Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 28 of 226
Found at i:12583551 original size:21 final size:21
Alignment explanation
Indices: 12583527--12583576 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
12583517 CATTGTTTCT
* *
12583527 AATCTCACTGCTACAATATCC
1 AATCTCACAGCTACAATAACC
* *
12583548 AATCTCACAGCTACAGTAACT
1 AATCTCACAGCTACAATAACC
12583569 AATCTCAC
1 AATCTCAC
12583577 CACCACCGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.06, T:0.26
Consensus pattern (21 bp):
AATCTCACAGCTACAATAACC
Found at i:12583999 original size:25 final size:24
Alignment explanation
Indices: 12583965--12584012 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
12583955 ATGTATTAAA
* *
12583965 ATATTTTAATAGTTATATAATAAC
1 ATATTTTAATAATTAAATAATAAC
12583989 ATATATTTAATAATTAAATAATAA
1 ATAT-TTTAATAATTAAATAATAA
12584013 TTTGAATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATTTTAATAATTAAATAATAAC
Found at i:12586694 original size:12 final size:12
Alignment explanation
Indices: 12586677--12586702 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12586667 AACATTGATA
12586677 TATAATATTACG
1 TATAATATTACG
12586689 TATAATATTACG
1 TATAATATTACG
12586701 TA
1 TA
12586703 AATTTCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
TATAATATTACG
Found at i:12587364 original size:20 final size:20
Alignment explanation
Indices: 12587339--12587398 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
12587329 GTAATCTTAT
12587339 AATCATAAATCATAACCATA
1 AATCATAAATCATAACCATA
*
12587359 AATCATTCAAAT--TAAACATA
1 AATCA-T-AAATCATAACCATA
12587379 AATCATATAATCATAACCAT
1 AATCATA-AATCATAACCAT
12587399 TTTAGTTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 17 0.52
21 7 0.21
22 4 0.12
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.28
Consensus pattern (20 bp):
AATCATAAATCATAACCATA
Found at i:12588063 original size:23 final size:23
Alignment explanation
Indices: 12588032--12588076 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
12588022 TACAATCAAC
12588032 ATTACACATATC-AACAAGCCATA
1 ATTACACAT-TCAAACAAGCCATA
*
12588055 ATTAGACATTCAAAACAAGCCA
1 ATTACACATTC-AAACAAGCCA
12588077 AAATAAGTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 8 0.42
24 9 0.47
ACGTcount: A:0.49, C:0.24, G:0.07, T:0.20
Consensus pattern (23 bp):
ATTACACATTCAAACAAGCCATA
Found at i:12588900 original size:3 final size:3
Alignment explanation
Indices: 12588892--12588943 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
12588882 AGTTAAAATA
12588892 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12588939 TAT TA
1 TAT TA
12588944 CTTAAAAGTT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:12588970 original size:5 final size:5
Alignment explanation
Indices: 12588962--12589009 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
12588952 TTAAGTATAA
* * * * *
12588962 ATATT ATATA ATGTT AGATT AGATT ATAAT ATATT ATATT ATATT ATA
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATA
12589010 AAATATAGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (5 bp):
ATATT
Found at i:12591513 original size:5 final size:5
Alignment explanation
Indices: 12591501--12591531 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
12591491 AAGGAAAATT
12591501 TCTT- TCTTC TCTTC TCTTC TCTTC TCTTC TC
1 TCTTC TCTTC TCTTC TCTTC TCTTC TCTTC TC
12591532 ACGTGGGTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (5 bp):
TCTTC
Found at i:12595263 original size:25 final size:26
Alignment explanation
Indices: 12595230--12595286 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 26
12595220 TATATATATT
* * *
12595230 ATAATAATAAATTAATGTATAATAAA
1 ATAATAATAAATAAATGAATAAAAAA
*
12595256 ATAA-AATAAGTAAATGAATAAAAAA
1 ATAATAATAAATAAATGAATAAAAAA
12595281 ATAATA
1 ATAATA
12595287 GAAAGCCAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (26 bp):
ATAATAATAAATAAATGAATAAAAAA
Found at i:12595749 original size:19 final size:20
Alignment explanation
Indices: 12595725--12595765 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
12595715 GAATTTAGGA
*
12595725 AAATATTGAATA-AAAATTG
1 AAATATTCAATATAAAATTG
*
12595744 AAATATTCAATATGAAATTG
1 AAATATTCAATATAAAATTG
12595764 AA
1 AA
12595766 TTGTGTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (20 bp):
AAATATTCAATATAAAATTG
Found at i:12608736 original size:29 final size:29
Alignment explanation
Indices: 12608702--12608771 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 29
12608692 TAAATTTTGT
*
12608702 TTTGATCACTTAATTAAAAAAAGTTATAA
1 TTTGATCAATTAATTAAAAAAAGTTATAA
12608731 TTTGATCATTGAATTAATTAAAAAAAGTTATAA
1 TTTGATC----AATTAATTAAAAAAAGTTATAA
12608764 TTTGATCA
1 TTTGATCA
12608772 TTGAACTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
29 8 0.22
33 28 0.78
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (29 bp):
TTTGATCAATTAATTAAAAAAAGTTATAA
Found at i:12608753 original size:33 final size:33
Alignment explanation
Indices: 12608711--12608776 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
12608701 TTTTGATCAC
12608711 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
1 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
12608744 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
1 TTAATTAAAAAAAGTTATAATTTGATCATTGAA
12608777 CTATTTGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (33 bp):
TTAATTAAAAAAAGTTATAATTTGATCATTGAA
Found at i:12608803 original size:30 final size:31
Alignment explanation
Indices: 12608769--12608843 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
12608759 TATAATTTGA
*
12608769 TCATTGAACTATTTGAAAG-TTTTACTTAAG
1 TCATTGAACTATTTAAAAGTTTTTACTTAAG
* *
12608799 TCATTGAACTATTCAAAAGTTTTTATTTAAG
1 TCATTGAACTATTTAAAAGTTTTTACTTAAG
*
12608830 TCATTGGACTATTT
1 TCATTGAACTATTT
12608844 TTTTTTTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 17 0.44
31 22 0.56
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (31 bp):
TCATTGAACTATTTAAAAGTTTTTACTTAAG
Found at i:12610939 original size:3 final size:3
Alignment explanation
Indices: 12610931--12610960 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12610921 AAATAAGCCC
12610931 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12610961 TGAATGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:12622070 original size:66 final size:66
Alignment explanation
Indices: 12621989--12622122 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
12621979 GACGAACATC
12621989 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
1 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
12622054 T
66 T
12622055 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
1 ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
12622120 T
66 T
12622121 AT
1 AT
12622123 GATCTTATTT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (66 bp):
ATTGAGACACAACCACCACCAATGCAAGTAAAGGCATACGTGCATATATTTAAGTGTTCACATAT
T
Found at i:12629275 original size:22 final size:23
Alignment explanation
Indices: 12629222--12629277 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
12629212 TTTAATTAAA
* * *
12629222 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
12629245 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
12629267 ATTAAAATTAA
1 ATTAAAATTAA
12629278 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:12629290 original size:16 final size:16
Alignment explanation
Indices: 12629253--12629292 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12629243 TTAATAAAAT
* *
12629253 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
12629269 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
12629285 TAAAATTA
1 TAAAATTA
12629293 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:12629398 original size:9 final size:9
Alignment explanation
Indices: 12629365--12629392 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12629355 TTTATCAAAT
12629365 TATTAATTG
1 TATTAATTG
12629374 TATTAATTG
1 TATTAATTG
12629383 TATTAATTG
1 TATTAATTG
12629392 T
1 T
12629393 TGTAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:12629402 original size:68 final size:68
Alignment explanation
Indices: 12629281--12629490 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
12629271 AAATTAATTG
*
12629281 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
12629344 TGA
66 TGA
12629347 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
12629412 TGA
66 TGA
*
12629415 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
12629480 TGA
66 TGA
12629483 TTAGTAAA
1 TTAGTAAA
12629491 ACAAACTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:12629445 original size:9 final size:9
Alignment explanation
Indices: 12629433--12629460 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12629423 TTTATCAAAT
12629433 TATTAATTG
1 TATTAATTG
12629442 TATTAATTG
1 TATTAATTG
12629451 TATTAATTG
1 TATTAATTG
12629460 T
1 T
12629461 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:12629587 original size:21 final size:22
Alignment explanation
Indices: 12629561--12629603 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12629551 AAACTTAAAA
12629561 TAAAAA-AAAACTAT-TATATTT
1 TAAAAATAAAA-TATATATATTT
12629582 TAAAAATAAAATATATATATTT
1 TAAAAATAAAATATATATATTT
12629604 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAAAATAAAATATATATATTT
Found at i:12629971 original size:25 final size:26
Alignment explanation
Indices: 12629925--12629991 Score: 109
Period size: 25 Copynumber: 2.6 Consensus size: 26
12629915 ACAATCATAG
*
12629925 TATAATATTTTTATAAATAAATATAT
1 TATAACATTTTTATAAATAAATATAT
12629951 TATAACATTTTTATAAA-AAATATAT
1 TATAACATTTTTATAAATAAATATAT
*
12629976 TATAACGTTTTTATAA
1 TATAACATTTTTATAA
12629992 TATGTTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 23 0.59
26 16 0.41
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (26 bp):
TATAACATTTTTATAAATAAATATAT
Found at i:12632470 original size:16 final size:16
Alignment explanation
Indices: 12632449--12632482 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
12632439 GTGATTTGAT
*
12632449 AAAAAATAAAAATTTA
1 AAAAAATAAAAAATTA
12632465 AAAAAATAAAAAATTA
1 AAAAAATAAAAAATTA
12632481 AA
1 AA
12632483 TGAATGGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAAAATAAAAAATTA
Found at i:12633091 original size:34 final size:34
Alignment explanation
Indices: 12633053--12633124 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
12633043 ATCCTGGTAA
* *
12633053 ATTTTTT-TTAATGATTTTTTGTTTCTTCTTTTAG
1 ATTTTTTCTGAATGA-TTTTTGTTTCTTATTTTAG
12633087 ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
1 ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
12633121 ATTT
1 ATTT
12633125 ATGATCTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 29 0.83
35 6 0.17
ACGTcount: A:0.17, C:0.06, G:0.10, T:0.68
Consensus pattern (34 bp):
ATTTTTTCTGAATGATTTTTGTTTCTTATTTTAG
Found at i:12635743 original size:14 final size:15
Alignment explanation
Indices: 12635721--12635753 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
12635711 AACTAATATT
*
12635721 TTATTTTTTA-AAAA
1 TTATGTTTTAGAAAA
12635735 TTATGTTTTAGAAAA
1 TTATGTTTTAGAAAA
12635750 TTAT
1 TTAT
12635754 ATTTCTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TTATGTTTTAGAAAA
Found at i:12640282 original size:50 final size:50
Alignment explanation
Indices: 12640222--12640410 Score: 270
Period size: 50 Copynumber: 3.8 Consensus size: 50
12640212 CCTTAAGATC
*
12640222 ATGAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * *
12640272 ACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
* * * * *
12640322 ATGAGATGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
**
12640372 ATGAGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 ATGAG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
12640411 TTTGGCATGT
Statistics
Matches: 122, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 93 0.76
51 29 0.24
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.19
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAG
Found at i:12647191 original size:13 final size:13
Alignment explanation
Indices: 12647173--12647205 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12647163 ATTTCCAGCA
12647173 TTTATGAATTTAT
1 TTTATGAATTTAT
12647186 TTTATGAATTTAT
1 TTTATGAATTTAT
*
12647199 TTGATGA
1 TTTATGA
12647206 TGATCCAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (13 bp):
TTTATGAATTTAT
Found at i:12647430 original size:50 final size:50
Alignment explanation
Indices: 12647300--12647541 Score: 277
Period size: 50 Copynumber: 4.7 Consensus size: 50
12647290 ATTTGGGTAA
* * *
12647300 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGTATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--AAGA-C--G
* *
12647356 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * *
12647406 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
* * * * *
12647456 AGATGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
**
12647506 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
12647542 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
50 92 0.56
51 29 0.18
52 1 0.01
53 3 0.02
55 2 0.01
56 38 0.23
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCAAGACG
Found at i:12647484 original size:100 final size:103
Alignment explanation
Indices: 12647300--12647549 Score: 344
Period size: 100 Copynumber: 2.4 Consensus size: 103
12647290 ATTTGGGTAA
*
12647300 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGTATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* * *
12647365 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* * * *
12647406 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGATGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
*
12647468 TAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
12647506 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
12647550 GTTATTATCA
Statistics
Matches: 130, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
100 50 0.38
101 39 0.30
105 2 0.02
106 39 0.30
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:12649995 original size:10 final size:10
Alignment explanation
Indices: 12649980--12650010 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
12649970 TATCAAATAG
12649980 ATAAAGTTTA
1 ATAAAGTTTA
12649990 ATAAAGTTTA
1 ATAAAGTTTA
12650000 ATAAAGTTTA
1 ATAAAGTTTA
12650010 A
1 A
12650011 AAAACCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (10 bp):
ATAAAGTTTA
Found at i:12651822 original size:8 final size:9
Alignment explanation
Indices: 12651808--12651840 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
12651798 CAGACGGTCT
12651808 TATATATACA
1 TATATAT-CA
12651818 TATATATCA
1 TATATATCA
12651827 TAT-TATCA
1 TATATATCA
12651835 TATATA
1 TATATA
12651841 CTTTTTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 7 0.32
10 7 0.32
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (9 bp):
TATATATCA
Found at i:12658815 original size:16 final size:16
Alignment explanation
Indices: 12658794--12658825 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12658784 TCATACAAAA
12658794 TGAGCTTCGACTACAC
1 TGAGCTTCGACTACAC
12658810 TGAGCTTCGACTACAC
1 TGAGCTTCGACTACAC
12658826 GTGTTGCAAT
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:0.31, G:0.19, T:0.25
Consensus pattern (16 bp):
TGAGCTTCGACTACAC
Found at i:12664622 original size:23 final size:22
Alignment explanation
Indices: 12664596--12664648 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
12664586 TACAGCGTCG
12664596 TAGAAATAATATAAATAAATAAA
1 TAGAAATAATATAAAT-AATAAA
*
12664619 TAG-AATCAATATACATAATAAA
1 TAGAAAT-AATATAAATAATAAA
12664641 -A-AAATAAT
1 TAGAAATAAT
12664649 CACATACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
20 3 0.11
21 4 0.15
22 9 0.33
23 11 0.41
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (22 bp):
TAGAAATAATATAAATAATAAA
Found at i:12665086 original size:21 final size:21
Alignment explanation
Indices: 12665047--12665087 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12665037 TTATACTACA
* *
12665047 AAAAATAAATATGCGTATATG
1 AAAAATAAATATACATATATG
*
12665068 AAAAATATATATACATATAT
1 AAAAATAAATATACATATAT
12665088 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAATAAATATACATATATG
Found at i:12665131 original size:25 final size:23
Alignment explanation
Indices: 12665098--12665152 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
12665088 ATATTTTTTA
12665098 AAAATAACTAAATATAA-AAAAAGAAT
1 AAAA-AACT-AAT-TAATAAAAA-AAT
12665124 AAAAAACTAATTAATAAAAAAAT
1 AAAAAACTAATTAATAAAAAAAT
12665147 AAAAAA
1 AAAAAA
12665153 ATGAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 12 0.43
24 8 0.29
25 4 0.14
26 4 0.14
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAAACTAATTAATAAAAAAAT
Found at i:12665153 original size:25 final size:24
Alignment explanation
Indices: 12665096--12665153 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
12665086 ATATATTTTT
*
12665096 TAAAAATAACTAAATATAAAAAAA
1 TAAAAAAAACTAAATATAAAAAAA
* *
12665120 GAATAAAAAACTAATTAATAAAAAAA
1 TAA-AAAAAACTAAAT-ATAAAAAAA
12665146 TAAAAAAA
1 TAAAAAAA
12665154 TGAAAAAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.07
25 15 0.54
26 11 0.39
ACGTcount: A:0.76, C:0.03, G:0.02, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTAAATATAAAAAAA
Found at i:12665661 original size:23 final size:22
Alignment explanation
Indices: 12665633--12665678 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12665623 CAAATTAAAT
*
12665633 TTCTAAGATTACAAAATCATATC
1 TTCTAAAATTAC-AAATCATATC
* *
12665656 TTCTAAAATTGCATATCATATC
1 TTCTAAAATTACAAATCATATC
12665678 T
1 T
12665679 AAGATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.39, C:0.17, G:0.04, T:0.39
Consensus pattern (22 bp):
TTCTAAAATTACAAATCATATC
Found at i:12665690 original size:19 final size:19
Alignment explanation
Indices: 12665634--12665729 Score: 93
Period size: 19 Copynumber: 4.8 Consensus size: 19
12665624 AAATTAAATT
*
12665634 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
* *
12665654 TCTTCTAAAATTGCATATCATA
1 ---TCTAAGATTACATATCATA
* *
12665676 TCTAAGATTATATATTATA
1 TCTAAGATTACATATCATA
*
12665695 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
12665714 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
12665730 CCTGAAGATT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
19 47 0.75
22 7 0.11
23 9 0.14
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.39
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:12666985 original size:3 final size:3
Alignment explanation
Indices: 12666977--12667004 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12666967 CTTTCTCCAG
12666977 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT C
12667005 CTTTGTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:12669284 original size:29 final size:30
Alignment explanation
Indices: 12669220--12669288 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
12669210 TATTAATTTA
12669220 TAATTTTATCATTTTTGAAGGAATTAAATAG
1 TAATTTTATCATTTTT-AAGGAATTAAATAG
*
12669251 AAATTATT-TCATTTTT-AGGAAGTTAAAT-G
1 TAATT-TTATCATTTTTAAGGAA-TTAAATAG
12669280 TAATTTTAT
1 TAATTTTAT
12669289 TATATATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
28 2 0.06
29 11 0.33
30 6 0.18
31 12 0.36
32 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.12, T:0.48
Consensus pattern (30 bp):
TAATTTTATCATTTTTAAGGAATTAAATAG
Found at i:12672586 original size:46 final size:45
Alignment explanation
Indices: 12672519--12672657 Score: 208
Period size: 46 Copynumber: 3.0 Consensus size: 45
12672509 CATGGAAAAG
12672519 TGTGAAACA-TAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
1 TGTGAAA-AGTAGGTATGGTATTCC-GTGAAGAAAACCATACTGAGT
* * *
12672565 TGTGAAAAGTAGGTATGGTATTTCGGTAAAGAAAAACATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTCCGTGAAGAAAACCATACTGAGT
12672611 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTCCGTGAAGAAAACCATACTGAGT
12672657 T
1 T
12672658 ATAGCCTTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
45 1 0.01
46 81 0.95
47 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.28
Consensus pattern (45 bp):
TGTGAAAAGTAGGTATGGTATTCCGTGAAGAAAACCATACTGAGT
Found at i:12676789 original size:23 final size:25
Alignment explanation
Indices: 12676759--12676815 Score: 77
Period size: 23 Copynumber: 2.4 Consensus size: 25
12676749 AAATTTTATT
12676759 ATTATAAATATTATACATTC-AT-A
1 ATTATAAATATTATACATTCAATCA
*
12676782 ATTATAAATA-TATATATTCAATCA
1 ATTATAAATATTATACATTCAATCA
12676806 ATTA-AAATAT
1 ATTATAAATAT
12676816 AAAGTCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.27
23 17 0.57
24 5 0.17
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATAAATATTATACATTCAATCA
Found at i:12676823 original size:21 final size:24
Alignment explanation
Indices: 12676759--12676823 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 24
12676749 AAATTTTATT
* *
12676759 ATTATAAATATTATACATTC-AT-A
1 ATTATAAATA-TATATAGTCAATCA
*
12676782 ATTATAAATATATATATTCAATCA
1 ATTATAAATATATATAGTCAATCA
12676806 ATTA-AAATATA-A-AGTCAA
1 ATTATAAATATATATAGTCAA
12676824 AACAGTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.13
22 9 0.24
23 19 0.50
24 5 0.13
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTATAAATATATATAGTCAATCA
Found at i:12688522 original size:51 final size:50
Alignment explanation
Indices: 12688395--12688532 Score: 179
Period size: 50 Copynumber: 2.7 Consensus size: 50
12688385 AAAGTAATGG
*
12688395 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGA
* * * * * * *
12688445 TCGCATGTGTAGTACTATGTGCAGGCTATTATGTGTACTGG-ATAGTTTCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAT-G-ATAGA
12688496 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
12688533 TCAGATGGTC
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
49 2 0.03
50 37 0.50
51 35 0.47
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGA
Found at i:12688556 original size:51 final size:48
Alignment explanation
Indices: 12688392--12688577 Score: 183
Period size: 51 Copynumber: 3.7 Consensus size: 48
12688382 GTGAAAGTAA
* *
12688392 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGG-ATGGT
* * * * *
12688442 AGGTCGCATGTGTAGTACTATGTGCAGGCTATTATGTGTACTGGATAGTT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTAC-GGAT-GGT
* * *
12688492 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CGGATGGT
* * *
12688542 CGTGGTCATATGTGTAGTACTATATGTAGGCTACTA
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTA
12688578 TGTGAACCGA
Statistics
Matches: 111, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
49 3 0.03
50 41 0.37
51 65 0.59
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (48 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACGGATGGT
Found at i:12690567 original size:45 final size:45
Alignment explanation
Indices: 12690502--12690650 Score: 196
Period size: 45 Copynumber: 3.4 Consensus size: 45
12690492 GGGTGTTACA
* *
12690502 GATTCCACCAGGTATCATTGATTATAAAGGTGGTTGCTGTGTGCT
1 GATTCCACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCT
*
12690547 GATTCCACCGGGTA-CTATTGATTATGAAGGTGGTTGCTATGTGCT
1 GATTCCACCGGGTATC-ATTGATTATAAAGGTGGTTGCTATGTGCT
* * * *
12690592 GATTCCACTGAGTATCATTGACTATAAGGGTGG-TGCTATGTGCT
1 GATTCCACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCT
*
12690636 GA-TCCACCGTGTATC
1 GATTCCACCGGGTATC
12690651 TGTTATTATT
Statistics
Matches: 92, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
43 11 0.12
44 14 0.15
45 66 0.72
46 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.34
Consensus pattern (45 bp):
GATTCCACCGGGTATCATTGATTATAAAGGTGGTTGCTATGTGCT
Found at i:12692914 original size:2 final size:2
Alignment explanation
Indices: 12692907--12692933 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12692897 GTAAAATTTA
12692907 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 A
12692934 AATCCATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12693174 original size:41 final size:41
Alignment explanation
Indices: 12693129--12693302 Score: 260
Period size: 41 Copynumber: 4.2 Consensus size: 41
12693119 ACTGGCACTT
* * *
12693129 AGCCTGCTAGACATAAAGTTTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
*
12693170 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCATCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
12693211 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGA-CA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGC-ATCA
** * *
12693252 AGCCTGCTAGACTTAAAGTCTGAAACATATCACTGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
12693293 AGCCTGCTAG
1 AGCCTGCTAG
12693303 GCACCGAGCT
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.01
41 120 0.98
42 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCATCA
Found at i:12694002 original size:2 final size:2
Alignment explanation
Indices: 12693997--12694035 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
12693987 ATTCGAACCT
12693997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
12694036 CATACCTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:12696894 original size:21 final size:23
Alignment explanation
Indices: 12696869--12696920 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 23
12696859 AAAAATAAAC
12696869 GCATGTAA-AAAA-TTTAATGTT
1 GCATGTAATAAAATTTTAATGTT
12696890 GCATGTATAATAAAATTTTAATGTT
1 GCATG--TAATAAAATTTTAATGTT
12696915 GCATGT
1 GCATGT
12696921 GTAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 5 0.19
23 4 0.15
24 4 0.15
25 14 0.52
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (23 bp):
GCATGTAATAAAATTTTAATGTT
Found at i:12696910 original size:25 final size:25
Alignment explanation
Indices: 12696876--12696927 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
12696866 AACGCATGTA
12696876 AAAAATTTAATGTTGCATGTATAAT
1 AAAAATTTAATGTTGCATGTATAAT
* *
12696901 AAAATTTTAATGTTGCATGTGTAAT
1 AAAAATTTAATGTTGCATGTATAAT
12696926 AA
1 AA
12696928 TAACACATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.42, C:0.04, G:0.13, T:0.40
Consensus pattern (25 bp):
AAAAATTTAATGTTGCATGTATAAT
Found at i:12697512 original size:5 final size:5
Alignment explanation
Indices: 12697502--12697550 Score: 98
Period size: 5 Copynumber: 9.8 Consensus size: 5
12697492 GTATTAAGTA
12697502 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
12697551 ATAAAACAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 44 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:12715756 original size:24 final size:24
Alignment explanation
Indices: 12715722--12715773 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
12715712 TTTTTAGAAG
* **
12715722 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
12715746 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
12715770 ATTT
1 ATTT
12715774 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:12743534 original size:2 final size:2
Alignment explanation
Indices: 12743527--12743551 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12743517 TAATAATGAA
12743527 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 A
12743552 ACCCTTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12743583 original size:30 final size:30
Alignment explanation
Indices: 12743543--12743599 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12743533 ATATATATAT
*
12743543 ATATATATAACCCTTTTCCGGATAGTCAAA
1 ATATACATAACCCTTTTCCGGATAGTCAAA
*
12743573 ATATACATAACCCTTTTCTGGATAGTC
1 ATATACATAACCCTTTTCCGGATAGTC
12743600 GGAAGCATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (30 bp):
ATATACATAACCCTTTTCCGGATAGTCAAA
Found at i:12748042 original size:21 final size:19
Alignment explanation
Indices: 12748016--12748057 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
12748006 TAAAAAATCC
12748016 AAAAATATCATAAAATTATTT
1 AAAAATATCAT-AAATT-TTT
*
12748037 AAAAATTTCATAAATTTTT
1 AAAAATATCATAAATTTTT
12748056 AA
1 AA
12748058 GATTTTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATATCATAAATTTTT
Found at i:12751609 original size:21 final size:21
Alignment explanation
Indices: 12751585--12751630 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12751575 AAACCTTAAA
*
12751585 TTAAAATATTA-AGTTTAGAAT
1 TTAAAAT-TTAGAGTTCAGAAT
*
12751606 TTAAGATTTAGAGTTCAGAAT
1 TTAAAATTTAGAGTTCAGAAT
12751627 TTAA
1 TTAA
12751631 GTGTTTGGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.43, C:0.02, G:0.13, T:0.41
Consensus pattern (21 bp):
TTAAAATTTAGAGTTCAGAAT
Found at i:12752294 original size:34 final size:38
Alignment explanation
Indices: 12752251--12752320 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 38
12752241 TAAAATATAA
12752251 TAAAAATAAAATC-C-TAA-ATG-CATT-AACTCAATT
1 TAAAAATAAAATCGCATAAGATGCCATTAAACTCAATT
12752284 TAAATAATAAAATCGCATAAGATGCCATTAAACTCAA
1 TAAA-AATAAAATCGCATAAGATGCCATTAAACTCAA
12752321 GCAAAAACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
33 4 0.13
34 9 0.29
35 1 0.03
36 3 0.10
37 3 0.10
38 4 0.13
39 7 0.23
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (38 bp):
TAAAAATAAAATCGCATAAGATGCCATTAAACTCAATT
Found at i:12753994 original size:29 final size:27
Alignment explanation
Indices: 12753953--12754010 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
12753943 TTTGTAATAT
* *
12753953 TAATGATTAAATTTAACAAAAAATATGAA
1 TAATAATTAAA-TTAA-AAAAAATATAAA
* *
12753982 TAATAATTTAATTAATAAAAATATAAA
1 TAATAATTAAATTAAAAAAAATATAAA
12754009 TA
1 TA
12754011 TTAAAAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
27 12 0.48
28 4 0.16
29 9 0.36
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (27 bp):
TAATAATTAAATTAAAAAAAATATAAA
Found at i:12756705 original size:17 final size:17
Alignment explanation
Indices: 12756683--12756718 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12756673 AAAGATATTA
12756683 TTCTTTAATTTGCACTT
1 TTCTTTAATTTGCACTT
**
12756700 TTCTTTTGTTTGCACTT
1 TTCTTTAATTTGCACTT
12756717 TT
1 TT
12756719 ATAAATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.08, T:0.64
Consensus pattern (17 bp):
TTCTTTAATTTGCACTT
Found at i:12779510 original size:21 final size:21
Alignment explanation
Indices: 12779486--12779526 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
12779476 TTTTAATAGT
*
12779486 TTTTTAATAT-TTTTTAGAAAA
1 TTTTTAA-ATCTTTTGAGAAAA
12779507 TTTTTAAATCTTTTGAGAAA
1 TTTTTAAATCTTTTGAGAAA
12779527 TATTCTAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (21 bp):
TTTTTAAATCTTTTGAGAAAA
Found at i:12795428 original size:27 final size:28
Alignment explanation
Indices: 12795376--12795431 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
12795366 AACTTGATCA
* *
12795376 AATCAAAATTTTATGTATAAAGTTACAC
1 AATCAAAATATTACGTATAAAGTTACAC
12795404 AATCAAAA-ATTACGTATACAA-TTACAC
1 AATCAAAATATTACGTATA-AAGTTACAC
12795431 A
1 A
12795432 TTAAATCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.30
Consensus pattern (28 bp):
AATCAAAATATTACGTATAAAGTTACAC
Found at i:12796622 original size:2 final size:2
Alignment explanation
Indices: 12796615--12796646 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12796605 ACATTATACA
12796615 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
12796647 CTTCTAACTC
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:12807904 original size:13 final size:13
Alignment explanation
Indices: 12807883--12807920 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
12807873 ACACTCAAAT
*
12807883 TTCTGAAAAGCAC
1 TTCTCAAAAGCAC
12807896 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
12807909 TTCTCAAAAGCA
1 TTCTCAAAAGCA
12807921 ATGAAGAACT
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:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:12810434 original size:20 final size:21
Alignment explanation
Indices: 12810397--12810454 Score: 91
Period size: 20 Copynumber: 2.8 Consensus size: 21
12810387 CGTGTTTTAC
12810397 TTTTTGTTCAGCTCTTATGAG
1 TTTTTGTTCAGCTCTTATGAG
12810418 TTTTTGTTCAGCT-TTATGAG
1 TTTTTGTTCAGCTCTTATGAG
* *
12810438 CTTCTGTTCAGCTCTTA
1 TTTTTGTTCAGCTCTTA
12810455 CAAGCTTCTG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.14, C:0.17, G:0.17, T:0.52
Consensus pattern (21 bp):
TTTTTGTTCAGCTCTTATGAG
Found at i:12810462 original size:21 final size:21
Alignment explanation
Indices: 12810401--12810466 Score: 89
Period size: 21 Copynumber: 3.2 Consensus size: 21
12810391 TTTTACTTTT
* *
12810401 TGTTCAGCTCTTATGAGTTTT
1 TGTTCAGCTCTTATGAGCTTC
12810422 TGTTCAGCT-TTATGAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
**
12810442 TGTTCAGCTCTTACAAGCTTC
1 TGTTCAGCTCTTATGAGCTTC
12810463 TGTT
1 TGTT
12810467 GGTGTATTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 18 0.45
21 22 0.55
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TGTTCAGCTCTTATGAGCTTC
Found at i:12810686 original size:20 final size:21
Alignment explanation
Indices: 12810643--12810688 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
12810633 GAATTTATGG
*
12810643 ATGATAGGAAATTGTCAGTGA
1 ATGATAGGAAATTGACAGTGA
*
12810664 ATGATAGGGAATTGACA-TGA
1 ATGATAGGAAATTGACAGTGA
12810684 ATGAT
1 ATGAT
12810689 TTTATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.28
Consensus pattern (21 bp):
ATGATAGGAAATTGACAGTGA
Found at i:12817280 original size:50 final size:50
Alignment explanation
Indices: 12817165--12817345 Score: 263
Period size: 50 Copynumber: 3.6 Consensus size: 50
12817155 ACATGCTAAA
* ** * * *
12817165 GCCATGTCCCAAACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTT-TCATCTCGGTGCCAAC
* **
12817216 GCCATGTCCTAGACATGGTCTTACGGGGGACCTTTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGGTGCCAAC
*
12817266 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGGTGCCAAC
12817316 GCCATGTCCCAGACATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
12817346 TCTCTTTACC
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 89 0.76
51 28 0.24
ACGTcount: A:0.20, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGGTGCCAAC
Found at i:12817722 original size:30 final size:28
Alignment explanation
Indices: 12817688--12817744 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
12817678 CCTCAACTCT
12817688 AACTTTGAAAAAATTACAATTTTGCCCCTA
1 AACTTTGAAAAAATTAC-ATTTT-CCCCTA
* * *
12817718 AACTTTTACATAATTACATTTTCCCCT
1 AACTTTGAAAAAATTACATTTTCCCCT
12817745 TCTATGGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 5 0.21
30 14 0.58
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.39
Consensus pattern (28 bp):
AACTTTGAAAAAATTACATTTTCCCCTA
Found at i:12823661 original size:26 final size:26
Alignment explanation
Indices: 12823603--12823655 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
12823593 CAGTAACGGA
*
12823603 AAGCTCACAAAGAACCTTTAATCGAG
1 AAGCTCACAAAGAACCTATAATCGAG
*
12823629 AAGCTCACAAAGAGCCATATAA-CGAG
1 AAGCTCACAAAGAACC-TATAATCGAG
12823655 A
1 A
12823656 CACTCATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 20 0.83
27 4 0.17
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (26 bp):
AAGCTCACAAAGAACCTATAATCGAG
Found at i:12824820 original size:41 final size:40
Alignment explanation
Indices: 12824688--12824821 Score: 109
Period size: 37 Copynumber: 3.4 Consensus size: 40
12824678 ACCAGTTTGG
* *
12824688 CACCCAATGCCTCATC-AGA-TAATTCGAAATAATAATTTGA
1 CACCCAATGCCTCATCGA-ATTAATTCG-AATAGTAAATTGA
* * * *
12824728 CACCCAGTGTCTCATCG-ATTAA-ACTG-A-AGTAAATTGG
1 CACCCAATGCCTCATCGAATTAATTC-GAATAGTAAATTGA
* *
12824765 CACCCAGTACCTCATCGAATTAATTCGAAGTAGTAAATTGA
1 CACCCAATGCCTCATCGAATTAATTCGAA-TAGTAAATTGA
*
12824806 CACCCAATGTCTCATC
1 CACCCAATGCCTCATC
12824822 AACTCGAAGT
Statistics
Matches: 73, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
37 22 0.30
38 7 0.10
39 4 0.05
40 18 0.25
41 22 0.30
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (40 bp):
CACCCAATGCCTCATCGAATTAATTCGAATAGTAAATTGA
Found at i:12830058 original size:25 final size:26
Alignment explanation
Indices: 12830024--12830095 Score: 94
Period size: 25 Copynumber: 2.8 Consensus size: 26
12830014 CACACCACAA
* *
12830024 CTCTTATGAGCATCCCGATAT-TTGG
1 CTCTTATGAGCTTCCCGATATAATGG
* *
12830049 CTCTCATGAGCTTCTCGAT-TAATGG
1 CTCTTATGAGCTTCCCGATATAATGG
12830074 CTCTTATGAGCTTCCCGATATA
1 CTCTTATGAGCTTCCCGATATA
12830096 CAGCTCGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 1 0.03
25 36 0.92
26 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (26 bp):
CTCTTATGAGCTTCCCGATATAATGG
Found at i:12830101 original size:25 final size:25
Alignment explanation
Indices: 12830024--12830140 Score: 87
Period size: 25 Copynumber: 4.7 Consensus size: 25
12830014 CACACCACAA
* * ***
12830024 CTCTTATGAGCATCCCGATATTTGG
1 CTCTCATGAGCTTCCCGATATACAG
*
12830049 CTCTCATGAGCTTCTCGAT-TA-ATGG
1 CTCTCATGAGCTTCCCGATATACA--G
*
12830074 CTCTTATGAGCTTCCCGATATACAG
1 CTCTCATGAGCTTCCCGATATACAG
* * *
12830099 CTC-GATTGAGCTTCCTGTTATACAG
1 CTCTCA-TGAGCTTCCCGATATACAG
*
12830124 CTCACATGAGCTTCCCG
1 CTCTCATGAGCTTCCCG
12830141 TTACATGGCT
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
24 2 0.03
25 68 0.92
26 3 0.04
27 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (25 bp):
CTCTCATGAGCTTCCCGATATACAG
Found at i:12830151 original size:25 final size:26
Alignment explanation
Indices: 12830029--12830173 Score: 81
Period size: 25 Copynumber: 5.8 Consensus size: 26
12830019 CACAACTCTT
* ** *
12830029 ATGAGCATCCCGA-TATTTGGCTCTC
1 ATGAGCTTCCCGATTACATGGCTCAC
* **
12830054 ATGAGCTTCTCGATTA-ATGGCTCTT
1 ATGAGCTTCCCGATTACATGGCTCAC
12830079 ATGAGCTTCCCGATATACA--GCTCGA-
1 ATGAGCTTCCCGAT-TACATGGCTC-AC
* * *
12830104 TTGAGCTTCCTGTTATACA--GCTCAC
1 ATGAGCTTCCCGAT-TACATGGCTCAC
*
12830129 ATGAGCTTCCCG-TTACATGGCTCAA
1 ATGAGCTTCCCGATTACATGGCTCAC
* * *
12830154 AAGAGTTTCCCGTTTACATG
1 ATGAGCTTCCCGATTACATG
12830174 CTCGTATAAG
Statistics
Matches: 98, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
23 4 0.04
24 2 0.02
25 80 0.82
26 11 0.11
27 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (26 bp):
ATGAGCTTCCCGATTACATGGCTCAC
Found at i:12832277 original size:20 final size:21
Alignment explanation
Indices: 12832233--12832277 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
12832223 GAAAACAGGG
12832233 GAAAAAGGAAAGAAAAAGAAA
1 GAAAAAGGAAAGAAAAAGAAA
* *
12832254 -AAAAAGGGAAG-GAAAGAAA
1 GAAAAAGGAAAGAAAAAGAAA
12832273 GAAAA
1 GAAAA
12832278 TTTGGGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (21 bp):
GAAAAAGGAAAGAAAAAGAAA
Found at i:12833077 original size:25 final size:25
Alignment explanation
Indices: 12833026--12833081 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
12833016 AGTTTAGCGC
* * ***
12833026 GCTCTCTTATTATTAGCACGTTGGT
1 GCTCTCTGATTACTAGCACGACAGT
12833051 GCTCTCTGATTACTAGCACGACAGT
1 GCTCTCTGATTACTAGCACGACAGT
12833076 GCTCTC
1 GCTCTC
12833082 CGTTTAGCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.36
Consensus pattern (25 bp):
GCTCTCTGATTACTAGCACGACAGT
Found at i:12834297 original size:13 final size:13
Alignment explanation
Indices: 12834274--12834307 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
12834264 TTTATTTTCT
12834274 AATAT-AATATTA
1 AATATAAATATTA
12834286 AATATAAATATTA
1 AATATAAATATTA
12834299 AATATAAAT
1 AATATAAAT
12834308 GCAATATCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.24
13 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAAATATTA
Found at i:12843707 original size:3 final size:3
Alignment explanation
Indices: 12843699--12843730 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
12843689 TTTCAGTTTT
*
12843699 TTC TTC TTC CTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
12843731 GTCACTCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TTC
Found at i:12844310 original size:40 final size:40
Alignment explanation
Indices: 12844255--12844333 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
12844245 GTTCCAAAAA
12844255 TACATAGCATATTGACATGTGATTTTGCAATTTCTAAATG
1 TACATAGCATATTGACATGTGATTTTGCAATTTCTAAATG
*
12844295 TACATAGCATATTGACATGTTATTTTGCAATTTCTAAAT
1 TACATAGCATATTGACATGTGATTTTGCAATTTCTAAAT
12844334 TGTAGGATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.42
Consensus pattern (40 bp):
TACATAGCATATTGACATGTGATTTTGCAATTTCTAAATG
Found at i:12847584 original size:20 final size:20
Alignment explanation
Indices: 12847559--12847599 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
12847549 ATTCATTGAC
12847559 CCAAATGTTGATTTTTGAGG
1 CCAAATGTTGATTTTTGAGG
12847579 CCAAATGTTGATTTTTGAGG
1 CCAAATGTTGATTTTTGAGG
12847599 C
1 C
12847600 TTATGATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (20 bp):
CCAAATGTTGATTTTTGAGG
Found at i:12848784 original size:3 final size:3
Alignment explanation
Indices: 12848776--12848810 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
12848766 TTTTATAGAA
12848776 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
12848811 AAAGGGGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:12851228 original size:10 final size:10
Alignment explanation
Indices: 12851192--12851220 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
12851182 GTATAATTAA
12851192 AATA-TTTTT
1 AATATTTTTT
12851201 AATATTTTTT
1 AATATTTTTT
12851211 AATATTTTTT
1 AATATTTTTT
12851221 GAATTTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATATTTTTT
Found at i:12860684 original size:5 final size:5
Alignment explanation
Indices: 12860674--12860707 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
12860664 TTGACAAAAC
12860674 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCT
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCT
12860708 GCTTTTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (5 bp):
CTCTT
Found at i:12860715 original size:15 final size:15
Alignment explanation
Indices: 12860674--12860715 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12860664 TTGACAAAAC
*
12860674 CTCTTCTCTTCTCTT
1 CTCTGCTCTTCTCTT
*
12860689 CTCTTCTCTTCTCTT
1 CTCTGCTCTTCTCTT
*
12860704 CTCTGCTTTTCT
1 CTCTGCTCTTCT
12860716 TACTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.60
Consensus pattern (15 bp):
CTCTGCTCTTCTCTT
Found at i:12870719 original size:15 final size:16
Alignment explanation
Indices: 12870701--12870738 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
12870691 ATTCCCAGCC
12870701 ATCATATTCCA-TCGA
1 ATCATATTCCATTCGA
* *
12870716 ATCACATTCCATTGGA
1 ATCATATTCCATTCGA
12870732 ATCATAT
1 ATCATAT
12870739 CATGGAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.34
Consensus pattern (16 bp):
ATCATATTCCATTCGA
Found at i:12871932 original size:6 final size:6
Alignment explanation
Indices: 12871891--12871932 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
12871881 ATGTTGATTA
* * *
12871891 GGTTTG GGTTTG GGTTTG GGTTTT GGTTTT GGTTTT GGTTTT
1 GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT GGTTTT
12871933 ATCACAGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (6 bp):
GGTTTT
Found at i:12871932 original size:12 final size:12
Alignment explanation
Indices: 12871891--12871931 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
12871881 ATGTTGATTA
*
12871891 GGTTTGGGTTTG
1 GGTTTGGGTTTT
12871903 GGTTTGGGTTTT
1 GGTTTGGGTTTT
*
12871915 GGTTTTGGTTTT
1 GGTTTGGGTTTT
12871927 GGTTT
1 GGTTT
12871932 TATCACAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.41, T:0.59
Consensus pattern (12 bp):
GGTTTGGGTTTT
Found at i:12875327 original size:2 final size:2
Alignment explanation
Indices: 12875320--12875358 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12875310 GTATATTCCT
12875320 TA TA 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 TA TA T
12875359 TATTATTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12891639 original size:45 final size:45
Alignment explanation
Indices: 12891585--12891718 Score: 213
Period size: 44 Copynumber: 3.0 Consensus size: 45
12891575 ATCCCGTCTT
*
12891585 TGTAA-CTTAACCATGA-TTACGTAACAACTAACGGAGCCCATTAC
1 TGTAATCTTAACCGT-ATTTACGTAACAACTAACGGAGCCCATTAC
12891629 TGTAATCTTAACCGTATTTACGT-ACAACTAACGGAGCCCATTAC
1 TGTAATCTTAACCGTATTTACGTAACAACTAACGGAGCCCATTAC
*
12891673 TGTAATCTCAACCGTATTTACGTAA-AACTAACGGAGCCCATTAC
1 TGTAATCTTAACCGTATTTACGTAACAACTAACGGAGCCCATTAC
12891717 TG
1 TG
12891719 ATTTTAACAG
Statistics
Matches: 85, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
44 70 0.82
45 15 0.18
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.28
Consensus pattern (45 bp):
TGTAATCTTAACCGTATTTACGTAACAACTAACGGAGCCCATTAC
Found at i:12903621 original size:31 final size:31
Alignment explanation
Indices: 12903586--12903660 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
12903576 AACAAAATTA
** *
12903586 AATAGTTGAATGATCAAAGTAGAAATTTACT
1 AATAGTTGAATGATCAAAAAAGAAACTTACT
*
12903617 AATAGTT-AGATAATCAAAAAAGAAACTTACT
1 AATAGTTGA-ATGATCAAAAAAGAAACTTACT
* *
12903648 AATAATTGGATGA
1 AATAGTTGAATGA
12903661 CTACTAATGC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (31 bp):
AATAGTTGAATGATCAAAAAAGAAACTTACT
Found at i:12914544 original size:29 final size:30
Alignment explanation
Indices: 12914491--12914549 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
12914481 TACGTTGACA
*
12914491 TAATATAGAAACAAATAATTATA-TTATTT
1 TAATATAAAAACAAATAATTATATTTATTT
*
12914520 TAATATAAAAATAAATAAATT-TATTTATTT
1 TAATATAAAAACAAAT-AATTATATTTATTT
12914550 AAACATGTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (30 bp):
TAATATAAAAACAAATAATTATATTTATTT
Found at i:12924767 original size:66 final size:66
Alignment explanation
Indices: 12924656--12924796 Score: 273
Period size: 66 Copynumber: 2.1 Consensus size: 66
12924646 AATAATATAG
12924656 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
1 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
12924721 A
66 A
*
12924722 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAATTAACTTACCATTCATTTATATTTA
1 AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
12924787 A
66 A
12924788 AGTAAGCAT
1 AGTAAGCAT
12924797 GCAAAATTCA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 74 1.00
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (66 bp):
AGTAAGCATATTATGCTTAGTAAGTTCGTATAATGGGAAAGTAACTTACCATTCATTTATATTTA
A
Found at i:12925366 original size:26 final size:26
Alignment explanation
Indices: 12925337--12925386 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
12925327 TGAGAGCCAC
*
12925337 TAATTAGGAAGCTCACAAAGAGCCTT
1 TAATCAGGAAGCTCACAAAGAGCCTT
* * *
12925363 TAATCGGGAAGTTCACGAAGAGCC
1 TAATCAGGAAGCTCACAAAGAGCC
12925387 ATATAACGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (26 bp):
TAATCAGGAAGCTCACAAAGAGCCTT
Found at i:12925396 original size:26 final size:26
Alignment explanation
Indices: 12925343--12925403 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
12925333 CCACTAATTA
*
12925343 GGAAGCTCACAAAGAGCCTTTAATCG
1 GGAAGCTCACAAAGAGCCTATAATCG
* *
12925369 GGAAGTTCACGAAGAGCCATATAA-CG
1 GGAAGCTCACAAAGAGCC-TATAATCG
*
12925395 GGATGCTCA
1 GGAAGCTCA
12925404 TAAGAGCTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.18
Consensus pattern (26 bp):
GGAAGCTCACAAAGAGCCTATAATCG
Found at i:12935604 original size:13 final size:13
Alignment explanation
Indices: 12935571--12935597 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12935561 CCAGTCAATC
12935571 ATTCAAAGCATAA
1 ATTCAAAGCATAA
12935584 ATTCAAAGCATAA
1 ATTCAAAGCATAA
12935597 A
1 A
12935598 GTTAAAGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (13 bp):
ATTCAAAGCATAA
Found at i:12946373 original size:13 final size:13
Alignment explanation
Indices: 12946355--12946406 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 13
12946345 AATGACTCGC
12946355 GACCGTGTGGCAT
1 GACCGTGTGGCAT
*
12946368 GACCGTGTGTGTCACGC
1 GACCGTGTG-G-CA--T
12946385 GACCGTGTGGCAT
1 GACCGTGTGGCAT
12946398 GACCGTGTG
1 GACCGTGTG
12946407 TGTCACACGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 18 0.55
14 1 0.03
15 4 0.12
16 1 0.03
17 9 0.27
ACGTcount: A:0.13, C:0.25, G:0.38, T:0.23
Consensus pattern (13 bp):
GACCGTGTGGCAT
Found at i:12946388 original size:17 final size:16
Alignment explanation
Indices: 12946368--12946423 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 16
12946358 CGTGTGGCAT
12946368 GACCGTGTGTGTCACGC
1 GACCGTGTGTGTCAC-C
*
12946385 GACCGTGTG-G-CA-T
1 GACCGTGTGTGTCACC
12946398 GACCGTGTGTGTCACAC
1 GACCGTGTGTGTCAC-C
12946415 GACCGTGTG
1 GACCGTGTG
12946424 ACAGCCCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 9 0.27
14 1 0.03
15 4 0.12
16 1 0.03
17 18 0.55
ACGTcount: A:0.14, C:0.27, G:0.36, T:0.23
Consensus pattern (16 bp):
GACCGTGTGTGTCACC
Found at i:12946388 original size:30 final size:30
Alignment explanation
Indices: 12946352--12946423 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
12946342 CAAAATGACT
12946352 CGCGACCGTGTGGCATGACCGTGTGTGTCA
1 CGCGACCGTGTGGCATGACCGTGTGTGTCA
12946382 CGCGACCGTGTGGCATGACCGTGTGTGTCA
1 CGCGACCGTGTGGCATGACCGTGTGTGTCA
*
12946412 CACGACCGTGTG
1 CGCGACCGTGTG
12946424 ACAGCCCATG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.14, C:0.28, G:0.36, T:0.22
Consensus pattern (30 bp):
CGCGACCGTGTGGCATGACCGTGTGTGTCA
Found at i:12951844 original size:2 final size:2
Alignment explanation
Indices: 12951837--12951874 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
12951827 CTCCCCACTT
12951837 TC TC TC TC TC TC 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 TC TC TC TC TC TC
12951875 GCTGCGTGCA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12977015 original size:2 final size:2
Alignment explanation
Indices: 12977008--12977035 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12976998 TACGAATGAA
12977008 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
12977036 CTCATACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:12983005 original size:11 final size:11
Alignment explanation
Indices: 12982975--12983008 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
12982965 AAACTAATCA
12982975 TCTCTCAATTAT
1 TCTCTCAATT-T
*
12982987 TTTCTCAATTT
1 TCTCTCAATTT
12982998 TCTCTCAATTT
1 TCTCTCAATTT
12983009 CATCTGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:12983084 original size:51 final size:51
Alignment explanation
Indices: 12983005--12983110 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
12982995 TTTTCTCTCA
* * *
12983005 ATTTCATCTGAATTTACTTTCAAATTCCT-TCCAAATTTCTCTCAAATCCAT
1 ATTTAATCTCAATTTACTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCAT
* * * * *
12983056 ATTTAATCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCT
1 ATTTAATCTCAATTTACTCTCAAATTCCTCTCAAATTTCTCTCAAATCCAT
12983107 ATTT
1 ATTT
12983111 TTAAATAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 45 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.46
Consensus pattern (51 bp):
ATTTAATCTCAATTTACTCTCAAATTCCTCTCAAATTTCTCTCAAATCCAT
Found at i:12987193 original size:45 final size:46
Alignment explanation
Indices: 12987091--12987195 Score: 140
Period size: 46 Copynumber: 2.3 Consensus size: 46
12987081 ATGTGCCGAC
* ** * *
12987091 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAAATACTGT
1 TACTGTTACTGTTACAGATTCAACACTTTGCGTGTCGAAATACAGT
* *
12987137 TACCGTTACTGTTACAGATTCAACACTTTGCGTGTTG-AATACAGT
1 TACTGTTACTGTTACAGATTCAACACTTTGCGTGTCGAAATACAGT
12987182 TACTGTTACTGTTA
1 TACTGTTACTGTTA
12987196 TTGCTACCGT
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 20 0.39
46 31 0.61
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (46 bp):
TACTGTTACTGTTACAGATTCAACACTTTGCGTGTCGAAATACAGT
Found at i:12987310 original size:19 final size:19
Alignment explanation
Indices: 12987282--12987322 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
12987272 ATAGGGGCAA
12987282 ATAAAATAAATTGACTGAT
1 ATAAAATAAATTGACTGAT
* *
12987301 ATAAATTAAATTGAGTGAT
1 ATAAAATAAATTGACTGAT
12987320 ATA
1 ATA
12987323 GTATATGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.34
Consensus pattern (19 bp):
ATAAAATAAATTGACTGAT
Found at i:12988438 original size:125 final size:126
Alignment explanation
Indices: 12988240--12988708 Score: 685
Period size: 125 Copynumber: 3.7 Consensus size: 126
12988230 TACTATTTGC
* * * *
12988240 TCAACTTGAAATTATTTTTTTCAGGACCTACTGTAGCAAAAGCGCGTCCACGACGGCGCGATTTC
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
* * *
12988305 ACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACA
66 ACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* * *
12988366 TCAACTCGAGATTA-TTTTTGCATGACCTACTGTAGCAAAAGTGCGTACAC-ATGGGCGCGATTT
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGA-GGGCGCGATTT
*
12988429 CACAAATTCTTCTAATAAAGCATCCTGCTTGAAGC-ATTTTTATACTATTTGCTCAGAAACG
65 CACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* * * *
12988490 TCAACTCGAAATTATTTTTTCCAGGACCTACTGTAGCAAAAGTGCGTCCACGAGCGCGCGATTTC
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
* * * *
12988555 ACAAATTCTTTTTATAAAGTATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAAAAACG
66 ACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
* *
12988616 TCAACTCGAAATTA-TTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTC
1 TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
* * *
12988680 AGAAATTCTTCTGATAAACCATCCTGCTT
66 ACAAATTCTTCTAATAAAGCATCCTGCTT
12988709 TGATTTTATC
Statistics
Matches: 307, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
124 38 0.12
125 218 0.71
126 51 0.17
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (126 bp):
TCAACTCGAAATTATTTTTTGCAGGACCTACTGTAGCAAAAGCGCGTACACGAGGGCGCGATTTC
ACAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTATACTATTTGCTCAGAAACG
Found at i:12988583 original size:250 final size:241
Alignment explanation
Indices: 12988151--12988708 Score: 857
Period size: 250 Copynumber: 2.3 Consensus size: 241
12988141 GGGTGTTACA
* * *
12988151 CTACTGTAGCAAAAGCGCGTTCACGTGGGCACGATTTTACAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
* *
12988216 TTGAAGCGTTTTTATACTATTTGCTCAACTTGAAATTATTTTTTTCAGGACCTACTGTAGCAAAA
66 TTGAAGCATTTTTATACTATTTGCTCAACTTGAAATTATTTTTTCCAGGACCTACTGTAGCAAAA
12988281 GCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTT
131 GCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTT
* * *
12988346 ATACTATTTGCTCAGAAACATCAACTCGAGATTATTTTTGCATGAC
196 ATACTATTTGCTCAAAAACATCAACTCGAAATTATTTTTGCAGGAC
* * *
12988392 CTACTGTAGCAAAAGTGCGTACACATGGGCGCGATTTCACAAATTCTTCTAATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
12988457 TTGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCCAGGACCTACT
66 TTGAAGCATTTTTATACTATTTGCTC---AAC-T----T-GAAATTATTTTTTCCAGGACCTACT
* * *
12988522 GTAGCAAAAGTGCGTCCACGA-GCGCGCGATTTCACAAATTCTTTTTATAAAGTATCCTGCTTGA
122 GTAGCAAAAGCGCGTCCACGACG-GCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGA
*
12988586 AGCGTTTTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTGCAGGAC
186 AGCGTTTTTTATACTATTTGCTCAAAAACATCAACTCGAAATTATTTTTGCAGGAC
* * *
12988642 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGACTTCAGAAATTCTTCTGATAAACCATCCTGC
1 CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
12988707 TT
66 TT
12988709 TGATTTTATC
Statistics
Matches: 286, Mismatches: 21, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
241 84 0.29
244 3 0.01
245 1 0.00
249 2 0.01
250 196 0.69
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (241 bp):
CTACTGTAGCAAAAGCGCGTACACGTGGGCGCGATTTCACAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTATACTATTTGCTCAACTTGAAATTATTTTTTCCAGGACCTACTGTAGCAAAA
GCGCGTCCACGACGGCGCGATTTCACAAATTCTTCTCATAAAGTATCCTGCTTGAAGCGTTTTTT
ATACTATTTGCTCAAAAACATCAACTCGAAATTATTTTTGCAGGAC
Found at i:12989249 original size:6 final size:6
Alignment explanation
Indices: 12989238--12989265 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12989228 ATATTGGGTT
12989238 CAATCA CAATCA CAATCA CAATCA CAAT
1 CAATCA CAATCA CAATCA CAATCA CAAT
12989266 ATTGTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (6 bp):
CAATCA
Found at i:13004385 original size:21 final size:21
Alignment explanation
Indices: 13004359--13004516 Score: 77
Period size: 21 Copynumber: 7.5 Consensus size: 21
13004349 TGTGTTTACT
*
13004359 TTCTGTTTAGCTCTCATGAGC
1 TTCTGTTCAGCTCTCATGAGC
* *
13004380 TTCTGTTCAACTCAT-ATGAGT
1 TTCTGTTCAGCTC-TCATGAGC
** * **
13004401 TTCCATTCAGCTATTTTGAGC
1 TTCTGTTCAGCTCTCATGAGC
* * * * *
13004422 TTCTGTTTAACCCTCGTGAGT
1 TTCTGTTCAGCTCTCATGAGC
* * *
13004443 TTCCGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTCATGAGC
* * * * *
13004464 TTCAGTTCAACCCTTATTG-GT
1 TTCTGTTCAGCTCTCA-TGAGC
* *
13004485 TTCTGTTTAGCTCACATGAGC
1 TTCTGTTCAGCTCTCATGAGC
13004506 TTCTGTTCAGC
1 TTCTGTTCAGC
13004517 CTTTGGGCTT
Statistics
Matches: 94, Mismatches: 39, Indels: 8
0.67 0.28 0.06
Matches are distributed among these distances:
20 3 0.03
21 89 0.95
22 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.41
Consensus pattern (21 bp):
TTCTGTTCAGCTCTCATGAGC
Found at i:13004442 original size:42 final size:42
Alignment explanation
Indices: 13004396--13004477 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 42
13004386 TCAACTCATA
** * *
13004396 TGAGTTTCCATTCAGCTATTTTGAGCTTCTGTTTAACCCTCG
1 TGAGTTTCCATTCAGCTATTACGAGCTTCAGTTCAACCCTCG
* *
13004438 TGAGTTTCCGTTCAGCTCTTACGAGCTTCAGTTCAACCCT
1 TGAGTTTCCATTCAGCTATTACGAGCTTCAGTTCAACCCT
13004478 TATTGGTTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.17, C:0.27, G:0.17, T:0.39
Consensus pattern (42 bp):
TGAGTTTCCATTCAGCTATTACGAGCTTCAGTTCAACCCTCG
Found at i:13004516 original size:63 final size:63
Alignment explanation
Indices: 13004358--13004516 Score: 160
Period size: 63 Copynumber: 2.5 Consensus size: 63
13004348 TTGTGTTTAC
* * * * *
13004358 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAACTCATATGAGTTTCCATTCAGCTATTTTGAG
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGCTCATACGAGCTTCCATTCAACCATTTTGAG
* * * * * * * *
13004421 CTTCTGTTTAACCCTCGTGAGTTTCCGTTCAGCTCTTACGAGCTT-CAGTTCAACCCTTATTG-G
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGCTCATACGAGCTTCCA-TTCAACCATT-TTGAG
*
13004484 TTTCTGTTTAGCTCACATGAGCTTCTGTTCAGC
1 TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGC
13004517 CTTTGGGCTT
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
62 2 0.03
63 69 0.93
64 3 0.04
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (63 bp):
TTTCTGTTTAGCTCTCATGAGCTTCTGTTCAGCTCATACGAGCTTCCATTCAACCATTTTGAG
Found at i:13005420 original size:42 final size:42
Alignment explanation
Indices: 13005361--13005442 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
13005351 TCAAAATTGT
* *
13005361 TCACACGACCTGTCACAC-AGGCGTGTGGTTTGGCCGTGTGTC
1 TCACACGACCTGTCACACGA-GCGTGTGGCTTGGCAGTGTGTC
* *
13005403 TCACACGGCCTAG-CACACGAGCTTGTGGCTTGGCAGTGTG
1 TCACACGACCT-GTCACACGAGCGTGTGGCTTGGCAGTGTG
13005443 ACCTAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.16, C:0.28, G:0.32, T:0.24
Consensus pattern (42 bp):
TCACACGACCTGTCACACGAGCGTGTGGCTTGGCAGTGTGTC
Found at i:13006253 original size:21 final size:21
Alignment explanation
Indices: 13006210--13006319 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
13006200 TGAATACGCC
*
13006210 AACAGAAGCTC--AAAAGCTG
1 AACAGAAGCTCATAAAAGCTA
* *
13006229 AATAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAAAGCTA
* *
13006250 AATAGAAGCTCGTAAAAGCTA
1 AACAGAAGCTCATAAAAGCTA
* * * *
13006271 AACAGAAGTTCATAAGAGTTG
1 AACAGAAGCTCATAAAAGCTA
*
13006292 AACAGAAGCTCGTAAAAGCTA
1 AACAGAAGCTCATAAAAGCTA
13006313 AACAGAA
1 AACAGAA
13006320 AGTAAAATAC
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 10 0.14
21 63 0.86
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAAAGCTA
Found at i:13006278 original size:42 final size:42
Alignment explanation
Indices: 13006210--13006319 Score: 152
Period size: 42 Copynumber: 2.7 Consensus size: 42
13006200 TGAATACGCC
* *
13006210 AACAGAAGCTC--AAAAGCTGAATAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCGTAAAAGCTAAACAGAAGCTCATAAGAGCTA
* * * *
13006250 AATAGAAGCTCGTAAAAGCTAAACAGAAGTTCATAAGAGTTG
1 AACAGAAGCTCGTAAAAGCTAAACAGAAGCTCATAAGAGCTA
13006292 AACAGAAGCTCGTAAAAGCTAAACAGAA
1 AACAGAAGCTCGTAAAAGCTAAACAGAA
13006320 AGTAAAATAC
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 10 0.16
42 51 0.84
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.16
Consensus pattern (42 bp):
AACAGAAGCTCGTAAAAGCTAAACAGAAGCTCATAAGAGCTA
Found at i:13011280 original size:24 final size:24
Alignment explanation
Indices: 13011225--13011302 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
13011215 GAGGATGAGA
* * *
13011225 TGGTGGGTGTGTTGGTGGCTTGGT
1 TGGTGGCTGAGTTGGAGGCTTGGT
* *
13011249 CGGGGGCTGAGTTGGAGGCTTGGT
1 TGGTGGCTGAGTTGGAGGCTTGGT
* * *
13011273 TGGTGGCTTAGTCGGGGGC-TGAGT
1 TGGTGGCTGAGTTGGAGGCTTG-GT
13011297 TGGTGG
1 TGGTGG
13011303 TTTAGGCGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.05, C:0.09, G:0.54, T:0.32
Consensus pattern (24 bp):
TGGTGGCTGAGTTGGAGGCTTGGT
Found at i:13011307 original size:24 final size:24
Alignment explanation
Indices: 13011271--13011352 Score: 83
Period size: 24 Copynumber: 3.4 Consensus size: 24
13011261 TGGAGGCTTG
* *
13011271 GTTGGTGGCTTAGTCGGGGGCTGA
1 GTTGGAGGTTTAGTCGGGGGCTGA
* * *
13011295 GTTGGTGGTTTAGGCGGGGGTTGA
1 GTTGGAGGTTTAGTCGGGGGCTGA
* * * *
13011319 GTTGGAGGTTTGGTTGGTGGCTTA
1 GTTGGAGGTTTAGTCGGGGGCTGA
13011343 GTTGGAGGTT
1 GTTGGAGGTT
13011353 GAACTGGTGG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.09, C:0.06, G:0.50, T:0.35
Consensus pattern (24 bp):
GTTGGAGGTTTAGTCGGGGGCTGA
Found at i:13011361 original size:60 final size:60
Alignment explanation
Indices: 13011249--13011398 Score: 169
Period size: 60 Copynumber: 2.5 Consensus size: 60
13011239 GTGGCTTGGT
* **
13011249 CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGGGGCTGAGTTGGTGGTTTAGG
1 CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAACTGGTGGTTTAGG
* * * * *
13011309 CGGGGGTTGAGTTGGAGGTTTGGTTGGTGGCTTAGTTGGAGGTTGAACTGGTGGCTT-GG
1 CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAACTGGTGGTTTAGG
* * *
13011368 -GTGGAGCAGAAGTTGGGGGCTTGGTTGGTGG
1 CG-GGGGCTG-AGTTGGAGGCTTGGTTGGTGG
13011399 TTGCACTGGC
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
58 1 0.01
59 6 0.08
60 68 0.91
ACGTcount: A:0.10, C:0.08, G:0.51, T:0.31
Consensus pattern (60 bp):
CGGGGGCTGAGTTGGAGGCTTGGTTGGTGGCTTAGTCGGAGGCTGAACTGGTGGTTTAGG
Found at i:13011372 original size:24 final size:24
Alignment explanation
Indices: 13011333--13011431 Score: 65
Period size: 24 Copynumber: 4.1 Consensus size: 24
13011323 GAGGTTTGGT
* *
13011333 TGGTGGCTTAGTTGGAGGTTGAAC
1 TGGTGGCTTGGGTGGAGGTTGAAC
** *
13011357 TGGTGGCTTGGGTGGA-GCAGAAGT
1 TGGTGGCTTGGGTGGAGGTTGAA-C
* * * *
13011381 TGGGGGCTTGGTTGGTGGTTGCAC
1 TGGTGGCTTGGGTGGAGGTTGAAC
* * * *
13011405 TGGCGCCTTGGGTGGTGGATGAAC
1 TGGTGGCTTGGGTGGAGGTTGAAC
13011429 TGG
1 TGG
13011432 AGGAGGAGTG
Statistics
Matches: 56, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
23 4 0.07
24 49 0.88
25 3 0.05
ACGTcount: A:0.12, C:0.11, G:0.47, T:0.29
Consensus pattern (24 bp):
TGGTGGCTTGGGTGGAGGTTGAAC
Found at i:13011503 original size:12 final size:12
Alignment explanation
Indices: 13011460--13011513 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
13011450 GGGCTTAGTG
*
13011460 GGTGGATGAGGAT
1 GGTGG-TGAGGGT
*
13011473 GGGGGTGAGGGT
1 GGTGGTGAGGGT
13011485 GAG-GGTGAGGGT
1 G-GTGGTGAGGGT
*
13011497 GGTGGTGATGGT
1 GGTGGTGAGGGT
13011509 GGTGG
1 GGTGG
13011514 GTTGGTGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 1 0.03
12 30 0.83
13 5 0.14
ACGTcount: A:0.13, C:0.00, G:0.65, T:0.22
Consensus pattern (12 bp):
GGTGGTGAGGGT
Found at i:13014470 original size:30 final size:30
Alignment explanation
Indices: 13014434--13014495 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
13014424 CCAAACACTT
13014434 AAGCCCATATAATATATAGTAAAGAATATC
1 AAGCCCATATAATATATAGTAAAGAATATC
13014464 AAGCCCATATAATATATAGTAAAGAATATC
1 AAGCCCATATAATATATAGTAAAGAATATC
13014494 AA
1 AA
13014496 AAAATAGTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (30 bp):
AAGCCCATATAATATATAGTAAAGAATATC
Found at i:13019449 original size:18 final size:19
Alignment explanation
Indices: 13019407--13019455 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
13019397 TCAAGATCTT
13019407 AAATTAATGTAGTCCAAAG
1 AAATTAATGTAGTCCAAAG
*
13019426 AAATTAATGTGGTCCAAA-
1 AAATTAATGTAGTCCAAAG
13019444 AAATTAAT-TAGT
1 AAATTAATGTAGT
13019456 AAATTTTCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 3 0.11
18 8 0.29
19 17 0.61
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (19 bp):
AAATTAATGTAGTCCAAAG
Done.