensus size: 286
2396530 TTTAGTTAAT
* *
2396540 AGTTTTCGGGTTAGTTCATTAGCTCTTGGTTAGACTCTGTAATCAAATGTTTCTCAAAGCAGTAA
1 AGTTTTCGGGTTAGTTAAGTAGCTCTTGGTTAGACTCTGTAATCAAATGTTTCT------AGTAA
** * *
2396605 CTCAAACACGATCATTCTAGGTTCTTCGAACGTGACTTGTTTACGTAATATATTCAATTAATGAA
60 CTCAAACACGATCATTCTAGGTTCTTCGAACAAGACTTGTTCACGTAATAGATTCAATTAATGAA
*
2396670 CTTCGTTTGGTGTATGTAATGAAGTTTCCGGGTTAGCTCAGTAGCTCTTGGTTAGACTGTAAAAT
125 CTTCGTTTGGTGTATGTAATGAAGTTTCCGGGTTAGCTCAATAGCTC---GTTAGACTGTAAAAT
* * * * *
2396735 CAAATGTTGCTTTAACTCGAACACAATTGTTCTAGGCTGTATGAAAAAGAGTTGTTTGCGTGATA
187 CAAATGTTGCTTTAACCCAAACACAATTGTTCTAGGCTCTATGAAAAAGAGTTGTTTACATGATA
2396800 CATCCAGTTGATGAACTTTGTT-TGGTGTATGTAATGA
252 CATCCAGTTGATGAACTTT-TTCT--TGTATGTAATGA
* * *
2396837 AGTTTTCGGGTTAGTTAAGTAGCTTTTGGTTAGACTGTGTAATCAAATGTTTCT-TTAACTCAAA
1 AGTTTTCGGGTTAGTTAAGTAGCTCTTGGTTAGACTCTGTAATCAAATGTTTCTAGTAACTCAAA
* * * * * * ***
2396901 CATGGTCATTCTAGGTTCTTTGAACAAGAGTTGTTCGCGTGATAGATTTGGTT-ATGAAC-TCTG
66 CACGATCATTCTAGGTTCTTCGAACAAGACTTGTTCACGTAATAGATTCAATTAATGAACTTC-G
* ** * **
2396964 TTTGGTTTATGTAATGAAGTTTTTGGGTTAGTTCAATAGCTC-TTAGACTGTGTAATCAAATGTT
130 TTTGGTGTATGTAATGAAGTTTCCGGGTTAGCTCAATAGCTCGTTAGACTGTAAAATCAAATGTT
* * * * * ***
2397028 GCTTTAACCCAAACACGATTGTTCTAGGCTCTGTGAACACGAGTT-TTTCACATGATAGATTTGG
195 GCTTTAACCCAAACACAATTGTTCTAGGCTCTATGAAAAAGAGTTGTTT-ACATGATACATCCAG
2397092 TTGATGAACTTTTTCTTGTATGTAATGA
259 TTGATGAACTTTTTCTTGTATGTAATGA
2397120 AGTTTTTCGGGTT
1 AG-TTTTCGGGTT
2397133 CTAATGTAAC
Statistics
Matches: 254, Mismatches: 38, Indels: 21
0.81 0.12 0.07
Matches are distributed among these distances:
283 14 0.06
284 15 0.06
285 80 0.31
288 2 0.01
289 44 0.17
290 49 0.19
297 50 0.20
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.39
Consensus pattern (286 bp):
AGTTTTCGGGTTAGTTAAGTAGCTCTTGGTTAGACTCTGTAATCAAATGTTTCTAGTAACTCAAA
CACGATCATTCTAGGTTCTTCGAACAAGACTTGTTCACGTAATAGATTCAATTAATGAACTTCGT
TTGGTGTATGTAATGAAGTTTCCGGGTTAGCTCAATAGCTCGTTAGACTGTAAAATCAAATGTTG
CTTTAACCCAAACACAATTGTTCTAGGCTCTATGAAAAAGAGTTGTTTACATGATACATCCAGTT
GATGAACTTTTTCTTGTATGTAATGA
Found at i:2398691 original size:148 final size:150
Alignment explanation
Indices: 2398464--2398752 Score: 440
Period size: 148 Copynumber: 1.9 Consensus size: 150
2398454 ATGGATGGAT
*
2398464 ATGCAATCTCCAAATTAGAATTTGTAAAAAAAACCCTTGCTTTGTTTGCATGATACTACATGTTG
1 ATGCAATCTCCAAATTAGAATTTGTAAAAAAAACCCTTGCTTTGCTTGCATGATACTACATGTTG
** * *
2398529 ATGTACTTTTGATGTTTGCCTTGCTTTAAAGTTCCTCTCATCTTCATTTTCATGTACATGAATGT
66 ATGTACTTCAGATGTTTGCCTTGCTTTAAAGTTCCTCTAATCTTCATTTTCATGTACATGAATGG
2398594 ATATATGTATGCATGTATGC
131 ATATATGTATGCATGTATGC
* * * *
2398614 ATGCATTCTCCAAATTAGAATTTGT-AAAACATCCCTTGC-TTGCTTGCATGATAC-ATCGTGTT
1 ATGCAATCTCCAAATTAGAATTTGTAAAAAAAACCCTTGCTTTGCTTGCATGATACTA-CATGTT
* *
2398676 GATGTACTTCAGATGTTTGCCTTGCTTTAAAGTTCCTCTAATCTTCATTTTCATGTATATGTATG
65 GATGTACTTCAGATGTTTGCCTTGCTTTAAAGTTCCTCTAATCTTCATTTTCATGTACATGAATG
*
2398741 GATCTATGTATG
130 GATATATGTATG
2398753 TATGCATGTG
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
147 1 0.01
148 89 0.71
149 12 0.10
150 24 0.19
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (150 bp):
ATGCAATCTCCAAATTAGAATTTGTAAAAAAAACCCTTGCTTTGCTTGCATGATACTACATGTTG
ATGTACTTCAGATGTTTGCCTTGCTTTAAAGTTCCTCTAATCTTCATTTTCATGTACATGAATGG
ATATATGTATGCATGTATGC
Found at i:2403014 original size:16 final size:16
Alignment explanation
Indices: 2402993--2403023 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2402983 TATTTTGAAA
2402993 TAATAAAAAGTACTAT
1 TAATAAAAAGTACTAT
2403009 TAATAAAAAGTACTA
1 TAATAAAAAGTACTA
2403024 ACTTAATAGT
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:0.58, C:0.06, G:0.06, T:0.29
Consensus pattern (16 bp):
TAATAAAAAGTACTAT
Found at i:2406741 original size:29 final size:30
Alignment explanation
Indices: 2406706--2406778 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
2406696 TATTGGGACC
* * * *
2406706 GGATCAAATTAGTGCCTCTATTATT-AAAG
1 GGATCAAATTAGTCCCTATACTATTAAAAA
*
2406735 GGATCAATTTAGTCCCTATACTATTAAAAA
1 GGATCAAATTAGTCCCTATACTATTAAAAA
*
2406765 GAATCAAATTAGTC
1 GGATCAAATTAGTC
2406779 TAGATGGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 21 0.58
30 15 0.42
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (30 bp):
GGATCAAATTAGTCCCTATACTATTAAAAA
Found at i:2407233 original size:120 final size:120
Alignment explanation
Indices: 2407020--2407258 Score: 451
Period size: 120 Copynumber: 2.0 Consensus size: 120
2407010 AATTGATGAA
2407020 GTCCCTATAATAAAGTGACCTCTATTGTACATTGACCAATTACTTCCTGTCCAACAAAGCAAACC
1 GTCCCTATAATAAAGTGACCTCTATTGTACATTGACCAATTACTTCCTGTCCAACAAAGCAAACC
2407085 CTAGCAATTCAATCACACAATTAACCCTAAACCCTAACACAGTAAACCGGCTAAC
66 CTAGCAATTCAATCACACAATTAACCCTAAACCCTAACACAGTAAACCGGCTAAC
* *
2407140 GTCCCTATAATAAAGTGACCTCTATTGTACGTTGACCAATTACTTCCTGTCCAACAAAGCAAATC
1 GTCCCTATAATAAAGTGACCTCTATTGTACATTGACCAATTACTTCCTGTCCAACAAAGCAAACC
*
2407205 CTAGCAATTCAATCACACAATTAACCCTAAACCCTAACACATTAAACCGGCTAA
66 CTAGCAATTCAATCACACAATTAACCCTAAACCCTAACACAGTAAACCGGCTAA
2407259 TGTTACTCAA
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 116 1.00
ACGTcount: A:0.37, C:0.29, G:0.09, T:0.24
Consensus pattern (120 bp):
GTCCCTATAATAAAGTGACCTCTATTGTACATTGACCAATTACTTCCTGTCCAACAAAGCAAACC
CTAGCAATTCAATCACACAATTAACCCTAAACCCTAACACAGTAAACCGGCTAAC
Found at i:2422354 original size:103 final size:103
Alignment explanation
Indices: 2422175--2422486 Score: 473
Period size: 103 Copynumber: 3.0 Consensus size: 103
2422165 AATTTATAAA
* *
2422175 ATAATTTTGTTTGTGAATTAAAAAAGGAGGACAAAGTCCTAACAGTAATAAGATTAGTATGATTC
1 ATAATTTTATTTGTGAATTAAAAGAGGAGGACAAAGTCCTAACAGTAATAAGATTAGTATGATTC
* *
2422240 GGACTTAGACCACACTTGGTACGGTGAATTGCCGATTT
66 GGACATAGACCACACTTGGTACGGTGAATTGACGATTT
* *
2422278 ATAATTTTATTTGTGAATTAAAAGAGAAGGACAAAGTCCTAACAGCAATAAGATTAGTATGATTC
1 ATAATTTTATTTGTGAATTAAAAGAGGAGGACAAAGTCCTAACAGTAATAAGATTAGTATGATTC
*
2422343 GGACATAGACCACACTTGGTACGGTGAATTGTCGATTT
66 GGACATAGACCACACTTGGTACGGTGAATTGACGATTT
* * * * *
2422381 ATAATTTTATTTGTGAATTAAAAGAGGAGGGCAAGGTCCTAATAGTAATAAGATTAGTACGATTT
1 ATAATTTTATTTGTGAATTAAAAGAGGAGGACAAAGTCCTAACAGTAATAAGATTAGTATGATTC
* * * *
2422446 GGACGTAGATCACACTTGATATGGTGAATT-ACGATTT
66 GGACATAGACCACACTTGGTACGGTGAATTGACGATTT
2422483 ATAA
1 ATAA
2422487 AAAAATAAAT
Statistics
Matches: 191, Mismatches: 18, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
102 10 0.05
103 181 0.95
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (103 bp):
ATAATTTTATTTGTGAATTAAAAGAGGAGGACAAAGTCCTAACAGTAATAAGATTAGTATGATTC
GGACATAGACCACACTTGGTACGGTGAATTGACGATTT
Found at i:2424078 original size:26 final size:27
Alignment explanation
Indices: 2424047--2424106 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
2424037 TATACATCTG
*
2424047 TTATATTTAAGTGTTTTAATTTGTTA-
1 TTATATTTAAATGTTTTAATTTGTTAC
*
2424073 TTATA-TTAAATTTTTTAATTTGTTAC
1 TTATATTTAAATGTTTTAATTTGTTAC
*
2424099 ATATATTT
1 TTATATTT
2424107 TTTATCCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 18 0.62
26 9 0.31
27 2 0.07
ACGTcount: A:0.30, C:0.02, G:0.07, T:0.62
Consensus pattern (27 bp):
TTATATTTAAATGTTTTAATTTGTTAC
Found at i:2428767 original size:51 final size:51
Alignment explanation
Indices: 2428654--2428759 Score: 203
Period size: 51 Copynumber: 2.1 Consensus size: 51
2428644 CTGATCACAT
2428654 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
2428705 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
2428756 TTAT
1 TTAT
2428760 TGCTTGTCGC
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:2431922 original size:31 final size:30
Alignment explanation
Indices: 2431853--2431923 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
2431843 AAGTGATAGC
*
2431853 TTCAGCTACCTGATCAGTTAAAAATGGTAG
1 TTCAGCTACCTGATCAGTGAAAAATGGTAG
* * * *
2431883 CTCTAGCTACCTGATCAGTGAATAGTGGTTG
1 TTC-AGCTACCTGATCAGTGAAAAATGGTAG
2431914 TTTCAGCTAC
1 -TTCAGCTAC
2431924 AAGTGACAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 2 0.06
31 29 0.88
32 2 0.06
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (30 bp):
TTCAGCTACCTGATCAGTGAAAAATGGTAG
Found at i:2432061 original size:48 final size:47
Alignment explanation
Indices: 2431942--2432064 Score: 158
Period size: 47 Copynumber: 2.6 Consensus size: 47
2431932 AGTGATTTCC
**
2431942 GTGTAAGA-TCATATCTGGGATATGGCATCGGAGTGATATGTGCATTT
1 GTGTAAGACT-ATATCTGGGATATGGCATCGGAGTGATATGTGCATAA
* * *
2431989 GTGTAAGACCATATCTGGGATATGGCATCGGTGTGATATGTGTATAA
1 GTGTAAGACTATATCTGGGATATGGCATCGGAGTGATATGTGCATAA
* *
2432036 GATGTAAGACTATAGCTGGGCTATGGCAT
1 G-TGTAAGACTATATCTGGGATATGGCAT
2432065 TTTAGTAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 42 0.64
48 24 0.36
ACGTcount: A:0.27, C:0.11, G:0.30, T:0.32
Consensus pattern (47 bp):
GTGTAAGACTATATCTGGGATATGGCATCGGAGTGATATGTGCATAA
Found at i:2435491 original size:12 final size:12
Alignment explanation
Indices: 2435474--2435499 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2435464 CATTCATTTT
2435474 TTACGATATTCA
1 TTACGATATTCA
2435486 TTACGATATTCA
1 TTACGATATTCA
2435498 TT
1 TT
2435500 TTAAATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (12 bp):
TTACGATATTCA
Found at i:2436471 original size:23 final size:23
Alignment explanation
Indices: 2436453--2436509 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
2436443 TGATTTTAGT
2436453 ATTTAAATTTTTTGAATTTTAAA
1 ATTTAAATTTTTTGAATTTTAAA
*
2436476 ATTTTAATTTTTTGAATTTTAAA
1 ATTTAAATTTTTTGAATTTTAAA
*
2436499 ATTTTAATTTT
1 ATTTAAATTTT
2436510 AATTCAGATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (23 bp):
ATTTAAATTTTTTGAATTTTAAA
Found at i:2437816 original size:205 final size:199
Alignment explanation
Indices: 2437361--2437829 Score: 557
Period size: 202 Copynumber: 2.3 Consensus size: 199
2437351 AAGTATATGT
* * * * *
2437361 ATCACAAACACGAACAAGGCTCGGAATAGATTATCCTCAATCCAAAGAACCATATAAAGATTGCA
1 ATCACAAACACAAACAAGGCTCTG--CA-ATTATCTTCAATCCGAAGAACCATATAAAGATTGCA
* * * *
2437426 TTGCAGGCTATACATAGAAAACAAATGCGCAACGACAAAATACATTGCCTTTCTCGAACCTGAAA
63 TCGCAGGCTATACATACAAAACAAATGCACAACAACAAAATACATTGCCTTTCTCGAACCTGAAA
*** * * * * *
2437491 TCTTTGGGACTTGTTCGACACTCGACCGTGAACACTGTGGCCTACTAACTAGAATTGCCCTACAT
128 TCTGCAGGACTTGCTCGACACTCGACCGGGAACACTATGACCTACTAACTAGAATTGCCCTACAA
2437556 AAACAGC
193 AAACAGC
2437563 ATCACAAACACAAACAAGGCTCTGCATAGATTATCTTCAATCCGAAGAACCATATAAAGATTGCA
1 ATCACAAACACAAACAAGGCTCTGC--A-ATTATCTTCAATCCGAAGAACCATATAAAGATTGCA
*
2437628 TCGCAGGCTATACATACAAAACAAATGCACAACAACAACAACATACATTGCCTTTCTCGTACCTG
63 TCGCAGGCTATACATACAAAACAAATGCACAACAAC-A-AA-ATACATTGCCTTTCTCGAACCTG
* *
2437693 AAATCTGCAGGACTTGCTCGACAGTCGACCGGGAATACCATAT-ACCTACTAACTAGAATTGCCT
125 AAATCTGCAGGACTTGCTCGACACTCGACCGGGAACA-C-TATGACCTACTAACTAGAATTGCC-
*
2437757 CATATAAAAACAGC
187 C-TACAAAAACAGC
* * * *
2437771 ATCACGAACACACACAAGGCTCTGC-ATTATCTCTGATAT-CGAAGAAACATATAAAGATT
1 ATCACAAACACAAACAAGGCTCTGCAATTATCT-TCA-ATCCGAAGAACCATATAAAGATT
2437830 CAACTCGAAT
Statistics
Matches: 231, Mismatches: 25, Indels: 19
0.84 0.09 0.07
Matches are distributed among these distances:
202 90 0.39
203 1 0.00
204 9 0.04
205 73 0.32
206 22 0.10
207 3 0.01
208 33 0.14
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.22
Consensus pattern (199 bp):
ATCACAAACACAAACAAGGCTCTGCAATTATCTTCAATCCGAAGAACCATATAAAGATTGCATCG
CAGGCTATACATACAAAACAAATGCACAACAACAAAATACATTGCCTTTCTCGAACCTGAAATCT
GCAGGACTTGCTCGACACTCGACCGGGAACACTATGACCTACTAACTAGAATTGCCCTACAAAAA
CAGC
Found at i:2439538 original size:20 final size:20
Alignment explanation
Indices: 2439493--2439540 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
2439483 TCATTTGTTA
*
2439493 ATTTGAAATTAAATTATTATT
1 ATTT-AAATTAAATTATGATT
*
2439514 TTTTAAATTAAATT-TGATAT
1 ATTTAAATTAAATTATGAT-T
2439534 ATTTAAA
1 ATTTAAA
2439541 AAAGAGTCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 17 0.74
21 3 0.13
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
ATTTAAATTAAATTATGATT
Found at i:2439835 original size:20 final size:20
Alignment explanation
Indices: 2439795--2439836 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2439785 ATTTTTTTAG
*
2439795 AAAATCATTAAAAATCTAAA
1 AAAATCATTAAAAATCCAAA
2439815 AAAATCA-TAAAAACTCCAAA
1 AAAATCATTAAAAA-TCCAAA
2439835 AA
1 AA
2439837 CGTTAACTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.67, C:0.14, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATCATTAAAAATCCAAA
Found at i:2440230 original size:18 final size:18
Alignment explanation
Indices: 2440194--2440229 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2440184 CTAGGTTTTT
2440194 TTTTAGAAAATATTAAAA
1 TTTTAGAAAATATTAAAA
*
2440212 TTTTATGAAAATTTTAAA
1 TTTTA-GAAAATATTAAA
2440230 TAATTATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTTTAGAAAATATTAAAA
Found at i:2446822 original size:14 final size:14
Alignment explanation
Indices: 2446803--2446832 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2446793 AGAAGCTATC
2446803 ATATATATGTATAT
1 ATATATATGTATAT
*
2446817 ATATATATGTGTAT
1 ATATATATGTATAT
2446831 AT
1 AT
2446833 GTTTGAAGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
ATATATATGTATAT
Found at i:2448146 original size:13 final size:13
Alignment explanation
Indices: 2448120--2448159 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2448110 TTAGGCTTAA
2448120 AAAAGGGCATAGGC
1 AAAA-GGCATAGGC
*
2448134 AAAAGGTATAGGC
1 AAAAGGCATAGGC
*
2448147 AAAGGGCATAGGC
1 AAAAGGCATAGGC
2448160 CTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.10
Consensus pattern (13 bp):
AAAAGGCATAGGC
Found at i:2452918 original size:29 final size:31
Alignment explanation
Indices: 2452850--2452929 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
2452840 ATCTCAAAAC
* *
2452850 TATACATGAACTATGGTTTAATGTGCAATTG
1 TATACATGAACTTTGATTTAATGTGCAATTG
** *
2452881 TATGTATGAACTTTGATTT-A-GTGCAATTT
1 TATACATGAACTTTGATTTAATGTGCAATTG
*
2452910 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
2452930 GATTCAATTC
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 14 0.35
30 11 0.28
31 15 0.38
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.45
Consensus pattern (31 bp):
TATACATGAACTTTGATTTAATGTGCAATTG
Found at i:2458156 original size:31 final size:31
Alignment explanation
Indices: 2458119--2458178 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
2458109 CAATCCAATG
2458119 ACTTAAATAAAAAC-TTATGAATAGTTTAATA
1 ACTTAAATAAAAACTTTA-GAATAGTTTAATA
*
2458150 ACTTAAATGAAAACTTTAGAATAGTTTAA
1 ACTTAAATAAAAACTTTAGAATAGTTTAA
2458179 GGACCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.35
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTAGAATAGTTTAATA
Found at i:2459405 original size:2 final size:2
Alignment explanation
Indices: 2459398--2459437 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
2459388 AGTACTCGAG
* * *
2459398 TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2459438 GGGAAGTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
TA
Found at i:2459894 original size:17 final size:18
Alignment explanation
Indices: 2459852--2459899 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
2459842 TACGTTTATT
*
2459852 TTATTTAAATTTAGATTTA
1 TTATTT-AATTTAGATGTA
*
2459871 TTTTTTAATTTA-ATGTA
1 TTATTTAATTTAGATGTA
*
2459888 TTATTTATTTTA
1 TTATTTAATTTA
2459900 TTATTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 14 0.56
18 6 0.24
19 5 0.20
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
TTATTTAATTTAGATGTA
Found at i:2465340 original size:2 final size:2
Alignment explanation
Indices: 2465333--2465366 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2465323 GAGTTGTTTT
2465333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2465367 TTGATCTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2468906 original size:18 final size:17
Alignment explanation
Indices: 2468861--2468895 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2468851 ATATATTATT
2468861 AAAA-ATTTATAAAAATA
1 AAAATATTTA-AAAAATA
2468878 AAAATATTTAAAAAATA
1 AAAATATTTAAAAAATA
2468895 A
1 A
2468896 TAATTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATATTTAAAAAATA
Found at i:2475484 original size:2 final size:2
Alignment explanation
Indices: 2475477--2475504 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2475467 TGTATGTGTT
2475477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2475505 GTATTGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2480467 original size:2 final size:2
Alignment explanation
Indices: 2480460--2480487 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2480450 GGTAGAGCAC
2480460 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
2480488 TCTGTCTTTT
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:2480550 original size:13 final size:13
Alignment explanation
Indices: 2480534--2480560 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2480524 AATATTAAAT
2480534 ATAGTAAATGTAA
1 ATAGTAAATGTAA
2480547 ATAGTAAATGTAA
1 ATAGTAAATGTAA
2480560 A
1 A
2480561 AATTATAGTA
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:0.56, C:0.00, G:0.15, T:0.30
Consensus pattern (13 bp):
ATAGTAAATGTAA
Found at i:2491373 original size:18 final size:18
Alignment explanation
Indices: 2491346--2491404 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
2491336 CTTGATCTGA
*
2491346 GTGGTTCTTCTGCTACGT
1 GTGGTGCTTCTGCTACGT
2491364 GTGGTGC-T-T-CT-C-T
1 GTGGTGCTTCTGCTACGT
*
2491377 -TGGTTCTTCTGCTACGT
1 GTGGTGCTTCTGCTACGT
2491394 GTGGTGCTTCT
1 GTGGTGCTTCT
2491405 CGTCATAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
12 5 0.16
13 2 0.06
14 2 0.06
15 4 0.12
16 2 0.06
17 2 0.06
18 15 0.47
ACGTcount: A:0.03, C:0.22, G:0.29, T:0.46
Consensus pattern (18 bp):
GTGGTGCTTCTGCTACGT
Found at i:2491383 original size:30 final size:30
Alignment explanation
Indices: 2491347--2491405 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
2491337 TTGATCTGAG
2491347 TGGTTCTTCTGCTACGTGTGGTGCTTCTCT
1 TGGTTCTTCTGCTACGTGTGGTGCTTCTCT
2491377 TGGTTCTTCTGCTACGTGTGGTGCTTCTC
1 TGGTTCTTCTGCTACGTGTGGTGCTTCTC
2491406 GTCATAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.03, C:0.24, G:0.27, T:0.46
Consensus pattern (30 bp):
TGGTTCTTCTGCTACGTGTGGTGCTTCTCT
Found at i:2493119 original size:17 final size:17
Alignment explanation
Indices: 2493097--2493131 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2493087 TCGGGCCCGT
2493097 ATGAAAATA-AAAACAAA
1 ATGAAAATACAAAA-AAA
2493114 ATGAAAATACAAAAAAA
1 ATGAAAATACAAAAAAA
2493131 A
1 A
2493132 ACCCCACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (17 bp):
ATGAAAATACAAAAAAA
Found at i:2496084 original size:131 final size:131
Alignment explanation
Indices: 2495841--2496091 Score: 412
Period size: 131 Copynumber: 1.9 Consensus size: 131
2495831 CATTCATTCA
* *
2495841 AAAATTCTTCAAAACGAAGACGAGATTCGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGT
1 AAAATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGT
* * *
2495906 TGGGTTACAATTTCGTGTTTGCTCAAAATAATCGAATATTACTTCAAAATTTCATTCATGTCTTT
66 TGGGTTACAATTTCGTGTTTACTCAAAATAATCGAATATCACATCAAAATTTCATTCATGTCTTT
2495971 T
131 T
* *
2495972 AAAATTCTTCAAAACGAAGACGAGATTTGATATTTAGCAATTCGTGGAATCGTGCCCTAACGTGT
1 AAAATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGT
* * *
2496037 TGGGTTGCAATTTCGTGTTTACTCAAAATAATCGAGTATCCCATCAAAATTTCAT
66 TGGGTTACAATTTCGTGTTTACTCAAAATAATCGAATATCACATCAAAATTTCAT
2496092 ATCTTCTAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 110 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Consensus pattern (131 bp):
AAAATTCTTCAAAACGAAGACGAGATTCGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGT
TGGGTTACAATTTCGTGTTTACTCAAAATAATCGAATATCACATCAAAATTTCATTCATGTCTTT
T
Found at i:2497982 original size:19 final size:19
Alignment explanation
Indices: 2497960--2497999 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2497950 TGCATTTACT
*
2497960 TTGCATTGCGTCATTTGCA
1 TTGCATTGCATCATTTGCA
*
2497979 TTGCATTGTATCATTTGCA
1 TTGCATTGCATCATTTGCA
2497998 TT
1 TT
2498000 AAATTTCCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCATTGCATCATTTGCA
Found at i:2500700 original size:29 final size:33
Alignment explanation
Indices: 2500641--2500704 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
2500631 TCGAAGCAAA
2500641 AAAACAAAATAAAAGAGAAGGAAAATTGAAAAGG
1 AAAACAAAATAAAAGAGAAGGAAAA-TGAAAAGG
*
2500675 AAAATAAAA-AAAAGAGAA-G-AAA-GAAAAGG
1 AAAACAAAATAAAAGAGAAGGAAAATGAAAAGG
2500704 A
1 A
2500705 GAGGCCAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
29 8 0.28
31 3 0.10
32 1 0.03
33 9 0.31
34 8 0.28
ACGTcount: A:0.72, C:0.02, G:0.20, T:0.06
Consensus pattern (33 bp):
AAAACAAAATAAAAGAGAAGGAAAATGAAAAGG
Found at i:2502022 original size:44 final size:44
Alignment explanation
Indices: 2501963--2502351 Score: 625
Period size: 44 Copynumber: 8.8 Consensus size: 44
2501953 AATCCAAGAT
* * *
2501963 GATTTGGTGTTTCTGTATTGGCGGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
* *
2502007 GATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
* *
2502051 GATTTGCCGTCTCTTTATTGGCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
* *
2502095 GATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
*
2502139 GATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
*
2502183 GATTTGGCGTCTCTTTATTGGCAGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
*
2502227 GATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
* *
2502271 GATTTGGCGTCTCTGTATTGTCAGAGGGCAGATCGAAGATAGCA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
* * *
2502315 GATTTGGCGTCTCTGTGTTGTCAGAGGGCAGATCGAA
1 GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAA
2502352 AATAACATAT
Statistics
Matches: 321, Mismatches: 24, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 321 1.00
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCGAAGATAGCA
Found at i:2502597 original size:17 final size:17
Alignment explanation
Indices: 2502575--2502609 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2502565 CCGGGCCCGT
2502575 ATGAAAATA-AAAACAAA
1 ATGAAAATACAAAA-AAA
2502592 ATGAAAATACAAAAAAA
1 ATGAAAATACAAAAAAA
2502609 A
1 A
2502610 ACCCCACAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (17 bp):
ATGAAAATACAAAAAAA
Found at i:2505507 original size:131 final size:131
Alignment explanation
Indices: 2505323--2505572 Score: 374
Period size: 131 Copynumber: 1.9 Consensus size: 131
2505313 CATTCATTCA
* * * * *
2505323 AAAATTATTCAAAATGAAAACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGT
1 AAAATTATTCAAAACGAAAACGAGATTCGATATTTAGAAATTCGCGGAATCGTGCCCTAACGTGT
* *
2505388 TGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATTACTTCAAAATTTCACTCATGTCTTT
66 TGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCACATCAAAATTTCACTCATGTCTTT
2505453 T
131 T
* * *
2505454 AAAATTCTTCAAAACGAAGACGAGATTCGATATTTAGAAATTCGTGGAATCGTGCCCTAACGTGT
1 AAAATTATTCAAAACGAAAACGAGATTCGATATTTAGAAATTCGCGGAATCGTGCCCTAACGTGT
** * *
2505519 TGGGTTGCAATTTCGTGTTTGCTCAAAATAATCGAGTATCCCATCAAAATTTCA
66 TGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCACATCAAAATTTCA
2505573 TATCTTCTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
131 105 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (131 bp):
AAAATTATTCAAAACGAAAACGAGATTCGATATTTAGAAATTCGCGGAATCGTGCCCTAACGTGT
TGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATCACATCAAAATTTCACTCATGTCTTT
T
Found at i:2505665 original size:126 final size:130
Alignment explanation
Indices: 2505369--2505672 Score: 352
Period size: 131 Copynumber: 2.4 Consensus size: 130
2505359 GCAATTCGCG
* * *
2505369 GAATCGTGCCCTAACGTGTTGGGTTGCAATTTCACGTTTGCTCAAAATAATCGAATATTACTTCA
1 GAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCACATCA
* * *
2505434 AAATTTCACTCATGTCTTTTAAAATTCTTCAAAACGAAGACGAGATTCGATATTTAGAAATTCGT
66 AAATTTCACTCA-GTCTTTAAAAATTCTTCAAAACGAAGACAAGATTCGACATTTAGAAATTCGT
*
2505499 G
130 A
* *
2505500 GAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGT-GTTTGCTCAAAATAATCGAGTATCCCATC
1 GAATCGTGCCCTAACGTGTTGGGTTGCAATTTC-TCGTTTGCTCAAAATAATCGAATATCACATC
* * * * *
2505564 AAAATTTCA-T-A-TCTTCTAAAAATT-TTTAAAACGAAGGCAATATTCGGCGTTT-GATAATTC
65 AAAATTTCACTCAGTCTT-TAAAAATTCTTCAAAACGAAGACAAGATTCGACATTTAGA-AATTC
2505624 G-A
128 GTA
* * * **
2505626 GAATCATGCCCTATCATGTTGGGTTGTGATTTCTCGTTTGCTCAAAA
1 GAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAA
2505673 CGATTGAACA
Statistics
Matches: 150, Mismatches: 19, Indels: 13
0.82 0.10 0.07
Matches are distributed among these distances:
125 1 0.01
126 42 0.28
127 31 0.21
128 7 0.05
129 1 0.01
130 1 0.01
131 67 0.45
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (130 bp):
GAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAATCGAATATCACATCA
AAATTTCACTCAGTCTTTAAAAATTCTTCAAAACGAAGACAAGATTCGACATTTAGAAATTCGTA
Found at i:2511030 original size:13 final size:13
Alignment explanation
Indices: 2511012--2511036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2511002 CCTGCTATAC
2511012 TAATATTATTTAT
1 TAATATTATTTAT
2511025 TAATATTATTTA
1 TAATATTATTTA
2511037 ATTTTTTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATATTATTTAT
Found at i:2513537 original size:26 final size:26
Alignment explanation
Indices: 2513500--2513592 Score: 89
Period size: 26 Copynumber: 3.6 Consensus size: 26
2513490 TGGTCCTTCA
* *
2513500 ACCAACCCAAACTCAAGCGACCTCCG
1 ACCAACTCAAACTCAAGGGACCTCCG
* * *
2513526 ACTAACTCAAACTCAAGGGTCCTCGG
1 ACCAACTCAAACTCAAGGGACCTCCG
* * * *
2513552 ACCCATTCAAACTCAAGGGACCTTCA
1 ACCAACTCAAACTCAAGGGACCTCCG
*
2513578 ACCCACTC-AACTCAA
1 ACCAACTCAAACTCAA
2513593 TCTCACTAGG
Statistics
Matches: 54, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
25 7 0.13
26 47 0.87
ACGTcount: A:0.34, C:0.39, G:0.12, T:0.15
Consensus pattern (26 bp):
ACCAACTCAAACTCAAGGGACCTCCG
Found at i:2514631 original size:70 final size:70
Alignment explanation
Indices: 2514518--2514657 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
2514508 TTTTCTAAGT
2514518 TAGTGTATAATTGTTTTTTAAGAATGATATCTTTGCAAATTTGTCACATGGTTTAGTAAAAGTGA
1 TAGTGTATAATTGTTTTTTAAGAATGATATCTTTGCAAATTTGTCACATGGTTTAGTAAAAGTGA
2514583 CAGAA
66 CAGAA
2514588 TAGTGTATAATTGTTTTTTAAGAATGATATCTTTGCAAATTTGTCACATGGTTTAGTAAAAGTGA
1 TAGTGTATAATTGTTTTTTAAGAATGATATCTTTGCAAATTTGTCACATGGTTTAGTAAAAGTGA
2514653 CAGAA
66 CAGAA
2514658 AACTATCTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.34, C:0.07, G:0.19, T:0.40
Consensus pattern (70 bp):
TAGTGTATAATTGTTTTTTAAGAATGATATCTTTGCAAATTTGTCACATGGTTTAGTAAAAGTGA
CAGAA
Found at i:2515542 original size:19 final size:18
Alignment explanation
Indices: 2515503--2515564 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 18
2515493 ATTATTTTAG
*
2515503 TATTTTTAATTTTTTATA
1 TATTTTTAATTTTCTATA
2515521 TATTCTTTAGATTTTCTAATA
1 TATT-TTTA-ATTTTCT-ATA
* *
2515542 TTTTTTTAAATTT-TATA
1 TATTTTTAATTTTCTATA
2515559 -ATTTTT
1 TATTTTT
2515565 TAAAAATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 5 0.14
17 3 0.08
18 5 0.14
19 8 0.22
20 10 0.27
21 6 0.16
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (18 bp):
TATTTTTAATTTTCTATA
Found at i:2515549 original size:20 final size:18
Alignment explanation
Indices: 2515505--2515567 Score: 56
Period size: 17 Copynumber: 3.4 Consensus size: 18
2515495 TATTTTAGTA
*
2515505 TTTTTAATTTTTTATATAT
1 TTTTTAATTTTTAATAT-T
*
2515524 TCTTTAGATTTTCTAATATT
1 TTTTTA-ATTTT-TAATATT
* *
2515544 TTTTTAAATTTT-ATAAT
1 TTTTTAATTTTTAATATT
2515561 TTTTTAA
1 TTTTTAA
2515568 AAATATAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
17 11 0.30
18 1 0.03
19 9 0.24
20 11 0.30
21 5 0.14
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTAATTTTTAATATT
Found at i:2516877 original size:30 final size:30
Alignment explanation
Indices: 2516843--2516899 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2516833 ACAGGCTGGC
*
2516843 ACATGGGCGTGTGGCCAACCCGTGTGGCTT
1 ACATGGGCGTGTGCCCAACCCGTGTGGCTT
* *
2516873 ACATGGGCTTGTGCCCAGCCCGTGTGG
1 ACATGGGCGTGTGCCCAACCCGTGTGG
2516900 AAATGCCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.12, C:0.28, G:0.37, T:0.23
Consensus pattern (30 bp):
ACATGGGCGTGTGCCCAACCCGTGTGGCTT
Found at i:2521594 original size:40 final size:40
Alignment explanation
Indices: 2521549--2521716 Score: 124
Period size: 40 Copynumber: 4.2 Consensus size: 40
2521539 CGGAATATAA
2521549 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * ** * * *
2521589 CCGGATAGAGTGTCTCGCACGAATGCCCTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* ** * * * *
2521629 CCGGATGTAGCCACTAGCGCAATTGCCTTTGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
2521669 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
2521709 CCGGATAT
1 CCGGATAT
2521717 CATTCAATTT
Statistics
Matches: 97, Mismatches: 29, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
39 1 0.01
40 95 0.98
41 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:2528211 original size:14 final size:14
Alignment explanation
Indices: 2528192--2528228 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
2528182 ATTTTTAGAC
2528192 CAACTTGCAAATCA
1 CAACTTGCAAATCA
2528206 CAACTTGCAAATCA
1 CAACTTGCAAATCA
2528220 CAACTTGCA
1 CAACTTGCA
2528229 CAATTAGGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.30, G:0.08, T:0.22
Consensus pattern (14 bp):
CAACTTGCAAATCA
Found at i:2528466 original size:29 final size:29
Alignment explanation
Indices: 2528410--2528466 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
2528400 TTGATCTTTA
* *
2528410 TACTTCATCCACATAACTTGGATTGTATG
1 TACTTCATCCACATAACTTAGATGGTATG
*
2528439 TACTTCATCCACATAACTTATATGGTAT
1 TACTTCATCCACATAACTTAGATGGTAT
2528467 TGTCTGCTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.39
Consensus pattern (29 bp):
TACTTCATCCACATAACTTAGATGGTATG
Found at i:2529599 original size:27 final size:26
Alignment explanation
Indices: 2529562--2529676 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
2529552 AGCATGGCTG
* *
2529562 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
2529588 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
2529616 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
2529643 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
2529670 CCAGAAC
1 CCAGAAC
2529677 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:2529621 original size:54 final size:54
Alignment explanation
Indices: 2529562--2529676 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
2529552 AGCATGGCTG
*
2529562 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
2529616 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
2529670 CCAGAAC
1 CCAGAAC
2529677 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:2535488 original size:40 final size:40
Alignment explanation
Indices: 2535417--2535499 Score: 105
Period size: 40 Copynumber: 2.1 Consensus size: 40
2535407 ATCATGCACT
* * * *
2535417 CAAGAACTCATGCACATAAGTTGTCCTGGTAAAGTATGTG
1 CAAGAACTCATACACATAAGTTGTCCGGGTAAAATACGTG
*
2535457 CAAGAATTCATACACATAAGTT-TCCCGGGTAAAATACGTG
1 CAAGAACTCATACACATAAGTTGT-CCGGGTAAAATACGTG
2535497 CAA
1 CAA
2535500 TAGGAGATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.03
40 36 0.97
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.25
Consensus pattern (40 bp):
CAAGAACTCATACACATAAGTTGTCCGGGTAAAATACGTG
Found at i:2536527 original size:34 final size:34
Alignment explanation
Indices: 2536482--2536549 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
2536472 CCAACGAGAG
2536482 ATGCATCAAATGAATACTGAATATGAAGAAGGAT
1 ATGCATCAAATGAATACTGAATATGAAGAAGGAT
* * *
2536516 ATGCATGAAATGAATATTGAATATGAAGATGGAT
1 ATGCATCAAATGAATACTGAATATGAAGAAGGAT
2536550 GGAGAGGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.22, T:0.26
Consensus pattern (34 bp):
ATGCATCAAATGAATACTGAATATGAAGAAGGAT
Found at i:2539377 original size:11 final size:11
Alignment explanation
Indices: 2539363--2539388 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2539353 TTAGTACTTA
2539363 TTTTTTTCTTT
1 TTTTTTTCTTT
2539374 TTTTTTTCTTT
1 TTTTTTTCTTT
2539385 TTTT
1 TTTT
2539389 CTTTTTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2539404 original size:19 final size:19
Alignment explanation
Indices: 2539363--2539404 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2539353 TTAGTACTTA
*
2539363 TTTTTTTCTTTTTTTTTTC
1 TTTTTTTCTTTTTTATTTC
2539382 TTTTTTTCTTTTTTGATTT-
1 TTTTTTTCTTTTTT-ATTTC
2539401 TTTT
1 TTTT
2539405 AAATTTTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.02, C:0.07, G:0.02, T:0.88
Consensus pattern (19 bp):
TTTTTTTCTTTTTTATTTC
Found at i:2539690 original size:118 final size:117
Alignment explanation
Indices: 2539548--2539759 Score: 372
Period size: 118 Copynumber: 1.8 Consensus size: 117
2539538 TTTTACCCAA
2539548 CACGTCACACAACCTTTTCGCGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
1 CACGTCACACAACCTTTTCGCGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
*
2539613 TCAGTCACGATTTGAGCCATACTCATAACCTCGGCTAGTGGAGTTTTACTTGT
66 TCAGTCACGA-TTAAGCCATACTCATAACCTCGGCTAGTGGAGTTTTACTTGT
2539666 CACGTCACACAACCTTTT-GACGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCA
1 CACGTCACACAACCTTTTCG-CGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCA
**
2539730 GTCAGTCACGATTAAGCTGTACTCATAACC
65 GTCAGTCACGATTAAGCCATACTCATAACC
2539760 ATGGAAAACA
Statistics
Matches: 90, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
117 17 0.19
118 73 0.81
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (117 bp):
CACGTCACACAACCTTTTCGCGCGAAGTAGAATGACAACCCAAGCACCCTACCCCGGTTACTCAG
TCAGTCACGATTAAGCCATACTCATAACCTCGGCTAGTGGAGTTTTACTTGT
Found at i:2540649 original size:16 final size:15
Alignment explanation
Indices: 2540624--2540688 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 15
2540614 AATATTTAAC
2540624 TAAAATAAAATAAAAA
1 TAAAA-AAAATAAAAA
2540640 TAAAAGAAAATAATAAA
1 TAAAA-AAAATAA-AAA
2540657 TAATAAAAGAA-AAAAA
1 TAA-AAAA-AATAAAAA
2540673 TAAATAAAAATAAAAA
1 TAAA-AAAAATAAAAA
2540689 GAAAGACTGG
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
15 3 0.07
16 26 0.60
17 10 0.23
18 4 0.09
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (15 bp):
TAAAAAAAATAAAAA
Found at i:2540672 original size:23 final size:23
Alignment explanation
Indices: 2540625--2540692 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 23
2540615 ATATTTAACT
2540625 AAAATAAAATAAAAATAAAAGAAA
1 AAAAT-AAATAAAAATAAAAGAAA
*
2540649 ATAATAAAT---AATAAAAGAAA
1 AAAATAAATAAAAATAAAAGAAA
2540669 AAAATAAATAAAAATAAAAAGAAA
1 AAAATAAATAAAAAT-AAAAGAAA
2540693 GACTGGGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 19 0.50
23 7 0.18
24 12 0.32
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAATAAATAAAAATAAAAGAAA
Found at i:2550415 original size:12 final size:12
Alignment explanation
Indices: 2550398--2550423 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2550388 CAGGATCTTT
2550398 CTGGATCTTGAA
1 CTGGATCTTGAA
2550410 CTGGATCTTGAA
1 CTGGATCTTGAA
2550422 CT
1 CT
2550424 CTAATGACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (12 bp):
CTGGATCTTGAA
Found at i:2550843 original size:27 final size:27
Alignment explanation
Indices: 2550813--2550865 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
2550803 CCTCCATAAC
*
2550813 ACACTAGTATAAT-ATAGCCTCCCAAAT
1 ACACCAGTAT-ATCATAGCCTCCCAAAT
* *
2550840 ACACCGGTATATCATATCCTCCCAAA
1 ACACCAGTATATCATAGCCTCCCAAA
2550866 CAATCCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.25
Consensus pattern (27 bp):
ACACCAGTATATCATAGCCTCCCAAAT
Found at i:2552020 original size:2 final size:2
Alignment explanation
Indices: 2552013--2552047 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2552003 TAATAATTAT
*
2552013 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2552048 CTTTTACTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2557180 original size:30 final size:30
Alignment explanation
Indices: 2557120--2557187 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
2557110 AAAAATAGTT
* *
2557120 AAATTTTAAATTTGGTTTATGTACTATGTTA
1 AAATTTGAAATTTGGCTTA-GTACTATGTTA
*
2557151 AAATTTGAAATTTGGCTTA-TACTTTTGTTA
1 AAATTTGAAATTTGGCTTAGTAC-TATGTTA
*
2557181 TAATTTG
1 AAATTTG
2557188 GTGTTTCAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 12 0.38
31 17 0.53
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.51
Consensus pattern (30 bp):
AAATTTGAAATTTGGCTTAGTACTATGTTA
Found at i:2570308 original size:16 final size:16
Alignment explanation
Indices: 2570283--2570314 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2570273 ATTCTAATAT
*
2570283 TTATATTTTTTAAAAA
1 TTATAATTTTTAAAAA
2570299 TTATAATTTTTAAAAA
1 TTATAATTTTTAAAAA
2570315 AACTAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTATAATTTTTAAAAA
Found at i:2570654 original size:21 final size:21
Alignment explanation
Indices: 2570630--2570670 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2570620 TTTACAAGAA
2570630 AAGTTAAAA-GTAAAAACTATC
1 AAGTTAAAAGGT-AAAACTATC
2570651 AAGTTAAAAGGTAAAACTAT
1 AAGTTAAAAGGTAAAACTAT
2570671 GTTGTTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTATC
Found at i:2574560 original size:19 final size:19
Alignment explanation
Indices: 2574538--2574579 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
2574528 TAAGTATAGG
2574538 AAAAAATCA-CAATTTAACA
1 AAAAAAT-ATCAATTTAACA
* *
2574557 AAAATATATCGATTTAACA
1 AAAAAATATCAATTTAACA
2574576 AAAA
1 AAAA
2574580 TGAATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.62, C:0.12, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAAATATCAATTTAACA
Found at i:2588252 original size:25 final size:27
Alignment explanation
Indices: 2588215--2588267 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
2588205 TCAAACATGC
2588215 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
2588241 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
2588267 A
1 A
2588268 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:2589780 original size:25 final size:25
Alignment explanation
Indices: 2589746--2589852 Score: 178
Period size: 25 Copynumber: 4.2 Consensus size: 25
2589736 CATGAAATTC
2589746 TTATCATGAAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
2589771 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAA-CCA
* *
2589797 TTATCATGGAATATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
*
2589822 TTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCA
2589847 TTATCA
1 TTATCA
2589853 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
25 55 0.71
26 23 0.29
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (25 bp):
TTATCATGAAACATTTACCTAACCA
Found at i:2589822 original size:51 final size:50
Alignment explanation
Indices: 2589746--2589852 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 50
2589736 CATGAAATTC
2589746 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAA-CCA
* * *
2589797 TTATCATGGAATATTTACCTAACCATTATCATGGAACATTTACCTAACCA
1 TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAACCA
2589847 TTATCA
1 TTATCA
2589853 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
50 9 0.17
51 44 0.83
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (50 bp):
TTATCATGAAACATTTACCTAACCATTATCATGAAACATTTACCTAACCA
Found at i:2594044 original size:25 final size:26
Alignment explanation
Indices: 2594007--2594055 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2593997 TCAAACATGC
2594007 ATTTAGGTCAATTTAACCCTAGGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* * *
2594033 ATTTCGGT-AATTTATCTCTAGGG
1 ATTTAGGTCAATTTAACCCTAGGG
2594056 TAAAACTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:2595577 original size:26 final size:26
Alignment explanation
Indices: 2595541--2595650 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
2595531 CATGAAATTC
*
2595541 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
2595567 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
2595593 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
2595619 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2595645 TTATCA
1 TTATCA
2595651 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2614626 original size:9 final size:9
Alignment explanation
Indices: 2614614--2614639 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2614604 TTTACTACTT
2614614 ACTTGCACC
1 ACTTGCACC
2614623 ACTTGCACC
1 ACTTGCACC
2614632 ACTTGCAC
1 ACTTGCAC
2614640 ATTGCAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.42, G:0.12, T:0.23
Consensus pattern (9 bp):
ACTTGCACC
Found at i:2614904 original size:29 final size:29
Alignment explanation
Indices: 2614848--2614904 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
2614838 TTGATCTTTA
* * *
2614848 TACTTCATCGACATAACTTGGATTGTATG
1 TACTTCATCCACATAACTTAGATGGTATG
*
2614877 TACTTCATCCACATAACTTATATGGTAT
1 TACTTCATCCACATAACTTAGATGGTAT
2614905 TGTCTGCTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (29 bp):
TACTTCATCCACATAACTTAGATGGTATG
Found at i:2622839 original size:47 final size:47
Alignment explanation
Indices: 2622729--2622853 Score: 142
Period size: 47 Copynumber: 2.7 Consensus size: 47
2622719 AATCAATAAG
* * ** *
2622729 TACCTACACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGGAG
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
* * *
2622776 TACCTATACCACGGCCCGTAGCCAAATCAAGGTAACTCCTCTCAAAA
1 TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
** * *
2622823 TATTTATATCATGGCCCATAGCCAAATCAAG
1 TACCTATACCATGGCCCGTAGCCAAATCAAG
2622854 ATATTCTTCA
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 65 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (47 bp):
TACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCCCAAAA
Found at i:2628156 original size:31 final size:30
Alignment explanation
Indices: 2628111--2628169 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
2628101 TATAAAAATA
*
2628111 GTTAAATTTCAAATTTGGTCTCTATACTAT
1 GTTAAAATTCAAATTTGGTCTCTATACTAT
*
2628141 GTTAAAATTCGAAATTTGGTCTTTATACT
1 GTTAAAATTC-AAATTTGGTCTCTATACT
2628170 TCTTTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (30 bp):
GTTAAAATTCAAATTTGGTCTCTATACTAT
Found at i:2630851 original size:41 final size:39
Alignment explanation
Indices: 2630788--2630876 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 39
2630778 TCACTTTGTT
* *
2630788 TTTTTTTTCTTTTTTTACTTTTGGTC-ATATTGTTTATTTA
1 TTTTTTTACTTTTTTTACTTTT-GTCTATA-TCTTTATTTA
* *
2630828 TTTTTTTACTTTTTTTAAGTTTTGTCTTTATCTTTATTTA
1 TTTTTTTACTTTTTTT-ACTTTTGTCTATATCTTTATTTA
2630868 TTTATTTTA
1 TTT-TTTTA
2630877 TTTATTATTA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
40 30 0.71
41 12 0.29
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.73
Consensus pattern (39 bp):
TTTTTTTACTTTTTTTACTTTTGTCTATATCTTTATTTA
Found at i:2630876 original size:13 final size:14
Alignment explanation
Indices: 2630854--2630882 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2630844 AAGTTTTGTC
2630854 TTTATCTTTATTTA
1 TTTATCTTTATTTA
2630868 TTTAT-TTTATTTA
1 TTTATCTTTATTTA
2630881 TT
1 TT
2630883 ATTATCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATCTTTATTTA
Found at i:2631010 original size:24 final size:25
Alignment explanation
Indices: 2630978--2631024 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
2630968 ATTATTCTAA
*
2630978 ATTTTAAATAT-TAATTTTTAAATT
1 ATTTAAAATATATAATTTTTAAATT
*
2631002 ATTTAAAATATATTATTTTTAAA
1 ATTTAAAATATATAATTTTTAAA
2631025 GATATAATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTAAAATATATAATTTTTAAATT
Found at i:2631095 original size:12 final size:13
Alignment explanation
Indices: 2631078--2631127 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 13
2631068 ATATTTTTTA
2631078 AATTTTAAATA-T
1 AATTTTAAATATT
2631090 AATTTTTATAAATTATT
1 AA--TTT-TAAA-TATT
2631107 AATTTTAAA-ATT
1 AATTTTAAATATT
2631119 AATTTTAAA
1 AATTTTAAA
2631128 GATATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 14 0.42
14 7 0.21
15 7 0.21
16 2 0.06
17 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAAATATT
Found at i:2631194 original size:24 final size:21
Alignment explanation
Indices: 2631166--2631229 Score: 67
Period size: 24 Copynumber: 2.8 Consensus size: 21
2631156 TTTAATATCT
2631166 TTAAAAATAATTTAAAACTCATAA
1 TTAAAAATAATTTAAAA--CA-AA
2631190 TTAAAAA-AATTATAAAACAAA
1 TTAAAAATAATT-TAAAACAAA
2631211 TTAAAATATATATTTAAAA
1 TTAAAA-ATA-ATTTAAAA
2631230 TATTATAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
21 8 0.22
22 3 0.08
23 10 0.28
24 15 0.42
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
TTAAAAATAATTTAAAACAAA
Found at i:2631317 original size:20 final size:20
Alignment explanation
Indices: 2631294--2631351 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
2631284 TTTTATATTA
2631294 TTAAAAAATATATTT-AATAT
1 TTAAAAAATATATTTAAAT-T
2631314 TT-AAAAATAATATTTAAATT
1 TTAAAAAAT-ATATTTAAATT
2631334 TTAAAAAA-ATAATTTAAA
1 TTAAAAAATAT-ATTTAAA
2631352 AATAATATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.24
20 18 0.53
21 8 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAAATATATTTAAATT
Found at i:2631324 original size:13 final size:13
Alignment explanation
Indices: 2631308--2631400 Score: 66
Period size: 13 Copynumber: 7.9 Consensus size: 13
2631298 AAAATATATT
2631308 TAATATTTAAAAA
1 TAATATTTAAAAA
2631321 TAATATTT----A
1 TAATATTTAAAAA
2631330 -AAT-TTTAAAAA
1 TAATATTTAAAAA
2631341 -AATAATTTAAAAA
1 TAAT-ATTTAAAAA
2631354 TAATATTT-AAAA
1 TAATATTTAAAAA
*
2631366 T--T-TTAAAAAA
1 TAATATTTAAAAA
*
2631376 TGAT-TTTAAAAA
1 TAATATTTAAAAA
2631388 TATATATTTAAAA
1 TA-ATATTTAAAA
2631401 TTTAAAAATA
Statistics
Matches: 65, Mismatches: 3, Indels: 23
0.71 0.03 0.25
Matches are distributed among these distances:
7 3 0.05
8 3 0.05
9 3 0.05
10 6 0.09
11 4 0.06
12 14 0.22
13 22 0.34
14 10 0.15
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (13 bp):
TAATATTTAAAAA
Found at i:2631372 original size:34 final size:35
Alignment explanation
Indices: 2631312--2631408 Score: 148
Period size: 33 Copynumber: 2.9 Consensus size: 35
2631302 TATATTTAAT
2631312 ATTTAAAAATAATATTT-AAATTTTAAAAAAAT-A
1 ATTTAAAAATAATATTTAAAATTTTAAAAAAATGA
2631345 ATTTAAAAATAATATTTAAAATTTT-AAAAAATGA
1 ATTTAAAAATAATATTTAAAATTTTAAAAAAATGA
*
2631379 TTTTAAAAATATATATTTAAAA-TTTAAAAA
1 ATTTAAAAATA-ATATTTAAAATTTTAAAAA
2631409 TATATGTATA
Statistics
Matches: 59, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
33 24 0.41
34 21 0.36
35 14 0.24
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (35 bp):
ATTTAAAAATAATATTTAAAATTTTAAAAAAATGA
Found at i:2631480 original size:4 final size:4
Alignment explanation
Indices: 2631465--2631502 Score: 60
Period size: 4 Copynumber: 9.5 Consensus size: 4
2631455 TAAAATTAAT
2631465 AATA AA-A AATA AATAA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AAT-A AATA AATA AATA AATA AATA AA
2631503 GATAAAGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.09
4 25 0.78
5 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:2631497 original size:21 final size:21
Alignment explanation
Indices: 2631465--2631508 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2631455 TAAAATTAAT
2631465 AATAAAAAATAAATAAA-ATA
1 AATAAAAAATAAATAAAGATA
2631485 AATAAATAAATAAATAAAGATA
1 AATAAA-AAATAAATAAAGATA
2631507 AA
1 AA
2631509 GACAAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (21 bp):
AATAAAAAATAAATAAAGATA
Found at i:2632296 original size:23 final size:21
Alignment explanation
Indices: 2632265--2632317 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
2632255 TTGAACAAGC
*
2632265 ATAAAGTATGTTAATATCATTTT
1 ATAATGTATGTTAATA-C-TTTT
* *
2632288 ATAATGTATTTTTATACTTTT
1 ATAATGTATGTTAATACTTTT
2632309 ATAATGTAT
1 ATAATGTAT
2632318 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
23 13 0.48
ACGTcount: A:0.36, C:0.04, G:0.08, T:0.53
Consensus pattern (21 bp):
ATAATGTATGTTAATACTTTT
Found at i:2632310 original size:21 final size:21
Alignment explanation
Indices: 2632284--2632323 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2632274 GTTAATATCA
2632284 TTTTATAATGTATTTTTATAC
1 TTTTATAATGTATTTTTATAC
2632305 TTTTATAATGTATTTTTAT
1 TTTTATAATGTATTTTTAT
2632324 TTTATTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTATAATGTATTTTTATAC
Found at i:2637581 original size:17 final size:18
Alignment explanation
Indices: 2637559--2637595 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
2637549 TTAGTTTGCT
2637559 CTATTGCAT-TATTC-CTC
1 CTATTGC-TCTATTCTCTC
2637576 CTATTGCTCTATTCTCTC
1 CTATTGCTCTATTCTCTC
2637594 CT
1 CT
2637596 TGTCAACCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.06
17 12 0.67
18 5 0.28
ACGTcount: A:0.14, C:0.32, G:0.05, T:0.49
Consensus pattern (18 bp):
CTATTGCTCTATTCTCTC
Found at i:2641198 original size:24 final size:25
Alignment explanation
Indices: 2641146--2641199 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
2641136 GAATATATAC
* *
2641146 ATAAGAAATATATAACTAATGGCAT
1 ATAAAAAATATATAACTAATGACAT
2641171 -TAAAAAATATAT-ACATAAT-ACAT
1 ATAAAAAATATATAAC-TAATGACAT
2641194 ATAAAA
1 ATAAAA
2641200 TACCTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (25 bp):
ATAAAAAATATATAACTAATGACAT
Found at i:2641727 original size:35 final size:33
Alignment explanation
Indices: 2641678--2641760 Score: 123
Period size: 35 Copynumber: 2.5 Consensus size: 33
2641668 GTGGCTAGGG
* *
2641678 TTTTTT-TATTTTTTTTTTGGGTTAGGTTTTTC
1 TTTTTTCTTTTTTTTTTTTGGGCTAGGTTTTTC
2641710 TTTTTTCTTCTTCTTTTTTTTGGGCTAGGTTTTTC
1 TTTTTTCTT-TT-TTTTTTTTGGGCTAGGTTTTTC
2641745 TTTTTTCTTTTTTTTT
1 TTTTTTCTTTTTTTTT
2641761 GGAGGGGCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
32 6 0.13
33 6 0.13
34 4 0.09
35 30 0.65
ACGTcount: A:0.04, C:0.08, G:0.12, T:0.76
Consensus pattern (33 bp):
TTTTTTCTTTTTTTTTTTTGGGCTAGGTTTTTC
Found at i:2642638 original size:74 final size:74
Alignment explanation
Indices: 2642515--2642888 Score: 462
Period size: 74 Copynumber: 4.9 Consensus size: 74
2642505 TTGAAAAACG
* * *
2642515 GAAATTGAAAATACCT-TGACGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATT
1 GAAATTGAAAATACCTCAG-CGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
*
2642579 TTTTTTACAACA
63 TTTTTAACAACA
*
2642591 GAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
2642656 TGAAACATACGA
66 T-TAACA-AC-A
* * * *
2642668 AAAATTGACAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
*
2642733 TTGACAACA
66 TTAACAACA
* *
2642742 GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACATCTCGCAATGTGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* *
2642807 TTGAAAAATA
66 TT-AACAACA
* * * *
2642817 TAAATTGAGAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 GAAATT--GAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
2642882 GTTTTTT
62 -TTTTTT
2642889 TTTTTTCTGA
Statistics
Matches: 260, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
74 102 0.39
75 14 0.05
76 25 0.10
77 80 0.31
79 33 0.13
80 6 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (74 bp):
GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
TTAACAACA
Found at i:2642792 original size:151 final size:151
Alignment explanation
Indices: 2642516--2642888 Score: 504
Period size: 151 Copynumber: 2.5 Consensus size: 151
2642506 TGAAAAACGG
* * *
2642516 AAATT-GAAAATACCT-TGACGTGTGACCTGAGGCTCAACTCGCCTCTCGCAATACGAGTTGATT
1 AAATTAGAAAATACCTCAG-CGTGT-ACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATT
* *
2642579 TTTTTTACAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
64 TTTTTGACAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACATCTCGCAATAT
2642644 GAGTTGA-TTTTTTGAAACATACGAA
129 GAGTTGATTTTTTTGAAA-A-A-GAA
*
2642669 AAATT-GACAATACCTCAGCGTGT-CCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
1 AAATTAGAAAATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
* *
2642732 TTTGACAACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACATCTCGCAATGTGA
66 TTTGACAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACATCTCGCAATATGA
* *
2642797 GTTGATTTTTTTGAAAAATAT
131 GTTGATTTTTTTGAAAAAGAA
* * * * *
2642818 AAATTGAGAAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATG
1 AAATT-AGAAAATACCTCAGCGTGT-ACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGAT-
2642883 TTTTTT
63 TTTTTT
2642889 TTTTTTCTGA
Statistics
Matches: 197, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
149 6 0.03
150 1 0.01
151 121 0.61
152 10 0.05
153 52 0.26
154 7 0.04
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (151 bp):
AAATTAGAAAATACCTCAGCGTGTACCCGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTT
TTTGACAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACATCTCGCAATATGA
GTTGATTTTTTTGAAAAAGAA
Found at i:2643046 original size:72 final size:73
Alignment explanation
Indices: 2642966--2643107 Score: 259
Period size: 72 Copynumber: 2.0 Consensus size: 73
2642956 ACTCATTTTG
*
2642966 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGTTCAACTCATTTCTCGCAATATGAGTTG-A
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
2643030 ATTTTGAA
66 ATTTTGAA
*
2643038 AACAGAAATTGAAATTACCTCAATGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
1 AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
2643103 ATTTT
66 ATTTT
2643108 TTTTTTTGAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
72 61 0.91
73 6 0.09
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (73 bp):
AACAGAAATTGAAATTACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAA
ATTTTGAA
Found at i:2643128 original size:81 final size:81
Alignment explanation
Indices: 2643031--2643180 Score: 214
Period size: 83 Copynumber: 1.8 Consensus size: 81
2643021 ATGAGTTGAA
* * * **
2643031 TTTTGAAAACAGAAATTGAAATTACCTCA-ATGTG-TCTTGAGGCTCAACTCATTTCTCGCAATA
1 TTTTGAAAACAGAAATTGAAAATACCTCACATGTGAAC-CGAGGCTCAACTCACCTCTCGCAATA
2643094 TGAGTTGAAATTTTTTT
65 TGAGTTGAAATTTTTTT
2643111 TTTTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAAT
1 TTTTGAAA-ACAGAAATTGAAAATACCTCA-CATGTGAACCGAGGCTCAACTCACCTCTCGCAAT
2643176 ATGAG
64 ATGAG
2643181 CTGATTTTGA
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
80 8 0.13
81 20 0.33
83 32 0.52
84 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (81 bp):
TTTTGAAAACAGAAATTGAAAATACCTCACATGTGAACCGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGAAATTTTTTT
Found at i:2643257 original size:54 final size:55
Alignment explanation
Indices: 2643157--2643262 Score: 144
Period size: 54 Copynumber: 1.9 Consensus size: 55
2643147 GAACCGAGGC
* *
2643157 TCAACTCACCTCTCGCAATATGAGCTGATTTTGAAAAAGTAGAAATT-AAAAGGT
1 TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
* * *
2643211 TCAACCCACCTCTCGCAATATGAGTTGATTCTTGAATAA-CATAAATTGAAAA
1 TCAACCCACCTCTCGCAATATGAGCTGATT-TTGAAAAAGCAGAAATTGAAAA
2643263 CAGAAATTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
54 34 0.76
55 11 0.24
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (55 bp):
TCAACCCACCTCTCGCAATATGAGCTGATTTTGAAAAAGCAGAAATTGAAAAGGT
Found at i:2643269 original size:13 final size:13
Alignment explanation
Indices: 2643242--2643275 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2643232 GAGTTGATTC
*
2643242 TTGAATAACATAAA
1 TTGAA-AACAGAAA
2643256 TTGAAAACAGAAA
1 TTGAAAACAGAAA
2643269 TTGAAAA
1 TTGAAAA
2643276 TACCTCAGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.24
Consensus pattern (13 bp):
TTGAAAACAGAAA
Found at i:2643323 original size:140 final size:140
Alignment explanation
Indices: 2643113--2643600 Score: 879
Period size: 140 Copynumber: 3.5 Consensus size: 140
2643103 ATTTTTTTTT
2643113 TTGAAAGACAGAAATTGAAAATACCTCAGCATGTGAACC-GAGGCTCAACTCACCTCTCGCAATA
1 TTGAAA-ACAGAAATTGAAAATACCTCAGC--GTG-ACCTGAGGCTCAACTCACCTCTCGCAATA
*
2643177 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACCTCTCGCAATATGAGTTGATTC
62 TGAGCTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTC
* *
2643242 TTGAATAACATAAA
127 TTGAACAACGTAAA
*
2643256 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCATCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
2643321 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
2643386 ACAACGTAAA
131 ACAACGTAAA
2643396 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
2643461 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCATTTCTCGCAATATGAGTTGATTCTTGA
66 CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
2643526 ACAACGTAAA
131 ACAACGTAAA
*
2643536 TTGAAAACAGAAATTGAAAATACCTCAGCGTAACCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
2643601 TTGAAATTAA
Statistics
Matches: 337, Mismatches: 7, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
139 3 0.01
140 305 0.91
142 23 0.07
143 6 0.02
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (140 bp):
TTGAAAACAGAAATTGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG
CTGATTTTGAAAAAGTAGAAATTAAAAGGTTCAACCCACTTCTCGCAATATGAGTTGATTCTTGA
ACAACGTAAA
Found at i:2643667 original size:72 final size:71
Alignment explanation
Indices: 2643533--2643698 Score: 235
Period size: 72 Copynumber: 2.3 Consensus size: 71
2643523 TGAACAACGT
* * * *
2643533 AAATTGAAAACAGAAATTGAAAATACCTCAGCGTAACCTGAGGCTCAACTCACCTCTCGCAATAT
1 AAATTAAAAACAAAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTAGCAATAT
2643598 GAGTTG
66 GAGTTG
**
2643604 AAATTAAAACACAAAAATTGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCTAGCAATA
1 AAATTAAAA-ACAAAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTAGCAATA
2643669 TGAGTTG
65 TGAGTTG
**
2643676 ATTTTGAAAAACAAAAATT-AAAA
1 AAATT-AAAAACAAAAATTGAAAA
2643699 GGCTTAACTC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 12 0.14
72 69 0.81
73 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.22
Consensus pattern (71 bp):
AAATTAAAAACAAAAATTGAAAATACCTCAGCGTAACCCGAGGCTCAACTCACCTCTAGCAATAT
GAGTTG
Found at i:2649450 original size:12 final size:12
Alignment explanation
Indices: 2649430--2649465 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
2649420 TGGGATATGC
*
2649430 AATGTATGAATG
1 AATGCATGAATG
2649442 AATGCATGAATG
1 AATGCATGAATG
2649454 AATGCATGAATG
1 AATGCATGAATG
2649466 TCAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.28
Consensus pattern (12 bp):
AATGCATGAATG
Found at i:2651549 original size:24 final size:25
Alignment explanation
Indices: 2651497--2651550 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
2651487 GAATATATAC
* *
2651497 ATAAGAAATATATAACTAATGGCAT
1 ATAAAAAATATATAACTAATGACAT
2651522 -TAAAAAATATAT-ACATAAT-ACAT
1 ATAAAAAATATATAAC-TAATGACAT
2651545 ATAAAA
1 ATAAAA
2651551 TACCTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.59, C:0.07, G:0.06, T:0.28
Consensus pattern (25 bp):
ATAAAAAATATATAACTAATGACAT
Found at i:2652090 original size:36 final size:34
Alignment explanation
Indices: 2652032--2652114 Score: 125
Period size: 36 Copynumber: 2.4 Consensus size: 34
2652022 GTGGCTAGGG
*
2652032 TTTTT-TTATTTTTTTTTT-GGTTAGGTTTTTCT
1 TTTTTCTTTTTTTTTTTTTGGGTTAGGTTTTTCT
2652064 TTTTTCTTCTTCTTTTTTTTTGGGTTAGGTTTTTCT
1 TTTTTCTT-TT-TTTTTTTTTGGGTTAGGTTTTTCT
2652100 TTTTTCTTTTTTTTT
1 TTTTTCTTTTTTTTT
2652115 GGAGGGGGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
32 5 0.11
33 2 0.04
34 6 0.13
35 11 0.24
36 22 0.48
ACGTcount: A:0.04, C:0.07, G:0.11, T:0.78
Consensus pattern (34 bp):
TTTTTCTTTTTTTTTTTTTGGGTTAGGTTTTTCT
Found at i:2660533 original size:2 final size:2
Alignment explanation
Indices: 2660526--2660570 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2660516 TTTCGACATC
2660526 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2660568 TA T
1 TA T
2660571 TTTTGGTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2661952 original size:16 final size:16
Alignment explanation
Indices: 2661922--2661969 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
2661912 GAAAATTAAT
2661922 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
2661937 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
2661954 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
2661969 A
1 A
2661970 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:2661968 original size:11 final size:11
Alignment explanation
Indices: 2661913--2661983 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
2661903 ATAGCTTAAG
*
2661913 AAAATTAATAT
1 AAAATTAAAAT
2661924 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
2661936 AATAA-T-AATT
1 AA-AATTAAAAT
*
2661946 AAAAAT-AAAT
1 AAAATTAAAAT
2661956 AAAATTAAAAT
1 AAAATTAAAAT
*
2661967 AAACTTAAAAT
1 AAAATTAAAAT
*
2661978 AGAATT
1 AAAATT
2661984 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:2672271 original size:16 final size:16
Alignment explanation
Indices: 2672241--2672288 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
2672231 GAAAATTAAT
2672241 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
2672256 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
2672273 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
2672288 A
1 A
2672289 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:2672287 original size:11 final size:11
Alignment explanation
Indices: 2672232--2672302 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
2672222 ATAGCTTAAG
*
2672232 AAAATTAATAT
1 AAAATTAAAAT
2672243 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
2672255 AATAA-T-AATT
1 AA-AATTAAAAT
*
2672265 AAAAAT-AAAT
1 AAAATTAAAAT
2672275 AAAATTAAAAT
1 AAAATTAAAAT
*
2672286 AAACTTAAAAT
1 AAAATTAAAAT
*
2672297 AGAATT
1 AAAATT
2672303 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:2673717 original size:20 final size:20
Alignment explanation
Indices: 2673692--2673735 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
2673682 TTAGGGTTAC
*
2673692 AGAACATT-ACTATACAAAAT
1 AGAACATTCAATAT-CAAAAT
2673712 AGAACATTCAATATCAAAAT
1 AGAACATTCAATATCAAAAT
2673732 AGAA
1 AGAA
2673736 ACACTTATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.23
Consensus pattern (20 bp):
AGAACATTCAATATCAAAAT
Found at i:2676223 original size:11 final size:11
Alignment explanation
Indices: 2676207--2676231 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2676197 TAATGTAATC
2676207 AATTTATCTGT
1 AATTTATCTGT
2676218 AATTTATCTGT
1 AATTTATCTGT
2676229 AAT
1 AAT
2676232 CTAATCAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (11 bp):
AATTTATCTGT
Found at i:2679522 original size:18 final size:18
Alignment explanation
Indices: 2679496--2679606 Score: 168
Period size: 18 Copynumber: 6.2 Consensus size: 18
2679486 TACGACCATT
2679496 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2679514 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
2679532 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2679550 TACGGTACTATTCAAGTA
1 TACGGTACTATTCACGTA
* * *
2679568 TACGGCACTATTTATGTA
1 TACGGTACTATTCACGTA
*
2679586 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2679604 TAC
1 TAC
2679607 AGTAGTTGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 83 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2689831 original size:22 final size:22
Alignment explanation
Indices: 2689805--2689866 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 22
2689795 CCAGTCTTTC
2689805 TTTTTATTTTTATTTATTTTTT
1 TTTTTATTTTTATTTATTTTTT
*
2689827 TTTTTA---TTATTTATTATTT
1 TTTTTATTTTTATTTATTTTTT
2689846 TTTTTATTTTTATTTTATTTT
1 TTTTTATTTTTA-TTTATTTT
2689867 AATAATTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
19 18 0.53
22 9 0.26
23 7 0.21
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTATTTTTATTTATTTTTT
Found at i:2689866 original size:16 final size:15
Alignment explanation
Indices: 2689805--2689867 Score: 83
Period size: 15 Copynumber: 4.0 Consensus size: 15
2689795 CCAGTCTTTC
2689805 TTTTTATTTTTATTTA
1 TTTTTATTTTT-TTTA
2689821 TTTTT-TTTTTTATTA
1 TTTTTATTTTTT-TTA
2689836 TTTATTATTTTTTTTA
1 TTT-TTATTTTTTTTA
2689852 TTTTTATTTTATTTTA
1 TTTTTATTTT-TTTTA
2689868 ATAATTTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 1 0.02
15 18 0.42
16 18 0.42
17 6 0.14
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTTTTTA
Found at i:2690045 original size:43 final size:42
Alignment explanation
Indices: 2689962--2690052 Score: 112
Period size: 42 Copynumber: 2.1 Consensus size: 42
2689952 TCCATGCTGT
* * * *
2689962 CAAACAGTTCTATTCCAGCCCAGAATGCCATATCTCTGCAGC
1 CAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCAGC
*
2690004 CAAACAGTCCTATTCCAGCCTTAGAATCCCCAAAAC-CTGCAGC
1 CAAACAGTCCTATTCCAGCC-CAGAAT-CCCAAAACTCTGCAGC
2690047 CAAACA
1 CAAACA
2690053 CCCCTTTTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
42 19 0.45
43 18 0.43
44 5 0.12
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.20
Consensus pattern (42 bp):
CAAACAGTCCTATTCCAGCCCAGAATCCCAAAACTCTGCAGC
Found at i:2704402 original size:15 final size:16
Alignment explanation
Indices: 2704382--2704422 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
2704372 AATTTTTTAA
2704382 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
2704397 AAATTATTAAAAATAAT
1 AAATTA-TAAAAATAAT
2704414 AAAGTTATA
1 AAA-TTATA
2704423 TTTTTATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 7 0.30
18 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:2704436 original size:75 final size:76
Alignment explanation
Indices: 2704301--2704452 Score: 170
Period size: 75 Copynumber: 2.0 Consensus size: 76
2704291 TATGTAGGTC
* * * *
2704301 TTTTAAAATTTTTAAAAATTTAAATTATAAGAGATAAAATTATACTTTTATCCTTGAT-AAAATT
1 TTTTAAAAATTATAAAAATATAAATTATAAGAAATAAAATTATACTTTTATCCTTGATAAAAATT
* *
2704365 TTGATTTAATT
66 ATAATTTAATT
*
2704376 TTTTAAAAATTATAAAAATATAAATTATTAA-AAATAATAAAGTTATATTTTTAT-C-T-ATAAA
1 TTTTAAAAATTATAAAAATATAAATTA-TAAGAAAT-A-AAA-TTATACTTTTATCCTTGATAAA
2704437 AATTATAATTTAATT
62 AATTATAATTTAATT
2704452 T
1 T
2704453 CAGACATGAA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
75 29 0.45
76 21 0.32
77 4 0.06
78 11 0.17
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (76 bp):
TTTTAAAAATTATAAAAATATAAATTATAAGAAATAAAATTATACTTTTATCCTTGATAAAAATT
ATAATTTAATT
Found at i:2709181 original size:3 final size:3
Alignment explanation
Indices: 2709173--2709289 Score: 234
Period size: 3 Copynumber: 39.0 Consensus size: 3
2709163 TTTTACAGTG
2709173 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2709221 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2709269 TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT
2709290 GTTATTAGGG
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 114 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2711569 original size:16 final size:16
Alignment explanation
Indices: 2711548--2711582 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
2711538 AATTTACTGT
2711548 CAATGTTTGATTGCTA
1 CAATGTTTGATTGCTA
2711564 CAATGTTTGATTGCTA
1 CAATGTTTGATTGCTA
2711580 CAA
1 CAA
2711583 CAAGAGTACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (16 bp):
CAATGTTTGATTGCTA
Found at i:2715236 original size:20 final size:20
Alignment explanation
Indices: 2715211--2715251 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2715201 TCGATAGTAG
2715211 CCAAAAGGGTTATGAGATAT
1 CCAAAAGGGTTATGAGATAT
2715231 CCAAAAGGGTTATGAGATAT
1 CCAAAAGGGTTATGAGATAT
2715251 C
1 C
2715252 TTCAGAAAAC
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:0.12, G:0.24, T:0.24
Consensus pattern (20 bp):
CCAAAAGGGTTATGAGATAT
Found at i:2718533 original size:16 final size:16
Alignment explanation
Indices: 2718514--2718544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2718504 ATTCTAGTTA
*
2718514 TTTTGGGTCATTTTAT
1 TTTTGGGTCACTTTAT
2718530 TTTTGGGTCACTTTA
1 TTTTGGGTCACTTTA
2718545 GGATAATTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTTGGGTCACTTTAT
Found at i:2719969 original size:45 final size:45
Alignment explanation
Indices: 2719919--2720009 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
2719909 TGAATAGCAG
2719919 TAAAACTTTTAAAAATATCCTTACATGATTGAATATCTTGATCAA
1 TAAAACTTTTAAAAATATCCTTACATGATTGAATATCTTGATCAA
2719964 TAAAACTTTTAAAAATATCCTTACATGATTGAATATCTTGATCAA
1 TAAAACTTTTAAAAATATCCTTACATGATTGAATATCTTGATCAA
2720009 T
1 T
2720010 TACAATCACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (45 bp):
TAAAACTTTTAAAAATATCCTTACATGATTGAATATCTTGATCAA
Found at i:2725464 original size:30 final size:30
Alignment explanation
Indices: 2725428--2725499 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
2725418 ATTATTAGAA
*
2725428 ATAAAATTATACTTTAACCCTTTAAAAATG
1 ATAAAATTATAATTTAACCCTTTAAAAATG
* * * *
2725458 ATAAAATTTTAATTTAATCTTTTAAAAATT
1 ATAAAATTATAATTTAACCCTTTAAAAATG
*
2725488 ATAAAAATATAA
1 ATAAAATTATAA
2725500 AGTATTAAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (30 bp):
ATAAAATTATAATTTAACCCTTTAAAAATG
Done.