Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr6
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: 26303135
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.30
Warning! 1968672 characters in sequence are not A, C, G, or T
File 7 of 66
Found at i:2343311 original size:19 final size:21
Alignment explanation
Indices: 2343278--2343318 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
2343268 GAAAACTTCC
2343278 TTTTTTTCAAGTTTG-ATTTT
1 TTTTTTTCAAGTTTGAATTTT
*
2343298 TTTTTTTGAA-TTTGAATTTT
1 TTTTTTTCAAGTTTGAATTTT
2343318 T
1 T
2343319 CCCTTCTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (21 bp):
TTTTTTTCAAGTTTGAATTTT
Found at i:2350351 original size:20 final size:20
Alignment explanation
Indices: 2350313--2350353 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2350303 AATATAATAT
* **
2350313 TATTTTATTTATTTTTTAAA
1 TATTTTATTAATTCCTTAAA
2350333 TATTTTATTAATTCCTTAAA
1 TATTTTATTAATTCCTTAAA
2350353 T
1 T
2350354 TCTAGCCATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTTTATTAATTCCTTAAA
Found at i:2350714 original size:19 final size:19
Alignment explanation
Indices: 2350690--2350727 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2350680 CTGCCAAACC
*
2350690 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
2350709 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
2350728 AGTCAAATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:2353574 original size:22 final size:22
Alignment explanation
Indices: 2353549--2353592 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2353539 TATTTCTTCT
*
2353549 TTTTCTTTCTAT-TTTGTTTTTG
1 TTTTATTTCTATCTTT-TTTTTG
*
2353571 TTTTATTTTTATCTTTTTTTTG
1 TTTTATTTCTATCTTTTTTTTG
2353593 GACTTTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (22 bp):
TTTTATTTCTATCTTTTTTTTG
Found at i:2356878 original size:19 final size:17
Alignment explanation
Indices: 2356846--2356881 Score: 54
Period size: 19 Copynumber: 2.0 Consensus size: 17
2356836 TATTTAGTTA
2356846 TTTTTTAATTAGTTTAT
1 TTTTTTAATTAGTTTAT
2356863 TTTTATTAAGTTAGTTTAT
1 TTTT-TTAA-TTAGTTTAT
2356882 CTTATACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 4 0.24
19 9 0.53
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (17 bp):
TTTTTTAATTAGTTTAT
Found at i:2357247 original size:22 final size:22
Alignment explanation
Indices: 2357219--2357264 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2357209 TTGAAGCCAA
2357219 GGGAGCATAGCAGCACTGATGG
1 GGGAGCATAGCAGCACTGATGG
*
2357241 GGGAGCATAGCATCACTGATGG
1 GGGAGCATAGCAGCACTGATGG
2357263 GG
1 GG
2357265 TGTGCCACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.41, T:0.15
Consensus pattern (22 bp):
GGGAGCATAGCAGCACTGATGG
Found at i:2369708 original size:13 final size:13
Alignment explanation
Indices: 2369690--2369756 Score: 66
Period size: 13 Copynumber: 5.0 Consensus size: 13
2369680 AAAAAATCCC
2369690 CAAATAATCTTAT
1 CAAATAATCTTAT
2369703 CAAATAAT-TTAT
1 CAAATAATCTTAT
*
2369715 AATTTATATAATCTTAT
1 CA---A-ATAATCTTAT
2369732 CAAATAATCTTAT
1 CAAATAATCTTAT
*
2369745 CACATAAT-TTAT
1 CAAATAATCTTAT
2369757 AATTTATATA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
12 9 0.20
13 25 0.54
14 1 0.02
15 1 0.02
16 5 0.11
17 5 0.11
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (13 bp):
CAAATAATCTTAT
Found at i:2369752 original size:42 final size:41
Alignment explanation
Indices: 2369690--2369779 Score: 162
Period size: 42 Copynumber: 2.2 Consensus size: 41
2369680 AAAAAATCCC
2369690 CAAATAATCTTATCAAATAATTTATAATTTATATAATCTTAT
1 CAAATAATCTTATCAAATAATTTATAATTTATATAAT-TTAT
*
2369732 CAAATAATCTTATCACATAATTTATAATTTATATAATTTAT
1 CAAATAATCTTATCAAATAATTTATAATTTATATAATTTAT
2369773 CAAATAA
1 CAAATAA
2369780 GATTATATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 11 0.23
42 36 0.77
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (41 bp):
CAAATAATCTTATCAAATAATTTATAATTTATATAATTTAT
Found at i:2374744 original size:17 final size:17
Alignment explanation
Indices: 2374722--2374759 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
2374712 ATTTAACTCT
* *
2374722 ATTATAAGTGTGTATTN
1 ATTATAAATGTGTATTC
2374739 ATTATAAATGTGTATTC
1 ATTATAAATGTGTATTC
2374756 ATTA
1 ATTA
2374760 AATGATGAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.47
Consensus pattern (17 bp):
ATTATAAATGTGTATTC
Found at i:2375509 original size:32 final size:32
Alignment explanation
Indices: 2375473--2375551 Score: 77
Period size: 35 Copynumber: 2.4 Consensus size: 32
2375463 ATTAAAAGCT
2375473 TGTCCTTTTCTTCAACTACATTGAAAGCAATG
1 TGTCCTTTTCTTCAACTACATTGAAAGCAATG
** * **
2375505 TGTCCATTAATAATTCAACTACATTGGAATTAATG
1 TGTCC-TT--TTCTTCAACTACATTGAAAGCAATG
*
2375540 TGACCTTTTCTT
1 TGTCCTTTTCTT
2375552 ATTAATAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
32 8 0.22
33 2 0.06
34 2 0.06
35 24 0.67
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (32 bp):
TGTCCTTTTCTTCAACTACATTGAAAGCAATG
Found at i:2375522 original size:35 final size:35
Alignment explanation
Indices: 2375483--2375586 Score: 100
Period size: 42 Copynumber: 2.8 Consensus size: 35
2375473 TGTCCTTTTC
2375483 TTCAACTACATTGAAAGCAATGTGTCCATTAATAA
1 TTCAACTACATTGAAAGCAATGTGTCCATTAATAA
* ** *
2375518 TTCAACTACATTGGAATTAATGTGACCTTTTCTTATTAATAA
1 TTCAACTACATTGAAAGCAATGTG------TC-CATTAATAA
*
2375560 TTCAACTATATTGAAAGCAATGTGTCC
1 TTCAACTACATTGAAAGCAATGTGTCC
2375587 TTTTCTGATT
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
35 21 0.40
36 2 0.04
41 2 0.04
42 28 0.53
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.37
Consensus pattern (35 bp):
TTCAACTACATTGAAAGCAATGTGTCCATTAATAA
Found at i:2375582 original size:42 final size:42
Alignment explanation
Indices: 2375510--2375600 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
2375500 CAATGTGTCC
* ** *
2375510 ATTAATAATTCAACTACATTGGAATTAATGTGACCTTTTCTT
1 ATTAATAATTCAACTACATTGAAAGCAATGTGACCTTTTCTG
* *
2375552 ATTAATAATTCAACTATATTGAAAGCAATGTGTCCTTTTCTG
1 ATTAATAATTCAACTACATTGAAAGCAATGTGACCTTTTCTG
2375594 ATTAATA
1 ATTAATA
2375601 CTTCTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (42 bp):
ATTAATAATTCAACTACATTGAAAGCAATGTGACCTTTTCTG
Found at i:2387567 original size:2 final size:2
Alignment explanation
Indices: 2387560--2387592 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2387550 AGATAGTAGA
*
2387560 AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2387593 CTGCGATACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2388927 original size:173 final size:173
Alignment explanation
Indices: 2388637--2388977 Score: 497
Period size: 173 Copynumber: 2.0 Consensus size: 173
2388627 CACTGTGTCT
* * *
2388637 GGCTGTTTAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTTTAAGTATATATG
1 GGCTGTTCAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTATAAGTATATATA
* * *
2388702 CAACTTAAAGAGGGATTTTCTCATTATTGATTTGCTTACTTATATCTTTAACTTTTTCATATTGT
66 CAACTTAAAGAGGGATTTCCTCATTATCGATTTGCTTACTTATATCTTTAAC-TTTTCATATTAT
* *
2388767 ATTGAT-TTCAATATTCTGTTCTATTATGCTCAATTCCTGTTTCG
130 AGTGATCTT-AATATTCTGTTCAATTATGCTCAATTCCTGTTTCG
* * * * *
2388811 GGCTGTTCAAATTATTTGGTTTCCTATTGGTTATCCTATGTGGTTTCTTGTTAT-AGTATATATA
1 GGCTGTTCAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTATAAGTATATATA
* * * *
2388875 CAATTTAAAGAGGGATTTCCTCTTTATCGATTTGTTTAGTTATATCTTTAACTTTTCATATTATA
66 CAACTTAAAGAGGGATTTCCTCATTATCGATTTGCTTACTTATATCTTTAACTTTTCATATTATA
2388940 GTGATCTTAATATTCTGTTCAATTATGCTCAATTCCTG
131 GTGATCTTAATATTCTGTTCAATTATGCTCAATTCCTG
2388978 ACAAATTGTT
Statistics
Matches: 149, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
172 45 0.30
173 57 0.38
174 47 0.32
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (173 bp):
GGCTGTTCAAATTATTCGGTTTCCTATTAGTTACCCTATGTGATTCCTTGTTATAAGTATATATA
CAACTTAAAGAGGGATTTCCTCATTATCGATTTGCTTACTTATATCTTTAACTTTTCATATTATA
GTGATCTTAATATTCTGTTCAATTATGCTCAATTCCTGTTTCG
Found at i:2397112 original size:14 final size:15
Alignment explanation
Indices: 2397075--2397115 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
2397065 TTAGTTATTT
2397075 TTAGTTATTTTCTAA
1 TTAGTTATTTTCTAA
2397090 TTAGTTTATTTT-T-A
1 TTAG-TTATTTTCTAA
2397104 TTAAGTTATTTT
1 TT-AGTTATTTT
2397116 ATTTTATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 10 0.42
15 7 0.29
16 7 0.29
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (15 bp):
TTAGTTATTTTCTAA
Found at i:2411865 original size:19 final size:18
Alignment explanation
Indices: 2411837--2411872 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2411827 TATTATATTA
*
2411837 TTTTTATTTTCATGTAAT
1 TTTTTATTTTAATGTAAT
2411855 TTTTTATTTTTAATGTAA
1 TTTTTA-TTTTAATGTAA
2411873 ATTACATCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.03, G:0.06, T:0.67
Consensus pattern (18 bp):
TTTTTATTTTAATGTAAT
Found at i:2413647 original size:17 final size:17
Alignment explanation
Indices: 2413625--2413658 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2413615 GCTAGGATTA
2413625 AAGATCATACTTAAGCT
1 AAGATCATACTTAAGCT
2413642 AAGATCATACTTAAGCT
1 AAGATCATACTTAAGCT
2413659 GGTAAATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
AAGATCATACTTAAGCT
Found at i:2415137 original size:25 final size:25
Alignment explanation
Indices: 2415089--2415166 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 25
2415079 AATTAAGGAA
2415089 AATTTTACCACCAGAAGTGGATGGAT
1 AATTTTACCACCA-AAGTGGATGGAT
*
2415115 AATTTTGCCACCAAAGTGGATGGAT
1 AATTTTACCACCAAAGTGGATGGAT
2415140 AATTTTACCACCAAAAGTGGATGGAT
1 AATTTTACCACC-AAAGTGGATGGAT
2415166 A
1 A
2415167 CCTTAACCCA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 23 0.47
26 26 0.53
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (25 bp):
AATTTTACCACCAAAGTGGATGGAT
Found at i:2415160 original size:22 final size:24
Alignment explanation
Indices: 2415089--2415161 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 24
2415079 AATTAAGGAA
*
2415089 AATTTTACCACCAGAAGTGGATGGAT
1 AATTTTACCACCA-AAG-AGATGGAT
* *
2415115 AATTTTGCCACCAAAGTGGATGGAT
1 AATTTTACCACCAAAG-AGATGGAT
2415140 AATTTTACCACCAAA-AG-TGGAT
1 AATTTTACCACCAAAGAGATGGAT
2415162 GGATACCTTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 5 0.11
23 1 0.02
25 26 0.59
26 12 0.27
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (24 bp):
AATTTTACCACCAAAGAGATGGAT
Found at i:2420274 original size:12 final size:11
Alignment explanation
Indices: 2420254--2420340 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 11
2420244 TTTTTTCTTC
2420254 CTTTCTCTCTTTT
1 CTTTCTC-C-TTT
2420267 CCTTTCTCCTTT
1 -CTTTCTCCTTT
*
2420279 CTTTCT--TTC
1 CTTTCTCCTTT
2420288 CTTTCTCCTTT
1 CTTTCTCCTTT
* *
2420299 C-TNCTTC-TT
1 CTTTCTCCTTT
2420308 C-TTCTCCTTT
1 CTTTCTCCTTT
2420318 C-TT-T-CTTT
1 CTTTCTCCTTT
2420326 CTTTTCTCCTTT
1 C-TTTCTCCTTT
2420338 CTT
1 CTT
2420341 CCAACTGATC
Statistics
Matches: 60, Mismatches: 6, Indels: 17
0.72 0.07 0.20
Matches are distributed among these distances:
8 5 0.08
9 16 0.27
10 11 0.18
11 12 0.20
12 8 0.13
13 1 0.02
14 7 0.12
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.64
Consensus pattern (11 bp):
CTTTCTCCTTT
Found at i:2420278 original size:7 final size:7
Alignment explanation
Indices: 2420247--2420339 Score: 65
Period size: 7 Copynumber: 13.7 Consensus size: 7
2420237 ACCAAGCTTT
2420247 TTTCTTCC
1 TTTC-TCC
2420255 TTTCTCTC
1 TTTCTC-C
2420263 TTT-TCC
1 TTTCTCC
2420269 TTTCTCC
1 TTTCTCC
2420276 TTTCT--
1 TTTCTCC
*
2420281 TTCTTTCC
1 TT-TCTCC
2420289 TTTCTCC
1 TTTCTCC
*
2420296 TTTCTNC
1 TTTCTCC
*
2420303 -TTCTTC
1 TTTCTCC
2420309 -TTCTCC
1 TTTCTCC
*
2420315 TTTCTTTC
1 TTTC-TCC
2420323 TTTCT--
1 TTTCTCC
2420328 TTTCTCC
1 TTTCTCC
2420335 TTTCT
1 TTTCT
2420340 TCCAACTGAT
Statistics
Matches: 70, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
5 7 0.10
6 16 0.23
7 31 0.44
8 16 0.23
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.65
Consensus pattern (7 bp):
TTTCTCC
Found at i:2420289 original size:13 final size:13
Alignment explanation
Indices: 2420273--2420332 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
2420263 TTTTCCTTTC
2420273 TCCTTTCTTTCTT
1 TCCTTTCTTTCTT
*
2420286 TCCTTTC-TCCTT
1 TCCTTTCTTTCTT
2420298 T-CTNCTTC-TTCTT
1 TCCT--TTCTTTCTT
2420311 CTCCTTTCTTTCTT
1 -TCCTTTCTTTCTT
*
2420325 TCTTTTCT
1 TCCTTTCT
2420333 CCTTTCTTCC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 2 0.05
12 5 0.13
13 24 0.62
14 6 0.15
15 2 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.65
Consensus pattern (13 bp):
TCCTTTCTTTCTT
Found at i:2420289 original size:20 final size:20
Alignment explanation
Indices: 2420247--2420340 Score: 113
Period size: 20 Copynumber: 4.7 Consensus size: 20
2420237 ACCAAGCTTT
*
2420247 TTTCTTCCTTTCTCTCTTTTCC
1 TTTC-TCCTTTCTTTC-TTTCC
2420269 TTTCTCCTTTCTTTCTTTCC
1 TTTCTCCTTTCTTTCTTTCC
2420289 TTTCTCCTTTCTNCTTC-TT-C
1 TTTCTCCTTTCT--TTCTTTCC
*
2420309 -TTCTCCTTTCTTTCTTTCT
1 TTTCTCCTTTCTTTCTTTCC
2420328 TTTCTCCTTTCTT
1 TTTCTCCTTTCTT
2420341 CCAACTGATC
Statistics
Matches: 65, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.05
18 2 0.03
19 11 0.17
20 30 0.46
21 12 0.18
22 7 0.11
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCTCCTTTCTTTCTTTCC
Found at i:2432937 original size:74 final size:74
Alignment explanation
Indices: 2432849--2432990 Score: 257
Period size: 74 Copynumber: 1.9 Consensus size: 74
2432839 AAACCTATAC
*
2432849 TTATAAATATGTATTCATTAAATGAAGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATGAAGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
2432914 TTAAACGTA
66 TTAAACGTA
* *
2432923 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATGAAGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
2432988 TTA
66 TTA
2432991 TTCCATTTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATGAAGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
TTAAACGTA
Found at i:2433691 original size:32 final size:32
Alignment explanation
Indices: 2433655--2433733 Score: 104
Period size: 35 Copynumber: 2.4 Consensus size: 32
2433645 TATTAAAGCT
2433655 TGTCCTTTTCTTCAACTACATTGAAAGCAATG
1 TGTCCTTTTCTTCAACTACATTGAAAGCAATG
** *
2433687 TGTCCATTAATAATTCAACTACATTGGAAGCAATG
1 TGTCC-TT--TTCTTCAACTACATTGAAAGCAATG
2433722 TGTCCTTTTCTT
1 TGTCCTTTTCTT
2433734 ATTAATAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
32 8 0.21
33 2 0.05
34 2 0.05
35 27 0.69
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (32 bp):
TGTCCTTTTCTTCAACTACATTGAAAGCAATG
Found at i:2433704 original size:35 final size:37
Alignment explanation
Indices: 2433665--2433768 Score: 140
Period size: 42 Copynumber: 2.7 Consensus size: 37
2433655 TGTCCTTTTC
2433665 TTCAACTACATTGAAAGCAATGTGTC-C-ATTAATAA
1 TTCAACTACATTGAAAGCAATGTGTCTCTATTAATAA
*
2433700 TTCAACTACATTGGAAGCAATGTGTCCTTTTCTTATTAATAA
1 TTCAACTACATTGAAAGCAATGTGT-C---TC-TATTAATAA
2433742 TTCAACTACATTGAAAGCAATGTGTCT
1 TTCAACTACATTGAAAGCAATGTGTCT
2433769 TTTTCTGATT
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
35 24 0.40
36 1 0.02
38 1 0.02
40 1 0.02
41 1 0.02
42 32 0.53
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (37 bp):
TTCAACTACATTGAAAGCAATGTGTCTCTATTAATAA
Found at i:2433739 original size:42 final size:42
Alignment explanation
Indices: 2433692--2433782 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
2433682 CAATGTGTCC
* *
2433692 ATTAATAATTCAACTACATTGGAAGCAATGTGTCCTTTTCTT
1 ATTAATAATTCAACTACATTGAAAGCAATGTGTCCTTTTCTG
*
2433734 ATTAATAATTCAACTACATTGAAAGCAATGTGTCTTTTTCTG
1 ATTAATAATTCAACTACATTGAAAGCAATGTGTCCTTTTCTG
2433776 ATTAATA
1 ATTAATA
2433783 CGTCTTATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (42 bp):
ATTAATAATTCAACTACATTGAAAGCAATGTGTCCTTTTCTG
Found at i:2434176 original size:26 final size:28
Alignment explanation
Indices: 2434140--2434193 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 28
2434130 GAAGCTAGAT
2434140 ATATAACTCTT-ATCC-GCTATCTTATC
1 ATATAACTCTTAATCCTGCTATCTTATC
*
2434166 ATATAACTCTTAATCCTTCTATCTTATC
1 ATATAACTCTTAATCCTGCTATCTTATC
2434194 CGCTATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 11 0.44
27 4 0.16
28 10 0.40
ACGTcount: A:0.28, C:0.26, G:0.02, T:0.44
Consensus pattern (28 bp):
ATATAACTCTTAATCCTGCTATCTTATC
Found at i:2436786 original size:75 final size:74
Alignment explanation
Indices: 2436704--2436843 Score: 237
Period size: 75 Copynumber: 1.9 Consensus size: 74
2436694 AAACCTATAC
*
2436704 TTATAAATATGTATTCATTAAATGACT-ATCATTGAAATATTTTTTTATTATAATTATTAGTAAG
1 TTATAAATATGTATTCATCAAATGA-TGATCATTGAAATA-TTTTTTATTATAATTATTAGTAAG
2436768 ATGTAAACTTA
64 ATGTAAACTTA
*
2436779 TTATAAATGTGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
1 TTATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
2436844 TTATTCCATT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
74 27 0.44
75 35 0.56
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.46
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGAT
GTAAACTTA
Found at i:2437617 original size:13 final size:13
Alignment explanation
Indices: 2437599--2437652 Score: 56
Period size: 13 Copynumber: 4.0 Consensus size: 13
2437589 AAAAATAAAT
2437599 ATTAATTTTTTAA
1 ATTAATTTTTTAA
2437612 ATTAATTTTTTAAA
1 ATTAATTTTTT-AA
2437626 ATTAAATATTTTT-A
1 ATT-AAT-TTTTTAA
* *
2437640 TTTTATTTTTTAA
1 ATTAATTTTTTAA
2437653 TATTTTAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
12 5 0.14
13 14 0.40
14 8 0.23
15 3 0.09
16 5 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATTAATTTTTTAA
Found at i:2437625 original size:28 final size:29
Alignment explanation
Indices: 2437594--2437656 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
2437584 TTAAAAAAAA
2437594 TAAATATT-AAT-TTTTTAAATTAATTTTT
1 TAAATATTAAATATTTTT-AATTAATTTTT
* *
2437622 TAAA-ATTAAATATTTTTATTTTATTTTT
1 TAAATATTAAATATTTTTAATTAATTTTT
2437650 T-AATATT
1 TAAATATT
2437657 TTAAGTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
27 5 0.17
28 20 0.67
29 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
TAAATATTAAATATTTTTAATTAATTTTT
Found at i:2437627 original size:14 final size:14
Alignment explanation
Indices: 2437594--2437630 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
2437584 TTAAAAAAAA
2437594 TAAATATTAATTTTT
1 TAAA-ATTAATTTTT
2437609 T-AAATTAATTTTT
1 TAAAATTAATTTTT
2437622 TAAAATTAA
1 TAAAATTAA
2437631 ATATTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 9 0.43
15 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TAAAATTAATTTTT
Found at i:2468269 original size:43 final size:43
Alignment explanation
Indices: 2468222--2468307 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
2468212 CCACTAATTT
2468222 ATTATGTTTGTGTACTGCTCTCTCCACATTGCACTCATTATTC
1 ATTATGTTTGTGTACTGCTCTCTCCACATTGCACTCATTATTC
*
2468265 ATTATGTTTGTGTACTGCTCTCTCCTCATTGCACTCATTATTC
1 ATTATGTTTGTGTACTGCTCTCTCCACATTGCACTCATTATTC
2468308 CATGGTATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.17, C:0.26, G:0.12, T:0.45
Consensus pattern (43 bp):
ATTATGTTTGTGTACTGCTCTCTCCACATTGCACTCATTATTC
Found at i:2471149 original size:2 final size:2
Alignment explanation
Indices: 2471144--2471172 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2471134 TTAAATAGAA
2471144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2471173 AATTTTACGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2474952 original size:59 final size:58
Alignment explanation
Indices: 2474833--2474953 Score: 136
Period size: 59 Copynumber: 2.1 Consensus size: 58
2474823 AACAAGAACT
* * * ** *
2474833 TCATATTTTTCATGCTTTGACGTCTTCTGCCACTACAATTTATCTGACACTGCAGTTG
1 TCATATTTTCCATGCTTTGACGTCTTCTGCCACTACAACTTATCTCACAAGGCAGCTG
* * *
2474891 TCATAATTTTCCATG-TATTGATGTCTTCTGCCACTATAGCTTATCTCACAAGGCAGCTG
1 TCAT-ATTTTCCATGCT-TTGACGTCTTCTGCCACTACAACTTATCTCACAAGGCAGCTG
2474950 TCAT
1 TCAT
2474954 GTGTCTATAG
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
58 5 0.10
59 47 0.90
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (58 bp):
TCATATTTTCCATGCTTTGACGTCTTCTGCCACTACAACTTATCTCACAAGGCAGCTG
Found at i:2477048 original size:18 final size:19
Alignment explanation
Indices: 2477022--2477071 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
2477012 ACACGTTTAC
*
2477022 TTAATCGTGTTAT-CGTGT
1 TTAAACGTGTTATACGTGT
2477040 TTAAACGTG-TATACGTGT
1 TTAAACGTGTTATACGTGT
2477058 TTAAACGTG-TATAC
1 TTAAACGTGTTATAC
2477072 ATTACACGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 3 0.10
18 27 0.90
ACGTcount: A:0.26, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TTAAACGTGTTATACGTGT
Found at i:2477203 original size:28 final size:24
Alignment explanation
Indices: 2477167--2477220 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
2477157 TATTTTAACC
*
2477167 TTATA-TATA-ATAATAAATTTTA
1 TTATATTATATATATTAAATTTTA
*
2477189 TGTATATTATTTATATTAAATTTTA
1 T-TATATTATATATATTAAATTTTA
2477214 TTATATT
1 TTATATT
2477221 TGATGTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.04
23 4 0.15
24 9 0.33
25 13 0.48
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATTATATATATTAAATTTTA
Found at i:2477246 original size:19 final size:19
Alignment explanation
Indices: 2477211--2477255 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2477201 ATATTAAATT
2477211 TTATTA-TATTTGATGTTA
1 TTATTATTATTTGATGTTA
**
2477229 TTATTATTATTTTTTGTTA
1 TTATTATTATTTGATGTTA
*
2477248 TAATTATT
1 TTATTATT
2477256 TTTATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (19 bp):
TTATTATTATTTGATGTTA
Found at i:2477335 original size:9 final size:9
Alignment explanation
Indices: 2477317--2477356 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
2477307 ATATTTTTAT
2477317 TTAATCGTG
1 TTAATCGTG
*
2477326 TTAATTGTG
1 TTAATCGTG
* *
2477335 TTAAACATG
1 TTAATCGTG
2477344 TTAATCGTG
1 TTAATCGTG
2477353 TTAA
1 TTAA
2477357 ACGTATTATT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (9 bp):
TTAATCGTG
Found at i:2477345 original size:18 final size:18
Alignment explanation
Indices: 2477324--2477358 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2477314 TATTTAATCG
*
2477324 TGTTAATTGTGTTAAACA
1 TGTTAATCGTGTTAAACA
2477342 TGTTAATCGTGTTAAAC
1 TGTTAATCGTGTTAAAC
2477359 GTATTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.17, T:0.43
Consensus pattern (18 bp):
TGTTAATCGTGTTAAACA
Found at i:2477748 original size:54 final size:53
Alignment explanation
Indices: 2477667--2477774 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 53
2477657 TTGATATTAC
*
2477667 TACTCAAAATATTCGCTAGAAAGTCATTTAATTTGAAAGAAATATAAATGAACT
1 TACTCAAAATATTCGCTAGAAAGTCATTTAA-TTAAAAGAAATATAAATGAACT
* * *
2477721 TACTCCAAATATTTGCTAGAAAGTCATTTAATTAAAAGGAATATAAATGAACT
1 TACTCAAAATATTCGCTAGAAAGTCATTTAATTAAAAGAAATATAAATGAACT
2477774 T
1 T
2477775 GGGTTATCTT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 21 0.42
54 29 0.58
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.32
Consensus pattern (53 bp):
TACTCAAAATATTCGCTAGAAAGTCATTTAATTAAAAGAAATATAAATGAACT
Found at i:2484277 original size:13 final size:13
Alignment explanation
Indices: 2484259--2484283 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2484249 TTTCAGAAAA
2484259 TTTATAAAATCAT
1 TTTATAAAATCAT
2484272 TTTATAAAATCA
1 TTTATAAAATCA
2484284 CAATTTCTCT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:2487029 original size:18 final size:18
Alignment explanation
Indices: 2486987--2487029 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2486977 TGACTTGATG
*
2486987 ATATTTAAATTTTTCTAA
1 ATATTAAAATTTTTCTAA
2487005 ATAATTAAAATTTTT-TAAA
1 AT-ATTAAAATTTTTCT-AA
2487024 ATATTA
1 ATATTA
2487030 TACCTAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATTAAAATTTTTCTAA
Found at i:2487914 original size:34 final size:34
Alignment explanation
Indices: 2487876--2487942 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
2487866 TATGGTGGAG
* * *
2487876 AAGCTTTGACTTTGACATGTAATATCTAGTGTTA
1 AAGCTTTAACCTTGACATGTAACATCTAGTGTTA
*
2487910 AAGCTTTAACCTTGACATGTAACATCTGGTGTT
1 AAGCTTTAACCTTGACATGTAACATCTAGTGTT
2487943 GAATCTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (34 bp):
AAGCTTTAACCTTGACATGTAACATCTAGTGTTA
Found at i:2489552 original size:60 final size:60
Alignment explanation
Indices: 2489435--2489724 Score: 345
Period size: 60 Copynumber: 4.9 Consensus size: 60
2489425 AGACATCATC
* *
2489435 ACCTACTCGTGGGAACTACCCACG-C-CGC-ATATGAATCGGGGCTTCAGGTCCGC-CTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGGCTTCAGGTCC-CTCTTT
* * *
2489492 ACTTACTCGTGGGAACTACCCACGTCACCCAATATAAATCGGGGCTTTAGGTCCCTCTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGGCTTCAGGTCCCTCTTT
* ** ** * * *
2489552 ACCTACTTGTGGGAACTACCCAATCCACTTAATATAAATCAGGGCTTCAGGTCGCTTTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGGCTTCAGGTCCCTCTTT
* * *
2489612 ACCTACTCGTGGGAACTACCCACGCCATCCAATATAAATCGTGGCTTCAGGTCCCCCTTT
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGGCTTCAGGTCCCTCTTT
* * * * * *
2489672 ACCTACTCGTGGAAACCACTCACGCCATCCAATACAAATCGGAGCTTCAGGTC
1 ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGGCTTCAGGTC
2489725 TCCCTTTTTA
Statistics
Matches: 197, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
57 23 0.12
58 1 0.01
59 3 0.02
60 170 0.86
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (60 bp):
ACCTACTCGTGGGAACTACCCACGCCACCCAATATAAATCGGGGCTTCAGGTCCCTCTTT
Found at i:2490420 original size:13 final size:12
Alignment explanation
Indices: 2490390--2490429 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2490380 GTGAAACCCA
2490390 TTATTATTATTT
1 TTATTATTATTT
*
2490402 TATATTTTTAATTT
1 T-TATTATT-ATTT
2490416 TTATTATTATTT
1 TTATTATTATTT
2490428 TT
1 TT
2490430 CTTCATCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 7 0.29
13 12 0.50
14 5 0.21
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (12 bp):
TTATTATTATTT
Found at i:2490596 original size:18 final size:17
Alignment explanation
Indices: 2490575--2490618 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
2490565 TCTCTTTCAC
*
2490575 TTTCTTTCCTTCTTTTCT
1 TTTCTTTCCTT-TCTTCT
2490593 TTTCTTTTCCTTTCTTCT
1 TTTC-TTTCCTTTCTTCT
*
2490611 TTTATTTC
1 TTTCTTTC
2490619 TCTTGGCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 4 0.17
18 12 0.52
19 7 0.30
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTTCCTTTCTTCT
Found at i:2490597 original size:10 final size:10
Alignment explanation
Indices: 2490562--2490608 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
2490552 CCCTTTCTCT
2490562 CTTTCTCTTTC
1 CTTTCT-TTTC
2490573 ACTTTC-TTTC
1 -CTTTCTTTTC
2490583 C-TTCTTTTC
1 CTTTCTTTTC
*
2490592 TTTTCTTTTC
1 CTTTCTTTTC
2490602 CTTTCTT
1 CTTTCTT
2490609 CTTTTATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
8 3 0.10
9 5 0.16
10 18 0.58
12 5 0.16
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (10 bp):
CTTTCTTTTC
Found at i:2490622 original size:24 final size:24
Alignment explanation
Indices: 2490553--2490622 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 24
2490543 CACCGTTCTC
*
2490553 CCTTTCTCTCTTTCTCTTTCAC-TTT
1 CCTTTCT-TCTTT-TCTTTCTCTTTT
2490578 -CTTTCCTTCTTTTCTTT-TCTTTT
1 CCTTT-CTTCTTTTCTTTCTCTTTT
*
2490601 CCTTTCTTCTTTTATTTCTCTT
1 CCTTTCTTCTTTTCTTTCTCTT
2490623 GGCAAGCCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 1 0.03
23 19 0.49
24 17 0.44
25 2 0.05
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (24 bp):
CCTTTCTTCTTTTCTTTCTCTTTT
Found at i:2491425 original size:34 final size:34
Alignment explanation
Indices: 2491369--2491490 Score: 102
Period size: 34 Copynumber: 3.6 Consensus size: 34
2491359 AGCAACACCC
*
2491369 AAACTTCAGCACTAAATTTTACATGTCAAGGTCA
1 AAACTTCAGCACTAAATGTTACATGTCAAGGTCA
* * * *
2491403 AAACTTTAGCCCTAGATGTTACATGTCAAGGTTA
1 AAACTTCAGCACTAAATGTTACATGTCAAGGTCA
* * * * * * * * *
2491437 AAGCTTCACCTCCAGATGTTACACGCCAAGATTA
1 AAACTTCAGCACTAAATGTTACATGTCAAGGTCA
2491471 AAACTTCAGCA-TCAAATGTT
1 AAACTTCAGCACT-AAATGTT
2491491 GCACGCTATT
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
34 69 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (34 bp):
AAACTTCAGCACTAAATGTTACATGTCAAGGTCA
Found at i:2491496 original size:34 final size:34
Alignment explanation
Indices: 2491418--2491580 Score: 128
Period size: 34 Copynumber: 4.8 Consensus size: 34
2491408 TTAGCCCTAG
* * * * * *
2491418 ATGTTACATGTCAAGGTTAAAGCTTCACCTCCAG
1 ATGTTACACGCCAAGATTAAAGCTTCAGCACCAA
* *
2491452 ATGTTACACGCCAAGATTAAAACTTCAGCATCAA
1 ATGTTACACGCCAAGATTAAAGCTTCAGCACCAA
* * ** **
2491486 ATGTTGCACGCTATTACCAAAGCTTCAGCACCAA
1 ATGTTACACGCCAAGATTAAAGCTTCAGCACCAA
* * * *
2491520 ATGTTACATGCCAAGGTTAAAGCTTCACCACCAG
1 ATGTTACACGCCAAGATTAAAGCTTCAGCACCAA
* * * *
2491554 ATATTACATGCCAAAATCAAAGCTTCA
1 ATGTTACACGCCAAGATTAAAGCTTCA
2491581 ACAGCATATA
Statistics
Matches: 99, Mismatches: 30, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 99 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (34 bp):
ATGTTACACGCCAAGATTAAAGCTTCAGCACCAA
Found at i:2491592 original size:34 final size:34
Alignment explanation
Indices: 2491503--2491602 Score: 112
Period size: 34 Copynumber: 3.0 Consensus size: 34
2491493 ACGCTATTAC
* * **
2491503 CAAAGCTTCAGCACCAAATGTTACATGCCAAGGT
1 CAAAGCTTCAACACCAAATATTACATGCCAAAAT
* * *
2491537 TAAAGCTTCACCACCAGATATTACATGCCAAAAT
1 CAAAGCTTCAACACCAAATATTACATGCCAAAAT
* *
2491571 CAAAGCTTCAACAGCATATATTACATG-CAAAA
1 CAAAGCTTCAACACCAAATATTACATGCCAAAA
2491603 GCTTCTTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
33 5 0.09
34 51 0.91
ACGTcount: A:0.41, C:0.25, G:0.12, T:0.22
Consensus pattern (34 bp):
CAAAGCTTCAACACCAAATATTACATGCCAAAAT
Found at i:2494608 original size:2 final size:2
Alignment explanation
Indices: 2494601--2494631 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2494591 NNNCTTTACT
2494601 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2494632 TTAAGTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2500800 original size:15 final size:15
Alignment explanation
Indices: 2500780--2500810 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2500770 GTATTTTAAC
*
2500780 AAGTAATTTAATTAT
1 AAGTAATTTAAATAT
2500795 AAGTAATTTAAATAT
1 AAGTAATTTAAATAT
2500810 A
1 A
2500811 TATTAGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
AAGTAATTTAAATAT
Found at i:2503479 original size:36 final size:36
Alignment explanation
Indices: 2503419--2503532 Score: 201
Period size: 36 Copynumber: 3.1 Consensus size: 36
2503409 CAGAATATAG
*
2503419 TCTGATACCACAAAATTAATTATTTTATGTTTACTTGT
1 TCTGATACCAC--AATTAATTATTTTATGTTTAATTGT
2503457 TCTGATACCACAATTAATTATTTTATGTTTAATTGT
1 TCTGATACCACAATTAATTATTTTATGTTTAATTGT
2503493 TCTGATACCACAATTAATTATTTTATGTTTAATTGT
1 TCTGATACCACAATTAATTATTTTATGTTTAATTGT
2503529 TCTG
1 TCTG
2503533 CTGTGTGTAC
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
36 64 0.85
38 11 0.15
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (36 bp):
TCTGATACCACAATTAATTATTTTATGTTTAATTGT
Found at i:2504477 original size:186 final size:187
Alignment explanation
Indices: 2504158--2504521 Score: 502
Period size: 186 Copynumber: 2.0 Consensus size: 187
2504148 TGGTGACAAA
*
2504158 TTTGTCTATGATCTAGTGTACATGGTTCTTTTGGAGAAGCTGGAATGATAGAGCTTTGTGGTGAT
1 TTTGTCTATGATCTAGTGTACATGGTTCTTTTGGAGAAGCTGGAATGATAGAACTTTGTGGTGAT
* * *
2504223 AAAGGTGGCAATCCTCTGAACTGTGCTGCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAGTTC
66 AAAGGTGCCAATCCTCTGAACTGTGATGCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAATTC
* * *
2504288 AGGTGAGGATAACTCTAGAGTCAATTG-GAAAGACATAGATTAGGTGGTGATAAAGGT
131 AGGTGAGGATAACTCTAGAGTCAA-CGAGAAAGACATAAAATAGGTGGTGATAAAGGT
* * *
2504345 TTTGTCTATGGTCTAGTGTCCATGGTTGTTTTGGAGGAA-CT-GAAT-AGTAGAACTTTGTGGTG
1 TTTGTCTATGATCTAGTGTACATGGTTCTTTTGGA-GAAGCTGGAATGA-TAGAACTTTGTGGTG
* * * * **
2504407 GTAAAGGTGCCAGTCCTCTGAACTGTGATTCATTACATGTTCTTGGTTTCCAGTAGAGTTGAAAT
64 ATAAAGGTGCCAATCCTCTGAACTGTGATGCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAAT
* * *
2504472 TCAGGTGTGGATGACTCTATAGTCAACGAGAAAGACATAAAATAGGTGGT
129 TCAGGTGAGGATAACTCTAGAGTCAACGAGAAAGACATAAAATAGGTGGT
2504522 TATTGTCGTC
Statistics
Matches: 155, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
185 2 0.01
186 116 0.75
187 34 0.22
188 3 0.02
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (187 bp):
TTTGTCTATGATCTAGTGTACATGGTTCTTTTGGAGAAGCTGGAATGATAGAACTTTGTGGTGAT
AAAGGTGCCAATCCTCTGAACTGTGATGCATTACATGTTCCTGGTTTAAAGTAGAGTTGAAATTC
AGGTGAGGATAACTCTAGAGTCAACGAGAAAGACATAAAATAGGTGGTGATAAAGGT
Found at i:2506364 original size:3 final size:3
Alignment explanation
Indices: 2506356--2506388 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2506346 CGCTTCCCAA
*
2506356 TCT TCT TCT TCT TCT TCT TCT TCT TCT TGT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
2506389 GTTTTCTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.30, G:0.03, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:2515151 original size:2 final size:2
Alignment explanation
Indices: 2515144--2515174 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2515134 GTAATGTCTC
*
2515144 TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2515175 CTACATGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:2521909 original size:33 final size:33
Alignment explanation
Indices: 2521865--2521953 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
2521855 CAATTATATT
*
2521865 ATTATATTATATCAACATATCACATCATCATCA
1 ATTATAATATATCAACATATCACATCATCATCA
2521898 ATTATAATATATCAACATA-CTACATCATCATCA
1 ATTATAATATATCAACATATC-ACATCATCATCA
*
2521931 ATTATAATATATCAACATGTCAC
1 ATTATAATATATCAACATATCAC
2521954 GTGATATAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
32 1 0.02
33 50 0.96
34 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.01, T:0.35
Consensus pattern (33 bp):
ATTATAATATATCAACATATCACATCATCATCA
Found at i:2524133 original size:26 final size:26
Alignment explanation
Indices: 2524057--2524141 Score: 79
Period size: 26 Copynumber: 3.4 Consensus size: 26
2524047 GTGCCTGAAT
* * *
2524057 ATTACGTGATTGAACATTTGTTGAGA
1 ATTACGTGACTGAATATTTGTTGAGC
* * *
2524083 ATTGCGTGACT---TGTTTGTAG-GC
1 ATTACGTGACTGAATATTTGTTGAGC
2524105 ATTACGTGACTGAATATTTGTTGAGC
1 ATTACGTGACTGAATATTTGTTGAGC
*
2524131 ATTGCGTGACT
1 ATTACGTGACT
2524142 TTGTCTACCT
Statistics
Matches: 45, Mismatches: 10, Indels: 8
0.71 0.16 0.13
Matches are distributed among these distances:
22 11 0.24
23 6 0.13
25 7 0.16
26 21 0.47
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.39
Consensus pattern (26 bp):
ATTACGTGACTGAATATTTGTTGAGC
Found at i:2525510 original size:190 final size:190
Alignment explanation
Indices: 2525300--2525706 Score: 541
Period size: 190 Copynumber: 2.1 Consensus size: 190
2525290 TATGTGTATG
* * * * *
2525300 GTGACATGTTGTTATGTATTGCATGACGTTCGGG-CAGTATGTGAATGGTTATGTTGGCATGACG
1 GTGACCTGTTGTTATGTATTGCGTGACATT-GGGCCAGTATGGGAATGGTTATGTTGGCATAACG
** * * * *
2525364 TGAGTGGATATTAGGCATGGAGTGACTTATTACTAGGTATTGCAAGATTG-CTTGTGCGTGATTG
65 TGAGTGGATATTAGGCATCAAGTGACTTATTACTAGGTATAGCAAGAATGTC-GGTGCGTGACTG
* * * *
2525428 ACTTGTACAATTTATCTTTTGTTTTAAGGCTTTTGTTCACTAGTTTGTAGGCTTTGCCTTGC
129 ACTTGTACAATTGATCTTTTGTTTCAAGGCTTTTGTTCACTAGTTTGTAGGCATTGCATTGC
* *
2525490 GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCATTATGGGACTGGTTATGTTGGCATAACGT
1 GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAGTATGGGAATGGTTATGTTGGCATAACGT
* *
2525555 GAGTGGATATTAGGCATCAAGTGACTTATTATTAGGTATAGCGAGAATGTCGGTGCGTGACTGAC
66 GAGTGGATATTAGGCATCAAGTGACTTATTACTAGGTATAGCAAGAATGTCGGTGCGTGACTGAC
* * * *
2525620 TTGTGCAGTTGATCTTTTGTTTCGAGGCTTTTGTTCACTAGTTTGTAGTCATTGCATTGC
131 TTGTACAATTGATCTTTTGTTTCAAGGCTTTTGTTCACTAGTTTGTAGGCATTGCATTGC
* *
2525680 GTGA-CTGGTTTTTATATATTGCGTGAC
1 GTGACCT-GTTGTTATGTATTGCGTGAC
2525707 CTGTTGTTAT
Statistics
Matches: 189, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
189 5 0.03
190 183 0.97
191 1 0.01
ACGTcount: A:0.20, C:0.13, G:0.28, T:0.40
Consensus pattern (190 bp):
GTGACCTGTTGTTATGTATTGCGTGACATTGGGCCAGTATGGGAATGGTTATGTTGGCATAACGT
GAGTGGATATTAGGCATCAAGTGACTTATTACTAGGTATAGCAAGAATGTCGGTGCGTGACTGAC
TTGTACAATTGATCTTTTGTTTCAAGGCTTTTGTTCACTAGTTTGTAGGCATTGCATTGC
Found at i:2525703 original size:22 final size:21
Alignment explanation
Indices: 2525675--2525733 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 21
2525665 TAGTCATTGC
*
2525675 ATTGCGTGACTGGTTTTTATAT
1 ATTGCGTGACT-GTTGTTATAT
*
2525697 ATTGCGTGACCTGTTGTTATGT
1 ATTGCGTGA-CTGTTGTTATAT
*
2525719 ATTGTGTGACATGTT
1 ATTGCGTGAC-TGTT
2525734 AGCACTATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.17, C:0.10, G:0.25, T:0.47
Consensus pattern (21 bp):
ATTGCGTGACTGTTGTTATAT
Found at i:2525960 original size:15 final size:14
Alignment explanation
Indices: 2525939--2526015 Score: 72
Period size: 15 Copynumber: 5.6 Consensus size: 14
2525929 ATAATATTAT
2525939 AATTAAAATAAAAA
1 AATTAAAATAAAAA
2525953 ACATTAAAATAAAAA
1 A-ATTAAAATAAAAA
* *
2525968 AAATAATAT-AAAA
1 AATTAAAATAAAAA
* *
2525981 AATCAAAAT--CAA
1 AATTAAAATAAAAA
2525993 AA-TAAAATAAAAGA
1 AATTAAAATAAAA-A
2526007 AATTAAAAT
1 AATTAAAAT
2526016 TTATATAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
11 5 0.10
12 4 0.08
13 11 0.22
14 10 0.20
15 20 0.40
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (14 bp):
AATTAAAATAAAAA
Found at i:2525988 original size:27 final size:29
Alignment explanation
Indices: 2525945--2526002 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 29
2525935 TTATAATTAA
*
2525945 AATAAAAAACATTAAAAT-AAAA-AAAAT
1 AATAAAAAACATCAAAATCAAAATAAAAT
2525972 AATATAAAAA-ATCAAAATCAAAATAAAAT
1 AATA-AAAAACATCAAAATCAAAATAAAAT
2526001 AA
1 AA
2526003 AAGAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 11 0.41
28 9 0.33
29 7 0.26
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (29 bp):
AATAAAAAACATCAAAATCAAAATAAAAT
Found at i:2526110 original size:33 final size:33
Alignment explanation
Indices: 2526066--2526128 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
2526056 AATATTAAAA
*
2526066 ATTATATTAAAAAATAAAAATAAAAAATATAAT
1 ATTATAATAAAAAATAAAAATAAAAAATATAAT
* *
2526099 ATTATAATAAAAAATGAAAATAAAATATAT
1 ATTATAATAAAAAATAAAAATAAAAAATAT
2526129 GACATTCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
ATTATAATAAAAAATAAAAATAAAAAATATAAT
Found at i:2533095 original size:23 final size:23
Alignment explanation
Indices: 2533034--2533096 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2533024 ACAATAAGTG
* *
2533034 AGTCACGCGATTCAAGATCAACT
1 AGTCACGCGATTCCATATCAACT
* *
2533057 AGTCACGCGATCCCATATCATCT
1 AGTCACGCGATTCCATATCAACT
*
2533080 AGTCACGTGATTCCATA
1 AGTCACGCGATTCCATA
2533097 ATAAGTGGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (23 bp):
AGTCACGCGATTCCATATCAACT
Found at i:2533613 original size:19 final size:19
Alignment explanation
Indices: 2533589--2533626 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2533579 CCATTTGACT
2533589 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
2533608 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
2533627 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:2536264 original size:22 final size:23
Alignment explanation
Indices: 2536205--2536264 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
2536195 TCGTGACATT
*
2536205 TTATGCATTGCATGACTGGTTTG
1 TTATGTATTGCATGACTGGTTTG
*
2536228 -TATGTATATG-ATGACT-TTTTG
1 TTATGTAT-TGCATGACTGGTTTG
*
2536249 TTATGTATTGCGTGAC
1 TTATGTATTGCATGAC
2536265 ATTGGGCTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 6 0.19
22 23 0.74
23 2 0.06
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (23 bp):
TTATGTATTGCATGACTGGTTTG
Found at i:2536612 original size:23 final size:23
Alignment explanation
Indices: 2536572--2536629 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
2536562 TGTCAATATC
*
2536572 AACTAGTCATGCGATTCCACAAA
1 AACTAGTCACGCGATTCCACAAA
* * * *
2536595 AACTAGTCACGTGCTTCCATAAT
1 AACTAGTCACGCGATTCCACAAA
*
2536618 AACTAGTAACGC
1 AACTAGTCACGC
2536630 CACTCCATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (23 bp):
AACTAGTCACGCGATTCCACAAA
Found at i:2536662 original size:23 final size:22
Alignment explanation
Indices: 2536636--2536725 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 22
2536626 ACGCCACTCC
2536636 ATATTTACTACTCACGCGAGTCA
1 ATATTTACTACTCACGCGA-TCA
** *
2536659 ATATCAACTACTTACGCGATTCTA
1 ATATTTACTACTCACGCGA-TC-A
*** *
2536683 A-ATCTTAACGGTTCACGCGATCC
1 ATAT-TT-ACTACTCACGCGATCA
2536706 ATATTTACTACTCACGCGAT
1 ATATTTACTACTCACGCGAT
2536726 TCCAAATCAA
Statistics
Matches: 49, Mismatches: 14, Indels: 9
0.68 0.19 0.12
Matches are distributed among these distances:
22 11 0.22
23 23 0.47
24 6 0.12
25 9 0.18
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (22 bp):
ATATTTACTACTCACGCGATCA
Found at i:2536678 original size:92 final size:92
Alignment explanation
Indices: 2536509--2536680 Score: 231
Period size: 92 Copynumber: 1.9 Consensus size: 92
2536499 GAATAAATAC
* * * * *
2536509 TCACGTCATTCCATAATAACTAGTAGCGGCACTCCATATATATTATTCAGGCATGTCAATATCAA
1 TCACGTCATTCCATAATAACTAGTAACGCCACTCCATATATACTACTCACGCATGTCAATATCAA
* *
2536574 CTAGTCATGCGATTCCACAAAAACTAG
66 CTACTCACGCGATTCCACAAAAACTAG
*
2536601 TCACGTGC-TTCCATAATAACTAGTAACGCCACTCCATATTTACTACTCACGCGA-GTCAATATC
1 TCACGT-CATTCCATAATAACTAGTAACGCCACTCCATATATACTACTCACGC-ATGTCAATATC
*
2536664 AACTACTTACGCGATTC
64 AACTACTCACGCGATTC
2536681 TAAATCTTAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
92 67 0.97
93 2 0.03
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.28
Consensus pattern (92 bp):
TCACGTCATTCCATAATAACTAGTAACGCCACTCCATATATACTACTCACGCATGTCAATATCAA
CTACTCACGCGATTCCACAAAAACTAG
Found at i:2537154 original size:26 final size:26
Alignment explanation
Indices: 2537123--2537174 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
2537113 AAAAAAGAAT
*
2537123 ACAAAGAATAATATGTAAATGATACA
1 ACAAAGAATAATATGGAAATGATACA
*
2537149 ACAAAGAATAATATGGACATGATACA
1 ACAAAGAATAATATGGAAATGATACA
2537175 GAATAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.13, T:0.21
Consensus pattern (26 bp):
ACAAAGAATAATATGGAAATGATACA
Found at i:2540908 original size:23 final size:22
Alignment explanation
Indices: 2540869--2540926 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
2540859 CTACAACAAG
*
2540869 AGTCACGCAATGCCTAATCAATT-
1 AGTCACGCAATGACTAA-C-ATTA
*
2540892 AGTCACGCAATTACTAACATTA
1 AGTCACGCAATGACTAACATTA
*
2540914 AATCACGCAATGA
1 AGTCACGCAATGA
2540927 TTTATAAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 12 0.40
23 15 0.50
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (22 bp):
AGTCACGCAATGACTAACATTA
Found at i:2546271 original size:56 final size:56
Alignment explanation
Indices: 2546172--2546283 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
2546162 TTGACTTCTG
*
2546172 ATCCTATAGTGAGACATGTAGTAATATGTCAAACTGTAAAAGAAGTTAAAAAGTAT
1 ATCCTATAGTGAGACATGTAGTAATATGTCAAACTGTAAAAGAAGATAAAAAGTAT
* * * * * *
2546228 ATCCTATAGTGAGACATTTAGTAGTATGTTAAATTGTAGAAGAAGATAGAAAGTAT
1 ATCCTATAGTGAGACATGTAGTAATATGTCAAACTGTAAAAGAAGATAAAAAGTAT
2546284 CTATGCTATC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (56 bp):
ATCCTATAGTGAGACATGTAGTAATATGTCAAACTGTAAAAGAAGATAAAAAGTAT
Found at i:2551853 original size:2 final size:2
Alignment explanation
Indices: 2551846--2551875 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2551836 GGAAAAATAC
2551846 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
2551876 TTTGTCTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2553611 original size:2 final size:2
Alignment explanation
Indices: 2553604--2553639 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2553594 TGACTAGGAG
2553604 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
2553640 TTTTTTTTTT
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
Found at i:2562047 original size:17 final size:17
Alignment explanation
Indices: 2562000--2562059 Score: 72
Period size: 17 Copynumber: 3.7 Consensus size: 17
2561990 AACATGATTA
2562000 AAAATA-ATATAATATT
1 AAAATATATATAATATT
* *
2562016 TAAATAT-TA-ATTATT
1 AAAATATATATAATATT
2562031 AAAATATATATAATATT
1 AAAATATATATAATATT
*
2562048 AATATATATATA
1 AAAATATATATA
2562060 TATAGTATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
15 11 0.31
16 9 0.25
17 16 0.44
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATATATATAATATT
Found at i:2562051 original size:15 final size:15
Alignment explanation
Indices: 2562002--2562062 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
2561992 CATGATTAAA
2562002 AATA-ATATAATATTT
1 AATATATATAATA-TT
2562017 AA-ATAT-TAATTATT
1 AATATATATAA-TATT
2562031 AAAATATATATAATATT
1 --AATATATATAATATT
2562048 AATATATATATATAT
1 AATATATATA-ATAT
2562063 AGTATTTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
14 6 0.15
15 16 0.41
16 6 0.15
17 8 0.21
18 3 0.08
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATATATAATATT
Found at i:2562079 original size:21 final size:21
Alignment explanation
Indices: 2562004--2562080 Score: 61
Period size: 21 Copynumber: 3.6 Consensus size: 21
2561994 TGATTAAAAA
*
2562004 TAATATA-ATATTTA-AATAT
1 TAATATACATATATATAATAT
*
2562023 TAATTATTAAAATATATATAATAT
1 TAA-TA-T-ACATATATATAATAT
* *
2562047 TAATATATATATATATAGTATT
1 TAATATACATATATATAATA-T
2562069 TAAT-TACATATA
1 TAATATACATATA
2562081 ANTATTTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
19 3 0.06
20 2 0.04
21 20 0.42
22 7 0.15
23 8 0.17
24 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
TAATATACATATATATAATAT
Found at i:2563963 original size:14 final size:16
Alignment explanation
Indices: 2563946--2563978 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2563936 ATAACATTAT
2563946 AAAAAT-AAA-AATAA
1 AAAAATCAAATAATAA
2563960 AAAAATCAAATAATAA
1 AAAAATCAAATAATAA
2563976 AAA
1 AAA
2563979 CTTGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 3 0.18
16 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAATCAAATAATAA
Found at i:2576324 original size:23 final size:23
Alignment explanation
Indices: 2576296--2576342 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2576286 TTCTTTCTTC
*
2576296 TCTTTAATTATTCTTTTCAGTTA
1 TCTTTAATTATTCTTTTAAGTTA
* *
2576319 TCTTTATTTGTTCTTTTAAGTTA
1 TCTTTAATTATTCTTTTAAGTTA
2576342 T
1 T
2576343 TTTTCATACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (23 bp):
TCTTTAATTATTCTTTTAAGTTA
Found at i:2576437 original size:14 final size:15
Alignment explanation
Indices: 2576418--2576456 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2576408 GTTTGATAAC
2576418 AAAGAAAAAGGAA-G
1 AAAGAAAAAGGAACG
*
2576432 AAAGAAAAAGTAACCG
1 AAAGAAAAAGGAA-CG
2576448 AAAGAAAAA
1 AAAGAAAAA
2576457 TATTGTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.55
16 10 0.45
ACGTcount: A:0.72, C:0.05, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAGAAAAAGGAACG
Found at i:2587503 original size:16 final size:16
Alignment explanation
Indices: 2587482--2587513 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2587472 ACAAAACAAA
2587482 CACATTTAGTTCCATG
1 CACATTTAGTTCCATG
2587498 CACATTTAGTTCCATG
1 CACATTTAGTTCCATG
2587514 GAGCATAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
CACATTTAGTTCCATG
Found at i:2590724 original size:32 final size:33
Alignment explanation
Indices: 2590658--2590738 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 33
2590648 TAATAATATT
* *
2590658 AAAATAATAAT-TTTATTTTTCATTAATTTTAA
1 AAAATAATAATAATAATTTTTCATTAATTTTAA
* *
2590690 AAATTATTAATATATAATTTTT-ATTAA-TTTAA
1 AAAATAATAATA-ATAATTTTTCATTAATTTTAA
2590722 AAAATAATAATAATAAT
1 AAAATAATAATAATAAT
2590739 AACATAGAGA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
31 5 0.12
32 24 0.59
33 5 0.12
34 7 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (33 bp):
AAAATAATAATAATAATTTTTCATTAATTTTAA
Found at i:2593643 original size:2 final size:2
Alignment explanation
Indices: 2593594--2593624 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2593584 TTTAAAAGTG
2593594 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2593625 ATAAACTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2593953 original size:2 final size:2
Alignment explanation
Indices: 2593946--2593982 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
2593936 CTTCTCTTCC
*
2593946 CT CT CT CT CT CT CT -T CT CT CT CT CT CT CT CT AT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2593983 GGGCATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:2593960 original size:17 final size:17
Alignment explanation
Indices: 2593938--2593976 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
2593928 CAAGGGGTCT
2593938 TCTCTTCCCTCTCTCTC
1 TCTCTTCCCTCTCTCTC
*
2593955 TCTCTTCTCTCTCTCTC
1 TCTCTTCCCTCTCTCTC
2593972 TCTCT
1 TCTCT
2593977 ATCTCTGGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (17 bp):
TCTCTTCCCTCTCTCTC
Found at i:2593964 original size:15 final size:15
Alignment explanation
Indices: 2593946--2593974 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2593936 CTTCTCTTCC
2593946 CTCTCTCTCTCTCTT
1 CTCTCTCTCTCTCTT
2593961 CTCTCTCTCTCTCT
1 CTCTCTCTCTCTCT
2593975 CTATCTCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (15 bp):
CTCTCTCTCTCTCTT
Found at i:2600516 original size:24 final size:24
Alignment explanation
Indices: 2600481--2600576 Score: 165
Period size: 24 Copynumber: 4.0 Consensus size: 24
2600471 ATTTATGGAA
2600481 GAAGGGAATGGGGGCATCACCCCT
1 GAAGGGAATGGGGGCATCACCCCT
* *
2600505 GAAGGGACTGGGAGCATCACCCCT
1 GAAGGGAATGGGGGCATCACCCCT
2600529 GAAGGGAATGGGGGCATCACCCCT
1 GAAGGGAATGGGGGCATCACCCCT
*
2600553 GAAGGGAATGGGGGCATCATCCCT
1 GAAGGGAATGGGGGCATCACCCCT
2600577 AAAACCGAAC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 67 1.00
ACGTcount: A:0.25, C:0.25, G:0.36, T:0.14
Consensus pattern (24 bp):
GAAGGGAATGGGGGCATCACCCCT
Found at i:2600626 original size:15 final size:15
Alignment explanation
Indices: 2600606--2600780 Score: 154
Period size: 15 Copynumber: 11.7 Consensus size: 15
2600596 AAGTATACTG
2600606 TCAAGAAGTATCCCA
1 TCAAGAAGTATCCCA
* * * *
2600621 TGAAGACGTAGCTCA
1 TCAAGAAGTATCCCA
2600636 TCAAGAAGTATCCCA
1 TCAAGAAGTATCCCA
* * *
2600651 TGAAGACA-TAGCTCA
1 TCAAGA-AGTATCCCA
2600666 TCAAGAAGTATCCCA
1 TCAAGAAGTATCCCA
* * *
2600681 TCAAGAAGCAGCTCA
1 TCAAGAAGTATCCCA
*
2600696 TCAAGAAATATCCCA
1 TCAAGAAGTATCCCA
* *
2600711 TCAAGAAGTAGCTCA
1 TCAAGAAGTATCCCA
*
2600726 TCAAGAAATATCCCA
1 TCAAGAAGTATCCCA
* * *
2600741 TCAAGAATTAGCTCA
1 TCAAGAAGTATCCCA
* *
2600756 TCAAGAAATATCCGA
1 TCAAGAAGTATCCCA
*
2600771 TCCAGAAGTA
1 TCAAGAAGTA
2600781 CCTTCTCAAG
Statistics
Matches: 122, Mismatches: 36, Indels: 4
0.75 0.22 0.02
Matches are distributed among these distances:
14 1 0.01
15 120 0.98
16 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (15 bp):
TCAAGAAGTATCCCA
Found at i:2600791 original size:30 final size:30
Alignment explanation
Indices: 2600606--2600780 Score: 244
Period size: 30 Copynumber: 5.8 Consensus size: 30
2600596 AAGTATACTG
* * *
2600606 TCAAGAAGTATCCCATGAAGACGTAGCTCA
1 TCAAGAAATATCCCATCAAGAAGTAGCTCA
* *
2600636 TCAAGAAGTATCCCATGAAGACA-TAGCTCA
1 TCAAGAAATATCCCATCAAGA-AGTAGCTCA
* *
2600666 TCAAGAAGTATCCCATCAAGAAGCAGCTCA
1 TCAAGAAATATCCCATCAAGAAGTAGCTCA
2600696 TCAAGAAATATCCCATCAAGAAGTAGCTCA
1 TCAAGAAATATCCCATCAAGAAGTAGCTCA
*
2600726 TCAAGAAATATCCCATCAAGAATTAGCTCA
1 TCAAGAAATATCCCATCAAGAAGTAGCTCA
* *
2600756 TCAAGAAATATCCGATCCAGAAGTA
1 TCAAGAAATATCCCATCAAGAAGTA
2600781 CCTTCTCAAG
Statistics
Matches: 134, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
29 1 0.01
30 133 0.99
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (30 bp):
TCAAGAAATATCCCATCAAGAAGTAGCTCA
Found at i:2607407 original size:15 final size:18
Alignment explanation
Indices: 2607382--2607421 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
2607372 TATTTTTATA
2607382 ATTTTACTTAATAA-ATT
1 ATTTTACTTAATAACATT
2607399 -TTTTA-TTAATAACATT
1 ATTTTACTTAATAACATT
2607415 ATTTTAC
1 ATTTTAC
2607422 GATTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 7 0.35
16 8 0.40
17 5 0.25
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTTACTTAATAACATT
Found at i:2607517 original size:22 final size:22
Alignment explanation
Indices: 2607488--2607558 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
2607478 TAATATTATT
2607488 AATAATTAAATTATTAATTTTA
1 AATAATTAAATTATTAATTTTA
* *
2607510 TATAATTAAATATATAAAGTTATTA
1 AATAATTAAAT-TATTAA-TT-TTA
2607535 AATTAATTAAAATTATTAAATTTT
1 AA-TAATT-AAATTATT-AATTTT
2607559 TTTACCTACA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 10 0.26
23 5 0.13
24 2 0.05
25 6 0.15
26 10 0.26
27 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (22 bp):
AATAATTAAATTATTAATTTTA
Found at i:2607543 original size:9 final size:8
Alignment explanation
Indices: 2607482--2607556 Score: 59
Period size: 8 Copynumber: 9.4 Consensus size: 8
2607472 AATAAGTAAT
2607482 ATTATT-A
1 ATTATTAA
*
2607489 ATAATTAA
1 ATTATTAA
2607497 ATTATT-A
1 ATTATTAA
*
2607504 ATT-TTAT
1 ATTATTAA
*
2607511 ATAATTAA
1 ATTATTAA
2607519 A-TATATAA
1 ATTAT-TAA
2607527 AGTTATTAA
1 A-TTATTAA
2607536 ATTAATTAAA
1 ATT-ATT-AA
2607546 ATTATTAA
1 ATTATTAA
2607554 ATT
1 ATT
2607557 TTTTTACCTA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
6 2 0.04
7 13 0.24
8 21 0.39
9 10 0.19
10 8 0.15
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (8 bp):
ATTATTAA
Found at i:2607939 original size:26 final size:27
Alignment explanation
Indices: 2607884--2607940 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
2607874 AAATTAAAAT
* * *
2607884 AAATTTTTATTTTTATTATATTTAATC
1 AAATTTTTATATTTATTATACTTAAAC
2607911 AAATTTTTATATTT-TTAT-CTTACAAC
1 AAATTTTTATATTTATTATACTTA-AAC
2607937 AAAT
1 AAAT
2607941 AAACGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 3 0.12
26 10 0.38
27 13 0.50
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATTTTTATATTTATTATACTTAAAC
Found at i:2609011 original size:15 final size:16
Alignment explanation
Indices: 2608991--2609024 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2608981 GTGAGTCGTC
*
2608991 ATAAATAAA-AAATAA
1 ATAAATAAAGAAAAAA
2609006 ATAAATAAAGAAAAAA
1 ATAAATAAAGAAAAAA
2609022 ATA
1 ATA
2609025 CCAAAACGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
ATAAATAAAGAAAAAA
Found at i:2619055 original size:21 final size:21
Alignment explanation
Indices: 2619029--2619093 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
2619019 CACAGTCCTG
*
2619029 AAGGCCATTGCTTTCAATGTC
1 AAGGCCATTGCTTTCAATATC
* * * *
2619050 AAGGCCATTTCCTTCTATCTC
1 AAGGCCATTGCTTTCAATATC
*
2619071 AAGGCCATTGCTCTCAATATC
1 AAGGCCATTGCTTTCAATATC
2619092 AA
1 AA
2619094 TGTCATTCCC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (21 bp):
AAGGCCATTGCTTTCAATATC
Found at i:2619106 original size:42 final size:42
Alignment explanation
Indices: 2619029--2619115 Score: 111
Period size: 42 Copynumber: 2.1 Consensus size: 42
2619019 CACAGTCCTG
* * * *
2619029 AAGGCCATTGCTTTCAATGTCAAGGCCATTTCCTTCTATCTC
1 AAGGCCATTGCTCTCAATATCAAGGCCATTCCCTTCAATCTC
* * *
2619071 AAGGCCATTGCTCTCAATATCAATGTCATTCCCTTCAATTTC
1 AAGGCCATTGCTCTCAATATCAAGGCCATTCCCTTCAATCTC
2619113 AAG
1 AAG
2619116 TTCATTTCCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (42 bp):
AAGGCCATTGCTCTCAATATCAAGGCCATTCCCTTCAATCTC
Found at i:2619108 original size:21 final size:21
Alignment explanation
Indices: 2619084--2619142 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2619074 GCCATTGCTC
2619084 TCAATATCAA-TGTCATTCCCT
1 TCAATATCAAGT-TCATTCCCT
* *
2619105 TCAATTTCAAGTTCATTTCCT
1 TCAATATCAAGTTCATTCCCT
* * *
2619126 TCCATTTCAAGCTCATT
1 TCAATATCAAGTTCATT
2619143 GCCATCATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.25, C:0.27, G:0.05, T:0.42
Consensus pattern (21 bp):
TCAATATCAAGTTCATTCCCT
Found at i:2620576 original size:17 final size:16
Alignment explanation
Indices: 2620550--2620584 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
2620540 ATATTTTTAA
2620550 TAAAAAATTTTAAAAT
1 TAAAAAATTTTAAAAT
*
2620566 TAAATAAATTTTAATAT
1 TAAA-AAATTTTAAAAT
2620583 TA
1 TA
2620585 CTTATTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAAAAATTTTAAAAT
Found at i:2634249 original size:72 final size:72
Alignment explanation
Indices: 2634167--2634314 Score: 287
Period size: 72 Copynumber: 2.1 Consensus size: 72
2634157 TAATAGATAA
2634167 TATTAATTTATCATTATATATTTTTATAAACTAATTATAAAAAATGGCATAATATTTAAAAAATC
1 TATTAATTTATCATTATATATTTTTATAAACTAATTATAAAAAATGGCATAATATTTAAAAAATC
2634232 TTTAAAC
66 TTTAAAC
*
2634239 TATTNATTTATCATTATATATTTTTATAAACTAATTATAAAAAATGGCATAATATTTAAAAAATC
1 TATTAATTTATCATTATATATTTTTATAAACTAATTATAAAAAATGGCATAATATTTAAAAAATC
2634304 TTTAAAC
66 TTTAAAC
2634311 TATT
1 TATT
2634315 TTAAAAATTC
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 75 1.00
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.44
Consensus pattern (72 bp):
TATTAATTTATCATTATATATTTTTATAAACTAATTATAAAAAATGGCATAATATTTAAAAAATC
TTTAAAC
Found at i:2634354 original size:29 final size:29
Alignment explanation
Indices: 2634321--2634394 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
2634311 TATTTTAAAA
2634321 ATTCAAATAAACTCTTAAATTTTTATTAT-
1 ATTCAAATAAA-TCTTAAATTTTTATTATG
* *
2634350 ATTCAATTAAATCTTTATATTTTTATTATG
1 ATTCAAATAAATC-TTAAATTTTTATTATG
*
2634380 AGTCAAATAAATCTT
1 ATTCAAATAAATCTT
2634395 TATACTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 2 0.05
29 26 0.67
30 11 0.28
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (29 bp):
ATTCAAATAAATCTTAAATTTTTATTATG
Found at i:2634393 original size:30 final size:29
Alignment explanation
Indices: 2634323--2634404 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 29
2634313 TTTTAAAAAT
* *
2634323 TCAAATAAA-CTCTTAAATTTTTATTATAT
1 TCAAATAAATCT-TTATATTTTTATTATAG
*
2634352 TCAATTAAATCTTTATATTTTTATTATGAG
1 TCAAATAAATCTTTATATTTTTATTAT-AG
*
2634382 TCAAATAAATCTTTATACTTTTA
1 TCAAATAAATCTTTATATTTTTA
2634405 ATTTAAATCA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 22 0.48
30 24 0.52
ACGTcount: A:0.38, C:0.10, G:0.02, T:0.50
Consensus pattern (29 bp):
TCAAATAAATCTTTATATTTTTATTATAG
Found at i:2634416 original size:30 final size:30
Alignment explanation
Indices: 2634323--2634419 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 30
2634313 TTTTAAAAAT
* * *
2634323 TCAAATAAA-CTCTTAAATTTTTATTAT-AT
1 TCAAATAAATCT-TTATATTTTAATTATAAA
* * * *
2634352 TCAATTAAATCTTTATATTTTTATTATGAG
1 TCAAATAAATCTTTATATTTTAATTATAAA
2634382 TCAAATAAATCTTTATACTTTTAATT-TAAA
1 TCAAATAAATCTTTATA-TTTTAATTATAAA
2634412 TCAAATAA
1 TCAAATAA
2634420 GTTTTTATCA
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.38
30 29 0.50
31 7 0.12
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.47
Consensus pattern (30 bp):
TCAAATAAATCTTTATATTTTAATTATAAA
Found at i:2634861 original size:28 final size:29
Alignment explanation
Indices: 2634812--2634881 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
2634802 CAAAATACAC
*
2634812 AAACTTGATTGAATTTAATAAAAGAA-TAA
1 AAACTT-ATTTAATTTAATAAAAGAATTAA
** * *
2634841 AAACTTATTTAATTTTTTAAAATAATTTA
1 AAACTTATTTAATTTAATAAAAGAATTAA
*
2634870 AAATTTATTTAA
1 AAACTTATTTAA
2634882 ACATTATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 15 0.44
29 19 0.56
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (29 bp):
AAACTTATTTAATTTAATAAAAGAATTAA
Found at i:2636410 original size:87 final size:87
Alignment explanation
Indices: 2636263--2636422 Score: 250
Period size: 87 Copynumber: 1.8 Consensus size: 87
2636253 TTAAAACTAG
* *
2636263 AGGACTTAGCTCAATTTTAGGTTCCAAATATGAATAAGATAACTCTATACCACATGGCATGTCCA
1 AGGACTTAGCTCAATTTTAAGTTCCAAATATGAATAAGATAACTCTATACCACATAGCATGTCCA
2636328 AAAAGTGAGCATGATAAAAAAT
66 AAAAGTGAGCATGATAAAAAAT
* **
2636350 AGGACTTAGCTTAATTTTAAGTTCCAAATAT-ACATAAGATAACTCTATAGTACATAGCATGTCC
1 AGGACTTAGCTCAATTTTAAGTTCCAAATATGA-ATAAGATAACTCTATACCACATAGCATGTCC
*
2636414 AAAAGGTGA
65 AAAAAGTGA
2636423 CCCGTGGTAT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
86 1 0.02
87 65 0.98
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (87 bp):
AGGACTTAGCTCAATTTTAAGTTCCAAATATGAATAAGATAACTCTATACCACATAGCATGTCCA
AAAAGTGAGCATGATAAAAAAT
Found at i:2639335 original size:18 final size:16
Alignment explanation
Indices: 2639314--2639390 Score: 57
Period size: 16 Copynumber: 4.7 Consensus size: 16
2639304 GTTATACATA
2639314 TATATATACATATAATAT
1 TATATATA-ATATAA-AT
*
2639332 TATATATAATATTAAT
1 TATATATAATATAAAT
* **
2639348 TATATTTTTTATAAA-
1 TATATATAATATAAAT
* *
2639363 TAAAAATAATATATAAT
1 TATATATAATATA-AAT
*
2639380 AATATATAATA
1 TATATATAATA
2639391 AAAAATAACA
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
15 8 0.18
16 15 0.34
17 13 0.30
18 8 0.18
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (16 bp):
TATATATAATATAAAT
Found at i:2639380 original size:10 final size:10
Alignment explanation
Indices: 2639367--2639391 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2639357 TATAAATAAA
2639367 AATAATATAT
1 AATAATATAT
2639377 AATAATATAT
1 AATAATATAT
2639387 AATAA
1 AATAA
2639392 AAAATAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATAATATAT
Found at i:2639480 original size:2 final size:2
Alignment explanation
Indices: 2639467--2639499 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2639457 TTAAAAGAAC
*
2639467 AT AT AT AC AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2639500 GTAAATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2640261 original size:140 final size:139
Alignment explanation
Indices: 2640009--2640283 Score: 401
Period size: 140 Copynumber: 2.0 Consensus size: 139
2639999 AGCATGCCAT
* *
2640009 ATTTATCTTGCAAATGGAGCGAGAATTTCGATAATGGGATTTCCCCGTGGAACTTGTAGAGACAA
1 ATTTATCTTGCAAATGGAGCGAGAATTCCGATAATGGGATTTCCCCGAGGAACTTGTAGAGACAA
* * *
2640074 GTTCTTCCGGAGATATTTCTAGGTGAGAAAAATTTCGAGACTTCACCAAAGCGTTGGGATGGTCT
66 GTTCTTCCGGAGATATCTCTAGGTGAGAAAAATTTCGAGACTTCACCAAAACGTTAGGATGGTCT
2640139 TCGANACCAC
131 TCGA-ACCAC
* * * * * *
2640149 ATTTATCTTGCAAATGGTGCGGGAGTTCCGATGATGGGATTTCCCCGAGGAGCTAT-TAGAGACG
1 ATTTATCTTGCAAATGGAGCGAGAATTCCGATAATGGGATTTCCCCGAGGAACT-TGTAGAGACA
*
2640213 AGTT-TTGCCGGGGATATCTCTAGGTGAGAAAAATTTCGAGACTTCACCAAAACGTTAGGATGGT
65 AGTTCTT-CCGGAGATATCTCTAGGTGAGAAAAATTTCGAGACTTCACCAAAACGTTAGGATGGT
2640277 CTTCGAA
129 CTTCGAA
2640284 TGATTTTCCA
Statistics
Matches: 121, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
139 3 0.02
140 117 0.97
141 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.28
Consensus pattern (139 bp):
ATTTATCTTGCAAATGGAGCGAGAATTCCGATAATGGGATTTCCCCGAGGAACTTGTAGAGACAA
GTTCTTCCGGAGATATCTCTAGGTGAGAAAAATTTCGAGACTTCACCAAAACGTTAGGATGGTCT
TCGAACCAC
Found at i:2654347 original size:21 final size:23
Alignment explanation
Indices: 2654307--2654352 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
2654297 TAAATATGAC
*
2654307 TAAATAAAGTTAATTTAATTGTT
1 TAAATAAAATTAATTTAATTGTT
2654330 TAAA-AAAATTAA-TTAATTGTT
1 TAAATAAAATTAATTTAATTGTT
2654351 TA
1 TA
2654353 TTTGATAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.50
22 7 0.32
23 4 0.18
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (23 bp):
TAAATAAAATTAATTTAATTGTT
Found at i:2657367 original size:68 final size:68
Alignment explanation
Indices: 2657253--2657390 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 68
2657243 CTATTTCGAC
* * * ** *
2657253 CTCGTTGACACACTAGCACATGTTGAATCCGCTGGCACATTAGCATATGTTGAAGATGATGTAAA
1 CTCGTTGACACACTAGCACATATTGAACCCACTACCACATTAGCATATGTTGAAAATGATGTAAA
2657318 ACA
66 ACA
* * * *
2657321 CTCGTTGGCACACTAGTACATATTGAACCCACTACCACATTGGCATATGTTGAAAATGGTGTAAA
1 CTCGTTGACACACTAGCACATATTGAACCCACTACCACATTAGCATATGTTGAAAATGATGTAAA
2657386 ACA
66 ACA
2657389 CT
1 CT
2657391 TAAATGTCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (68 bp):
CTCGTTGACACACTAGCACATATTGAACCCACTACCACATTAGCATATGTTGAAAATGATGTAAA
ACA
Found at i:2657783 original size:13 final size:13
Alignment explanation
Indices: 2657765--2657802 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2657755 TTAACTACTT
*
2657765 GATTTATCCATGA
1 GATTTAACCATGA
2657778 GATTTAACCATGA
1 GATTTAACCATGA
2657791 GATTTAACCATG
1 GATTTAACCATG
2657803 TAATTAATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (13 bp):
GATTTAACCATGA
Found at i:2666787 original size:40 final size:40
Alignment explanation
Indices: 2666742--2666824 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
2666732 TATATTTACT
2666742 TGTTAGTTTTTACTCAAAGTTTTTCATGCATTCCCTGTGC
1 TGTTAGTTTTTACTCAAAGTTTTTCATGCATTCCCTGTGC
2666782 TGTTAGTTTTTACTCAAAGTTTTTCATGCATTCCCTGTGC
1 TGTTAGTTTTTACTCAAAGTTTTTCATGCATTCCCTGTGC
2666822 TGT
1 TGT
2666825 ATATTTGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.17, C:0.19, G:0.16, T:0.48
Consensus pattern (40 bp):
TGTTAGTTTTTACTCAAAGTTTTTCATGCATTCCCTGTGC
Found at i:2671650 original size:24 final size:24
Alignment explanation
Indices: 2671623--2671672 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
2671613 GGTAGAAGAA
2671623 CAAAATGAGGAAAAAACTGAACAG
1 CAAAATGAGGAAAAAACTGAACAG
2671647 CAAAATGAGGAAAAAACTGAACAG
1 CAAAATGAGGAAAAAACTGAACAG
2671671 CA
1 CA
2671673 GATGTGCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.14, G:0.20, T:0.08
Consensus pattern (24 bp):
CAAAATGAGGAAAAAACTGAACAG
Found at i:2674070 original size:4 final size:4
Alignment explanation
Indices: 2674061--2674133 Score: 74
Period size: 4 Copynumber: 18.2 Consensus size: 4
2674051 ATCATAATAC
* * * *
2674061 ATAT ATAT ATAT ATAT ATAT ATAT GTAC ATAT ACAT ATAT ATAT ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
2674109 ACAT ACAT ACAT ATAC ATAT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT A
2674134 AATGAATTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 57 1.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:2674070 original size:6 final size:6
Alignment explanation
Indices: 2674061--2674133 Score: 74
Period size: 6 Copynumber: 12.2 Consensus size: 6
2674051 ATCATAATAC
* * * *
2674061 ATATAT ATATAT ATATAT ATATAT GTACAT ATACAT ATATAT ATATAC
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * *
2674109 ACATAC ATACAT ATACAT ATATAT A
1 ATATAT ATATAT ATATAT ATATAT A
2674134 AATGAATTAA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (6 bp):
ATATAT
Found at i:2674076 original size:10 final size:10
Alignment explanation
Indices: 2674061--2674133 Score: 74
Period size: 10 Copynumber: 7.3 Consensus size: 10
2674051 ATCATAATAC
2674061 ATATATATAT
1 ATATATATAT
2674071 ATATATATAT
1 ATATATATAT
* *
2674081 ATATGTACAT
1 ATATATATAT
*
2674091 ATACATATAT
1 ATATATATAT
* *
2674101 ATATATACAC
1 ATATATATAT
* *
2674111 ATACATACAT
1 ATATATATAT
*
2674121 ATACATATAT
1 ATATATATAT
2674131 ATA
1 ATA
2674134 AATGAATTAA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 52 1.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (10 bp):
ATATATATAT
Found at i:2674092 original size:20 final size:20
Alignment explanation
Indices: 2674061--2674133 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2674051 ATCATAATAC
* *
2674061 ATATATATATATATATATAT
1 ATATATACATATACATATAT
*
2674081 ATATGTACATATACATATAT
1 ATATATACATATACATATAT
* *
2674101 ATATATACACATACATACAT
1 ATATATACATATACATATAT
* *
2674121 ATACATATATATA
1 ATATATACATATA
2674134 AATGAATTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (20 bp):
ATATATACATATACATATAT
Found at i:2676453 original size:24 final size:23
Alignment explanation
Indices: 2676424--2676473 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2676414 TTAAGAAAAT
*
2676424 TTAAAAAGAAAATAGTGTTTTAA
1 TTAAAAAGAAAATAGTATTTTAA
2676447 TTAAAAAGAAAATAGTATTTTAA
1 TTAAAAAGAAAATAGTATTTTAA
2676470 TTAA
1 TTAA
2676474 TCTCTCAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (23 bp):
TTAAAAAGAAAATAGTATTTTAA
Done.