Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 121 of 145
Found at i:40369462 original size:15 final size:15
Alignment explanation
Indices: 40369442--40369472 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40369432 AATCCTTAAT
40369442 CCATACTCCATAAAC
1 CCATACTCCATAAAC
*
40369457 CCATACTCCCTAAAC
1 CCATACTCCATAAAC
40369472 C
1 C
40369473 TTAAAATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.45, G:0.00, T:0.19
Consensus pattern (15 bp):
CCATACTCCATAAAC
Found at i:40369560 original size:92 final size:92
Alignment explanation
Indices: 40369453--40369634 Score: 314
Period size: 92 Copynumber: 2.0 Consensus size: 92
40369443 CATACTCCAT
*
40369453 AAACCCATACTCCCTAAACCTTAAAATA-TGAATTCCTAAA-TCGGCCTTAAATCTTAAATAAAT
1 AAACCCATACTCCCTAAACCTTAAAATAGT-AACTCCTAAACT-GGCCTTAAATCTTAAATAAAT
*
40369516 CATATACCCTAAACCAAAAACCCTAAAAA
64 CATATACCCTAAACCAAAAACCATAAAAA
40369545 AAACCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACTGGCCTTAAATCTTAAATAAATCA
1 AAACCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACTGGCCTTAAATCTTAAATAAATCA
40369610 TATACCCTAAACCAAAAACCATAAA
66 TATACCCTAAACCAAAAACCATAAA
40369635 CTATAGTGAT
Statistics
Matches: 86, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
92 84 0.98
93 2 0.02
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (92 bp):
AAACCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACTGGCCTTAAATCTTAAATAAATCA
TATACCCTAAACCAAAAACCATAAAAA
Found at i:40370000 original size:41 final size:40
Alignment explanation
Indices: 40369914--40370053 Score: 167
Period size: 41 Copynumber: 3.5 Consensus size: 40
40369904 TTTTTAGTGA
* * *
40369914 CGCTTTTCCAAAAACGCCGCT-AAGCCCCTAGCATTAGCGA
1 CGCTTTTTCAAAAACGCCGCTAAAGCCCC-AACATTAGCGG
*
40369954 CGCTTTTTGAAAAACGCCGCTAAAGGCCCCAACATTAGCGG
1 CGCTTTTTCAAAAACGCCGCTAAA-GCCCCAACATTAGCGG
* *
40369995 CGCTTTTTCAAAAACGCCGCTAAATCCCCCATA-ATTATCGG
1 CGCTTTTTCAAAAACGCCGCTAAA-GCCCCA-ACATTAGCGG
*
40370036 CGCTTTTTGAAAAACGCC
1 CGCTTTTTCAAAAACGCC
40370054 TTGAAAACGA
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
40 19 0.22
41 63 0.72
42 6 0.07
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (40 bp):
CGCTTTTTCAAAAACGCCGCTAAAGCCCCAACATTAGCGG
Found at i:40373432 original size:37 final size:37
Alignment explanation
Indices: 40373391--40373484 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
40373381 CTGAAAGTAA
* * * *
40373391 CTCAAACGACTAAATTTTATTGTTATACTGAGTGAAG
1 CTCAAACGAGTAAATTCTACTGTTATACTGAATGAAG
* * * *
40373428 CTCAAATGAGAAAATTCTACTGTTATGCTGAATGGAG
1 CTCAAACGAGTAAATTCTACTGTTATACTGAATGAAG
*
40373465 CTCAAACGAGTAAAATCTAC
1 CTCAAACGAGTAAATTCTAC
40373485 AAATATACTA
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (37 bp):
CTCAAACGAGTAAATTCTACTGTTATACTGAATGAAG
Found at i:40379137 original size:23 final size:23
Alignment explanation
Indices: 40379080--40379140 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
40379070 CTGGTGGTTT
*
40379080 ATCCGCATATCTACTGGCAATTC
1 ATCCGCATATCTACTAGCAATTC
** *
40379103 ATCTACAAATCTACTAGCAATTC
1 ATCCGCATATCTACTAGCAATTC
*
40379126 ATCCGCTTATCTACT
1 ATCCGCATATCTACT
40379141 GGTGGTATTT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.33
Consensus pattern (23 bp):
ATCCGCATATCTACTAGCAATTC
Found at i:40384217 original size:9 final size:9
Alignment explanation
Indices: 40384200--40384236 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
40384190 TGAGTTTTTG
40384200 AATTCGAAT
1 AATTCGAAT
*
40384209 AACTCGAAT
1 AATTCGAAT
40384218 AATTCGAAT
1 AATTCGAAT
40384227 AATTCGAAT
1 AATTCGAAT
40384236 A
1 A
40384237 TTAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:40384867 original size:30 final size:28
Alignment explanation
Indices: 40384833--40384895 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
40384823 AAAAAACCCT
40384833 TTTTTAAAAAAATTTACCGAAATGGGCCA
1 TTTTT-AAAAAATTTACCGAAATGGGCCA
* ** *
40384862 CTTTTTTAATTATTTACCGGAATGGGCCA
1 -TTTTTAAAAAATTTACCGAAATGGGCCA
40384891 TTTTT
1 TTTTT
40384896 CGCGAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.17
29 19 0.66
30 5 0.17
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.41
Consensus pattern (28 bp):
TTTTTAAAAAATTTACCGAAATGGGCCA
Found at i:40385401 original size:125 final size:124
Alignment explanation
Indices: 40385174--40385454 Score: 415
Period size: 125 Copynumber: 2.3 Consensus size: 124
40385164 TTATTTGGAG
* **
40385174 TTGACATTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGATGCTATCAGAGAAGAAATTATG
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGATGCTATCAGAGAAGAAATTATG
* *
40385238 AAATCATGCCCTCGTGGACGCGATTTCGGTACAGTTGGTCATGTAAGAAATAATT-TTTT
65 AAATCACGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
*
40385297 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAAGATGCTAT-ATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACC-AGATGCTATCA-GAGAAGAAATTA
* *
40385361 TGAAATCGCGCCTTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
63 TGAAATCACGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
* *
40385423 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
40385455 GCCCTCATGG
Statistics
Matches: 143, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 5 0.03
124 30 0.21
125 98 0.69
126 10 0.07
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGATGCTATCAGAGAAGAAATTATGA
AATCACGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAATTATTTT
Found at i:40388695 original size:29 final size:29
Alignment explanation
Indices: 40388635--40389292 Score: 610
Period size: 29 Copynumber: 22.0 Consensus size: 29
40388625 NNNNNNNNNN
** *
40388635 ATTAAATTAGGTTAGTGTTTAGGGTTTTTA
1 ATTAAATTAAATTAG-GGTTAGGGTTTTTA
**
40388665 ATTAAATTAGGTTAGGGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
**
40388694 ATTAAATTAGGTTAGGGTTTAGGG-TTTTA
1 ATTAAATTAAATTAGGG-TTAGGGTTTTTA
40388723 ATTAAATTAAATTAGGGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
* *
40388752 ATCAAATTAAGTTAGGGTTTAGGG---TT-
1 ATTAAATTAAATTAGGG-TTAGGGTTTTTA
*
40388778 -TT-AATTAAATTA-GGTTAGGATTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
*
40388804 ATTAAATTAAATTAGAGTTAGGG-TTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
**
40388832 ATTAAATTAGGTTAGGGTTTAGGG-TTTTA
1 ATTAAATTAAATTAGGG-TTAGGGTTTTTA
*
40388861 ATTAAATTAAACTAGGGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
40388890 ATTAAATTAAATTAGGGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
40388919 ATTTAGGGTTTTTAATTAAATTA-GGTTAGGGTTAGAGTTTA
1 A-TTA--------AATTAAATTAGGGTTAGGGTT----TTTA
* * *
40388960 GGGTTTTTAATTAAATTAGGTTTAGGGTTAGAGTTTA
1 ----ATTAAATTAAATTAGGGTTAGGGTT----TTTA
* **
40388997 GGGTTTAAATTAGGTTAGGGTTAAGGGTTTTTA
1 ---ATTAAATTAAATTAGGGTT-AGGGTTTTTA
**
40389030 ATTAAAATGGGTTAGGGTTAGGGTTAGGG-TTTTA
1 ATT-AAA----TTA-AATTAGGGTTAGGGTTTTTA
40389064 ATTAAATTAAATTAGGGTTAGGG-TTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
** *
40389092 ATTAAATTAGGTTAGGGTTTAAGG-TTTTA
1 ATTAAATTAAATTAGGG-TTAGGGTTTTTA
*
40389121 ATTAAATTAAACTAGGGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
* *
40389150 ATTAAATTAAACTAGGATTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
*
40389179 ATTAAATTAAATTAGGGTTAGTGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
40389208 ATTAAATTAAATTAGGGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
*
40389237 ATTAAATTAAATTA-GGTTTGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
40389265 ATTAAATTAAATTA-GGTTAGGGTTTTTA
1 ATTAAATTAAATTAGGGTTAGGGTTTTTA
40389293 GNNNNNNNNN
Statistics
Matches: 547, Mismatches: 42, Indels: 80
0.82 0.06 0.12
Matches are distributed among these distances:
22 5 0.01
23 2 0.00
24 9 0.02
25 3 0.01
27 4 0.01
28 118 0.22
29 263 0.48
30 32 0.06
31 3 0.01
33 7 0.01
34 8 0.01
35 7 0.01
36 37 0.07
37 33 0.06
38 10 0.02
41 4 0.01
44 2 0.00
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.45
Consensus pattern (29 bp):
ATTAAATTAAATTAGGGTTAGGGTTTTTA
Found at i:40388926 original size:14 final size:14
Alignment explanation
Indices: 40388907--40388935 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
40388897 TAAATTAGGG
40388907 TTAGGGTTTTTAAT
1 TTAGGGTTTTTAAT
40388921 TTAGGGTTTTTAAT
1 TTAGGGTTTTTAAT
40388935 T
1 T
40388936 AAATTAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.59
Consensus pattern (14 bp):
TTAGGGTTTTTAAT
Found at i:40388989 original size:43 final size:41
Alignment explanation
Indices: 40388878--40389002 Score: 124
Period size: 37 Copynumber: 3.2 Consensus size: 41
40388868 TAAACTAGGG
**
40388878 TTAGGGTTTTTAATTAAATTAAATTAGGGTTAGGGTTTTTAAT
1 TTAGGGTTTTTAATTAAATT--ATTAGGGTTAGGGTTTAGAAT
*
40388921 TTAGGGTTTTTAATT-AA--ATTA-GGTTAGGG-TTAGAGT
1 TTAGGGTTTTTAATTAAATTATTAGGGTTAGGGTTTAGAAT
* *
40388957 TTAGGGTTTTTAATT-AA--ATTAGGTTTAGGG-TTAGAGT
1 TTAGGGTTTTTAATTAAATTATTAGGGTTAGGGTTTAGAAT
40388994 TTAGGGTTT
1 TTAGGGTTT
40389003 AAATTAGGTT
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
36 25 0.32
37 31 0.40
38 4 0.05
42 2 0.03
43 15 0.19
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (41 bp):
TTAGGGTTTTTAATTAAATTATTAGGGTTAGGGTTTAGAAT
Found at i:40389008 original size:36 final size:36
Alignment explanation
Indices: 40388891--40389008 Score: 157
Period size: 36 Copynumber: 3.2 Consensus size: 36
40388881 GGGTTTTTAA
** *
40388891 TTAAATTAAATTAGGGTTAGGGTTTTTAATTTAGGGTT
1 TTAAATTAAATTA-GGTTAGGG-TTAGAGTTTAGGGTT
*
40388929 TTTAATTAAATTAGGTTAGGGTTAGAGTTTAGGGTT
1 TTAAATTAAATTAGGTTAGGGTTAGAGTTTAGGGTT
*
40388965 TTTAATTAAATTAGGTTTAGGGTTAGAGTTTAGGG-T
1 TTAAATTAAATTAGG-TTAGGGTTAGAGTTTAGGGTT
40389001 TTAAATTA
1 TTAAATTA
40389009 GGTTAGGGTT
Statistics
Matches: 74, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
36 35 0.47
37 27 0.36
38 12 0.16
ACGTcount: A:0.30, C:0.00, G:0.25, T:0.46
Consensus pattern (36 bp):
TTAAATTAAATTAGGTTAGGGTTAGAGTTTAGGGTT
Found at i:40389015 original size:36 final size:37
Alignment explanation
Indices: 40388894--40389002 Score: 166
Period size: 37 Copynumber: 2.9 Consensus size: 37
40388884 TTTTTAATTA
* ** *
40388894 AATTAAATTAGGGTTAGGGTTTTTAATTTAGGGTTTTT
1 AATTAAATTAGGTTTAGGG-TTAGAGTTTAGGGTTTTT
40388932 AATTAAATTAGG-TTAGGGTTAGAGTTTAGGGTTTTT
1 AATTAAATTAGGTTTAGGGTTAGAGTTTAGGGTTTTT
40388968 AATTAAATTAGGTTTAGGGTTAGAGTTTAGGGTTT
1 AATTAAATTAGGTTTAGGGTTAGAGTTTAGGGTTT
40389003 AAATTAGGTT
Statistics
Matches: 67, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
36 27 0.40
37 28 0.42
38 12 0.18
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.46
Consensus pattern (37 bp):
AATTAAATTAGGTTTAGGGTTAGAGTTTAGGGTTTTT
Found at i:40389098 original size:23 final size:22
Alignment explanation
Indices: 40389068--40389111 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40389058 GTTTTAATTA
40389068 AATTAAATTAGGGTTAGGGTTTT
1 AATTAAATTA-GGTTAGGGTTTT
40389091 AATTAAATTAGGTTAGGGTTT
1 AATTAAATTAGGTTAGGGTTT
40389112 AAGGTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.25, T:0.43
Consensus pattern (22 bp):
AATTAAATTAGGTTAGGGTTTT
Found at i:40392226 original size:5 final size:5
Alignment explanation
Indices: 40392216--40392244 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
40392206 GAACAAATAT
40392216 ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTC
40392245 AAATTCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:40392495 original size:22 final size:21
Alignment explanation
Indices: 40392467--40392524 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
40392457 ATGCAATCTT
*
40392467 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
40392488 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
40392511 AGATTTGATTTGTA
1 AGATATGATTTGTA
40392525 GATACCTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:40396225 original size:74 final size:75
Alignment explanation
Indices: 40396158--40396321 Score: 278
Period size: 74 Copynumber: 2.2 Consensus size: 75
40396148 AATTTATTGT
* *
40396158 TATTTAGTTATAAATACAATTACTAAAGAATTTCTTTTATGAAATAAGGATTTTACTTTTAATTA
1 TATTTAGTAACAAATACAATTACTAAAGAATTTCTTTTATGAAATAAGGATTTTACTTTTAATTA
40396223 A-TTATAAAA
66 ATTTATAAAA
40396232 TATTTAGTAACAAATACAATTACTAAAGAATTTCTTTTATGAAATAAGGATTTTACTTTTAATTA
1 TATTTAGTAACAAATACAATTACTAAAGAATTTCTTTTATGAAATAAGGATTTTACTTTTAATTA
40396297 A-TTATAAAA
66 ATTTATAAAA
*
40396306 TAATATAGTAACAAAT
1 T-ATTTAGTAACAAAT
40396322 GATAAATTAT
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
74 73 0.85
75 13 0.15
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (75 bp):
TATTTAGTAACAAATACAATTACTAAAGAATTTCTTTTATGAAATAAGGATTTTACTTTTAATTA
ATTTATAAAA
Found at i:40396350 original size:74 final size:74
Alignment explanation
Indices: 40396195--40396350 Score: 183
Period size: 74 Copynumber: 2.1 Consensus size: 74
40396185 GAATTTCTTT
* * *
40396195 TATGAAATAAGGATTTTACTTTTAATTAATTATAAAATATTTAGTAACAAATACAATTACTAAAG
1 TATGAAATAAGGATTTTACTTTTAATTAATTATAAAATATATAGTAACAAATAAAATTACTAAAC
** ***
40396260 AATTTCTTT
66 AACGTCACA
40396269 TATGAAATAAGGATTTTACTTTTAATTAATTATAAAATAATATAGTAACAAATGATAAATTA-T-
1 TATGAAATAAGGATTTTACTTTTAATTAATTATAAAAT-ATATAGTAACAAAT-A-AAATTACTA
*
40396332 AACCACGTCACA
63 AACAACGTCACA
40396344 TA-GAAAT
1 TATGAAAT
40396351 TATTATTATT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
74 43 0.61
75 20 0.29
76 2 0.03
77 5 0.07
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.38
Consensus pattern (74 bp):
TATGAAATAAGGATTTTACTTTTAATTAATTATAAAATATATAGTAACAAATAAAATTACTAAAC
AACGTCACA
Found at i:40398528 original size:31 final size:31
Alignment explanation
Indices: 40398490--40398552 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
40398480 AAAGATAACC
40398490 TAAGCTTCACACTTATGGTTCCTTCTTTGAA
1 TAAGCTTCACACTTATGGTTCCTTCTTTGAA
40398521 TAAGCTTCACACTTATGGTTCCTTCTTTGAA
1 TAAGCTTCACACTTATGGTTCCTTCTTTGAA
40398552 T
1 T
40398553 TACATAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (31 bp):
TAAGCTTCACACTTATGGTTCCTTCTTTGAA
Found at i:40409401 original size:77 final size:77
Alignment explanation
Indices: 40409291--40409435 Score: 272
Period size: 77 Copynumber: 1.9 Consensus size: 77
40409281 AATAAAATTA
*
40409291 TATCCATTTTATAGACATATAATTCATATCAAATTAGTCCCTAGAGTTCAACAATTTTCTAAAAT
1 TATCCATTTTATAGACATATAATTCATATCAAATTAGTCCCTAGAGTTCAACAATTTTATAAAAT
40409356 TGTTATTTCCAT
66 TGTTATTTCCAT
*
40409368 TATCCATTTTATAGACATATCATTCATATCAAATTAGTCCCTAGAGTTCAACAATTTTATAAAAT
1 TATCCATTTTATAGACATATAATTCATATCAAATTAGTCCCTAGAGTTCAACAATTTTATAAAAT
40409433 TGT
66 TGT
40409436 ACATTCCATT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 66 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.41
Consensus pattern (77 bp):
TATCCATTTTATAGACATATAATTCATATCAAATTAGTCCCTAGAGTTCAACAATTTTATAAAAT
TGTTATTTCCAT
Found at i:40409624 original size:28 final size:28
Alignment explanation
Indices: 40409587--40409684 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
40409577 ACAAAGTGTA
40409587 AATAACGATAAGCACCGAAGTGCAAAAT
1 AATAACGATAAGCACCGAAGTGCAAAAT
* * * *
40409615 AATAATGATAAGAACCAAAGTGCAAAGTTT
1 AATAACGATAAGCACCGAAGTGCAAA--AT
* * *
40409645 TACAACGATAAGCACCGAAGTGCGAAAT
1 AATAACGATAAGCACCGAAGTGCAAAAT
40409673 AAT-ACGATAAGC
1 AATAACGATAAGC
40409685 GCTCTAATTT
Statistics
Matches: 55, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
27 9 0.16
28 25 0.45
30 21 0.38
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.17
Consensus pattern (28 bp):
AATAACGATAAGCACCGAAGTGCAAAAT
Found at i:40412146 original size:21 final size:21
Alignment explanation
Indices: 40412113--40412153 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40412103 CAAGTGCATT
* * *
40412113 AGCTTTTATGAGCTTTTGTTC
1 AGCTCTTAGGAGCTTCTGTTC
40412134 AGCTCTTAGGAGCTTCTGTT
1 AGCTCTTAGGAGCTTCTGTT
40412154 GGCGTGTTCG
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:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (21 bp):
AGCTCTTAGGAGCTTCTGTTC
Found at i:40414426 original size:21 final size:23
Alignment explanation
Indices: 40414387--40414428 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
40414377 GTTAGGAGTG
*
40414387 TTACACCATCCATCTTTACACTT
1 TTACACCATCCATCATTACACTT
40414410 TTAC-CCAT-CATCATTACAC
1 TTACACCATCCATCATTACAC
40414429 CTTAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 4 0.22
23 4 0.22
ACGTcount: A:0.29, C:0.36, G:0.00, T:0.36
Consensus pattern (23 bp):
TTACACCATCCATCATTACACTT
Found at i:40416728 original size:20 final size:20
Alignment explanation
Indices: 40416670--40416728 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
40416660 GCCCGAATTA
*
40416670 TATTAAATATATAT-TTATT
1 TATTAAATATATATATTTTT
* *
40416689 T-TT-AATCAAATATACTTTT
1 TATTAAAT-ATATATATTTTT
40416708 TATTAAATATATATATTTTT
1 TATTAAATATATATATTTTT
40416728 T
1 T
40416729 GACTTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
17 3 0.10
18 7 0.23
19 5 0.16
20 13 0.42
21 3 0.10
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTAAATATATATATTTTT
Found at i:40426317 original size:9 final size:9
Alignment explanation
Indices: 40426303--40426334 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
40426293 NNNNNNNGGT
40426303 TAATTCGGG
1 TAATTCGGG
*
40426312 TAATTCGGT
1 TAATTCGGG
40426321 TAATTCGGG
1 TAATTCGGG
40426330 TAATT
1 TAATT
40426335 TAGTTAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (9 bp):
TAATTCGGG
Found at i:40426323 original size:18 final size:18
Alignment explanation
Indices: 40426300--40426361 Score: 90
Period size: 18 Copynumber: 3.4 Consensus size: 18
40426290 NNNNNNNNNN
*
40426300 GGTTAATTCGGGTAATTC
1 GGTTAATTCGGGTAATTA
40426318 GGTTAATTCGGGTAATTTA
1 GGTTAATTCGGGTAA-TTA
*
40426337 -GTTAATTCGGTTAATTA
1 GGTTAATTCGGGTAATTA
40426354 GGTTAATT
1 GGTTAATT
40426362 TTTAACCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.08
18 35 0.88
19 2 0.05
ACGTcount: A:0.26, C:0.06, G:0.24, T:0.44
Consensus pattern (18 bp):
GGTTAATTCGGGTAATTA
Found at i:40427182 original size:19 final size:19
Alignment explanation
Indices: 40427158--40427195 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40427148 AAGTTAATAA
40427158 CAAATTTGATTACGGTGGG
1 CAAATTTGATTACGGTGGG
*
40427177 CAAATTTGATTATGGTGGG
1 CAAATTTGATTACGGTGGG
40427196 TGACAGTGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.32, T:0.34
Consensus pattern (19 bp):
CAAATTTGATTACGGTGGG
Found at i:40429529 original size:20 final size:20
Alignment explanation
Indices: 40429504--40429542 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40429494 CAAATTAATA
40429504 ATTATTGCATTAATTAAACC
1 ATTATTGCATTAATTAAACC
40429524 ATTATTGCATTAATTAAAC
1 ATTATTGCATTAATTAAAC
40429543 ATTTCTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (20 bp):
ATTATTGCATTAATTAAACC
Found at i:40439249 original size:4 final size:4
Alignment explanation
Indices: 40439232--40439275 Score: 70
Period size: 4 Copynumber: 11.0 Consensus size: 4
40439222 TTAATGACTA
* *
40439232 ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC GTAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
40439276 GTACGTATGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:40439280 original size:12 final size:12
Alignment explanation
Indices: 40439233--40439282 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
40439223 TAATGACTAA
* *
40439233 TACATATATACA
1 TACATACATACG
*
40439245 TACATACATACA
1 TACATACATACG
40439257 TACATACATACG
1 TACATACATACG
*
40439269 TACATACGTACG
1 TACATACATACG
40439281 TA
1 TA
40439283 TGTAACTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (12 bp):
TACATACATACG
Found at i:40440388 original size:23 final size:23
Alignment explanation
Indices: 40440362--40440439 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
40440352 TTGTGGGAGC
*
40440362 TTATTGACACTTTGGTGCTG-TTG
1 TTATTGGCACTTTGGTGC-GATTG
*
40440385 TTATTGGCACTTTCGTGCGATTG
1 TTATTGGCACTTTGGTGCGATTG
*
40440408 TGATTGGCACTTTGGTGCGATTG
1 TTATTGGCACTTTGGTGCGATTG
* *
40440431 ATACTGGCA
1 TTATTGGCA
40440440 ATACAATGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 1 0.02
23 46 0.98
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (23 bp):
TTATTGGCACTTTGGTGCGATTG
Found at i:40447189 original size:14 final size:14
Alignment explanation
Indices: 40447172--40447203 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
40447162 AGCACGGTAG
40447172 AAAAGAAAAAAAGA
1 AAAAGAAAAAAAGA
*
40447186 AAAAGAAAAGAAGA
1 AAAAGAAAAAAAGA
40447200 AAAA
1 AAAA
40447204 CTAATGACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAAAGA
Found at i:40447342 original size:30 final size:28
Alignment explanation
Indices: 40447272--40447346 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
40447262 TTACCTTAAG
40447272 TTACATTTTAGTCACTTATGTTTGAAATT
1 TTACATTTTAGTCAC-TATGTTTGAAATT
*
40447301 TTACGTTTTAGTCACTATG-TT-AACATGT
1 TTACATTTTAGTCACTATGTTTGAA-AT-T
40447329 TGTAACATTTTAGTCACT
1 T-T-ACATTTTAGTCACT
40447347 GAGTCGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 6 0.15
29 15 0.38
30 13 0.32
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (28 bp):
TTACATTTTAGTCACTATGTTTGAAATT
Found at i:40478987 original size:18 final size:18
Alignment explanation
Indices: 40478960--40479017 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
40478950 ATTTACTAAA
*
40478960 ATAATCATTTTAAATTTT
1 ATAATAATTTTAAATTTT
* * *
40478978 ATAATTATTTTATATTTA
1 ATAATAATTTTAAATTTT
*
40478996 ATTAATAATTTTAATTTTT
1 A-TAATAATTTTAAATTTT
40479015 ATA
1 ATA
40479018 TGATTTATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
18 18 0.56
19 14 0.44
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
ATAATAATTTTAAATTTT
Found at i:40479036 original size:37 final size:37
Alignment explanation
Indices: 40478948--40479038 Score: 89
Period size: 37 Copynumber: 2.5 Consensus size: 37
40478938 TTGTCTTGAA
* * *
40478948 ATATT-TACTAAAATAATCATTTTAAATTTTATAATT
1 ATATTATATTAAATTAATAATTTTAAATTTTATAATT
* * *
40478984 ATTTTATATTTAATTAATAATTTTAATTTTTATATGATT
1 ATATTATATTAAATTAATAATTTTAAATTTTATA--ATT
40479023 -TATTATA-TAAATTAAT
1 ATATTATATTAAATTAAT
40479039 GTAAATTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
36 4 0.09
37 31 0.70
38 6 0.14
39 3 0.07
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (37 bp):
ATATTATATTAAATTAATAATTTTAAATTTTATAATT
Found at i:40484379 original size:67 final size:67
Alignment explanation
Indices: 40484269--40484402 Score: 223
Period size: 67 Copynumber: 2.0 Consensus size: 67
40484259 TAGAATATGA
* *
40484269 ATTATGTATCCCATTTTTTATTGAATTTCCATTATTGTTTTAACTTCAATTATTTACATATATTT
1 ATTATGTATCCCATTTTGTATTGAATTTCCATTATTGTATTAACTTCAATTATTTACATATATTT
40484334 GC
66 GC
* * *
40484336 ATTATGTATCTCATTTTGTATTGAATTTCCATTCTTGTATTAACTTCAATTATTTATATATATTT
1 ATTATGTATCCCATTTTGTATTGAATTTCCATTATTGTATTAACTTCAATTATTTACATATATTT
40484401 GC
66 GC
40484403 GTAAACTTGA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.54
Consensus pattern (67 bp):
ATTATGTATCCCATTTTGTATTGAATTTCCATTATTGTATTAACTTCAATTATTTACATATATTT
GC
Found at i:40484485 original size:27 final size:26
Alignment explanation
Indices: 40484394--40484486 Score: 70
Period size: 27 Copynumber: 3.7 Consensus size: 26
40484384 ATTATTTATA
* *
40484394 TATATTTGCGTAAACTTGATTGTCACG
1 TATATTTGCATAAACTTGATAG-CACG
* *
40484421 TATATTTGCATGAACATG-TA--AC-
1 TATATTTGCATAAACTTGATAGCACG
* **
40484443 -ATATTTGAATGGACTTGATAGGCACG
1 TATATTTGCATAAACTTGATA-GCACG
40484469 TATATTTGCATAAACTTG
1 TATATTTGCATAAACTTG
40484487 TATCAAACAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
21 14 0.28
22 2 0.04
23 2 0.04
25 2 0.04
26 1 0.02
27 29 0.58
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (26 bp):
TATATTTGCATAAACTTGATAGCACG
Found at i:40487035 original size:17 final size:16
Alignment explanation
Indices: 40487013--40487059 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
40487003 AGGGATAAAT
*
40487013 TTATATTAAATTGAATA
1 TTATATGAAATTGAA-A
40487030 TTATATGAAATTGAAA
1 TTATATGAAATTGAAA
40487046 TTA-AT--AATTGAAA
1 TTATATGAAATTGAAA
40487059 T
1 T
40487060 AAACTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 9 0.31
15 2 0.07
16 4 0.14
17 14 0.48
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
TTATATGAAATTGAAA
Found at i:40489828 original size:22 final size:23
Alignment explanation
Indices: 40489785--40489840 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
40489775 AAGCTATCTT
*
40489785 AATAAACATACACTTCAAAATAA
1 AATAAACATACACTGCAAAATAA
*
40489808 AATAAACATAC-GTGCAAAATAA
1 AATAAACATACACTGCAAAATAA
*
40489830 TATAAACATAC
1 AATAAACATAC
40489841 TCACACTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.59, C:0.16, G:0.04, T:0.21
Consensus pattern (23 bp):
AATAAACATACACTGCAAAATAA
Found at i:40491664 original size:26 final size:26
Alignment explanation
Indices: 40491628--40491694 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
40491618 GGGTGAGCAT
* *
40491628 AAGAAACTCAGTGTGCGTTCAATCAC
1 AAGAAAATCAGTGTGCGTCCAATCAC
40491654 AAGAAAATCAGTGTGCGTCCAATCAC
1 AAGAAAATCAGTGTGCGTCCAATCAC
40491680 AAGAAAATCAGTGTG
1 AAGAAAATCAGTGTG
40491695 AAACAGTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (26 bp):
AAGAAAATCAGTGTGCGTCCAATCAC
Found at i:40498350 original size:19 final size:20
Alignment explanation
Indices: 40498318--40498355 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40498308 TTTTATAATA
40498318 ATTTTATGAATAATTAATTC
1 ATTTTATGAATAATTAATTC
*
40498338 ATTTTA-GATTAATTAATT
1 ATTTTATGAATAATTAATT
40498356 TGAAGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
ATTTTATGAATAATTAATTC
Found at i:40500852 original size:42 final size:41
Alignment explanation
Indices: 40500627--40500866 Score: 277
Period size: 41 Copynumber: 5.8 Consensus size: 41
40500617 TTAATTTAAA
* * *
40500627 CAGATTCACCGGCACTTAACCTGTTAGGCTTA-AAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGATAGGCTTATAA-CCTGGTT
* * *
40500669 CAGATCACCAGCACTTAGCCTGCTAGGCTTATAGCCTGGTT
1 CAGATCACCGGCACTTAGCCTGATAGGCTTATAACCTGGTT
*
40500710 CAGATCACCAGCACTTAGCCTGATAGGCTTATAACCTGGTT
1 CAGATCACCGGCACTTAGCCTGATAGGCTTATAACCTGGTT
*
40500751 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTT
1 CAGATCACCGGCACTTAGCCTGATAGGCTTATAACCTGGTT
* * * * *
40500792 CAGATCACCGACACTTAGCCTGTTAGGTTTTAAAACCTGATT
1 CAGATCACCGGCACTTAGCCTGATAGG-CTTATAACCTGGTT
** * *
40500834 CAG-TACACCGGCTTTTAGCCTGGTAGACTTATA
1 CAGAT-CACCGGCACTTAGCCTGATAGGCTTATA
40500867 GTCTGAAATA
Statistics
Matches: 174, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
41 138 0.79
42 36 0.21
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGATAGGCTTATAACCTGGTT
Found at i:40507558 original size:41 final size:41
Alignment explanation
Indices: 40507508--40507755 Score: 320
Period size: 41 Copynumber: 6.0 Consensus size: 41
40507498 TTAATTTAAA
** *
40507508 CAGATTCACCGGCACTTAGCCTATTAGGCTTA-AAGCTTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAA-CCTGATT
*
40507550 CAGATCACCGACACTTAGCCTGCTAGGCTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
**
40507591 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAGGCTCG-TT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCT-GATT
*
40507632 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGGTT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
40507673 CAGATCACCGGCAGTTAGCCTGCTAGGCTTATAACCTGGTT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* * * * *
40507714 CAAATCACCGACACTTAGCCTGTTAGGTTTTAAAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGG-CTTATAACCTGATT
40507756 TAGTACACTA
Statistics
Matches: 185, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
40 1 0.01
41 166 0.90
42 18 0.10
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:40507732 original size:123 final size:124
Alignment explanation
Indices: 40507508--40507740 Score: 353
Period size: 123 Copynumber: 1.9 Consensus size: 124
40507498 TTAATTTAAA
* *
40507508 CAGATTCACCGGCACTTAGCCTATTAGGCTTAAAGCTTGATTCAGATCACCGACACTTAGCCTGC
1 CAGATTCACCGGCACTTAGCCTACTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGC
* *
40507573 TAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGGCTCGTT
66 TAGGCTTATAACCTGATTCAAATCACCGACACTTAGCCTGCTAGGCTTATAGGCTCGTT
* * * *
40507632 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAA-CCTGGTTCAGATCACCGGCAGTTAGCCTG
1 CAGATTCACCGGCACTTAGCCTACTAGGCTTA-AAGCCTGATTCAGATCACCGACACTTAGCCTG
* *
40507695 CTAGGCTTATAACCTGGTTCAAATCACCGACACTTAGCCTGTTAGG
65 CTAGGCTTATAACCTGATTCAAATCACCGACACTTAGCCTGCTAGG
40507741 TTTTAAAACC
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
123 92 0.94
124 6 0.06
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (124 bp):
CAGATTCACCGGCACTTAGCCTACTAGGCTTAAAGCCTGATTCAGATCACCGACACTTAGCCTGC
TAGGCTTATAACCTGATTCAAATCACCGACACTTAGCCTGCTAGGCTTATAGGCTCGTT
Found at i:40508228 original size:78 final size:77
Alignment explanation
Indices: 40508136--40508313 Score: 191
Period size: 78 Copynumber: 2.3 Consensus size: 77
40508126 TTCGAATGTC
* * * *
40508136 ACATATACCTATATAATTTCATACCCTA-TTTCAATAACAA-AACTTATACATGTACATATATAC
1 ACATATACATATATAATTTCATACCCTACATTCAA-AACAAGAACTTATACATGTACACACATAC
40508199 ATATTCAAATCTA
65 ATATTCAAATCTA
* * * * * * *
40508212 CCATATATACATATATAATTTTATA-CTTACATTCGAAACAAGTACTTATACTTGTATACACATA
1 --ACATATACATATATAATTTCATACCCTACATTCAAAACAAGAACTTATACATGTACACACATA
* *
40508276 CATTTTCAAATTTA
64 CATATTCAAATCTA
40508290 ACATATACATATATAATTTCATAC
1 ACATATACATATATAATTTCATAC
40508314 TTATACTCAA
Statistics
Matches: 82, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
76 21 0.26
77 8 0.10
78 53 0.65
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (77 bp):
ACATATACATATATAATTTCATACCCTACATTCAAAACAAGAACTTATACATGTACACACATACA
TATTCAAATCTA
Found at i:40508562 original size:153 final size:156
Alignment explanation
Indices: 40508387--40508687 Score: 357
Period size: 153 Copynumber: 1.9 Consensus size: 156
40508377 TATATTATAC
* * *
40508387 ATATATATATGTAACATCCATACTTTTAA-TAAAATCCAAGAATTTATACTCA-TATATACATAC
1 ATATATAAATATAACATACATACTTTTAACT-AAATCCAAGAATTTAT--TCAGTATATACATAC
* * * * * *
40508450 CTATTCAAACCTCTTGTA-A-ACATATATAACATTCA-AC-ATTAACTAAATTCAA-AACTTATT
63 ATATCCAAA-CT-TTATATATACAAATATAACATACATACTATTAACTAAATTCAAGAACTTATA
40508510 CATGTATATACACATA-TATCCGAACTTTAT
126 CATGTATATACACATATTATCCGAACTTTAT
* *
40508540 ATATATAAATATAACATACATACTTTTAACTAAATTCAAGAATTTATTCATGTATATACATATAT
1 ATATATAAATATAACATACATACTTTTAACTAAATCCAAGAATTTATTCA-GTATATACATACAT
* * *
40508605 ATCCGAACTTTATATATATAAATATAACATACATACTTTTAACTAAATTCAAGAACTTATACATG
65 ATCCAAACTTTATATATACAAATATAACATACATACTATTAACTAAATTCAAGAACTTATACATG
*
40508670 TATATACATATATTATCC
130 TATATACACATATTATCC
40508688 ACTATTAGTT
Statistics
Matches: 124, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
151 7 0.06
152 3 0.02
153 70 0.56
154 3 0.02
155 14 0.11
156 22 0.18
157 5 0.04
ACGTcount: A:0.44, C:0.16, G:0.03, T:0.37
Consensus pattern (156 bp):
ATATATAAATATAACATACATACTTTTAACTAAATCCAAGAATTTATTCAGTATATACATACATA
TCCAAACTTTATATATACAAATATAACATACATACTATTAACTAAATTCAAGAACTTATACATGT
ATATACACATATTATCCGAACTTTAT
Found at i:40508605 original size:78 final size:78
Alignment explanation
Indices: 40508488--40508687 Score: 357
Period size: 78 Copynumber: 2.6 Consensus size: 78
40508478 ACATTCAACA
*
40508488 TTAACTAAATTCAA-AACTTATTCATGTATATACACATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
40508552 AACATACATACTT
66 AACATACATACTT
*
40508565 TTAACTAAATTCAAGAATTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
40508630 AACATACATACTT
66 AACATACATACTT
*
40508643 TTAACTAAATTCAAGAACTTATACATGTATATACATATATTATCC
1 TTAACTAAATTCAAGAACTTATTCATGTATATACATATA-TATCC
40508688 ACTATTAGTT
Statistics
Matches: 117, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
77 14 0.12
78 98 0.84
79 5 0.04
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (78 bp):
TTAACTAAATTCAAGAACTTATTCATGTATATACATATATATCCGAACTTTATATATATAAATAT
AACATACATACTT
Found at i:40511072 original size:43 final size:43
Alignment explanation
Indices: 40510999--40511307 Score: 322
Period size: 43 Copynumber: 7.3 Consensus size: 43
40510989 TGTTTTGAGG
* ** *
40510999 TATGTTCTTTAGCGGCCTTCCTGGGGAAAGCGCCGCTAAAGGT
1 TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
*
40511042 TATGTTCTTTAGCGGCGTTCGTGGGAAAAGCGCCGCTAAAGGT
1 TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
* * * *
40511085 CATGTTCTTTAGCGGAGTTTATGGGGAAAGCGCCGCTAAAGGT
1 TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
* *
40511128 CT-TGTTCTTTAGCGGCGTTTGTGGGAATAGCGCCGCTAAAAGT
1 -TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
** * * *
40511171 TATGTTCTCAATCGGCGTTTGTGGGGAAAGCGCTGCTAAAGGT
1 TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
* * * * *
40511214 CATGTTCTATAGTGGCGTTTGCGGG-AAAGCGTCGCTAAAGGT
1 TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
* *** **
40511256 TAT-TT-TTTAACGGCGTTTGCAAGAAAAATGCCGCTAAAGG-
1 TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
*
40511296 TCTGTTCTTTAG
1 TATGTTCTTTAG
40511308 TGGCTTTTTT
Statistics
Matches: 221, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
40 15 0.07
41 17 0.08
42 22 0.10
43 167 0.76
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (43 bp):
TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGT
Found at i:40514240 original size:13 final size:13
Alignment explanation
Indices: 40514222--40514253 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
40514212 GACACACGGG
40514222 CGTGTGGTCTGGT
1 CGTGTGGTCTGGT
40514235 CGTGTGGTCTGGT
1 CGTGTGGTCTGGT
40514248 CGTGTG
1 CGTGTG
40514254 ACTCAAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.47, T:0.38
Consensus pattern (13 bp):
CGTGTGGTCTGGT
Found at i:40516507 original size:10 final size:10
Alignment explanation
Indices: 40516466--40516506 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
40516456 CAAAATTAAA
40516466 TTAAAATA-T
1 TTAAAATATT
*
40516475 ATAAAATATT
1 TTAAAATATT
40516485 TTAAAATATT
1 TTAAAATATT
40516495 TTAAAATTATT
1 TTAAAA-TATT
40516506 T
1 T
40516507 ATAATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 7 0.25
10 16 0.57
11 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
TTAAAATATT
Found at i:40516507 original size:20 final size:20
Alignment explanation
Indices: 40516466--40516515 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
40516456 CAAAATTAAA
40516466 TTAAAATA-TATAAAATATT
1 TTAAAATATTATAAAATATT
*
40516485 TTAAAATATTTTAAAAT-TAT
1 TTAAAATATTATAAAATAT-T
*
40516505 TTATAATATTA
1 TTAAAATATTA
40516516 ATCATAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTAAAATATTATAAAATATT
Found at i:40516989 original size:17 final size:17
Alignment explanation
Indices: 40516937--40516992 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
40516927 TATTTTGAAA
40516937 TTAAAAATATAT-TAATTT
1 TTAAAAATATATAT-A-TT
*
40516955 TTAAAAA-ATGTGAT-TT
1 TTAAAAATATAT-ATATT
40516971 TTAAAAATATATATATT
1 TTAAAAATATATATATT
40516988 TTAAA
1 TTAAA
40516993 GATAAAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
16 11 0.34
17 13 0.41
18 7 0.22
19 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (17 bp):
TTAAAAATATATATATT
Found at i:40517253 original size:20 final size:20
Alignment explanation
Indices: 40517228--40517267 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40517218 GGTTTAGAGG
*
40517228 GAAGTAAAATTTTTGAAGGA
1 GAAGTAAAACTTTTGAAGGA
*
40517248 GAAGTAAAACTTTTGGAGGA
1 GAAGTAAAACTTTTGAAGGA
40517268 AAGCAAAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.03, G:0.28, T:0.28
Consensus pattern (20 bp):
GAAGTAAAACTTTTGAAGGA
Found at i:40521814 original size:5 final size:5
Alignment explanation
Indices: 40521804--40521855 Score: 61
Period size: 5 Copynumber: 10.2 Consensus size: 5
40521794 GAACAAATAT
* *
40521804 ATTCG ATTCG ATTCG ATTCG ATTCG AATTCC ATCTC- ACTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG ATTCG ATTCG
40521855 A
1 A
40521856 GAAAACTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 33 0.80
6 6 0.15
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (5 bp):
ATTCG
Found at i:40525150 original size:16 final size:17
Alignment explanation
Indices: 40525091--40525155 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 17
40525081 TTACTCCTGA
40525091 AAAAACTACCCACTCTT
1 AAAAACTACCCACTCTT
* **
40525108 AGAAAACAACCCACTAAT
1 A-AAAACTACCCACTCTT
* *
40525126 -ATAAGTACCCACTCTT
1 AAAAACTACCCACTCTT
*
40525142 AAAAA-TACCAACTC
1 AAAAACTACCCACTC
40525156 ACAAATATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
16 19 0.53
17 4 0.11
18 13 0.36
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAAACTACCCACTCTT
Found at i:40531759 original size:186 final size:185
Alignment explanation
Indices: 40531445--40531819 Score: 615
Period size: 186 Copynumber: 2.0 Consensus size: 185
40531435 ATAAGTTAAT
*
40531445 TTCAATCAATTAATAACAACAATGAGCCTAGTGGTTCAATGATTAAGCTTCTATGTACTCTTTGG
1 TTCAATCAATTAATAACAACAATGAGCCTAATGGTTCAATGATTAAGCTTCTATGTACTCTTTGG
* * * * * *
40531510 TTTGGTGTTCAAATCCTTATGAAAGTAATAGGGAAATGTTTTATTTTGAATTGTTTTGTGTGGTA
66 TTTGGTATTCAAATCCCTATGAAAGCAATAAGGAAACGTTTTATTTTGAATTGCTTTGTGTGGTA
*
40531575 GTTTATTTTTTTTTGGTTAATTAAACTTCCTAGGAACCTCCTATATTTATTCCATA
131 GTTTA-TTTTTTTTGGTTAATTAAACTTCCCAGGAACCTCCTATATTTATTCCATA
* *
40531631 TTCAATCAATTAATGACAACAATGAGCCTAATGGTTCAATGATTAAGCTTTTATGTACTCTTTGG
1 TTCAATCAATTAATAACAACAATGAGCCTAATGGTTCAATGATTAAGCTTCTATGTACTCTTTGG
**
40531696 TTTGGTATTTGAATCCCTATGAAAGCAATAAGGAAACGTTTTATTTTGAATTGCTTTGTGTGGTA
66 TTTGGTATTCAAATCCCTATGAAAGCAATAAGGAAACGTTTTATTTTGAATTGCTTTGTGTGGTA
* *
40531761 GTTTATTTTTTTTGGTTAATTAAACTTCCCAGGAACCTCCTGTGTTTATTCCATA
131 GTTTATTTTTTTTGGTTAATTAAACTTCCCAGGAACCTCCTATATTTATTCCATA
40531816 TTCA
1 TTCA
40531820 TTTTCCATTT
Statistics
Matches: 175, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
185 51 0.29
186 124 0.71
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (185 bp):
TTCAATCAATTAATAACAACAATGAGCCTAATGGTTCAATGATTAAGCTTCTATGTACTCTTTGG
TTTGGTATTCAAATCCCTATGAAAGCAATAAGGAAACGTTTTATTTTGAATTGCTTTGTGTGGTA
GTTTATTTTTTTTGGTTAATTAAACTTCCCAGGAACCTCCTATATTTATTCCATA
Found at i:40539253 original size:21 final size:21
Alignment explanation
Indices: 40539227--40539280 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
40539217 TTAAAATAAA
40539227 TTTAACCAAGTTAAAATGATT
1 TTTAACCAAGTTAAAATGATT
*
40539248 TTTAACTC-A-TCAAAATGATT
1 TTTAAC-CAAGTTAAAATGATT
* *
40539268 TTCAAACAAGTTA
1 TTTAACCAAGTTA
40539281 GAATTGCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
19 1 0.04
20 15 0.58
21 9 0.35
22 1 0.04
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (21 bp):
TTTAACCAAGTTAAAATGATT
Found at i:40552882 original size:41 final size:41
Alignment explanation
Indices: 40552837--40552918 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
40552827 AAGAAAAGAC
*
40552837 AAAGATTTATTAATAATTCAAATTTATGTTGATGATATTAT
1 AAAGATTTATTAATAATTCAAATTTATATTGATGATATTAT
40552878 AAAGATTTATTAATAATTCAAATTTATATTGATGATATTAT
1 AAAGATTTATTAATAATTCAAATTTATATTGATGATATTAT
40552919 TTTTGGTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (41 bp):
AAAGATTTATTAATAATTCAAATTTATATTGATGATATTAT
Found at i:40556494 original size:20 final size:20
Alignment explanation
Indices: 40556469--40556555 Score: 97
Period size: 20 Copynumber: 4.3 Consensus size: 20
40556459 ATTTTAAAAT
40556469 CAAGTCAAAATGATTTTAAC
1 CAAGTCAAAATGATTTTAAC
*
40556489 CAAGTCAAAATGATTTCAAC
1 CAAGTCAAAATGATTTTAAC
* *
40556509 CAAGTTAAAATCATTTTAA-
1 CAAGTCAAAATGATTTTAAC
* *
40556528 CACA-TCAAAAAGATTTTCAAA
1 CA-AGTCAAAATGATTTT-AAC
40556549 CAAGTCA
1 CAAGTCA
40556556 GAATTGCTCC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 12 0.21
20 39 0.70
21 5 0.09
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (20 bp):
CAAGTCAAAATGATTTTAAC
Found at i:40556525 original size:40 final size:40
Alignment explanation
Indices: 40556459--40556555 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 40
40556449 TTTTAAAACA
* * *
40556459 ATTTTAAAATCAAGTCAAAATGATTTTAAC-CAAGTCAAAATG
1 ATTTTCAAA-CAAGTCAAAATCATTTTAACAC-A-TCAAAAAG
* *
40556501 A-TTTCAACCAAGTTAAAATCATTTTAACACATCAAAAAG
1 ATTTTCAAACAAGTCAAAATCATTTTAACACATCAAAAAG
40556540 ATTTTCAAACAAGTCA
1 ATTTTCAAACAAGTCA
40556556 GAATTGCTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
39 8 0.17
40 31 0.67
41 6 0.13
42 1 0.02
ACGTcount: A:0.47, C:0.15, G:0.07, T:0.30
Consensus pattern (40 bp):
ATTTTCAAACAAGTCAAAATCATTTTAACACATCAAAAAG
Found at i:40562990 original size:23 final size:23
Alignment explanation
Indices: 40562958--40563006 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
40562948 TGTGTAACTT
*
40562958 TTCATCTTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
40562981 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
40563004 TTC
1 TTC
40563007 TAACTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:40567266 original size:23 final size:23
Alignment explanation
Indices: 40567234--40567282 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
40567224 TGTGTAACTT
*
40567234 TTCATCTTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
40567257 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
40567280 TTC
1 TTC
40567283 TAACTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:40568955 original size:25 final size:27
Alignment explanation
Indices: 40568927--40568976 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40568917 TTTAAGCATT
*
40568927 AAACAATA-AGTTAA-AACACTCATAA
1 AAACAACATAGTTAATAACACTCATAA
*
40568952 AAACAACATATTTAATAACACTCAT
1 AAACAACATAGTTAATAACACTCAT
40568977 GCACAAGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.56, C:0.18, G:0.02, T:0.24
Consensus pattern (27 bp):
AAACAACATAGTTAATAACACTCATAA
Found at i:40569155 original size:75 final size:75
Alignment explanation
Indices: 40569070--40569210 Score: 187
Period size: 75 Copynumber: 1.9 Consensus size: 75
40569060 AATATGAAGA
* * *
40569070 ACACATAATGCAAGTAT-TAAAGGATGCTAGTGTATTAATGCAAAACATTAAAT-AATGATGCAT
1 ACACATAATGCAAGTATCTAAA-GATGCAAATGTATTAATGCAAAACATT-AATCAAAGATGCAT
40569133 TTAATAAACAAG
64 TTAATAAACAAG
* * * *
40569145 ACACTTAATGCAAGTTTCTAAAGATGCAAATGTATTAATGTAAGACATTAATCAAAGATGCATTT
1 ACACATAATGCAAGTATCTAAAGATGCAAATGTATTAATGCAAAACATTAATCAAAGATGCATTT
40569210 A
66 A
40569211 TCCGACAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
74 3 0.05
75 50 0.88
76 4 0.07
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (75 bp):
ACACATAATGCAAGTATCTAAAGATGCAAATGTATTAATGCAAAACATTAATCAAAGATGCATTT
AATAAACAAG
Found at i:40569226 original size:75 final size:75
Alignment explanation
Indices: 40569075--40569228 Score: 170
Period size: 75 Copynumber: 2.1 Consensus size: 75
40569065 GAAGAACACA
* * *
40569075 TAATGCAAGTATTAAAGGATGCTAGTGTATTAATGCAAAACATTAAATAATGATGCATTTAATAA
1 TAATGCAAGTATTAAAGGATGCAAATGTATTAATGCAAAACATTAAATAAAGATGCATTTAATAA
* *
40569140 ACAAGACACT
66 ACAAAAAACT
* * *
40569150 TAATGCAAGTTTCTAAA-GATGCAAATGTATTAATGTAAGACATT-AATCAAAGATGCATTT-AT
1 TAATGCAAGTAT-TAAAGGATGCAAATGTATTAATGCAAAACATTAAAT-AAAGATGCATTTAAT
**
40569212 CCGACAAAAAACT
64 -AAACAAAAAACT
40569225 TAAT
1 TAAT
40569229 AATGCAAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
74 5 0.08
75 57 0.86
76 4 0.06
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (75 bp):
TAATGCAAGTATTAAAGGATGCAAATGTATTAATGCAAAACATTAAATAAAGATGCATTTAATAA
ACAAAAAACT
Found at i:40573721 original size:13 final size:12
Alignment explanation
Indices: 40573705--40573797 Score: 51
Period size: 12 Copynumber: 7.3 Consensus size: 12
40573695 CATTTTCAGC
40573705 TCTTTTTTTCTTT
1 TCTTTTTTT-TTT
40573718 TCTTTTTTTTTT
1 TCTTTTTTTTTT
*
40573730 TGAACTCTTTTCTTTT
1 T---CT-TTTTTTTTT
*
40573746 TCTTTTTCTTTT
1 TCTTTTTTTTTT
* * *
40573758 TCATTTTTCTTA
1 TCTTTTTTTTTT
* *
40573770 TCTTATTCTTTT
1 TCTTTTTTTTTT
* * *
40573782 TCATTCTTTTTC
1 TCTTTTTTTTTT
40573794 TCTT
1 TCTT
40573798 GTTCATTTTC
Statistics
Matches: 60, Mismatches: 16, Indels: 9
0.71 0.19 0.11
Matches are distributed among these distances:
12 38 0.63
13 11 0.18
15 2 0.03
16 9 0.15
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.75
Consensus pattern (12 bp):
TCTTTTTTTTTT
Found at i:40573794 original size:6 final size:6
Alignment explanation
Indices: 40573709--40573783 Score: 64
Period size: 6 Copynumber: 12.0 Consensus size: 6
40573699 TTCAGCTCTT
*
40573709 TTTTTC -TTTTC TTTTTT TTTTTGAAC TCTTTTC TTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTT---C T-TTTTC TTTTTC TTTTTC TTTTTC
* *
40573760 ATTTTTC -TTATC TTATTC TTTTTC
1 -TTTTTC TTTTTC TTTTTC TTTTTC
40573784 ATTCTTTTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
5 9 0.16
6 34 0.61
7 8 0.14
9 1 0.02
10 4 0.07
ACGTcount: A:0.07, C:0.16, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:40573797 original size:24 final size:23
Alignment explanation
Indices: 40573739--40573807 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
40573729 TTGAACTCTT
40573739 TTCTTTTTCT-TTTTCTTTTTCA
1 TTCTTTTTCTCTTTTCTTTTTCA
*
40573761 TT-TTTCTTATCTTATTCTTTTTCA
1 TTCTTT-TTCTCTT-TTCTTTTTCA
*
40573785 TTCTTTTTCTCTTGTTCATTTTC
1 TTCTTTTTCTCTT-TTCTTTTTC
40573808 TCTCGACTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.08
22 5 0.13
23 2 0.05
24 26 0.67
25 3 0.08
ACGTcount: A:0.07, C:0.19, G:0.01, T:0.72
Consensus pattern (23 bp):
TTCTTTTTCTCTTTTCTTTTTCA
Found at i:40579852 original size:17 final size:18
Alignment explanation
Indices: 40579825--40579873 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
40579815 AAAATATGAA
*
40579825 TCAATTTTTTTTTAAATT
1 TCAAATTTTTTTTAAATT
* **
40579843 T-TAATTTTTTTTGGATT
1 TCAAATTTTTTTTAAATT
40579860 TCAAATTTTTTTTA
1 TCAAATTTTTTTTA
40579874 CTTTGATCTT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (18 bp):
TCAAATTTTTTTTAAATT
Found at i:40581113 original size:75 final size:75
Alignment explanation
Indices: 40581012--40581151 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 75
40581002 AATATAAAGA
* * *
40581012 ACACATAATGCAGGTATTAAAGGATGCTAGTGTATTAATGCAAAACATTAAACAAAGATGCATTT
1 ACACATAATGCAAGTATTAAAGGATGCGAATGTATTAATGCAAAACATTAAACAAAGATGCATTT
40581077 TTTAAACAAG
66 TTTAAACAAG
* * * * *
40581087 ACACTTAATGCAAGTTTGTAAA-GATGCGAATGTATTAATGCAAGATATTAATCAAAGATGCATT
1 ACACATAATGCAAGTAT-TAAAGGATGCGAATGTATTAATGCAAAACATTAAACAAAGATGCATT
40581151 T
65 T
40581152 ATCCCACAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 52 0.93
76 4 0.07
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (75 bp):
ACACATAATGCAAGTATTAAAGGATGCGAATGTATTAATGCAAAACATTAAACAAAGATGCATTT
TTTAAACAAG
Found at i:40581166 original size:75 final size:75
Alignment explanation
Indices: 40581011--40581170 Score: 187
Period size: 75 Copynumber: 2.1 Consensus size: 75
40581001 TAATATAAAG
* * * *
40581011 AACACATAATGCAGGTATTAAAGGATGCTAGTGTATTAATGCAAAACATTAAACAAAGATGCATT
1 AACACTTAATGCAAGTATTAAAGGATGCGAATGTATTAATGCAAAACATTAAACAAAGATGCATT
* *
40581076 TTTTAAACAA
66 TATCAAACAA
* * * * *
40581086 GACACTTAATGCAAGTTTGTAAA-GATGCGAATGTATTAATGCAAGATATTAATCAAAGATGCAT
1 AACACTTAATGCAAGTAT-TAAAGGATGCGAATGTATTAATGCAAAACATTAAACAAAGATGCAT
**
40581150 TTATCCCACAA
65 TTATCAAACAA
40581161 AACACTTAAT
1 AACACTTAAT
40581171 AATGCAAAAC
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
75 66 0.94
76 4 0.06
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (75 bp):
AACACTTAATGCAAGTATTAAAGGATGCGAATGTATTAATGCAAAACATTAAACAAAGATGCATT
TATCAAACAA
Found at i:40581879 original size:71 final size:71
Alignment explanation
Indices: 40581759--40582120 Score: 307
Period size: 71 Copynumber: 5.1 Consensus size: 71
40581749 GTATATTACA
* * * * * * *
40581759 AAGGCTCGCAAG-TCCAATACCGCAGCCTCTAACATAGTTAGCGAGAGTTACAAACTCCTAAATG
1 AAGGCTCGCAAGAT-CAAAACCACAACCTCCAACACAATTAGCGAGAGTTACAAACTCCTAACTG
*
40581823 TCATATT
65 TCACATT
* * * * * **
40581830 AAGGCTCGCATGATTAAACCCACAACCTCCAACACAATTAGTGAGAGTTACAAACTTCTAGTTGT
1 AAGGCTCGCAAGATCAAAACCACAACCTCCAACACAATTAGCGAGAGTTACAAACTCCTAACTGT
40581895 CACATT
66 CACATT
* * ** * * * * *
40581901 AAGGCTCGTAAGATCAAAATCGTAGCCTCCAATACAATTAGCGAGAGTTGCAAACTCCCAACTAT
1 AAGGCTCGCAAGATCAAAACCACAACCTCCAACACAATTAGCGAGAGTTACAAACTCCTAACTGT
40581966 CACATT
66 CACATT
* * ** * * *
40581972 AAGGCTCGTAAGATCAAAATCATTGA-CTCCAACACAGTTAGCGAGAGTGACAAACT-TTCAACT
1 AAGGCTCGCAAGATCAAAACCA-CAACCTCCAACACAATTAGCGAGAGTTACAAACTCCT-AACT
40582035 GTCACATT
64 GTCACATT
* * ** * * * *
40582043 AAGGCTCGCAGGATTAAAACTGCAGCCTTCAACACAATTAGCGAGAGTTACAAACTCCCAGCTGT
1 AAGGCTCGCAAGATCAAAACCACAACCTCCAACACAATTAGCGAGAGTTACAAACTCCTAACTGT
*
40582108 CATATT
66 CACATT
*
40582114 AAAGCTC
1 AAGGCTC
40582121 CCAATTGTCA
Statistics
Matches: 229, Mismatches: 57, Indels: 10
0.77 0.19 0.03
Matches are distributed among these distances:
71 227 0.99
72 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (71 bp):
AAGGCTCGCAAGATCAAAACCACAACCTCCAACACAATTAGCGAGAGTTACAAACTCCTAACTGT
CACATT
Found at i:40582018 original size:142 final size:142
Alignment explanation
Indices: 40581759--40582120 Score: 363
Period size: 142 Copynumber: 2.5 Consensus size: 142
40581749 GTATATTACA
* * * * * * * *
40581759 AAGGCTCGCAAG-TCCAATACCGCAGCCTCTAACATAGTTAGCGAGAGTTACAAACTCCTAAATG
1 AAGGCTCGCAAGAT-CAAAACTGCAGCCTCCAACACAATTAGCGAGAGTTACAAACTCCCAACTA
* * * * * ** ** * *
40581823 TCATATTAAGGCTCGCATGATTAAACCCA-CAACCTCCAACACAATTAGTGAGAGTTACAAAC-T
65 TCACATTAAAGCTCGTAAGATCAAAATCATTGA-CTCCAACACAATTAGCGAGAGTGACAAACTT
**
40581886 TCTAGTTGTCACATT
129 TC-AACTGTCACATT
* * * *
40581901 AAGGCTCGTAAGATCAAAA-TCGTAGCCTCCAATACAATTAGCGAGAGTTGCAAACTCCCAACTA
1 AAGGCTCGCAAGATCAAAACT-GCAGCCTCCAACACAATTAGCGAGAGTTACAAACTCCCAACTA
* *
40581965 TCACATTAAGGCTCGTAAGATCAAAATCATTGACTCCAACACAGTTAGCGAGAGTGACAAACTTT
65 TCACATTAAAGCTCGTAAGATCAAAATCATTGACTCCAACACAATTAGCGAGAGTGACAAACTTT
40582030 CAACTGTCACATT
130 CAACTGTCACATT
* * * * *
40582043 AAGGCTCGCAGGATTAAAACTGCAGCCTTCAACACAATTAGCGAGAGTTACAAACTCCCAGCTGT
1 AAGGCTCGCAAGATCAAAACTGCAGCCTCCAACACAATTAGCGAGAGTTACAAACTCCCAACTAT
*
40582108 CATATTAAAGCTC
66 CACATTAAAGCTC
40582121 CCAATTGTCA
Statistics
Matches: 179, Mismatches: 36, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
142 173 0.97
143 6 0.03
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (142 bp):
AAGGCTCGCAAGATCAAAACTGCAGCCTCCAACACAATTAGCGAGAGTTACAAACTCCCAACTAT
CACATTAAAGCTCGTAAGATCAAAATCATTGACTCCAACACAATTAGCGAGAGTGACAAACTTTC
AACTGTCACATT
Found at i:40582251 original size:64 final size:64
Alignment explanation
Indices: 40582148--40582272 Score: 171
Period size: 64 Copynumber: 2.0 Consensus size: 64
40582138 GCTTGCAGTA
* **
40582148 TTAAAACCGCAACCTCTAACATTGTTAGAGAGAGCTACAAACTCCCAAG-TGTCATATTAAGAGT
1 TTAAAACCGCAACCTCCAACACAGTTAGAGAGAGCTACAAACTCCC-AGCTGTCATATTAAGAGT
* * * *
40582212 TTAAAATCGCAGCCTCCAACACAGTTAGTGAGAGTTACAAACTCCCAGCTGTCATATTAAG
1 TTAAAACCGCAACCTCCAACACAGTTAGAGAGAGCTACAAACTCCCAGCTGTCATATTAAG
40582273 GCTCGCGAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
63 2 0.04
64 51 0.96
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (64 bp):
TTAAAACCGCAACCTCCAACACAGTTAGAGAGAGCTACAAACTCCCAGCTGTCATATTAAGAGT
Found at i:40582356 original size:71 final size:71
Alignment explanation
Indices: 40582214--40583006 Score: 484
Period size: 71 Copynumber: 11.0 Consensus size: 71
40582204 TTAAGAGTTT
* * * ** *
40582214 AAAATCGCAGCCTCCAACACAGTTAGTGAGAGTTACAAACTCCCAGCTGTCATATTAAGGCTCGC
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
40582279 -GAGATC
66 AG-GATC
* * ** * ** ** * * *
40582285 AAAACCACAACCTCTAACACAGCTAGCGATTGTTGTAAATTCCCAACTGTCACATTAAGGCTCAC
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
40582350 AGGATC
66 AGGATC
* * * * * * * **
40582356 AAAATTGCAGCCTCCAACATAGTTAGCAAAATTTACAAACTCCCAACTGTCATATTAAGGCTCAT
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
*
40582421 AGGATT
66 AGGATC
* * * * *
40582427 AAAATCGCAGCCTCCAACATAATTAGCAAGACTTACAAACTCCCAACTATCATATTAAGGCTCGC
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
40582492 AGGATC
66 AGGATC
* *
40582498 AAAATCGCATCCTCTAACACAATTAGCGAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
40582563 AGGAT-
66 AGGATC
* * * * * * * *
40582568 TAAATCCGCAACCTCTAAAATAGTTAGCGAGAGTTACAAACTCCCAACTATCATAATAAGGCTTG
1 AAAAT-CGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCG
*
40582633 CAGGATT
65 CAGGATC
* * * * * * * ** *
40582640 AAAATCGTAGCCTCCAATAGAGTTAGCAAGAGATACAAACTCCCAGTTGTCATATTAAGGCTCCC
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
*
40582705 AATTG-TC
66 -A-GGATC
* * ** * * * * ** ** * *
40582712 ATATTAAGGCTCACAGGA-TTAAAACTGCAACCTCTA-AAACAGTTGCAAACTCTTAGTTGTTAC
1 A-A--AA---TCGCA--ACCTCTAAC-ACAA--T-TAGCAAGAGTTACAAACTCCCAACTGTCAT
40582775 ATTAAGGCTCGCAGGATC
54 ATTAAGGCTCGCAGGATC
* * * * * * ** *
40582793 AAAACCACAGCCTCCAACACAATTAGCGAGAGTTACAAACTCCTAGTTGTCATATTAAGGTTCGC
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
*
40582858 AAGATC
66 AGGATC
* * * * * * * ** * *
40582864 AAAA-CTGTAGCCTCTAACATAGTTAGCGAGAGTTGCAAACTCCTAGTTGTTACATTAAGGCTCG
1 AAAATC-GCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCG
40582928 CAGGATC
65 CAGGATC
* * * * *
40582935 AAAACCGCAGCCTCCAACACAATTAGCGAGAGTTGCAAACTCCCATCTAGCTGTCA-ACTTAAGG
1 AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCA---A-CTGTCATA-TTAAGG
40582999 CTCGCAGG
61 CTCGCAGG
40583007 TCCAATGCCA
Statistics
Matches: 573, Mismatches: 122, Indels: 50
0.77 0.16 0.07
Matches are distributed among these distances:
70 7 0.01
71 475 0.83
72 9 0.02
73 5 0.01
74 5 0.01
75 24 0.04
78 5 0.01
79 3 0.01
80 3 0.01
81 4 0.01
82 31 0.05
83 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (71 bp):
AAAATCGCAACCTCTAACACAATTAGCAAGAGTTACAAACTCCCAACTGTCATATTAAGGCTCGC
AGGATC
Found at i:40582406 original size:142 final size:142
Alignment explanation
Indices: 40582118--40583006 Score: 648
Period size: 142 Copynumber: 6.2 Consensus size: 142
40582108 CATATTAAAG
* * * * * * *
40582118 CTCCCAATTGTCATATTCAGGCTTGCAGTATTAAAACCGCAACCTCTAACATTGTTAGAGAGAGC
1 CTCCCAACTGTCATATTAAGGCTCGCAGGATTAAAACCGCAACCTCTAACATAGTTAGCGAGAGT
* * * * *
40582183 TACAAACTCCCAAGTGTCATATTAA-----G-A-GTTTAAAATCGCAGCCTCCAACACAGTTAGT
66 TACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTCCAACACAGTTAGC
*
40582241 GAGAGTTACAAA
131 AAGAGTTACAAA
* * * * * **
40582253 CTCCCAGCTGTCATATTAAGGCTCGC-GAGATCAAAACCACAACCTCTAACACAGCTAGCGATTG
1 CTCCCAACTGTCATATTAAGGCTCGCAG-GATTAAAACCGCAACCTCTAACATAGTTAGCGAGAG
** * * * * * *
40582317 TTGTAAATTCCCAACTGTCACATTAAGGCTCACAGGATCAAAATTGCAGCCTCCAACATAGTTAG
65 TTACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTCCAACACAGTTAG
* *
40582382 CAAAATTTACAAA
130 CAAGAGTTACAAA
** * * * * * *
40582395 CTCCCAACTGTCATATTAAGGCTCATAGGATTAAAATCGCAGCCTCCAACATAATTAGCAAGACT
1 CTCCCAACTGTCATATTAAGGCTCGCAGGATTAAAACCGCAACCTCTAACATAGTTAGCGAGAGT
* * *
40582460 TACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCATCCTCTAACACAATTAGC
66 TACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTCCAACACAGTTAGC
*
40582525 GAGAGTTACAAA
131 AAGAGTTACAAA
* *
40582537 CTCCCAACTGTCATATTAAGGCTCGCAGGATTAAATCCGCAACCTCTAAAATAGTTAGCGAGAGT
1 CTCCCAACTGTCATATTAAGGCTCGCAGGATTAAAACCGCAACCTCTAACATAGTTAGCGAGAGT
* * * * * *
40582602 TACAAACTCCCAACTATCATAATAAGGCTTGCAGGATTAAAATCGTAGCCTCCAATAGAGTTAGC
66 TACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTCCAACACAGTTAGC
*
40582667 AAGAGATACAAA
131 AAGAGTTACAAA
** * * ** * *** *
40582679 CTCCCAGTTGTCATATTAAGGCTCCCAATTGTCATATTAAGGCTCACAGGAT-TAAAACTGCAAC
1 CTCCCAACTGTCATATTAAGGCTCGC-A--G---GATTAAAAC-CGCAACCTCTAACA-T---A-
* ** * * ** ** * * * * *
40582743 CTCTA-AAACAGTTGCAAACTCTTAGTTGTTACATTAAGGCTCGCAGGATCAAAACCACAGCCTC
54 GT-TAGCGAGAGTTACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTC
* *
40582807 CAACACAATTAGCGAGAGTTACAAA
118 CAACACAGTTAGCAAGAGTTACAAA
* ** * * * * * *
40582832 CTCCTAGTTGTCATATTAAGGTTCGCAAGATCAAAACTGTAGCCTCTAACATAGTTAGCGAGAGT
1 CTCCCAACTGTCATATTAAGGCTCGCAGGATTAAAACCGCAACCTCTAACATAGTTAGCGAGAGT
* * ** * * * * *
40582897 TGCAAACTCCTAGTTGTTACATTAAGGCTCGCAGGATCAAAACCGCAGCCTCCAACACAATTAGC
66 TACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTCCAACACAGTTAGC
* *
40582962 GAGAGTTGCAAA
131 AAGAGTTACAAA
40582974 CTCCCATCTAGCTGTCA-ACTTAAGGCTCGCAGG
1 CTCCCA---A-CTGTCATA-TTAAGGCTCGCAGG
40583007 TCCAATGCCA
Statistics
Matches: 588, Mismatches: 137, Indels: 47
0.76 0.18 0.06
Matches are distributed among these distances:
134 1 0.00
135 69 0.12
141 3 0.01
142 374 0.64
143 3 0.01
145 2 0.00
146 21 0.04
147 9 0.02
148 11 0.02
149 5 0.01
152 2 0.00
153 86 0.15
154 2 0.00
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (142 bp):
CTCCCAACTGTCATATTAAGGCTCGCAGGATTAAAACCGCAACCTCTAACATAGTTAGCGAGAGT
TACAAACTCCCAACTATCATATTAAGGCTCGCAGGATCAAAATCGCAGCCTCCAACACAGTTAGC
AAGAGTTACAAA
Found at i:40582544 original size:213 final size:213
Alignment explanation
Indices: 40582212--40582702 Score: 617
Period size: 213 Copynumber: 2.3 Consensus size: 213
40582202 TATTAAGAGT
**
40582212 TTAAAATCGCAGCCTCCAACACAGTTAGTGAGAGTTACAAACTCCCAGCTGTCATATTAAGGCTC
1 TTAAAATCGCAGCCTCCAACACAGTTAGCAAGAGTTACAAACTCCCAGCTGTCATATTAAGGCTC
* ** ** *
40582277 GCGAGATCAAAACCACAACCTCTAACACAGCTAGCGATTGTTGTAAATTCCCAACTGTCACATTA
66 GCGAGATCAAAACCACAACCTCTAACACAACTAGCGAGAGTTACAAACTCCCAACTGTCACATTA
* * * * *
40582342 AGGCTCACAGGATCAAAAT-TGCAGCCTCCAACATAGTTAGCAAAATTTACAAACTCCCAACTGT
131 AGGCTCACAGGAT-AAAATCCGCAACCTCCAAAATAGTTAGCAAAAGTTACAAACTCCCAACTAT
* *
40582406 CATATTAAGGCTCATAGGA
195 CATAATAAGGCTCACAGGA
* * * * *
40582425 TTAAAATCGCAGCCTCCAACATAATTAGCAAGACTTACAAACTCCCAACTATCATATTAAGGCTC
1 TTAAAATCGCAGCCTCCAACACAGTTAGCAAGAGTTACAAACTCCCAGCTGTCATATTAAGGCTC
* * * * *
40582490 GC-AGGATCAAAATCGCATCCTCTAACACAATTAGCGAGAGTTACAAACTCCCAACTGTCATATT
66 GCGA-GATCAAAACCACAACCTCTAACACAACTAGCGAGAGTTACAAACTCCCAACTGTCACATT
* * * * *
40582554 AAGGCTCGCAGGATTAAATCCGCAACCTCTAAAATAGTTAGCGAGAGTTACAAACTCCCAACTAT
130 AAGGCTCACAGGATAAAATCCGCAACCTCCAAAATAGTTAGCAAAAGTTACAAACTCCCAACTAT
**
40582619 CATAATAAGGCTTGCAGGA
195 CATAATAAGGCTCACAGGA
* * * * *
40582638 TTAAAATCGTAGCCTCCAATAGAGTTAGCAAGAGATACAAACTCCCAGTTGTCATATTAAGGCTC
1 TTAAAATCGCAGCCTCCAACACAGTTAGCAAGAGTTACAAACTCCCAGCTGTCATATTAAGGCTC
40582703 CCAATTGTCA
Statistics
Matches: 235, Mismatches: 41, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
212 5 0.02
213 230 0.98
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (213 bp):
TTAAAATCGCAGCCTCCAACACAGTTAGCAAGAGTTACAAACTCCCAGCTGTCATATTAAGGCTC
GCGAGATCAAAACCACAACCTCTAACACAACTAGCGAGAGTTACAAACTCCCAACTGTCACATTA
AGGCTCACAGGATAAAATCCGCAACCTCCAAAATAGTTAGCAAAAGTTACAAACTCCCAACTATC
ATAATAAGGCTCACAGGA
Found at i:40582703 original size:21 final size:21
Alignment explanation
Indices: 40582679--40582723 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
40582669 GAGATACAAA
*
40582679 CTCCCAGTTGTCATATTAAGG
1 CTCCCAATTGTCATATTAAGG
40582700 CTCCCAATTGTCATATTAAGG
1 CTCCCAATTGTCATATTAAGG
40582721 CTC
1 CTC
40582724 ACAGGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (21 bp):
CTCCCAATTGTCATATTAAGG
Found at i:40583260 original size:67 final size:68
Alignment explanation
Indices: 40583071--40583303 Score: 326
Period size: 68 Copynumber: 3.4 Consensus size: 68
40583061 GCCCAAGTAT
* * *
40583071 AAAACAGCTCACGGGCCTACTTCCCAGCTGATATCCTAAAGGCTCGCCAGTTTAATATTACGACC
1 AAAACAGCTCGCGGACCTACTTCCCAGCTGATATCCTAAAGGCTCGCCAGTTTAATATCACGACC
40583136 TCC
66 TCC
* * * * * * ** *
40583139 AAAATAGCTCGCGGACATATTTCCCAGTTGATATTCTAAAGGCTCGCCAATTTAATATCGTGATC
1 AAAACAGCTCGCGGACCTACTTCCCAGCTGATATCCTAAAGGCTCGCCAGTTTAATATCACGACC
40583204 TCC
66 TCC
40583207 AAAACAGCTACG-GG-CCTACTTCCCAGCTGATATCCTAAAGGCTCGCCAGTTTAATATCACGAC
1 AAAACAGCT-CGCGGACCTACTTCCCAGCTGATATCCTAAAGGCTCGCCAGTTTAATATCACGAC
40583270 CTCC
65 CTCC
40583274 AAAACAGCTCGCGGACCTACGTTCCCAGCT
1 AAAACAGCTCGCGGACCTAC-TTCCCAGCT
40583304 CGTATTATAG
Statistics
Matches: 140, Mismatches: 21, Indels: 7
0.83 0.12 0.04
Matches are distributed among these distances:
66 2 0.01
67 56 0.40
68 71 0.51
69 11 0.08
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.24
Consensus pattern (68 bp):
AAAACAGCTCGCGGACCTACTTCCCAGCTGATATCCTAAAGGCTCGCCAGTTTAATATCACGACC
TCC
Found at i:40592175 original size:502 final size:502
Alignment explanation
Indices: 40591233--40592722 Score: 2784
Period size: 502 Copynumber: 3.0 Consensus size: 502
40591223 CTTCAGAATA
*
40591233 TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCGAAAATTCTTCTCTTTTTCTC
1 TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCAAAAATTCTTCTCTTTTTCTC
* ** * *
40591298 TCAATATTTTTCAATGTTTCGGTGATAGAAAAAGGCATGGTTTGTTCATTAATCTTTGCAGAGGT
66 TCAATATTTTCCAATGTTTCAATGATAGAAAAAGGCAAGGTTTGTTCATTAATCTCTGCAGAGGT
* *
40591363 GCTACTGCTTCAATCATCGTGTTGTTGTATCCTGGGAGACAGTCGACCAACGTTTCTCCAAGTAC
131 GCTACTGCTTCGATCATCGTGTTGTTGTATCCTGGGAGACAATCGACCAACGTTTCTCCAAGTAC
* * * *
40591428 CGTAGGAGTGGCAAAATCTGTCTTAAAGAAACTGTGTAAAATAAGCCTCAACATCTAGTAAAATT
196 CGTAGGAGCGGCCAAATTTGTCTTAAAGAAAATGTGTAAAATAAGCCTCAACATCTAGTAAAATT
* * * * *
40591493 CGATTCTTTATTTGATATCTGGTTTTTTAATCTTATTTATTTGTTTTTCATACTTGATATTTTAA
261 CGATTATTTATTTGATAACTGGTTTTCTAATCTTATTTATTGGTTTTTCATGCTTGATATTTTAA
40591558 ATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTTG
326 ATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTTG
40591623 CTAACGTGTTATTTGTCCAACAATCTTAAGACAGATTTTATTATTTTGCAATTCTCTAATTCGAG
391 CTAACGTGTTATTTGTCCAACAATCTTAAGACAGATTTTATTATTTTGCAATTCTCTAATTCGAG
40591688 ACGAACGAGACACTAAGGCGAAAGAAAGAAAAATCCAAGACAAAATT
456 ACGAACGAGACACTAAGGCGAAAGAAAGAAAAATCCAAGACAAAATT
40591735 TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCAAAAATTCTTCTCTTTTTCTC
1 TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCAAAAATTCTTCTCTTTTTCTC
40591800 TCAATATTTTCCAATGTTTCAATGATAGAAAAAGGCAAGGTTTGTTCATTAATCTCTGCAGAGGT
66 TCAATATTTTCCAATGTTTCAATGATAGAAAAAGGCAAGGTTTGTTCATTAATCTCTGCAGAGGT
40591865 GCTACTGCTTCGATCATCGTGTTGTTGTATCCTGGGAGACAATCGACCAACGTTTCTCCAAGTAC
131 GCTACTGCTTCGATCATCGTGTTGTTGTATCCTGGGAGACAATCGACCAACGTTTCTCCAAGTAC
40591930 CGTAGGAGCGGCCAAATTTGTCTTAAAGAAAATGTGTAAAATAAGCCTCAACATCTAGTAAAATT
196 CGTAGGAGCGGCCAAATTTGTCTTAAAGAAAATGTGTAAAATAAGCCTCAACATCTAGTAAAATT
40591995 CGATTATTTATTTGATAACTGGTTTTCTAATCTTATTTATTGGTTTTTCATGCTTGATATTTTAA
261 CGATTATTTATTTGATAACTGGTTTTCTAATCTTATTTATTGGTTTTTCATGCTTGATATTTTAA
40592060 ATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTTG
326 ATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTTG
40592125 CTAACGTGTTATTTGTCCAACAATCTTAAGACAGATTTTATTATTTTGCAATTCTCTAATTCGAG
391 CTAACGTGTTATTTGTCCAACAATCTTAAGACAGATTTTATTATTTTGCAATTCTCTAATTCGAG
40592190 ACGAACGAGACACTAAGGCGAAAGAAAGAAAAATCCAAGACAAAATT
456 ACGAACGAGACACTAAGGCGAAAGAAAGAAAAATCCAAGACAAAATT
40592237 TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCAAAAATTCTTCTCTTTTTCTC
1 TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCAAAAATTCTTCTCTTTTTCTC
40592302 TCAATATTTTCCAATGTTTCAATGATAGAAAAAGGCAAGGTTTGTTCATTAATCTCTGCAGAGGT
66 TCAATATTTTCCAATGTTTCAATGATAGAAAAAGGCAAGGTTTGTTCATTAATCTCTGCAGAGGT
40592367 GCTACTGCTTCGATCATCGTGTTGTTGTATCCTGGGAGACAATCGACCAACGTTTCTCCAAGTAC
131 GCTACTGCTTCGATCATCGTGTTGTTGTATCCTGGGAGACAATCGACCAACGTTTCTCCAAGTAC
40592432 CGTAGGAGC-GCCAAATTTGGTCTTAAAGAAAATGTGTAAAATAAGCCTCAACATCTAGTAAAAT
196 CGTAGGAGCGGCCAAATTT-GTCTTAAAGAAAATGTGTAAAATAAGCCTCAACATCTAGTAAAAT
40592496 TCGATTATTTATTTGATAACTGGTTTTCTAATCTTATTTATTGGTTTTTCATGCTTGATATTTTA
260 TCGATTATTTATTTGATAACTGGTTTTCTAATCTTATTTATTGGTTTTTCATGCTTGATATTTTA
40592561 AATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTT
325 AATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTT
* *
40592626 GCTAACGTGTTATTTGTCCAACAATCTTAAGACAAATTTTATTATTTTGCAATTCTCTAATCCGA
390 GCTAACGTGTTATTTGTCCAACAATCTTAAGACAGATTTTATTATTTTGCAATTCTCTAATTCGA
*
40592691 GACGAACGAGACACCAAGGCGAAAGAAAGAAA
455 GACGAACGAGACACTAAGGCGAAAGAAAGAAA
40592723 GAAAAGTTTG
Statistics
Matches: 967, Mismatches: 20, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
501 9 0.01
502 958 0.99
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (502 bp):
TTTTACACTGAGAGACTCTCTAAAACCGAGTTTATTTTGCTCTCAAAAATTCTTCTCTTTTTCTC
TCAATATTTTCCAATGTTTCAATGATAGAAAAAGGCAAGGTTTGTTCATTAATCTCTGCAGAGGT
GCTACTGCTTCGATCATCGTGTTGTTGTATCCTGGGAGACAATCGACCAACGTTTCTCCAAGTAC
CGTAGGAGCGGCCAAATTTGTCTTAAAGAAAATGTGTAAAATAAGCCTCAACATCTAGTAAAATT
CGATTATTTATTTGATAACTGGTTTTCTAATCTTATTTATTGGTTTTTCATGCTTGATATTTTAA
ATACAAATTATTTATTTTATTTTATTTTATATAAATAGTTTTTTATTTATACATATATTTGTTTG
CTAACGTGTTATTTGTCCAACAATCTTAAGACAGATTTTATTATTTTGCAATTCTCTAATTCGAG
ACGAACGAGACACTAAGGCGAAAGAAAGAAAAATCCAAGACAAAATT
Found at i:40592964 original size:87 final size:85
Alignment explanation
Indices: 40592861--40593257 Score: 378
Period size: 87 Copynumber: 4.6 Consensus size: 85
40592851 GGGATTTATT
* * *
40592861 ATTTATTCCCGTCGTTCAATAGATTTTATTCAAATTTTAATTTTATTTCCAAAGCGAGTGTTAAA
1 ATTTATTCCCGCCGTTCAACAGATTTTATTC-AATTTTTATTTTATTTCCAAA-CGAGTGTTAAA
40592926 ATTAAATAAAATCTGTTTCGGG
64 ATTAAATAAAATCTGTTTCGGG
* *
40592948 AGTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTTTATTTTATTTCCAAAACG-GTGTTAAA
1 ATTTATTCCCGCCGTTCAACAGATTTTATT-CAATTTTTATTTTATTTCC-AAACGAGTGTTAAA
* *
40593012 ATCAAATAAAATATGTTTCGGG
64 ATTAAATAAAATCTGTTTCGGG
* * * **
40593034 ATTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTTTTATTTAGTTTCCAAACAAGAAATT-A
1 ATTTATTCCCGCCGTTCAACAGATTTTATTCAATTTTTAT-TTTA-TTTCCAAACGAG-TGTTAA
* *
40593098 AATTAAATGAAATCTATTTCGGG
63 AATTAAATAAAATCTGTTTCGGG
*** * * * *
40593121 ATTTATTCCATTCGTTTAACAGATTTTATTCAGTTTTGATTTTGTTTCC-AA--A---TTAAAAT
1 ATTTATTCCCGCCGTTCAACAGATTTTATTCAATTTTTATTTTATTTCCAAACGAGTGTTAAAAT
*
40593180 TGAATTGAATAATCTGTTTCGGG
66 T-AAAT-AA-AATCTGTTTCGGG
* ** * * * * *
40593203 ATTTATTCCCGCCATTTGATAGATTTTATTCGATCTTGATTTTGTTTCCAAACGA
1 ATTTATTCCCGCCGTTCAACAGATTTTATTCAATTTTTATTTTATTTCCAAACGA
40593258 AGACTTAATC
Statistics
Matches: 258, Mismatches: 39, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
78 2 0.01
79 5 0.02
80 3 0.01
81 1 0.00
82 53 0.21
83 2 0.01
84 2 0.01
85 13 0.05
86 68 0.26
87 103 0.40
88 6 0.02
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (85 bp):
ATTTATTCCCGCCGTTCAACAGATTTTATTCAATTTTTATTTTATTTCCAAACGAGTGTTAAAAT
TAAATAAAATCTGTTTCGGG
Found at i:40593120 original size:173 final size:172
Alignment explanation
Indices: 40592861--40593172 Score: 405
Period size: 173 Copynumber: 1.8 Consensus size: 172
40592851 GGGATTTATT
* * * **
40592861 ATTTATTCCCGTCGTTCAATAGATTTTATTCAAATTTTAATTTTATTTCCAAAGCGAGTGTTAAA
1 ATTTATTCCCGCCGTTCAACAGATTTTATTCAAATTTTAATTTTATTTCCAAAGCAAGAATTAAA
* * * *
40592926 ATTAAATAAAATCTGTTTCGGGAGTTATTCCCGCCGTTCAACAGATTTTATTCCATTTTTTATTT
66 ATTAAATAAAATCTATTTCGGGAGTTATTCCAGCCGTTCAACAGATTTTATT-CAGTTTTGATTT
40592991 TATTTCCAAAACGGTGTTAAAATCAAATAAAATATGTTTCGGG
130 TATTTCCAAAACGGTGTTAAAATCAAATAAAATATGTTTCGGG
* **
40593034 ATTTATTCCCGCCGTTCAACAGATTTTATTC-CATTTTTTTATTTAGTTTCCAAA-CAAGAAATT
1 ATTTATTCCCGCCGTTCAACAGATTTTATTCAAATTTTAAT-TTTA-TTTCCAAAGCAAG-AATT
* * ** *
40593097 -AAATTAAATGAAATCTATTTCGGGATTTATTCCATTCGTTTAACAGATTTTATTCAGTTTTGAT
63 AAAATTAAATAAAATCTATTTCGGGAGTTATTCCAGCCGTTCAACAGATTTTATTCAGTTTTGAT
*
40593161 TTTGTTTCCAAA
128 TTTATTTCCAAA
40593173 TTAAAATTGA
Statistics
Matches: 118, Mismatches: 18, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
172 25 0.21
173 83 0.70
174 10 0.08
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (172 bp):
ATTTATTCCCGCCGTTCAACAGATTTTATTCAAATTTTAATTTTATTTCCAAAGCAAGAATTAAA
ATTAAATAAAATCTATTTCGGGAGTTATTCCAGCCGTTCAACAGATTTTATTCAGTTTTGATTTT
ATTTCCAAAACGGTGTTAAAATCAAATAAAATATGTTTCGGG
Found at i:40596514 original size:14 final size:14
Alignment explanation
Indices: 40596495--40596534 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
40596485 TTAGTTTCGT
40596495 TTTTTTTATTTTTA
1 TTTTTTTATTTTTA
40596509 TTTTTTTCA-TTTTA
1 TTTTTTT-ATTTTTA
40596523 TTTTATTTATTT
1 TTTT-TTTATTT
40596535 ATTTCGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:40597100 original size:3 final size:3
Alignment explanation
Indices: 40597092--40597117 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40597082 TTTTTAAATT
40597092 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40597118 TCTATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40597174 original size:27 final size:26
Alignment explanation
Indices: 40597144--40597219 Score: 64
Period size: 27 Copynumber: 2.8 Consensus size: 26
40597134 CATGCACTAT
*
40597144 TTTTATATAATATATATATGCATTTTC
1 TTTTATATAATATATATATGCA-TTGC
* * *
40597171 TTTTTTAT-ATAGTATACACGCATTGC
1 TTTTATATAATA-TATATATGCATTGC
**
40597197 TTCTTACGTAATATATATATGCA
1 TT-TTATATAATATATATATGCA
40597220 AAAAAATATT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
26 8 0.22
27 26 0.70
28 3 0.08
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.49
Consensus pattern (26 bp):
TTTTATATAATATATATATGCATTGC
Found at i:40601975 original size:12 final size:12
Alignment explanation
Indices: 40601960--40602019 Score: 50
Period size: 12 Copynumber: 4.9 Consensus size: 12
40601950 ATTCAATAAA
*
40601960 AAAATCAAAATC
1 AAAATCAAAAAC
40601972 AAAATCAAAAAAC
1 AAAATC-AAAAAC
*
40601985 AAAAT-AGAAAAA
1 AAAATCA-AAAAC
**
40601997 AAAATCAAAGTC
1 AAAATCAAAAAC
*
40602009 AAAAGCAAAAA
1 AAAATCAAAAA
40602020 AAGAGAAATC
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
11 1 0.03
12 25 0.68
13 11 0.30
ACGTcount: A:0.73, C:0.12, G:0.05, T:0.10
Consensus pattern (12 bp):
AAAATCAAAAAC
Found at i:40602895 original size:7 final size:7
Alignment explanation
Indices: 40602881--40602914 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40602871 GAAATGGAGG
40602881 ATGAAAA
1 ATGAAAA
*
40602888 ACGAAAA
1 ATGAAAA
40602895 ATG-AAA
1 ATGAAAA
40602901 ATGAAAA
1 ATGAAAA
40602908 ATGAAAA
1 ATGAAAA
40602915 GTAATAACGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (7 bp):
ATGAAAA
Found at i:40602906 original size:13 final size:13
Alignment explanation
Indices: 40602885--40602914 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40602875 TGGAGGATGA
40602885 AAAACGAAAAATG
1 AAAACGAAAAATG
*
40602898 AAAATGAAAAATG
1 AAAACGAAAAATG
40602911 AAAA
1 AAAA
40602915 GTAATAACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.73, C:0.03, G:0.13, T:0.10
Consensus pattern (13 bp):
AAAACGAAAAATG
Found at i:40604596 original size:219 final size:219
Alignment explanation
Indices: 40604332--40604799 Score: 735
Period size: 219 Copynumber: 2.1 Consensus size: 219
40604322 GCCACCGACC
* * * * *
40604332 CTTATCTCCCTAAAGTTGCAGCGGAGTAGACTGAGAAAGCAGGTCTTATTCCCCTGAAGTTGCAG
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAGCAGGTCTTATCCCCCTAAAGTTACAG
* * **
40604397 TGGGGCAGATCGAAGAGATTCAAATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAG
66 TGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAG
40604462 TAATCCTATCTCCCTGAGATTACAGTGGAGC-AGATTAAAGTAATAGATCTTATCTATCTGAAGT
131 TAATCCTATCTCCCTGAGATTACAGTGGAGCGA-ATTAAAGTAATAGATCTTATCTATCTGAAGT
**
40604526 TACAGCAGAGTGGATCGCATCAGGT
195 TACAGCAGAGTGGATCGCATCAAAT
*
40604551 CTTATCTCCATGAAGTTGCAGCGGAGCAGACTGAGTAAA-CAGGTCTTATCCCCCTAAAGTTACA
1 CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAG-AAAGCAGGTCTTATCCCCCTAAAGTTACA
40604615 GTGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCA
65 GTGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCA
* *
40604680 GTAATCCTATCTCCTTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGT
130 GTAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTATCTGAAGT
* *
40604745 TACAGTAGAGTGGATTGCATCAAAT
195 TACAGCAGAGTGGATCGCATCAAAT
*
40604770 CTTATCTCCCTG-AGATTACAGCGGAGCAGA
1 CTTATCTCCCTGAAG-TTGCAGCGGAGCAGA
40604800 TTGAAGCCAG
Statistics
Matches: 228, Mismatches: 18, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
218 2 0.01
219 222 0.97
220 4 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (219 bp):
CTTATCTCCCTGAAGTTGCAGCGGAGCAGACTGAGAAAGCAGGTCTTATCCCCCTAAAGTTACAG
TGGGGCAGATCGAAGAGATTCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAG
TAATCCTATCTCCCTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTATCTGAAGTT
ACAGCAGAGTGGATCGCATCAAAT
Found at i:40604789 original size:85 final size:86
Alignment explanation
Indices: 40604642--40605017 Score: 248
Period size: 85 Copynumber: 4.3 Consensus size: 86
40604632 GATTCAAATA
* * * * * * * * *
40604642 TTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGATTACAGT
1 TTATCTCTCTGAGATTACAGCAGAGCGGATTAAAGTCA-TAATCTTATCTCCCTGAGATTACAGT
40604707 GGAGC-GAATTAAAGTAATAGATC
65 GGAGCAG-ATTAAAGTAATA-ATC
* * ** *
40604730 TTATCTCTCTGA-AGTTACAGTAGAGTGGATTGCA-TCA-AATCTTATCTCCCTGAGATTACAGC
1 TTATCTCTCTGAGA-TTACAGCAGAGCGGATTAAAGTCATAATCTTATCTCCCTGAGATTACAGT
* * *
40604792 GGAGCAGATTGAAGCCAGTAATC
65 GGAGCAGATTAAAG-TAATAATC
* ** * * *
40604815 CTATCTC-CTTGAGATTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGA-AGTTACA
1 TTATCTCTC-TGAGATTACAGCAGAGCGGATTAAAGTCATA-ATCTTATCTCCCTGAGA-TTACA
* ** ** *
40604878 GTAGAGTGGATTGCA-TCA-AATC
63 GTGGAGCAGATTAAAGTAATAATC
* * * * * *
40604900 TTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGATTACAGT
1 TTATCTCTCTGAGATTACAGCAGAGCGGATTAAAGTCA-TAATCTTATCTCCCTGAGATTACAGT
40604965 GGAGCAGATTAAAGTAATAGATC
65 GGAGCAGATTAAAGTAATA-ATC
* * *
40604988 TTATCTTTCT-AAAGTTACAGCAGAGTGGAT
1 TTATCTCTCTGAGA-TTACAGCAGAGCGGAT
40605018 CACATCAAGT
Statistics
Matches: 220, Mismatches: 52, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
84 1 0.00
85 121 0.55
86 13 0.06
87 8 0.04
88 77 0.35
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (86 bp):
TTATCTCTCTGAGATTACAGCAGAGCGGATTAAAGTCATAATCTTATCTCCCTGAGATTACAGTG
GAGCAGATTAAAGTAATAATC
Found at i:40604795 original size:129 final size:129
Alignment explanation
Indices: 40604635--40605040 Score: 697
Period size: 129 Copynumber: 3.1 Consensus size: 129
40604625 TCGAAGAGAT
* * *
40604635 TCAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
1 TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
40604700 TTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
66 TTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
40604764 TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
1 TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
40604829 TTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
66 TTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
*
40604893 TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCCTGAGA
1 TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
* * * **
40604958 TTACAGTGGAGC-AGATTAAAGTAATAGATCTTATCTTTCTAAAGTTACAGCAGAGTGGATCACA
66 TTACAGTGGAGCGA-ATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
* *
40605022 TCAAGTCTTATCCCCCTGA
1 TCAAATCTTATCTCCCTGA
40605041 AGTCACAGTG
Statistics
Matches: 265, Mismatches: 11, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
128 1 0.00
129 264 1.00
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (129 bp):
TCAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATCTCCTTGAGA
TTACAGTGGAGCGAATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATTGCA
Found at i:40605007 original size:44 final size:43
Alignment explanation
Indices: 40604419--40604993 Score: 345
Period size: 44 Copynumber: 13.2 Consensus size: 43
40604409 AAGAGATTCA
* *
40604419 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-TAAT
* *
40604463 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGTAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTAAT
** ** ** * * *
40604506 AGATCTTATCTATCTGA-AGTTACAGCAGAGTGGATCGCA-TCA-
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTAAT
** * * * *
40604548 GGTCTTATCTCCATGA-AGTTGCAGCGGAGCAGACTG-AGTAA-
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTAAT
* * * *
40604589 ACAGGTCTTATCCCCCT-AAAGTTACAGTGGGGCAGATCGAAG-AGATT
1 A-A--TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTA-A-T
* * ** * *
40604636 CAAATATTATCTCCCTAAGATTACAACGGAGCAGATTGAAGCCAGT
1 --AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-TAAT
* * *
40604682 AATCCTATCTCCTTGAGATTACAGTGGAGC-GAATTAAAGTAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAG-ATTGAAGTAAT
* * ** * *
40604725 AGATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATTGCA-TCA-
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTAAT
* * *
40604767 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-TAAT
* * *
40604811 AATCCTATCTCCTTGAGATTACAGTGGAGC-GAATTAAAGTAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAG-ATTGAAGTAAT
* * ** * *
40604854 AGATCTTATCTCTCTGA-AGTTACAGTAGAGTGGATTGCA-TCA-
1 A-ATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGTAAT
* * *
40604896 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-TAAT
* *
40604940 AATCCTATCTCCCTGAGATTACAGTGGAGCAGATTAAAGTAAT
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTAAT
40604983 AGATCTTATCT
1 A-ATCTTATCT
40604994 TTCTAAAGTT
Statistics
Matches: 399, Mismatches: 99, Indels: 66
0.71 0.18 0.12
Matches are distributed among these distances:
40 1 0.00
41 85 0.21
42 4 0.01
43 24 0.06
44 247 0.62
45 5 0.01
46 28 0.07
47 2 0.01
48 2 0.01
49 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (43 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGTAAT
Found at i:40605146 original size:44 final size:43
Alignment explanation
Indices: 40605023--40605151 Score: 116
Period size: 44 Copynumber: 2.9 Consensus size: 43
40605013 TGGATCACAT
* * **
40605023 CAAGTCTTATCCCCCTGAAGTCACAGTGGGACA-AATCGAAGATGA
1 CAAGTCTTATCCCCCTGAAGTTACAGTGGG-CAGACT-G-AGAAAA
* * * * * *
40605068 CAAATCTTATCTCCTTGAGGTTGCAATGGAGCAGACTGAGAAAA
1 CAAGTCTTATCCCCCTGAAGTTACAGTGG-GCAGACTGAGAAAA
40605112 CAAGTCTTATCCCCCTGAAGTTACAGTGAGGCAGACTGAG
1 CAAGTCTTATCCCCCTGAAGTTACAGTG-GGCAGACTGAG
40605152 CATAGCAAAT
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
44 36 0.55
45 26 0.40
46 3 0.05
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.22
Consensus pattern (43 bp):
CAAGTCTTATCCCCCTGAAGTTACAGTGGGCAGACTGAGAAAA
Found at i:40606198 original size:6 final size:6
Alignment explanation
Indices: 40606183--40606240 Score: 93
Period size: 6 Copynumber: 9.8 Consensus size: 6
40606173 TTAGTTTCGT
40606183 TTTTTA -TTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT-
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
40606229 TTATTTA TTTTT
1 TT-TTTA TTTTT
40606241 TTCGCTTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
5 7 0.14
6 40 0.82
7 2 0.04
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:40606806 original size:3 final size:3
Alignment explanation
Indices: 40606798--40606823 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40606788 TTTTTAAATT
40606798 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
40606824 TCTATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40621656 original size:2 final size:2
Alignment explanation
Indices: 40621649--40621673 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40621639 TATGAAAAAT
40621649 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 T
40621674 GATTATTTTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40627546 original size:2 final size:2
Alignment explanation
Indices: 40627535--40627565 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
40627525 AAAATAAAAG
40627535 TA TA -A 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
40627566 ACAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:40628672 original size:21 final size:21
Alignment explanation
Indices: 40628648--40628692 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
40628638 TGTATTAATC
*
40628648 TTTTTTTT-ATATAATT-TTGA
1 TTTTTTTTAAT-TAATTAATGA
40628668 TTTTTTTTAATTAATTAATGA
1 TTTTTTTTAATTAATTAATGA
40628689 TTTT
1 TTTT
40628693 AAAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTTTTAATTAATTAATGA
Found at i:40628914 original size:19 final size:19
Alignment explanation
Indices: 40628898--40628937 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
40628888 GCATTTAATT
40628898 AATT-TTTTAAAATTTAAA
1 AATTATTTTAAAATTTAAA
*
40628916 AATTATTTTAAAAATTAAA
1 AATTATTTTAAAATTTAAA
40628935 AAT
1 AAT
40628938 CATTAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATTTTAAAATTTAAA
Found at i:40628954 original size:22 final size:22
Alignment explanation
Indices: 40628929--40628977 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
40628919 TATTTTAAAA
*
40628929 ATTAAAAATCAT-TAAAATTATT
1 ATTAAAAAT-ATAAAAAATTATT
40628951 ATTAAAAATATAAAAAATTATT
1 ATTAAAAATATAAAAAATTATT
40628973 -TTAAA
1 ATTAAA
40628978 TATTTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAAAAATATAAAAAATTATT
Found at i:40628970 original size:28 final size:27
Alignment explanation
Indices: 40628914--40628970 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 27
40628904 TTAAAATTTA
40628914 AAAATTATTTTAAAAATTAAAAATCATT
1 AAAATTATTTTAAAAATTAAAAA-CATT
40628942 AAAATTATTATTAAAAATATAAAAA-ATT
1 AAAATTATT-TTAAAAAT-TAAAAACATT
40628970 A
1 A
40628971 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 13 0.48
29 8 0.30
30 6 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (27 bp):
AAAATTATTTTAAAAATTAAAAACATT
Found at i:40628987 original size:31 final size:29
Alignment explanation
Indices: 40628914--40628988 Score: 82
Period size: 31 Copynumber: 2.6 Consensus size: 29
40628904 TTAAAATTTA
40628914 AAAATTA-TTTTAAAAATTAAAAATCATT
1 AAAATTATTTTTAAAAATTAAAAATCATT
* *
40628942 AAAATTATTATTAAAAATATAAAAAATTATTT
1 AAAATTATTTTTAAAAAT-T-AAAAATCA-TT
*
40628974 TAAA-TATTTTTAAAA
1 AAAATTATTTTTAAAA
40628989 TTTTTAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
28 7 0.18
29 9 0.23
30 1 0.03
31 17 0.44
32 5 0.13
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (29 bp):
AAAATTATTTTTAAAAATTAAAAATCATT
Found at i:40628988 original size:21 final size:22
Alignment explanation
Indices: 40628929--40628990 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
40628919 TATTTTAAAA
40628929 ATTAAAAATCA-TTAAAATTATT
1 ATTAAAAAT-ATTTAAAATTATT
**
40628951 ATTAAAAATATAAAAAATTATT
1 ATTAAAAATATTTAAAATTATT
* *
40628973 -TTAAATATTTTTAAAATT
1 ATTAAAAATATTTAAAATT
40628991 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATTAAAAATATTTAAAATTATT
Found at i:40633526 original size:17 final size:17
Alignment explanation
Indices: 40633504--40633537 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40633494 ATATCAACGG
* *
40633504 AATAAAATATTTTAAAA
1 AATAAAAAACTTTAAAA
40633521 AATAAAAAACTTTAAAA
1 AATAAAAAACTTTAAAA
40633538 TTAACTTAAT
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:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAAAAACTTTAAAA
Found at i:40634976 original size:6 final size:6
Alignment explanation
Indices: 40634965--40634992 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40634955 CAACGAGAAA
40634965 TTGGGT TTGGGT TTGGGT TTGGGT TTGG
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGG
40634993 CTTGGAACAT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
TTGGGT
Found at i:40636278 original size:15 final size:17
Alignment explanation
Indices: 40636260--40636298 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
40636250 CTTTTGAATA
40636260 TTACAATTTTC-CC-TT
1 TTACAATTTTCTCCATT
40636275 TTAC--TTTTCTCCATT
1 TTACAATTTTCTCCATT
40636290 TTACAATTT
1 TTACAATTT
40636299 AGTTTATACC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
13 5 0.25
14 2 0.10
15 10 0.50
17 3 0.15
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (17 bp):
TTACAATTTTCTCCATT
Found at i:40636551 original size:14 final size:14
Alignment explanation
Indices: 40636532--40636569 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
40636522 GTTTGCCAGT
40636532 AAAATG-TTTTCTGG
1 AAAATGATTTT-TGG
40636546 AAAATGATTTTTGG
1 AAAATGATTTTTGG
40636560 AAAATGATTT
1 AAAATGATTT
40636570 ATTTTTCTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.37, C:0.03, G:0.18, T:0.42
Consensus pattern (14 bp):
AAAATGATTTTTGG
Found at i:40636582 original size:20 final size:19
Alignment explanation
Indices: 40636553--40636590 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
40636543 TGGAAAATGA
40636553 TTTTTGGAAAATGATTTAT
1 TTTTTGGAAAATGATTTAT
40636572 TTTTCTGGAAAATGATTTA
1 TTTT-TGGAAAATGATTTA
40636591 CTGAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (19 bp):
TTTTTGGAAAATGATTTAT
Found at i:40636597 original size:34 final size:33
Alignment explanation
Indices: 40636538--40636602 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
40636528 CAGTAAAATG
*
40636538 TTTTCTGGAAAATGATTTTTGGAAAATGATTTAT
1 TTTTCTGGAAAATGATTTCTGGAAAAT-ATTTAT
40636572 TTTTCTGGAAAATGATTTACT-GAAAATATTT
1 TTTTCTGGAAAATGATTT-CTGGAAAATATTT
40636603 TCTGGTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 24 0.83
35 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.15, T:0.46
Consensus pattern (33 bp):
TTTTCTGGAAAATGATTTCTGGAAAATATTTAT
Found at i:40637798 original size:35 final size:35
Alignment explanation
Indices: 40637752--40637821 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
40637742 TGTCATTGTC
*
40637752 AATCATTTCAATATCCAACAAGCTTAAAACATAAT
1 AATCAATTCAATATCCAACAAGCTTAAAACATAAT
*
40637787 AATCAATTCAATATCCAACAAGGTTAAAACATAAT
1 AATCAATTCAATATCCAACAAGCTTAAAACATAAT
40637822 CAATATCTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.50, C:0.19, G:0.04, T:0.27
Consensus pattern (35 bp):
AATCAATTCAATATCCAACAAGCTTAAAACATAAT
Found at i:40639501 original size:22 final size:22
Alignment explanation
Indices: 40639473--40639538 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
40639463 GCATTAATAA
40639473 TTTTTTGAGAAATTAAGCTACT
1 TTTTTTGAGAAATTAAGCTACT
** *
40639495 TTTTTTGTA-ATTTTAA--TAAT
1 TTTTTTG-AGAAATTAAGCTACT
40639515 TTTTTTGAGAAATTAAGCTACT
1 TTTTTTGAGAAATTAAGCTACT
40639537 TT
1 TT
40639539 CATTGTACCA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.03
20 15 0.44
22 17 0.50
23 1 0.03
ACGTcount: A:0.30, C:0.06, G:0.11, T:0.53
Consensus pattern (22 bp):
TTTTTTGAGAAATTAAGCTACT
Found at i:40639530 original size:20 final size:20
Alignment explanation
Indices: 40639465--40639530 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
40639455 TTATAATTGC
40639465 ATTAATAA-TTTTTTGAGAA
1 ATTAATAATTTTTTTGAGAA
* *
40639484 ATTAAGCTACTTTTTTTGTA-AT
1 ATTAA--TAATTTTTTTG-AGAA
*
40639506 TTTAATAATTTTTTTGAGAA
1 ATTAATAATTTTTTTGAGAA
40639526 ATTAA
1 ATTAA
40639531 GCTACTTTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
19 6 0.17
20 15 0.42
21 2 0.06
22 12 0.33
23 1 0.03
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (20 bp):
ATTAATAATTTTTTTGAGAA
Found at i:40639545 original size:42 final size:41
Alignment explanation
Indices: 40639466--40639545 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
40639456 TATAATTGCA
**
40639466 TTAATAATTTTTTGAGAAATTAAGCTACTTTTTTTGTAATT
1 TTAATAATTTTTTGAGAAATTAAGCTACTTTCATTGTAATT
40639507 TTAATAATTTTTTTGAGAAATTAAGCTACTTTCATTGTA
1 TTAATAA-TTTTTTGAGAAATTAAGCTACTTTCATTGTA
40639546 CCAATACTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 7 0.19
42 29 0.81
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (41 bp):
TTAATAATTTTTTGAGAAATTAAGCTACTTTCATTGTAATT
Found at i:40650056 original size:24 final size:24
Alignment explanation
Indices: 40650022--40650073 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40650012 TTTCTAGAAG
* **
40650022 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
40650046 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
40650070 ATTT
1 ATTT
40650074 GAATTTGATT
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:40650084 original size:24 final size:24
Alignment explanation
Indices: 40650039--40650084 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
40650029 ATTTATGAGT
*
40650039 ATAATATATTTAGCATTTATTAAC
1 ATAATATATTTAGAATTTATTAAC
40650063 ATAATATATTT-GAATTTGATTA
1 ATAATATATTTAGAATTT-ATTA
40650085 GAATTAGGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (24 bp):
ATAATATATTTAGAATTTATTAAC
Found at i:40654460 original size:24 final size:24
Alignment explanation
Indices: 40654426--40654477 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40654416 TTTCTCAAAG
* * *
40654426 ATTTAGTATTTATGGGTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
40654450 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
40654474 ATTT
1 ATTT
40654478 GAATTTGATT
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:0.35, C:0.04, G:0.12, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:40654488 original size:24 final size:24
Alignment explanation
Indices: 40654443--40654489 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40654433 ATTTATGGGT
*
40654443 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGAATTTATTAGC
40654467 ATAATATATTT-GAATTTGATTAG
1 ATAATATATTTAGAATTT-ATTAG
40654490 AAATAGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGAATTTATTAGC
Found at i:40655830 original size:39 final size:39
Alignment explanation
Indices: 40655776--40655854 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
40655766 CCTCACCCTC
40655776 TAACCATTTTCTTTATTGCTGGATCCTTTATCCTATATT
1 TAACCATTTTCTTTATTGCTGGATCCTTTATCCTATATT
* * * *
40655815 TAACCATTTTCTTTATTGTTTGATCCTTTCTCTTATATT
1 TAACCATTTTCTTTATTGCTGGATCCTTTATCCTATATT
40655854 T
1 T
40655855 GCTACTACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (39 bp):
TAACCATTTTCTTTATTGCTGGATCCTTTATCCTATATT
Found at i:40661131 original size:51 final size:51
Alignment explanation
Indices: 40661050--40661265 Score: 310
Period size: 51 Copynumber: 4.3 Consensus size: 51
40661040 ACTTCTGATC
40661050 AGTGACAAGTGATAAGT-AGTAGCTTCAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGA-TAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
40661101 AGTGGCAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAGCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* * * *
40661152 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTAATCAGTGACA
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
* * * *
40661203 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAGGGACT
1 AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
*
40661253 AGTGATAAGTGAT
1 AGTGACAAGTGAT
40661266 CATACGTAAG
Statistics
Matches: 149, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
50 33 0.22
51 115 0.77
52 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:40661212 original size:102 final size:101
Alignment explanation
Indices: 40661050--40661265 Score: 342
Period size: 102 Copynumber: 2.1 Consensus size: 101
40661040 ACTTCTGATC
* *
40661050 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGCAAGTGATA
1 AGTGACAAGTGATAAGTAGTAACTTCAGCTACACTTATCTAATCAGTGACAAGTGGCAAGTGATA
*
40661115 AGTGATAGCTTCAGCTACACTTATCTGAGCAGTGACA
66 AGTGATAGCTT-AGCTACACTTATCTGAGCAGGGACA
* *
40661152 AGTGACAAGTGATAAGTGGTAACTTTAGCTACACTTATCTAATCAGTGACAAGTGGCAAGTGATA
1 AGTGACAAGTGATAAGTAGTAACTTCAGCTACACTTATCTAATCAGTGACAAGTGGCAAGTGATA
* * *
40661217 AGTGGTAGCTTAGCTACACTTATCTGATCAGGGACT
66 AGTGATAGCTTAGCTACACTTATCTGAGCAGGGACA
*
40661253 AGTGATAAGTGAT
1 AGTGACAAGTGAT
40661266 CATACGTAAG
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
101 34 0.32
102 71 0.68
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (101 bp):
AGTGACAAGTGATAAGTAGTAACTTCAGCTACACTTATCTAATCAGTGACAAGTGGCAAGTGATA
AGTGATAGCTTAGCTACACTTATCTGAGCAGGGACA
Done.