Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 9 of 135
Found at i:4034866 original size:37 final size:36
Alignment explanation
Indices: 4034820--4034889 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 36
4034810 GAGACTCACC
*
4034820 AATTAAAATAATTATA-TAAATATATAATTATTATAT
1 AATTAAAATAATTACACTAAA-ATATAATTATTATAT
*
4034856 AATTACAAATAATTACACTAAAATTTAATTATTA
1 AATTA-AAATAATTACACTAAAATATAATTATTA
4034890 AGTTCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 5 0.17
37 21 0.70
38 4 0.13
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (36 bp):
AATTAAAATAATTACACTAAAATATAATTATTATAT
Found at i:4042700 original size:23 final size:23
Alignment explanation
Indices: 4042621--4042855 Score: 123
Period size: 23 Copynumber: 10.5 Consensus size: 23
4042611 AAAACGGAAC
* * *
4042621 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
4042643 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
4042665 GGGCAACATAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
4042691 AAACAGAGAGTATACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
4042711 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* **
4042730 AATCAGAGAGCACATGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
4042753 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
4042776 AATA-ACAGAGCACGA-GACGTGCT
1 AA-ACAGAGAGCAC-ACAAAGTGCT
**
4042799 AAACAGAGAGCACACACTGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* **
4042822 AATCAGAGAGCACACACTGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
4042845 AATCAGAGAGC
1 AAACAGAGAGC
4042856 GCGCTAGTGT
Statistics
Matches: 164, Mismatches: 33, Indels: 31
0.72 0.14 0.14
Matches are distributed among these distances:
16 9 0.05
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 19 0.12
23 109 0.66
24 1 0.01
25 12 0.07
26 7 0.04
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.14
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:4042786 original size:46 final size:45
Alignment explanation
Indices: 4042714--4042855 Score: 167
Period size: 46 Copynumber: 3.1 Consensus size: 45
4042704 ACAAAGTACT
* * *
4042714 GAGCACACAAAGTGCTAATCAGAGAGCACATGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACA-GAAGTGCTAAACAGA
* * *
4042760 GAGCACACACAGTGCTAATAACAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAATCAGAGAGCAC-AGAAGTGCTAAACAGA
* * * *
4042806 GAGCACACACTGTGCTAATCAGAGAGCACACACTGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACAGA-AGTGCTAAACAGA
4042852 GAGC
1 GAGC
4042856 GCGCTAGTGT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
45 2 0.02
46 79 0.96
47 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.25, T:0.14
Consensus pattern (45 bp):
GAGCACACACAGTGCTAATCAGAGAGCACAGAAGTGCTAAACAGA
Found at i:4049449 original size:32 final size:31
Alignment explanation
Indices: 4049413--4049521 Score: 84
Period size: 30 Copynumber: 3.5 Consensus size: 31
4049403 CAACTTAAAA
* *
4049413 AAAAAAGTGTCAAGTTTTG-GTACTAAATTAGG
1 AAAAAA-TATCAAG-TTTGAGTACGAAATTAGG
4049445 AAAAAATATCAAGTTTGAGTACGAAATTA-G
1 AAAAAATATCAAGTTTGAGTACGAAATTAGG
* * *
4049475 ACCAAAAA-A-AAAGTTT-ACGTACCAAATTAGTA
1 A--AAAAATATCAAGTTTGA-GTACGAAATTAG-G
4049507 AAAAAATATCAAGTT
1 AAAAAATATCAAGTT
4049522 CAGGTACCAA
Statistics
Matches: 63, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
29 1 0.02
30 27 0.43
31 18 0.29
32 17 0.27
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.27
Consensus pattern (31 bp):
AAAAAATATCAAGTTTGAGTACGAAATTAGG
Found at i:4050730 original size:58 final size:61
Alignment explanation
Indices: 4050664--4050804 Score: 171
Period size: 62 Copynumber: 2.3 Consensus size: 61
4050654 TCAAAAGAAA
*
4050664 AAGATGAATAGTGAGGTTCCTTGCAAAG-TCTTCAAAT-TT-AGGGAATATATTCCAAAAC
1 AAGATGAATAGTGAGATTCCTTGCAAAGTTCTTCAAATATTCAGGGAATATATTCCAAAAC
* * * * * *
4050722 TAGATGAATGGTGAGATTCCTTGCTAAGTTTTTGAAATGATTCAGGGAATATATTCTAAAAC
1 AAGATGAATAGTGAGATTCCTTGCAAAGTTCTTCAAAT-ATTCAGGGAATATATTCCAAAAC
*
4050784 AAGATGAATAATGTAGATTCC
1 AAGATGAATAGTG-AGATTCC
4050805 CTGTAAAGGT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 24 0.35
59 7 0.10
61 2 0.03
62 28 0.41
63 7 0.10
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (61 bp):
AAGATGAATAGTGAGATTCCTTGCAAAGTTCTTCAAATATTCAGGGAATATATTCCAAAAC
Found at i:4055177 original size:26 final size:26
Alignment explanation
Indices: 4055138--4055195 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
4055128 GTTTAGAATT
* *
4055138 TTTTATTTAAAATTTAAAGTTTAGGC
1 TTTTATTTAAAATTCAAAGTTTAGGA
* *
4055164 TTTTATTTAGAATTCAAAGTTTATGA
1 TTTTATTTAAAATTCAAAGTTTAGGA
4055190 TTTTAT
1 TTTTAT
4055196 GACAGTATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.53
Consensus pattern (26 bp):
TTTTATTTAAAATTCAAAGTTTAGGA
Found at i:4061369 original size:86 final size:86
Alignment explanation
Indices: 4061255--4061513 Score: 473
Period size: 86 Copynumber: 3.0 Consensus size: 86
4061245 CATAGAAAAT
4061255 TAACAAATGTGATTGATCTTGAGCAAAGGGAAAAGGTGAATCTTGGAGGTTAAAAGTTAATGCGA
1 TAACAAATGTGATTGATCTTGAGCAAAGGGAAAAGGTGAATCTTGGAGGTTAAAAGTTAATGCGA
4061320 AACAGGAATGAAAATGATTAC
66 AACAGGAATGAAAATGATTAC
* * *
4061341 TAACAAATGTGATTGATCCTGAGCAAAGGGCAAAGGTGAATATTGGAGGTTAAAAGTTAATGCGA
1 TAACAAATGTGATTGATCTTGAGCAAAGGGAAAAGGTGAATCTTGGAGGTTAAAAGTTAATGCGA
*
4061406 AACAAGAATGAAAATGATTAC
66 AACAGGAATGAAAATGATTAC
*
4061427 TAACAAATGTGATTGATCTTGAGCAAAGGGAAAAGGTGAATCTTGGAGGTTAAAAGTTGATGCGA
1 TAACAAATGTGATTGATCTTGAGCAAAGGGAAAAGGTGAATCTTGGAGGTTAAAAGTTAATGCGA
4061492 AACAGGAATGAAAATGATTAC
66 AACAGGAATGAAAATGATTAC
4061513 T
1 T
4061514 CTTGGTTTGA
Statistics
Matches: 164, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
86 164 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.24
Consensus pattern (86 bp):
TAACAAATGTGATTGATCTTGAGCAAAGGGAAAAGGTGAATCTTGGAGGTTAAAAGTTAATGCGA
AACAGGAATGAAAATGATTAC
Found at i:4062500 original size:23 final size:24
Alignment explanation
Indices: 4062465--4062509 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
4062455 CAAAAGATAT
*
4062465 TTTATCAATAA-TTATATTAAATAA
1 TTTATCAAAAATTTA-ATTAAATAA
4062489 TTTA-CAAAAATTTAATTAAAT
1 TTTATCAAAAATTTAATTAAAT
4062510 CAAAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTATCAAAAATTTAATTAAATAA
Found at i:4063478 original size:308 final size:308
Alignment explanation
Indices: 4062920--4063846 Score: 1658
Period size: 308 Copynumber: 3.0 Consensus size: 308
4062910 AGTGACAAGA
4062920 ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTATAATTTTTTACACATACGGAATGAAC
1 ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTATAATTTTTTACACATACGGAATGAAC
*
4062985 TTGAACAAATTATTGTCCTGATACATTTAAACTTGAACAATCATTTGTTCAGATTTATTTTAGAT
66 TTGAACAAACTATTGTCCTGATACATTTAAACTTGAACAATCATTTGTTCAGATTTATTTTAGAT
4063050 ATAATTTTAATAATTTTAATTTTTTATAAGTATCATTTGAATTTGTAG-TTTTTTTTTTCCTAAA
131 AT-ATTTTAATAATTTTAATTTTTTATAAGTATCATTTGAATTTGTAGTTTTTTTTTTTCCTAAA
*
4063114 ACACTTCTAGAACTTAACATTTGTTGACATTTTTCATAACAAACACCACAAAAAATAACATGTAG
195 ACACTTCTAGAACTTAACATTTATTGACATTTTTCATAACAAACACCACAAAAAATAACATGTAG
* *
4063179 CAGTATTTTATTGACAAAAGCCGTTAGTTTTAAAAATTACCATAATTTT
260 CAGTATTTTATTGACAAAAGCCGTTAGTTTTAAAAATTAGCATCATTTT
*
4063228 ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTAAAATTTTTTACACATACGGAATGAAC
1 ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTATAATTTTTTACACATACGGAATGAAC
* **
4063293 TTGAACAAACTATTGTCCAGATACATTTAAACTTGGGCAATCATTTGTTCAGATTTATTTTAGAT
66 TTGAACAAACTATTGTCCTGATACATTTAAACTTGAACAATCATTTGTTCAGATTTATTTTAGAT
4063358 ATATTTTTAATAATTTTAATTTTTTATAAGTATCATTTGAATTTGTAGTTTTTTTTTTTCCTAAA
131 ATA-TTTTAATAATTTTAATTTTTTATAAGTATCATTTGAATTTGTAGTTTTTTTTTTTCCTAAA
4063423 ACACTTCTAGAACTTAACATTTATTGACA-TTTTCATAACAAACACCACAAAAAATAACATGTAG
195 ACACTTCTAGAACTTAACATTTATTGACATTTTTCATAACAAACACCACAAAAAATAACATGTAG
*
4063487 CAGTATTTTATTGACAAAAGCCGTTAGTTTTAAAAATTAGCATCATTTC
260 CAGTATTTTATTGACAAAAGCCGTTAGTTTTAAAAATTAGCATCATTTT
4063536 ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTATAATTTTTTACACATACGGAATGAAC
1 ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTATAATTTTTTACACATACGGAATGAAC
4063601 TTGAACAAACTATTGTCCTGATACATTTAAACTTGAACAATCATTTGTTCAGATTTATTTTAG--
66 TTGAACAAACTATTGTCCTGATACATTTAAACTTGAACAATCATTTGTTCAGATTTATTTTAGAT
*
4063664 ATA---T-AT--TTTTAATTTTTTATAAGTATCATTTGAATTTGTAGTTTTTTTTCTTCCTAAAA
131 ATATTTTAATAATTTTAATTTTTTATAAGTATCATTTGAATTTGTAGTTTTTTTTTTTCCTAAAA
4063723 CACTTCTAGAACTTAACATTTATTGACATTTTTCATAACAAACACCACAAAAAATAACATGTAGC
196 CACTTCTAGAACTTAACATTTATTGACATTTTTCATAACAAACACCACAAAAAATAACATGTAGC
* *
4063788 AGCATTTTATTGACAAAAACCGTTAGTTTTAAAAATTAGCATCATTTT
261 AGTATTTTATTGACAAAAGCCGTTAGTTTTAAAAATTAGCATCATTTT
4063836 ATTTAAAAATT
1 ATTTAAAAATT
4063847 TATAGTTTAT
Statistics
Matches: 599, Mismatches: 17, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
299 80 0.13
300 92 0.15
301 2 0.00
302 1 0.00
306 3 0.01
307 1 0.00
308 376 0.63
309 44 0.07
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (308 bp):
ATTTAAAAATTAAAATATATAAAATTGTAAAAAAAATTATAATTTTTTACACATACGGAATGAAC
TTGAACAAACTATTGTCCTGATACATTTAAACTTGAACAATCATTTGTTCAGATTTATTTTAGAT
ATATTTTAATAATTTTAATTTTTTATAAGTATCATTTGAATTTGTAGTTTTTTTTTTTCCTAAAA
CACTTCTAGAACTTAACATTTATTGACATTTTTCATAACAAACACCACAAAAAATAACATGTAGC
AGTATTTTATTGACAAAAGCCGTTAGTTTTAAAAATTAGCATCATTTT
Found at i:4082229 original size:3 final size:3
Alignment explanation
Indices: 4082221--4082256 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
4082211 TCCAGATTAA
4082221 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4082257 TTTAGAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4088059 original size:16 final size:17
Alignment explanation
Indices: 4088040--4088082 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
4088030 ATTACATTAT
4088040 ATATAAAAATAATAC-A
1 ATATAAAAATAATACAA
*
4088056 ATAT-AAAATATTACAA
1 ATATAAAAATAATACAA
*
4088072 ATTTAAAAATA
1 ATATAAAAATA
4088083 CGGGTCGACC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
16 8 0.35
17 6 0.26
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (17 bp):
ATATAAAAATAATACAA
Found at i:4090299 original size:2 final size:2
Alignment explanation
Indices: 4090292--4090323 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4090282 CATATTGTAC
4090292 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
4090324 CATTATGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4092228 original size:16 final size:18
Alignment explanation
Indices: 4092189--4092229 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
4092179 TAAGCTCGAA
4092189 AAAGCTCGAGTTCGACAG
1 AAAGCTCGAGTTCGACAG
4092207 -AA-CTCGAGTTC-A-AG
1 AAAGCTCGAGTTCGACAG
4092221 AAAGCTCGA
1 AAAGCTCGA
4092230 AAATGATCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.10
15 3 0.14
16 14 0.67
17 2 0.10
ACGTcount: A:0.37, C:0.22, G:0.24, T:0.17
Consensus pattern (18 bp):
AAAGCTCGAGTTCGACAG
Found at i:4092561 original size:25 final size:26
Alignment explanation
Indices: 4092513--4092603 Score: 77
Period size: 25 Copynumber: 3.7 Consensus size: 26
4092503 ATTTTAATAC
*
4092513 TATAATTATATATTTATAATAAATATA
1 TATAATTA-ATAATTATAATAAATATA
* *
4092540 TATAATTAATAATTATTA-AAATCTA
1 TATAATTAATAATTATAATAAATATA
* *
4092565 TAAAATTAA-ACTT-TAAT-AATA-A
1 TATAATTAATAATTATAATAAATATA
4092587 TATAA-TAATATATTATA
1 TATAATTAATA-ATTATA
4092604 TAACTATTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
21 3 0.06
22 6 0.12
23 7 0.14
24 5 0.10
25 14 0.27
26 8 0.16
27 8 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (26 bp):
TATAATTAATAATTATAATAAATATA
Found at i:4092881 original size:16 final size:16
Alignment explanation
Indices: 4092862--4092894 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4092852 TATATAATGT
4092862 ACTACTATTATA-TATA
1 ACTA-TATTATATTATA
4092878 ACTATATTATATTATA
1 ACTATATTATATTATA
4092894 A
1 A
4092895 ATTATAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (16 bp):
ACTATATTATATTATA
Found at i:4093127 original size:234 final size:245
Alignment explanation
Indices: 4092668--4093197 Score: 565
Period size: 234 Copynumber: 2.2 Consensus size: 245
4092658 TAGATTAGTT
* *
4092668 GTATCACATGATATTATAATGTTTAATCATCGATGCATGTATATATAAACTATTAATATATGATG
1 GTATTACATGATATTATAATGTTTAATCATTGATGCA--TATATAT-AACTATTAATATATGA-G
* * *
4092733 TGATATGATATAACATTATATAACATAGTAGGAGGACTAACTTTAAATGTATGAAAAGTATAAAG
62 TGATATGATATAACATTATATAACATAGTAGGAGGACT-A-TTCAAATATATGAAAAATATAAAG
* * * * *
4092798 ACTCTGAGCACTTTTCAACTAGTATAATAATAAATAATAACATATAATAAGTAATATATAATGTA
125 ACTCTAAACACTTTTCAACCAGCATAATAATAAACAATAACATATAATAAGTAATATATAATGTA
* * **
4092863 CTACTATTATATATAAC-----TATATTATATTATAAATTATAAT-AAAGGATAGA
190 CTACTATTATATATAACGATATTATATTATATTATAGATCATAATAAAAAAATAGA
*
4092913 GTATTACATGATATTATAATGTTTAATCATTTATGCATATATATAACTATT-A-ATAT-A-TGAT
1 GTATTACATGATATTATAATGTTTAATCATTGATGCATATATATAACTATTAATATATGAGTGAT
* * * ** *
4092974 ATGATATAGCATTATATAATATAGTAGGAAGG-CT-TTCACATATATGAAAAATATAGGGGCT-T
66 ATGATATAACATTATATAACATAGTAGG-AGGACTATTCAAATATATGAAAAATATAAAGACTCT
* *
4093036 AAA-ACATATTTCAACCAGCATAATAATAAACAATAATATATAATAATTAATATACAATTAATGT
130 AAACAC-T-TTTCAACCAGCATAATAATAAACAATAACATATAATAAGTAATAT---A-TAATGT
* *
4093100 ACTACTATTATATAT-A-GGTA-T-TATTATATTATAGATCATAATAAAAAAATATA
189 ACTACTATTATATATAACGATATTATATTATATTATAGATCATAATAAAAAAATAGA
* * *
4093153 TTATTACATGATATTTTAATGTTTAATCGTTGATGCATATATATA
1 GTATTACATGATATTATAATGTTTAATCATTGATGCATATATATA
4093198 TATAAACTAT
Statistics
Matches: 245, Mismatches: 28, Indels: 29
0.81 0.09 0.10
Matches are distributed among these distances:
232 2 0.01
233 3 0.01
234 60 0.24
237 34 0.14
238 24 0.10
239 20 0.08
240 53 0.22
241 1 0.00
242 7 0.03
243 7 0.03
245 34 0.14
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.38
Consensus pattern (245 bp):
GTATTACATGATATTATAATGTTTAATCATTGATGCATATATATAACTATTAATATATGAGTGAT
ATGATATAACATTATATAACATAGTAGGAGGACTATTCAAATATATGAAAAATATAAAGACTCTA
AACACTTTTCAACCAGCATAATAATAAACAATAACATATAATAAGTAATATATAATGTACTACTA
TTATATATAACGATATTATATTATATTATAGATCATAATAAAAAAATAGA
Found at i:4094512 original size:3 final size:3
Alignment explanation
Indices: 4094499--4094561 Score: 119
Period size: 3 Copynumber: 21.3 Consensus size: 3
4094489 CACTGAGAGA
4094499 AAG AA- AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4094546 AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG A
4094562 GTAAGCGAGA
Statistics
Matches: 59, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 57 0.97
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4097683 original size:6 final size:6
Alignment explanation
Indices: 4097672--4097700 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4097662 CCCCCCCTCT
4097672 CCATCA CCATCA CCATCA CCATCA CCATC
1 CCATCA CCATCA CCATCA CCATCA CCATC
4097701 CATAACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.52, G:0.00, T:0.17
Consensus pattern (6 bp):
CCATCA
Found at i:4101312 original size:84 final size:81
Alignment explanation
Indices: 4101192--4101388 Score: 202
Period size: 84 Copynumber: 2.4 Consensus size: 81
4101182 CCATTGTTGC
* ** * * *
4101192 TATTATTCATATACCTTTTACCCCCTTAAATAGAAAGA-C-TTGTGTTTCTATTTCAT-TCTTTG
1 TATTATTCATATACCTTTCAAACCCTTAAATAGAAAGATCAATATG--TCTATTTCATCT-TTTA
* *
4101254 TTATTTTTTGTACAAATTTTGT
63 TTATTTTTTATAC-AA--TTAT
* * * * *
4101276 TATTATTCATATATCTTTCAAACCTTTAAGTCGAAAGATCAATATGTCTATTTGATCTTTTATTA
1 TATTATTCATATACCTTTCAAACCCTTAAATAGAAAGATCAATATGTCTATTTCATCTTTTATTA
4101341 TTTTTTATACAATTAT
66 TTTTTTATACAATTAT
4101357 TATTATTCATATACCTTTCAAACCCTTAAATA
1 TATTATTCATATACCTTTCAAACCCTTAAATA
4101389 TGTGGATTGG
Statistics
Matches: 93, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
81 31 0.33
83 2 0.02
84 55 0.59
85 2 0.02
86 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (81 bp):
TATTATTCATATACCTTTCAAACCCTTAAATAGAAAGATCAATATGTCTATTTCATCTTTTATTA
TTTTTTATACAATTAT
Found at i:4103256 original size:2 final size:2
Alignment explanation
Indices: 4103249--4103283 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4103239 AACATTCAAC
4103249 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4103284 CATTTAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4103409 original size:23 final size:21
Alignment explanation
Indices: 4103378--4103426 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
4103368 AAAATAAAAC
*
4103378 AAATCAATTTAAATTATAAGTAA
1 AAATAAATTTAAA-TA-AAGTAA
*
4103401 AAATAAATTTAAATAAATTAA
1 AAATAAATTTAAATAAAGTAA
4103422 AAATA
1 AAATA
4103427 TTAAATACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.42
22 2 0.08
23 12 0.50
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATAAATTTAAATAAAGTAA
Found at i:4104218 original size:21 final size:21
Alignment explanation
Indices: 4104190--4104229 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4104180 TTTAAATTTT
4104190 AAAATATAAAAA-TTAGAGAA
1 AAAATATAAAAACTTAGAGAA
4104210 AAAAGTATAAAAACTTAGAG
1 AAAA-TATAAAAACTTAGAG
4104230 CATATTTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.20
Consensus pattern (21 bp):
AAAATATAAAAACTTAGAGAA
Found at i:4106297 original size:22 final size:23
Alignment explanation
Indices: 4106272--4106324 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
4106262 CATCAACTCA
*
4106272 ATTAAAAAAAATAAAATTAA-A-T
1 ATTAAAAAAAAT-AAACTAATATT
*
4106294 ATT-AAATAAATAAACTAATATT
1 ATTAAAAAAAATAAACTAATATT
4106316 ATTAAAAAA
1 ATTAAAAAA
4106325 TACGTTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 6 0.24
21 8 0.32
22 7 0.28
23 4 0.16
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
ATTAAAAAAAATAAACTAATATT
Found at i:4110642 original size:46 final size:46
Alignment explanation
Indices: 4110589--4110683 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
4110579 TTTGAAGTAA
*
4110589 ATAAAAGCACTAACAATTGATGTCTAAGCCCTCTTTTCTTTGGCAT
1 ATAAAAGCACTAACAATTGATGTCTAAACCCTCTTTTCTTTGGCAT
4110635 ATAAAAGCACTAACAATTGATGTCTAAACCCTCTTTTCTTTGGCAT
1 ATAAAAGCACTAACAATTGATGTCTAAACCCTCTTTTCTTTGGCAT
4110681 ATA
1 ATA
4110684 TGAAAATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.35
Consensus pattern (46 bp):
ATAAAAGCACTAACAATTGATGTCTAAACCCTCTTTTCTTTGGCAT
Found at i:4112287 original size:2 final size:2
Alignment explanation
Indices: 4112280--4112330 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4112270 ACAATTACAA
4112280 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
4112322 AG AG AG AG A
1 AG AG AG AG A
4112331 CGGTAACTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4113245 original size:19 final size:19
Alignment explanation
Indices: 4113221--4113258 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4113211 TTCGTCGTCT
4113221 TTTCAAGTAACTTTTTAAA
1 TTTCAAGTAACTTTTTAAA
4113240 TTTCAAGTAACTTTTTAAA
1 TTTCAAGTAACTTTTTAAA
4113259 GCACTTTAGT
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:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (19 bp):
TTTCAAGTAACTTTTTAAA
Found at i:4115197 original size:9 final size:9
Alignment explanation
Indices: 4115183--4115249 Score: 53
Period size: 9 Copynumber: 7.1 Consensus size: 9
4115173 CAAAATTATT
4115183 TTTTTAAAA
1 TTTTTAAAA
4115192 TTTTTAAAA
1 TTTTTAAAA
* **
4115201 ATTTTAACT
1 TTTTTAAAA
*
4115210 TTCTTTATATAT
1 TT-TTTA-A-AA
4115222 TTTTTAAAA
1 TTTTTAAAA
* *
4115231 TTGTTATAA
1 TTTTTAAAA
4115240 TTTTTAAAA
1 TTTTTAAAA
4115249 T
1 T
4115250 ATATAAATTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 32 0.71
10 5 0.11
11 5 0.11
12 3 0.07
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:4122607 original size:3 final size:3
Alignment explanation
Indices: 4122594--4122630 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
4122584 TGTACATCCT
*
4122594 TTA TGA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
4122631 AGATGAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:4137894 original size:15 final size:15
Alignment explanation
Indices: 4137874--4137903 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4137864 AAAAAATTGG
*
4137874 TATAAATTATTATAA
1 TATAAAGTATTATAA
4137889 TATAAAGTATTATAA
1 TATAAAGTATTATAA
4137904 ATTTACATGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
TATAAAGTATTATAA
Found at i:4154880 original size:20 final size:20
Alignment explanation
Indices: 4154852--4154942 Score: 75
Period size: 20 Copynumber: 4.6 Consensus size: 20
4154842 TTACATCAGC
*
4154852 AAATAATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
4154872 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
4154892 AAATTA--TTAAAATTAATTTA
1 AAATTATTTTAAAATT-A-TTA
* *
4154912 AAATTAATTTAAATTTATT-
1 AAATTATTTTAAAATTATTA
*
4154931 AAATAATTTTAA
1 AAATTATTTTAA
4154943 TTTCCAATTT
Statistics
Matches: 59, Mismatches: 4, Indels: 17
0.74 0.05 0.21
Matches are distributed among these distances:
16 6 0.10
17 1 0.02
18 1 0.02
19 10 0.17
20 23 0.39
21 3 0.05
22 15 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:4154914 original size:11 final size:11
Alignment explanation
Indices: 4154890--4154924 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4154880 TTTTAAAATA
4154890 TAAAATT-A-T
1 TAAAATTAATT
4154899 TAAAATTAATT
1 TAAAATTAATT
4154910 TAAAATTAATT
1 TAAAATTAATT
4154921 TAAA
1 TAAA
4154925 TTTATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 7 0.29
10 1 0.04
11 16 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAAATTAATT
Found at i:4155623 original size:29 final size:30
Alignment explanation
Indices: 4155598--4155670 Score: 112
Period size: 29 Copynumber: 2.4 Consensus size: 30
4155588 ATTAAAATTA
4155598 TTTAATAATTTTATTATTTCAAAAAAATAAT
1 TTTAATAATTTTA-TATTTCAAAAAAATAAT
* *
4155629 TTTAATAATTTTATATTT-TAAAATATAAT
1 TTTAATAATTTTATATTTCAAAAAAATAAT
4155658 TTTAATAATTTTA
1 TTTAATAATTTTA
4155671 AAATTATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 22 0.55
30 5 0.12
31 13 0.32
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTAATAATTTTATATTTCAAAAAAATAAT
Found at i:4155637 original size:9 final size:9
Alignment explanation
Indices: 4155623--4155675 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
4155613 ATTTCAAAAA
4155623 AATAATTTT
1 AATAATTTT
4155632 AATAATTTT
1 AATAATTTT
4155641 -AT-ATTTT
1 AATAATTTT
4155648 AA-AA---T
1 AATAATTTT
4155653 -ATAATTTT
1 AATAATTTT
4155661 AATAATTTT
1 AATAATTTT
4155670 AA-AATT
1 AATAATT
4155676 ATTTATTGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 15
0.71 0.00 0.29
Matches are distributed among these distances:
4 1 0.03
5 3 0.08
7 5 0.14
8 9 0.24
9 19 0.51
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATAATTTT
Found at i:4155658 original size:20 final size:22
Alignment explanation
Indices: 4155633--4155674 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4155623 AATAATTTTA
4155633 ATAATTTT-AT-ATTTTAAAAT
1 ATAATTTTAATAATTTTAAAAT
4155653 ATAATTTTAATAATTTTAAAAT
1 ATAATTTTAATAATTTTAAAAT
4155675 TATTTATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
22 10 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATTTTAATAATTTTAAAAT
Found at i:4158000 original size:16 final size:17
Alignment explanation
Indices: 4157979--4158015 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
4157969 CAATTGAATC
*
4157979 AAATTTTT-ATTATTTT
1 AAATTTTTAATAATTTT
4157995 AAATTTTTAATAATTTT
1 AAATTTTTAATAATTTT
4158012 AAAT
1 AAAT
4158016 CAAATCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AAATTTTTAATAATTTT
Found at i:4159699 original size:22 final size:23
Alignment explanation
Indices: 4159671--4159714 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4159661 CAATAAAAAA
*
4159671 CTGAATTAT-TTGTTTTATTATG
1 CTGAATTATATTATTTTATTATG
*
4159693 CTGAATTCTATTATTTTATTAT
1 CTGAATTATATTATTTTATTAT
4159715 TTTATTTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (23 bp):
CTGAATTATATTATTTTATTATG
Found at i:4160272 original size:29 final size:27
Alignment explanation
Indices: 4160240--4160321 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 27
4160230 TTTAAGTCTT
4160240 TTAAAAGTTAGTAAAAAAAATTGGGCCTC
1 TTAAAA-TTA-TAAAAAAAATTGGGCCTC
* *
4160269 TTAAAAACTTAAAAAAAAAATTGGACCTC
1 TT-AAAA-TTATAAAAAAAATTGGGCCTC
*
4160298 TTAAAAAT-TAAAAAAAATTGGGCC
1 TTAAAATTATAAAAAAAATTGGGCC
4160322 CTTTTAGCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
26 14 0.30
27 1 0.02
28 4 0.09
29 20 0.43
30 7 0.15
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (27 bp):
TTAAAATTATAAAAAAAATTGGGCCTC
Found at i:4160303 original size:28 final size:29
Alignment explanation
Indices: 4160252--4160314 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
4160242 AAAAGTTAGT
* *
4160252 AAAAAAAATTGGGCCTCTTAAAAACTTAA
1 AAAAAAAATTGGACCTCTTAAAAAATTAA
4160281 AAAAAAAATTGGACCTCTT-AAAAATTAA
1 AAAAAAAATTGGACCTCTTAAAAAATTAA
4160309 AAAAAA
1 AAAAAA
4160315 TTGGGCCCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 14 0.44
29 18 0.56
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (29 bp):
AAAAAAAATTGGACCTCTTAAAAAATTAA
Found at i:4161403 original size:29 final size:32
Alignment explanation
Indices: 4161360--4161422 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 32
4161350 ACTGTATACA
* *
4161360 TAAACTTTGATTTTG-TGCAATT-TTATATAT
1 TAAACTTTGATTTTGATCCAATTCTTATAAAT
*
4161390 TAAATTTTGA-TTTGATCCAATTCTTATAAAT
1 TAAACTTTGATTTTGATCCAATTCTTATAAAT
4161421 TA
1 TA
4161423 TTAACACAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 4 0.14
30 15 0.54
31 9 0.32
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.51
Consensus pattern (32 bp):
TAAACTTTGATTTTGATCCAATTCTTATAAAT
Found at i:4176863 original size:16 final size:15
Alignment explanation
Indices: 4176842--4176880 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4176832 CTCTTTTCCC
*
4176842 TATTTTCATATTATCA
1 TATTTTCA-ATTATAA
4176858 TATTTTC-ATTATAA
1 TATTTTCAATTATAA
4176872 TATTTTCAA
1 TATTTTCAA
4176881 CAATTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 1 0.05
16 7 0.33
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTTTCAATTATAA
Found at i:4177408 original size:27 final size:26
Alignment explanation
Indices: 4177359--4177409 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
4177349 TTAGGATTCA
*
4177359 AGATTCGAGTTTAAGTTCGAGGTTTG
1 AGATTCGAGTTTAAGTTCAAGGTTTG
4177385 AGATTCG-GATTTGAAGTTCAAGGTT
1 AGATTCGAG-TTT-AAGTTCAAGGTT
4177410 CAAGGTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 1 0.05
26 10 0.45
27 11 0.50
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.37
Consensus pattern (26 bp):
AGATTCGAGTTTAAGTTCAAGGTTTG
Found at i:4193585 original size:59 final size:60
Alignment explanation
Indices: 4193461--4193585 Score: 139
Period size: 59 Copynumber: 2.1 Consensus size: 60
4193451 AATTAAATCT
* * * * *
4193461 AAAAAAAAGCTTAGGTACCAATTTAGAAAAAAATGTCAAGTTCAGGTATCAAATTGGGTC
1 AAAAAAAAGCTTAGGTACCAATTAAGAAAAAAATGTCAAATTCAGATATCAAATTAGGTA
* * *
4193521 CAAAAAAAG-TTAGGTACCAAGTTAAG-AAAAATTGTCAAATTCAGATA-CTAATTTAGGTA
1 AAAAAAAAGCTTAGGTACCAA-TTAAGAAAAAAATGTCAAATTCAGATATC-AAATTAGGTA
4193580 AAAAAA
1 AAAAAA
4193586 TTTAAATATC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
58 1 0.02
59 41 0.76
60 12 0.22
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.25
Consensus pattern (60 bp):
AAAAAAAAGCTTAGGTACCAATTAAGAAAAAAATGTCAAATTCAGATATCAAATTAGGTA
Found at i:4197333 original size:17 final size:17
Alignment explanation
Indices: 4197313--4197346 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4197303 TAAGGGATTA
4197313 TAAATAAAAATAAACAT
1 TAAATAAAAATAAACAT
* *
4197330 TAAATCAAAATATACAT
1 TAAATAAAAATAAACAT
4197347 GTATCTTAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAATAAAAATAAACAT
Found at i:4210345 original size:24 final size:24
Alignment explanation
Indices: 4210313--4210369 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
4210303 GCAACATTGG
4210313 CAGCTGCAGCAGCAGCCT-TTGCAA
1 CAGCTGCAGCAGCAG-CTATTGCAA
* * *
4210337 CAGCAGCAGCTGCTGCTATTGCAA
1 CAGCTGCAGCAGCAGCTATTGCAA
4210361 CAGCTGCAG
1 CAGCTGCAG
4210370 AAGTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.25, C:0.32, G:0.26, T:0.18
Consensus pattern (24 bp):
CAGCTGCAGCAGCAGCTATTGCAA
Found at i:4212906 original size:28 final size:28
Alignment explanation
Indices: 4212874--4212931 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
4212864 AACCCATGAG
*
4212874 AATGATAACATGAAAATTGTGGGCGGAA
1 AATGATAACATGAAAATTGTGGGAGGAA
4212902 AATGATAACATGAAAATTGTGGGAGGAA
1 AATGATAACATGAAAATTGTGGGAGGAA
4212930 AA
1 AA
4212932 CAGAAAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.21
Consensus pattern (28 bp):
AATGATAACATGAAAATTGTGGGAGGAA
Found at i:4219649 original size:18 final size:21
Alignment explanation
Indices: 4219628--4219667 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4219618 TTTTTTGGCC
4219628 ATCAA-CTTT-TTTT-TTTCA
1 ATCAATCTTTCTTTTCTTTCA
4219646 ATCAATCTTTCTTTTCTTTCA
1 ATCAATCTTTCTTTTCTTTCA
4219667 A
1 A
4219668 AAGGTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 4 0.21
21 6 0.32
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (21 bp):
ATCAATCTTTCTTTTCTTTCA
Found at i:4219756 original size:21 final size:24
Alignment explanation
Indices: 4219722--4219771 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
4219712 ATTGAATTAA
*
4219722 TTTTTTAGATAATT-ACGTTTATT
1 TTTTTTAGATAATTGACGGTTATT
*
4219745 TTTTTTA-A-AATTGAGGGTTATT
1 TTTTTTAGATAATTGACGGTTATT
4219767 TTTTT
1 TTTTT
4219772 AATTTAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.62
Consensus pattern (24 bp):
TTTTTTAGATAATTGACGGTTATT
Found at i:4220155 original size:18 final size:18
Alignment explanation
Indices: 4220107--4220148 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
4220097 TCAAAAGCAC
*
4220107 TTTTGAAACAAAAAGTAT
1 TTTTGAAACAAAAAATAT
4220125 TTTTGAAACAAAAAATAT
1 TTTTGAAACAAAAAATAT
4220143 TTTTGA
1 TTTTGA
4220149 GATAAAAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (18 bp):
TTTTGAAACAAAAAATAT
Found at i:4220429 original size:37 final size:37
Alignment explanation
Indices: 4220388--4220465 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
4220378 GCTTGGCCAA
*
4220388 AAATGATAAATTGTATGTTGGTATATACAAAAGTTGT
1 AAATGATAAATTGAATGTTGGTATATACAAAAGTTGT
4220425 AAATGATAAATTGAATGTTGGTATATACAAAAGTTGT
1 AAATGATAAATTGAATGTTGGTATATACAAAAGTTGT
4220462 AAAT
1 AAAT
4220466 TTTCTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (37 bp):
AAATGATAAATTGAATGTTGGTATATACAAAAGTTGT
Found at i:4231151 original size:31 final size:30
Alignment explanation
Indices: 4231113--4231170 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
4231103 TGCATCAAAT
4231113 CAAAGTTCATGTATCAAA-TTGCATATTAGAC
1 CAAAGTTCATGTAT-AAACTTG-ATATTAGAC
4231144 CAAAGTTCATGTATAAACTTGATATTA
1 CAAAGTTCATGTATAAACTTGATATTA
4231171 TCCCTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (30 bp):
CAAAGTTCATGTATAAACTTGATATTAGAC
Found at i:4235012 original size:25 final size:26
Alignment explanation
Indices: 4234974--4235058 Score: 84
Period size: 26 Copynumber: 3.2 Consensus size: 26
4234964 AAAATAATTT
*
4234974 AAAAA-TATAAAAATATT-TTGAAAAA
1 AAAAATTAT-AAAATATTCATGAAAAA
* **
4234999 AAAAATTATAAAATGTTCATGAAATT
1 AAAAATTATAAAATATTCATGAAAAA
*
4235025 AAAAATTATAAAATGTTCATGAAATTAA
1 AAAAATTATAAAATATTCATGAAA--AA
4235053 AAAAAT
1 AAAAAT
4235059 AGTATTTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
25 12 0.24
26 32 0.64
28 6 0.12
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (26 bp):
AAAAATTATAAAATATTCATGAAAAA
Found at i:4238046 original size:46 final size:46
Alignment explanation
Indices: 4237935--4238089 Score: 203
Period size: 46 Copynumber: 3.5 Consensus size: 46
4237925 AAATTAAAAA
* *
4237935 TCATTAAGTTAAAAAGTAAAATTACATCGTTTTAATAAATGTTTA-
1 TCATTAAGTTAAAAAGTAAAATTATATCGTTTTGATAAATGTTTAC
* * *
4237980 T-TTTAAGTTAAAAGGTAAAATTATATTGTTTTGATAAATGTTTAC
1 TCATTAAGTTAAAAAGTAAAATTATATCGTTTTGATAAATGTTTAC
* *
4238025 TCATTAAGTTAAAAAGTAAAATTATATCATTTTGATAAATATTTAC
1 TCATTAAGTTAAAAAGTAAAATTATATCGTTTTGATAAATGTTTAC
*
4238071 TC---AAGTTAAAAAGCAAAAT
1 TCATTAAGTTAAAAAGTAAAAT
4238090 CATTAAGTTA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
43 16 0.16
44 38 0.39
45 2 0.02
46 41 0.42
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.40
Consensus pattern (46 bp):
TCATTAAGTTAAAAAGTAAAATTATATCGTTTTGATAAATGTTTAC
Found at i:4260300 original size:16 final size:18
Alignment explanation
Indices: 4260265--4260304 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
4260255 ATTATCAAAA
*
4260265 AATATTTTAATTATTAAT
1 AATATTATAATTATTAAT
4260283 AATATTATAA-TA-TAAT
1 AATATTATAATTATTAAT
4260299 AATATT
1 AATATT
4260305 TTATAAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 2 0.10
18 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATATTATAATTATTAAT
Found at i:4260308 original size:18 final size:19
Alignment explanation
Indices: 4260265--4260310 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 19
4260255 ATTATCAAAA
*
4260265 AATATTTTA-ATTATTAAT
1 AATATTTTATAATATTAAT
4260283 AATA--TTATAATA-TAAT
1 AATATTTTATAATATTAAT
4260299 AATATTTTATAA
1 AATATTTTATAA
4260311 ACAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 11 0.46
17 3 0.12
18 10 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTTATAATATTAAT
Found at i:4276359 original size:2 final size:2
Alignment explanation
Indices: 4276352--4276384 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4276342 TAAGCTTTAT
4276352 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4276385 TGTGTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4288960 original size:15 final size:16
Alignment explanation
Indices: 4288941--4288980 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
4288931 TAATTTTTAA
4288941 AAAATTATGA-AATAAT
1 AAAATTAT-ACAATAAT
4288957 -AAATTATACAATAAT
1 AAAATTATACAATAAT
4288972 AAAATTATA
1 AAAATTATA
4288981 TTTTGACTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 13 0.59
16 8 0.36
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AAAATTATACAATAAT
Found at i:4308288 original size:19 final size:19
Alignment explanation
Indices: 4308264--4308314 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 19
4308254 TGTTTCTTTT
*
4308264 AATAAACATTATATTATCA
1 AATAAACATTATATTATAA
*
4308283 AATAAA-A-AATATTATAA
1 AATAAACATTATATTATAA
4308300 AACTAAACATCTATA
1 AA-TAAACAT-TATA
4308315 ATAATATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 10 0.40
18 5 0.20
19 7 0.28
21 3 0.12
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
AATAAACATTATATTATAA
Found at i:4323060 original size:16 final size:18
Alignment explanation
Indices: 4323041--4323077 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
4323031 AATACAATGC
*
4323041 AAAATCA-AACTAATAAA
1 AAAATCATAACAAATAAA
4323058 AAAAT-ATAACAAATAAA
1 AAAATCATAACAAATAAA
4323075 AAA
1 AAA
4323078 TCGAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAATCATAACAAATAAA
Found at i:4324389 original size:20 final size:20
Alignment explanation
Indices: 4324364--4324405 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
4324354 GCCTAATGAC
4324364 TTATCTTGTATAATTTTTTG
1 TTATCTTGTATAATTTTTTG
*
4324384 TTATCTTGTATAGTTTTTTG
1 TTATCTTGTATAATTTTTTG
4324404 TT
1 TT
4324406 CTATTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.67
Consensus pattern (20 bp):
TTATCTTGTATAATTTTTTG
Found at i:4324873 original size:30 final size:30
Alignment explanation
Indices: 4324837--4324970 Score: 136
Period size: 30 Copynumber: 4.6 Consensus size: 30
4324827 GGATCCCAAA
* * **
4324837 AAGTTTAAGTATCAACTTAAAAAAATTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAAGTC
4324867 AAGTTTAAGTACCAAATTAAAAAAAAAGTC
1 AAGTTTAAGTACCAAATTAAAAAAAAAGTC
* *
4324897 AAGTTTGAGTACCAAATTGAACAAAAAA---
1 AAGTTTAAGTACCAAATT-AAAAAAAAAGTC
4324925 AA--TTAAGTACCAAATTAGAAAAAAATA-TC
1 AAGTTTAAGTACCAAATTA-AAAAAAA-AGTC
*
4324954 AAGTTCAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
4324971 GTTATATTAA
Statistics
Matches: 88, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
25 1 0.01
26 19 0.22
27 1 0.01
28 2 0.02
29 2 0.02
30 43 0.49
31 20 0.23
ACGTcount: A:0.53, C:0.11, G:0.10, T:0.25
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAAAAAAAAAGTC
Found at i:4324913 original size:88 final size:88
Alignment explanation
Indices: 4324786--4324970 Score: 214
Period size: 87 Copynumber: 2.1 Consensus size: 88
4324776 AAAAGATTAG
* * * * ** *
4324786 GTACCAAATTAAGAAAAAGAGTCAAGTTCAGGTATCAAATTGGATCCCAAAAAGTTTAAGTATCA
1 GTACCAAATTAAGAAAAAAAGTCAAGTTCAGGTACCAAATT-GA-ACAAAAAAAATTAAGTACCA
* * * *
4324851 ACTTA-AAAAAATTGTCAAGTTTAA
64 AATTAGAAAAAAATATCAAGTTCAA
*
4324875 GTACCAAATTAA-AAAAAAAGTCAAGTT-TGAGTACCAAATTGAACAAAAAAAATTAAGTACCAA
1 GTACCAAATTAAGAAAAAAAGTCAAGTTCAG-GTACCAAATTGAACAAAAAAAATTAAGTACCAA
4324938 ATTAGAAAAAAATATCAAGTTCAA
65 ATTAGAAAAAAATATCAAGTTCAA
4324962 GTACCAAAT
1 GTACCAAAT
4324971 GTTATATTAA
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
86 19 0.23
87 28 0.34
88 23 0.28
89 12 0.15
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (88 bp):
GTACCAAATTAAGAAAAAAAGTCAAGTTCAGGTACCAAATTGAACAAAAAAAATTAAGTACCAAA
TTAGAAAAAAATATCAAGTTCAA
Found at i:4324957 original size:25 final size:26
Alignment explanation
Indices: 4324904--4324957 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
4324894 GTCAAGTTTG
*
4324904 AGTACCAAATTGAACAAAAAAAATTA
1 AGTACCAAATTGAACAAAAAAAATCA
*
4324930 AGTACCAAATT-AGA-AAAAAATATCA
1 AGTACCAAATTGA-ACAAAAAAAATCA
4324955 AGT
1 AGT
4324958 TCAAGTACCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.59, C:0.11, G:0.09, T:0.20
Consensus pattern (26 bp):
AGTACCAAATTGAACAAAAAAAATCA
Found at i:4325050 original size:27 final size:26
Alignment explanation
Indices: 4325020--4325076 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 26
4325010 TTTTTAATTT
4325020 TTAAATTCAATTAGTTATAATATTTGA
1 TTAAATT-AATTAGTTATAATATTTGA
4325047 TT--A--AATTAGTTATAATATTTGA
1 TTAAATTAATTAGTTATAATATTTGA
4325069 TTAAATTA
1 TTAAATTA
4325077 GTTAACTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
22 21 0.81
24 1 0.04
25 1 0.04
26 1 0.04
27 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (26 bp):
TTAAATTAATTAGTTATAATATTTGA
Found at i:4325056 original size:22 final size:22
Alignment explanation
Indices: 4325028--4325080 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
4325018 TTTTAAATTC
4325028 AATTAGTTATAATATTTGATTA
1 AATTAGTTATAATATTTGATTA
4325050 AATTAGTTATAATATTTGATTA
1 AATTAGTTATAATATTTGATTA
4325072 AATTAGTTA
1 AATTAGTTA
4325081 ACTTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
AATTAGTTATAATATTTGATTA
Found at i:4330781 original size:22 final size:21
Alignment explanation
Indices: 4330734--4330787 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
4330724 TTAATAATAT
*
4330734 ATAATACAATATTATTACTTTA
1 ATAATA-AATATTATTACTTAA
4330756 ATAATAAATATTAATTA-TTAA
1 ATAATAAATATT-ATTACTTAA
*
4330777 CATAATTAATA
1 -ATAATAAATA
4330788 CTGTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
ATAATAAATATTATTACTTAA
Found at i:4334140 original size:2 final size:2
Alignment explanation
Indices: 4334133--4334170 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
4334123 GAAGTGGCTT
4334133 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
4334171 GTTGTAACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4339249 original size:18 final size:20
Alignment explanation
Indices: 4339228--4339266 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4339218 TACTGAAATT
4339228 TAATGA-CTAAAAAA-ATAA
1 TAATGAGCTAAAAAATATAA
4339246 TAATGATGCTAAAAAATATAA
1 TAATGA-GCTAAAAAATATAA
4339267 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.26
Consensus pattern (20 bp):
TAATGAGCTAAAAAATATAA
Found at i:4343105 original size:14 final size:14
Alignment explanation
Indices: 4343060--4343112 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
4343050 AAAAGAAAAA
* *
4343060 TTAGTTACTAAATT
1 TTAGTTATTTAATT
*
4343074 ATTAGTAAGTTTATATT
1 -TTAGTTA-TTTA-ATT
4343091 TTAGTTATTTAATT
1 TTAGTTATTTAATT
4343105 TTAGTTAT
1 TTAGTTAT
4343113 AAAATGATCA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 11 0.34
15 10 0.31
16 8 0.25
17 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (14 bp):
TTAGTTATTTAATT
Found at i:4344121 original size:25 final size:25
Alignment explanation
Indices: 4344082--4344132 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
4344072 TAATATAGAT
*
4344082 AATTTTTTTTAAATT-TAAAAAATA
1 AATTTTTTATAAATTCTAAAAAATA
4344106 AATTTTTTATAGAATTCTAAAAAATA
1 AATTTTTTATA-AATTCTAAAAAATA
4344132 A
1 A
4344133 TTATAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 4 0.17
26 10 0.42
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AATTTTTTATAAATTCTAAAAAATA
Found at i:4344175 original size:20 final size:18
Alignment explanation
Indices: 4344138--4344189 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
4344128 AATAATTATA
*
4344138 AATTTTAAAAAGTTAAAAT
1 AATTATAAAAA-TTAAAAT
4344157 AATATATAAAAATTGAAAAT
1 AAT-TATAAAAATT-AAAAT
**
4344177 TGTTATAAAAATT
1 AATTATAAAAATT
4344190 TTAAAAAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (18 bp):
AATTATAAAAATTAAAAT
Found at i:4344312 original size:21 final size:21
Alignment explanation
Indices: 4344286--4344346 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
4344276 TTTTATAAAA
4344286 AAATATTTTA-AACCTTTTTTT
1 AAATATTTTACAA-CTTTTTTT
4344307 AAATATATTTACAA-TTTTTTT
1 AAATAT-TTTACAACTTTTTTT
*
4344328 AAAAATTTTACAACTTTTT
1 AAATATTTTACAACTTTTT
4344347 ACAATTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 7 0.19
21 23 0.64
22 4 0.11
23 2 0.06
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (21 bp):
AAATATTTTACAACTTTTTTT
Found at i:4353626 original size:19 final size:20
Alignment explanation
Indices: 4353584--4353626 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
4353574 ACATAATAAC
* *
4353584 AATTATAAATAATTTATTTT
1 AATTATAAATAATATATTTA
*
4353604 AATTATTAA-AATATATTTA
1 AATTATAAATAATATATTTA
4353623 AATT
1 AATT
4353627 TGAATCAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
AATTATAAATAATATATTTA
Found at i:4353725 original size:7 final size:7
Alignment explanation
Indices: 4353713--4353742 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
4353703 TACACACCAT
4353713 AAAACTC
1 AAAACTC
4353720 AAAACTC
1 AAAACTC
4353727 AAAACTC
1 AAAACTC
4353734 AAAACTC
1 AAAACTC
4353741 AA
1 AA
4353743 TATCAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.60, C:0.27, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAACTC
Found at i:4360775 original size:15 final size:15
Alignment explanation
Indices: 4360755--4360800 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4360745 ACAAAATGAT
4360755 AACATAAATGATTAA
1 AACATAAATGATTAA
*
4360770 AACATAACAT--TTCA
1 AACATAA-ATGATTAA
*
4360784 AACATAAGTGATTAA
1 AACATAAATGATTAA
4360799 AA
1 AA
4360801 TGTAATTTGA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.40
15 12 0.48
16 2 0.08
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (15 bp):
AACATAAATGATTAA
Found at i:4361155 original size:23 final size:21
Alignment explanation
Indices: 4361133--4361171 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4361123 TTTTAATTAA
4361133 TAATT-TTATTAAAAAATATT
1 TAATTCTTATTAAAAAATATT
4361153 TAATTCTTATTAAAAAATA
1 TAATTCTTATTAAAAAATA
4361172 ATAACTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TAATTCTTATTAAAAAATATT
Found at i:4364580 original size:18 final size:18
Alignment explanation
Indices: 4364557--4364592 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
4364547 GAATGGATCT
*
4364557 TTAATTAAATAAATTTAA
1 TTAATTAAAAAAATTTAA
4364575 TTAATTAAAAAAATTTAA
1 TTAATTAAAAAAATTTAA
4364593 ACCCTAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TTAATTAAAAAAATTTAA
Found at i:4367445 original size:27 final size:27
Alignment explanation
Indices: 4367415--4367474 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
4367405 TTTGTGCATA
*
4367415 TTATTTTTATTT-TT-TTTAAATATTATG
1 TTATTTTAATTTATTATTT-AATATT-TG
*
4367442 TTATTTTAATTTATTATTTAATATTTT
1 TTATTTTAATTTATTATTTAATATTTG
4367469 TTATTT
1 TTATTT
4367475 ATCGAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 18 0.62
28 8 0.28
29 3 0.10
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (27 bp):
TTATTTTAATTTATTATTTAATATTTG
Found at i:4367454 original size:22 final size:22
Alignment explanation
Indices: 4367412--4367454 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
4367402 AAGTTTGTGC
* *
4367412 ATATTATTTTTATTTTTTTTAA
1 ATATTATTGTTATTTTATTTAA
4367434 ATATTA-TGTTATTTTAATTTA
1 ATATTATTGTTATTTT-ATTTA
4367455 TTATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
ATATTATTGTTATTTTATTTAA
Found at i:4388094 original size:2 final size:2
Alignment explanation
Indices: 4388087--4388138 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
4388077 AAAATGTTCC
4388087 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
4388129 TA TA TA TA TA
1 TA TA TA TA TA
4388139 AAGGTTTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4389268 original size:24 final size:22
Alignment explanation
Indices: 4389211--4389280 Score: 122
Period size: 22 Copynumber: 3.2 Consensus size: 22
4389201 CTGCTGGGGA
4389211 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
4389233 AACAGAAGCACACACAGTGCTG
1 AACAGAAGCACACACAGTGCTG
* *
4389255 ATCAGAAGCACACACAGTGTTG
1 AACAGAAGCACACACAGTGCTG
4389277 AACA
1 AACA
4389281 ATAAGCGCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.21, T:0.11
Consensus pattern (22 bp):
AACAGAAGCACACACAGTGCTG
Found at i:4393905 original size:27 final size:28
Alignment explanation
Indices: 4393874--4393940 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
4393864 CTTTAATTAC
*
4393874 TAATATAATT-TT-GTCTTTATATTTTTA
1 TAATATAATTATTAGT-TTAATATTTTTA
*
4393901 TAATATTATTAATTAGTTTAATATTTTTA
1 TAATATAATT-ATTAGTTTAATATTTTTA
*
4393930 TAATGTAATTA
1 TAATATAATTA
4393941 AATAGTTCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 9 0.27
28 1 0.03
29 21 0.64
30 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.04, T:0.58
Consensus pattern (28 bp):
TAATATAATTATTAGTTTAATATTTTTA
Found at i:4393926 original size:29 final size:30
Alignment explanation
Indices: 4393892--4393961 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
4393882 TTTTGTCTTT
* * *
4393892 ATATTTTTATAATATTATTAATTAGTT-TA
1 ATATTTTTATAATATAATTAAATAGTTCAA
*
4393921 ATATTTTTATAATGTAATTAAATAGTTCAA
1 ATATTTTTATAATATAATTAAATAGTTCAA
4393951 ATAATTTTTAT
1 AT-ATTTTTAT
4393962 TATTGTTCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 24 0.69
30 3 0.09
31 8 0.23
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
ATATTTTTATAATATAATTAAATAGTTCAA
Found at i:4399681 original size:23 final size:23
Alignment explanation
Indices: 4399654--4399703 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
4399644 TACAATGACT
4399654 AAAATGGATCAAATTAAGGTATA
1 AAAATGGATCAAATTAAGGTATA
4399677 AAAATGGATCAAATTAAGGTATA
1 AAAATGGATCAAATTAAGGTATA
4399700 AAAA
1 AAAA
4399704 CTAAAATCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.16, T:0.24
Consensus pattern (23 bp):
AAAATGGATCAAATTAAGGTATA
Found at i:4402864 original size:41 final size:38
Alignment explanation
Indices: 4402764--4402867 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
4402754 TTCGAAGCAA
* *
4402764 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
4402801 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
4402839 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
4402868 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:4403796 original size:13 final size:12
Alignment explanation
Indices: 4403726--4403807 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
4403716 CATATACATA
*
4403726 TATATATATTAGT
1 TATA-ATATTAAT
*
4403739 TAATAATAATAA-
1 T-ATAATATTAAT
*
4403751 TATAATACTAAT
1 TATAATATTAAT
*
4403763 TA-AATAATAATT
1 TATAATATTAA-T
*
4403775 TATATTATTATAT
1 TATAATATTA-AT
4403788 TATAATATTAAT
1 TATAATATTAAT
4403800 TAATAATA
1 T-ATAATA
4403808 AATTAAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:4404539 original size:6 final size:6
Alignment explanation
Indices: 4404528--4404554 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4404518 GTCACCAAAA
4404528 TCTAAC TCTAAC TCTAAC TCTAAC TCT
1 TCTAAC TCTAAC TCTAAC TCTAAC TCT
4404555 CCTTTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (6 bp):
TCTAAC
Found at i:4404693 original size:31 final size:31
Alignment explanation
Indices: 4404658--4404723 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
4404648 CAAGTTATAT
* * *
4404658 TTTAATTGTGTTTTAATTATTTAAATAATCA
1 TTTAATTATGTTTTAATCATTTAAATAATAA
*
4404689 TTTAATTATGTTTTAATCATTTAGATAATAA
1 TTTAATTATGTTTTAATCATTTAAATAATAA
4404720 TTTA
1 TTTA
4404724 TTTAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.55
Consensus pattern (31 bp):
TTTAATTATGTTTTAATCATTTAAATAATAA
Found at i:4404836 original size:36 final size:31
Alignment explanation
Indices: 4404729--4404824 Score: 192
Period size: 31 Copynumber: 3.1 Consensus size: 31
4404719 ATTTATTTAA
4404729 AATATTATATTTTAATCACTTAAGTAACGAT
1 AATATTATATTTTAATCACTTAAGTAACGAT
4404760 AATATTATATTTTAATCACTTAAGTAACGAT
1 AATATTATATTTTAATCACTTAAGTAACGAT
4404791 AATATTATATTTTAATCACTTAAGTAACGAT
1 AATATTATATTTTAATCACTTAAGTAACGAT
4404822 AAT
1 AAT
4404825 GGATCCCTAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (31 bp):
AATATTATATTTTAATCACTTAAGTAACGAT
Found at i:4408825 original size:2 final size:2
Alignment explanation
Indices: 4408818--4408843 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4408808 CATATTCCTC
4408818 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
4408844 GGGAAGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4408916 original size:17 final size:17
Alignment explanation
Indices: 4408894--4408930 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
4408884 AAATAATTAC
4408894 AAGAAGATGAAAAGTTA
1 AAGAAGATGAAAAGTTA
4408911 AAGAAGATGAAAAGTTA
1 AAGAAGATGAAAAGTTA
4408928 AAG
1 AAG
4408931 GTCAAGGGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.16
Consensus pattern (17 bp):
AAGAAGATGAAAAGTTA
Found at i:4411196 original size:15 final size:15
Alignment explanation
Indices: 4411153--4411198 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
4411143 TTAACACTAG
**
4411153 TTTAAATAAAAAATA
1 TTTAAATAAATTATA
4411168 -TTAAA-AAATATATA
1 TTTAAATAAAT-TATA
4411182 TTTAAATAAATTATA
1 TTTAAATAAATTATA
4411197 TT
1 TT
4411199 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 11 0.42
16 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAATAAATTATA
Found at i:4411203 original size:18 final size:15
Alignment explanation
Indices: 4411168--4411207 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 15
4411158 ATAAAAAATA
4411168 TTAAAAAATATATAT
1 TTAAAAAATATATAT
4411183 TTAAATAAATTATATTAT
1 TTAAA-AAA-TATA-TAT
4411201 TTAAAAA
1 TTAAAAA
4411208 TATTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 5 0.23
16 3 0.14
17 6 0.27
18 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TTAAAAAATATATAT
Found at i:4414026 original size:77 final size:77
Alignment explanation
Indices: 4413943--4414098 Score: 206
Period size: 77 Copynumber: 2.0 Consensus size: 77
4413933 CTCGATTAGC
* * * * * *
4413943 ATGAGTATTATTGTTAAAG-TAGAAGGATGTGGGTTTGAGTGCATTGAAGCGCATTATTCTTTTA
1 ATGAGTATTATTCTTAAAGCAAG-AGGATATGGGTTTGAGTGCATTGAAACGCATTATCCTCTTA
* *
4414007 TTTATAGGTTGGA
65 GTTATAAGTTGGA
* *
4414020 ATGAGTATTATTCTTAATGCAAGAGGATATGGGTTTGAGTGTATTGAAACGCATTATCCTCTTAG
1 ATGAGTATTATTCTTAAAGCAAGAGGATATGGGTTTGAGTGCATTGAAACGCATTATCCTCTTAG
4414085 TTATAAGTTGGA
66 TTATAAGTTGGA
4414097 AT
1 AT
4414099 TTAAAATGAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
77 66 0.97
78 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.39
Consensus pattern (77 bp):
ATGAGTATTATTCTTAAAGCAAGAGGATATGGGTTTGAGTGCATTGAAACGCATTATCCTCTTAG
TTATAAGTTGGA
Found at i:4418547 original size:117 final size:117
Alignment explanation
Indices: 4418341--4418573 Score: 448
Period size: 117 Copynumber: 2.0 Consensus size: 117
4418331 TTACCAGTTT
4418341 TAACTTATTCCCAAGTACTAGGATTAGGAACCACTCAGACTTGTTGTTGCTTAATAGAATGGATC
1 TAACTTATTCCCAAGTACTAGGATTAGGAACCACTCAGACTTGTTGTTGCTTAATAGAATGGATC
* *
4418406 AATTTCATCATTTGCTTCACCTTATATTATGTGTCCCTTCCTCACACCCAAG
66 AACTTCATCATTTGCTTCACCTTATATTATGTGCCCCTTCCTCACACCCAAG
4418458 TAACTTATTCCCAAGTACTAGGATTAGGAACCACTCAGACTTGTTGTTGCTTAATAGAATGGATC
1 TAACTTATTCCCAAGTACTAGGATTAGGAACCACTCAGACTTGTTGTTGCTTAATAGAATGGATC
4418523 AACTTCATCATTTGCTTCACCTTATATTATGTGCCCCTTCCTCACACCCAA
66 AACTTCATCATTTGCTTCACCTTATATTATGTGCCCCTTCCTCACACCCAA
4418574 TTATATTTTA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.27, C:0.25, G:0.13, T:0.34
Consensus pattern (117 bp):
TAACTTATTCCCAAGTACTAGGATTAGGAACCACTCAGACTTGTTGTTGCTTAATAGAATGGATC
AACTTCATCATTTGCTTCACCTTATATTATGTGCCCCTTCCTCACACCCAAG
Found at i:4420701 original size:11 final size:11
Alignment explanation
Indices: 4420685--4420712 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4420675 TTCAGCTAAA
4420685 AAAAAATTTTT
1 AAAAAATTTTT
4420696 AAAAAATTTTT
1 AAAAAATTTTT
4420707 AAAAAA
1 AAAAAA
4420713 CGTTTTCAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
AAAAAATTTTT
Found at i:4421366 original size:15 final size:16
Alignment explanation
Indices: 4421331--4421370 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
4421321 TCCATAAACC
*
4421331 TAATTTAAAAACATTA
1 TAATTTAATAACATTA
*
4421347 GAATTTAATAA-ATTA
1 TAATTTAATAACATTA
4421362 TAATTTAAT
1 TAATTTAAT
4421371 GCATGATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (16 bp):
TAATTTAATAACATTA
Found at i:4421413 original size:18 final size:17
Alignment explanation
Indices: 4421377--4421412 Score: 58
Period size: 15 Copynumber: 2.2 Consensus size: 17
4421367 TAATGCATGA
4421377 TATTTAAAGTTATTTAT
1 TATTTAAAGTTATTTAT
4421394 TATTTAAA-TT-TTTAT
1 TATTTAAAGTTATTTAT
4421409 TATT
1 TATT
4421413 AATGGCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.47
16 2 0.11
17 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTAAAGTTATTTAT
Found at i:4421602 original size:19 final size:18
Alignment explanation
Indices: 4421569--4421608 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
4421559 TTAAATGTTA
4421569 AATATTATTTATAATTAT
1 AATATTATTTATAATTAT
* *
4421587 AATATTAATTTTTAATTTT
1 AATATT-ATTTATAATTAT
4421606 AAT
1 AAT
4421609 TAGTATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTTATAATTAT
Found at i:4423582 original size:38 final size:38
Alignment explanation
Indices: 4423531--4423604 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
4423521 TTTTTAAGAG
*
4423531 AATACCTAATAAAATAA-ATAAAATGACATTGTTATAAA
1 AATACCTAATAAAAGAACA-AAAATGACATTGTTATAAA
* *
4423569 AATACCTAATAAAAGAACAAAATTGATATTGTTATA
1 AATACCTAATAAAAGAACAAAAATGACATTGTTATA
4423605 TACATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 31 0.97
39 1 0.03
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (38 bp):
AATACCTAATAAAAGAACAAAAATGACATTGTTATAAA
Found at i:4424885 original size:10 final size:10
Alignment explanation
Indices: 4424870--4424905 Score: 63
Period size: 10 Copynumber: 3.5 Consensus size: 10
4424860 CTCACTTCTA
4424870 TTTCTCTTTC
1 TTTCTCTTTC
4424880 TTTCTCTTTC
1 TTTCTCTTTC
4424890 TTTCTCTTTCC
1 TTTCTCTTT-C
4424901 TTTCT
1 TTTCT
4424906 ATCTTTCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.76
11 6 0.24
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTCTCTTTC
Found at i:4424889 original size:16 final size:16
Alignment explanation
Indices: 4424865--4424905 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
4424855 GAAAACTCAC
*
4424865 TTCTATTTCTCTT-TCT
1 TTCTCTTTCT-TTCTCT
4424881 TTCTCTTTCTTTCTCT
1 TTCTCTTTCTTTCTCT
4424897 TTC-CTTTCT
1 TTCTCTTTCT
4424906 ATCTTTCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.68
Consensus pattern (16 bp):
TTCTCTTTCTTTCTCT
Found at i:4431020 original size:31 final size:30
Alignment explanation
Indices: 4430951--4431030 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 30
4430941 AAAATTGAAC
*
4430951 TAAATCAAAATTTCATGTATGAAATCATACA
1 TAAATCAAAA-TTCATGTATGAAATCACACA
* *
4430982 -AAATCAAAATTCATGTATGATATTACACA
1 TAAATCAAAATTCATGTATGAAATCACACA
4431011 TTAAATCAAAATTCATGTAT
1 -TAAATCAAAATTCATGTAT
4431031 AATTTTAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 17 0.39
30 9 0.20
31 18 0.41
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.34
Consensus pattern (30 bp):
TAAATCAAAATTCATGTATGAAATCACACA
Found at i:4432971 original size:29 final size:31
Alignment explanation
Indices: 4432930--4432994 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 31
4432920 AATTATTATT
* *
4432930 ATTTTTATAATTTTTAAAAA-TTAAATTA-A
1 ATTTTTATAATTTTAAAAAATTTAAAATATA
*
4432959 ATTTTTATTATTTTAAAAAATTTAAAATATA
1 ATTTTTATAATTTTAAAAAATTTAAAATATA
4432990 ATTTT
1 ATTTT
4432995 ATTTTTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 18 0.58
30 7 0.23
31 6 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTTTATAATTTTAAAAAATTTAAAATATA
Found at i:4433022 original size:36 final size:37
Alignment explanation
Indices: 4432914--4433023 Score: 109
Period size: 36 Copynumber: 3.0 Consensus size: 37
4432904 TGGGAGAGAG
* * * *
4432914 AAATTAAATTATTATTATTTTTATAATTTTTAAAAATT
1 AAATTAAATTTTTATTA-ATTTAAAAATTTTAAAAATT
* *
4432952 AAATTAAATTTTTATTATTTTAAAAAATTT-AAAA-T
1 AAATTAAATTTTTATTAATTTAAAAATTTTAAAAATT
**
4432987 ATAATTTTATTTTTATTAATTT-AAAATTTTAAAAATT
1 A-AATTAAATTTTTATTAATTTAAAAATTTTAAAAATT
4433024 TAAAAAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
35 9 0.15
36 25 0.41
37 11 0.18
38 16 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (37 bp):
AAATTAAATTTTTATTAATTTAAAAATTTTAAAAATT
Found at i:4434459 original size:15 final size:15
Alignment explanation
Indices: 4434439--4434468 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4434429 TGTTTCTTTT
4434439 TCTTCATTAAATTTC
1 TCTTCATTAAATTTC
4434454 TCTTCATTAAATTTC
1 TCTTCATTAAATTTC
4434469 ACTTGTGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
TCTTCATTAAATTTC
Found at i:4447750 original size:16 final size:16
Alignment explanation
Indices: 4447729--4447761 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4447719 ATGATAGAAT
4447729 TTTTCAA-TAATAAAAA
1 TTTTCAATTAA-AAAAA
4447745 TTTTCAATTAAAAAAA
1 TTTTCAATTAAAAAAA
4447761 T
1 T
4447762 ATAAAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.81
17 3 0.19
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
TTTTCAATTAAAAAAA
Found at i:4472569 original size:14 final size:14
Alignment explanation
Indices: 4472550--4472582 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4472540 AGTATTCTTT
*
4472550 ATTAATGTTTTATG
1 ATTAATGTTTAATG
4472564 ATTAATGTTTAATG
1 ATTAATGTTTAATG
4472578 -TTAAT
1 ATTAAT
4472583 AATTGTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (14 bp):
ATTAATGTTTAATG
Found at i:4494628 original size:17 final size:17
Alignment explanation
Indices: 4494589--4494631 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4494579 AAAATATTTA
* *
4494589 TTTTA-ATATTTTTAGT
1 TTTTATATATTTTAAAT
4494605 TTATTATATATTTTAAAT
1 TT-TTATATATTTTAAAT
4494623 TTTTATATA
1 TTTTATATA
4494632 AAATAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 10 0.43
18 11 0.48
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTATATATTTTAAAT
Found at i:4498783 original size:6 final size:6
Alignment explanation
Indices: 4498758--4498802 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
4498748 ACAATTCATA
* * *
4498758 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
4498803 ATTTTGATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:4501143 original size:30 final size:30
Alignment explanation
Indices: 4501098--4501369 Score: 345
Period size: 30 Copynumber: 9.1 Consensus size: 30
4501088 ATCAAAAGGT
4501098 CCCC-AAACTTTTCTAAAATTACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
*** * *
4501127 CTTTTAAACCTTTCTAAAATCACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
*
4501157 CCCCTAAACTTTTCTAAAATTACATTTTGA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* *
4501187 CCCCTAAACTTTTCCAAAATCACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
*
4501217 -CCCTAAACTTTTCAAAAATTACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
*
4501246 CCCCTAAACTTTTCCAAAATTACATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
* * *
4501276 CCTCTAAACTTTTCCAAAATTTCATTTTAA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
4501306 CCCCTAAAACTTTT-TCAAAATTACATTTTGAA
1 CCCCT-AAACTTTTCT-AAAATTACATTTT-AA
* * *
4501338 -CCCTAAACTTTTCCAAAATCACATTTTGA
1 CCCCTAAACTTTTCTAAAATTACATTTTAA
4501367 CCC
1 CCC
4501370 TCGAGCTTCT
Statistics
Matches: 211, Mismatches: 25, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
29 29 0.14
30 156 0.74
31 24 0.11
32 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (30 bp):
CCCCTAAACTTTTCTAAAATTACATTTTAA
Found at i:4501244 original size:89 final size:88
Alignment explanation
Indices: 4501098--4501369 Score: 368
Period size: 89 Copynumber: 3.0 Consensus size: 88
4501088 ATCAAAAGGT
* ** * *
4501098 CCCC-AAACTTTTCTAAAATTACATTTTAACTTTTAAACCTTTCTAAAATCACATTTTAACCCCT
1 CCCCTAAACTTTTCCAAAATTACATTTTAAC-CCTAAACTTTTC-AAAATTACATTTTAACCCCT
*
4501162 AAACTTTTCTAAAATTACATTTTGA
64 AAACTTTTCCAAAATTACATTTTGA
*
4501187 CCCCTAAACTTTTCCAAAATCACATTTTAACCCTAAACTTTTCAAAAATTACATTTTAACCCCTA
1 CCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTC-AAAATTACATTTTAACCCCTA
*
4501252 AACTTTTCCAAAATTACATTTTAA
65 AACTTTTCCAAAATTACATTTTGA
* *
4501276 CCTCTAAACTTTTCCAAAATTTCATTTTAACCCCTAAAACTTTTTCAAAATTACATTTTGAA-CC
1 CCCCTAAACTTTTCCAAAATTACATTTTAA-CCCT-AAAC-TTTTCAAAATTACATTTT-AACCC
*
4501340 CTAAACTTTTCCAAAATCACATTTTGA
62 CTAAACTTTTCCAAAATTACATTTTGA
4501367 CCC
1 CCC
4501370 TCGAGCTTCT
Statistics
Matches: 163, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
89 82 0.50
90 28 0.17
91 46 0.28
92 7 0.04
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.38
Consensus pattern (88 bp):
CCCCTAAACTTTTCCAAAATTACATTTTAACCCTAAACTTTTCAAAATTACATTTTAACCCCTAA
ACTTTTCCAAAATTACATTTTGA
Found at i:4502914 original size:19 final size:19
Alignment explanation
Indices: 4502867--4502906 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4502857 CTTTCTTTCA
* *
4502867 AAATATGATTATTTTAAAT
1 AAATATTATTATTTAAAAT
4502886 AAATATTATTATTTAAAAT
1 AAATATTATTATTTAAAAT
4502905 AA
1 AA
4502907 TTTTTATTGA
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:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (19 bp):
AAATATTATTATTTAAAAT
Found at i:4504301 original size:2 final size:2
Alignment explanation
Indices: 4504296--4504321 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4504286 AAACATTTAT
4504296 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
4504322 CTTCCTTTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4507519 original size:6 final size:6
Alignment explanation
Indices: 4507508--4507552 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
4507498 TTTGTGGTCA
* * * *
4507508 AAATTG AAATTG AAAGTG AAAGTG AAAGTG AAATTG GAATTG AAA
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAA
4507553 GCGATATGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.24
Consensus pattern (6 bp):
AAATTG
Found at i:4509724 original size:2 final size:2
Alignment explanation
Indices: 4509717--4509767 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
4509707 ATGTAACATC
4509717 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
4509759 TA TA TA TA T
1 TA TA TA TA T
4509768 GATAGAAGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4521240 original size:15 final size:15
Alignment explanation
Indices: 4521220--4521253 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4521210 CACACACTTG
4521220 TCTTCTTCATCTTCA
1 TCTTCTTCATCTTCA
4521235 TCTTCTTCATCTTCA
1 TCTTCTTCATCTTCA
4521250 TCTT
1 TCTT
4521254 TAATTACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.12, C:0.32, G:0.00, T:0.56
Consensus pattern (15 bp):
TCTTCTTCATCTTCA
Found at i:4521522 original size:16 final size:16
Alignment explanation
Indices: 4521482--4521525 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
4521472 GGTTTAGGGT
*
4521482 TTAAAAATTCTAATTAA
1 TTAAAAATT-TATTTAA
4521499 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
4521513 TTAAAAATTTATT
1 TTAAAAATTTATT
4521526 CTTATCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:4522204 original size:29 final size:30
Alignment explanation
Indices: 4522149--4522207 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
4522139 ATCTCAAAAT
* *
4522149 TATACATGAATTTTGATTTAATGTGCAATTG
1 TATACATGAATTTTAATTT-AGGTGCAATTG
4522180 TATACATGAATTTTAATTT-GGTGCAATT
1 TATACATGAATTTTAATTTAGGTGCAATT
4522208 ATACACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
31 18 0.69
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (30 bp):
TATACATGAATTTTAATTTAGGTGCAATTG
Found at i:4522218 original size:29 final size:29
Alignment explanation
Indices: 4522146--4522218 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
4522136 TAAATCTCAA
* *
4522146 AATTATACA-TGAATTTTGATTTAATGTGC
1 AATTATACACTGAATTTTAATTT-AGGTGC
4522175 AATTGTATACA-TGAATTTTAATTT-GGTGC
1 AA-T-TATACACTGAATTTTAATTTAGGTGC
4522204 AATTATACACGTGAA
1 AATTATACAC-TGAA
4522219 ACTTTGATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 6 0.16
28 1 0.03
29 12 0.32
30 1 0.03
31 18 0.47
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (29 bp):
AATTATACACTGAATTTTAATTTAGGTGC
Found at i:4522427 original size:30 final size:29
Alignment explanation
Indices: 4522393--4522456 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4522383 AATTTACAAG
*
4522393 AATTGAATC-AAATCAAAATTTCATGTATAC
1 AATTGAA-CAAAAT-AAAAGTTCATGTATAC
* *
4522423 AATTGCACAAAATTAAAGTTCATGTATAC
1 AATTGAACAAAATAAAAGTTCATGTATAC
4522452 AATTG
1 AATTG
4522457 CACATTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 20 0.67
30 10 0.33
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.33
Consensus pattern (29 bp):
AATTGAACAAAATAAAAGTTCATGTATAC
Done.