Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold387
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: 397658
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.23
Warning! 113954 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:123498 original size:21 final size:21
Alignment explanation
Indices: 123457--123500 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
123447 CTCCCCTTTA
* *
123457 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
123478 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
123499 TC
1 TC
123501 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:126097 original size:13 final size:13
Alignment explanation
Indices: 126079--126104 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
126069 CAATTTTTTG
126079 TGTATCGATACAT
1 TGTATCGATACAT
126092 TGTATCGATACAT
1 TGTATCGATACAT
126105 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:126843 original size:21 final size:21
Alignment explanation
Indices: 126802--126846 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
126792 CTCTCCTTTA
* *
126802 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
126823 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
126844 TCT
1 TCT
126847 TATCAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.24, C:0.31, G:0.04, T:0.40
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:130670 original size:15 final size:15
Alignment explanation
Indices: 130650--130680 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
130640 ATTTCGTTTA
*
130650 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
130665 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
130680 G
1 G
130681 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:132496 original size:21 final size:21
Alignment explanation
Indices: 132467--132511 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
132457 AAGTTTTCAT
*
132467 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
132487 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
132509 TTT
1 TTT
132512 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:134748 original size:13 final size:13
Alignment explanation
Indices: 134730--134755 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
134720 CAATTTTTTG
134730 TGTATCGATACAT
1 TGTATCGATACAT
134743 TGTATCGATACAT
1 TGTATCGATACAT
134756 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:141968 original size:20 final size:19
Alignment explanation
Indices: 141913--141968 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
141903 AAAACCCTTA
*
141913 AAAGTATCGATACATAATTC
1 AAAGTATCGATACAT-GTTC
141933 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATGTT-C
*
141953 AATGTATCGATACATG
1 AAAGTATCGATACATG
141969 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 2 0.06
20 31 0.94
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
AAAGTATCGATACATGTTC
Found at i:142045 original size:13 final size:13
Alignment explanation
Indices: 142027--142052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
142017 TACAGCAAGT
142027 ATGTATCGATACA
1 ATGTATCGATACA
142040 ATGTATCGATACA
1 ATGTATCGATACA
142053 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:142574 original size:34 final size:35
Alignment explanation
Indices: 142511--142577 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
142501 CTAAGTGATT
142511 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
142547 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
142578 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:147496 original size:13 final size:13
Alignment explanation
Indices: 147478--147503 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
147468 TACAGCAAGT
147478 ATGTATCGATACA
1 ATGTATCGATACA
147491 ATGTATCGATACA
1 ATGTATCGATACA
147504 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:148025 original size:34 final size:35
Alignment explanation
Indices: 147962--148028 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
147952 CTAAGTGATT
147962 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
147998 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
148029 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:150119 original size:15 final size:15
Alignment explanation
Indices: 150099--150129 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
150089 TAAAAATGTC
*
150099 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
150114 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
150129 C
1 C
150130 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:274873 original size:56 final size:52
Alignment explanation
Indices: 274813--274940 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 52
274803 AAATAACGAG
**
274813 GTTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTTTTGGAAA-TAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGAAAAAATTAATG----TTTT-GAAAGTAAAATCGGA
* * *
274869 GTTGGAGTATCCCCGATTAT-AGAAAATTAATGTTTTGAAAGTAAAATCGGA
1 GTTGGAGTATCCTCGATTGTGAAAAAATTAATGTTTTGAAAGTAAAATCGGA
*
274920 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCTCGATTGTG
274941 GAGAATTGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
50 4 0.06
51 31 0.50
55 9 0.15
56 18 0.29
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.35
Consensus pattern (52 bp):
GTTGGAGTATCCTCGATTGTGAAAAAATTAATGTTTTGAAAGTAAAATCGGA
Found at i:277318 original size:13 final size:13
Alignment explanation
Indices: 277300--277325 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
277290 ACAAAGATCC
277300 ATGTATCGATACA
1 ATGTATCGATACA
277313 ATGTATCGATACA
1 ATGTATCGATACA
277326 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:277321 original size:33 final size:33
Alignment explanation
Indices: 277279--277345 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
277269 AAAATTTCCA
***
277279 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
277312 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
277345 A
1 A
277346 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:277389 original size:19 final size:18
Alignment explanation
Indices: 277365--277432 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
277355 CAGTAGCTAA
277365 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
277384 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
277399 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
277416 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
277433 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:277405 original size:13 final size:13
Alignment explanation
Indices: 277387--277411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277377 ACAATACTTA
277387 TGTATCGATACAT
1 TGTATCGATACAT
277400 TGTATCGATACA
1 TGTATCGATACA
277412 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:277409 original size:32 final size:32
Alignment explanation
Indices: 277368--277430 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
277358 TAGCTAATTA
*
277368 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
277400 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
277431 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:277512 original size:21 final size:21
Alignment explanation
Indices: 277488--277544 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
277478 CATTTGTAGG
* *
277488 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCAAAAA
277509 ATGTATCGATACATTCAAAAA
1 ATGTATCGATACATTCAAAAA
277530 ATGTATCGATACATT
1 ATGTATCGATACATT
277545 TAATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.18, G:0.11, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCAAAAA
Found at i:281551 original size:23 final size:22
Alignment explanation
Indices: 281517--281559 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
281507 ATACATTTTG
*
281517 GCTTAATGTATTGATACATCAA
1 GCTTAATCTATTGATACATCAA
281539 GCTTAAATCTATTGATACATC
1 GCTT-AATCTATTGATACATC
281560 CATAAATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (22 bp):
GCTTAATCTATTGATACATCAA
Found at i:281844 original size:25 final size:23
Alignment explanation
Indices: 281791--281845 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 23
281781 CCCATTTACT
*
281791 AATTTTATTTATTTATTTTGGCC
1 AATTTTATTTATTTATTTTGACC
*
281814 ACATTTTATTTAATTTATATTTGATC
1 A-ATTTTATTT-ATTTAT-TTTGACC
281840 AATTTT
1 AATTTT
281846 TCACCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 9 0.33
25 11 0.41
26 6 0.22
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.60
Consensus pattern (23 bp):
AATTTTATTTATTTATTTTGACC
Found at i:285010 original size:13 final size:13
Alignment explanation
Indices: 284992--285017 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
284982 CAATTTTTTG
284992 TGTATCGATACAT
1 TGTATCGATACAT
285005 TGTATCGATACAT
1 TGTATCGATACAT
285018 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:285082 original size:21 final size:21
Alignment explanation
Indices: 285056--285131 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
285046 CTGCCAAGAA
285056 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
****
285077 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
285097 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
285118 ATGTATCGATACAT
1 ATGTATCGATACAT
285132 TGCAACATGT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:285101 original size:20 final size:20
Alignment explanation
Indices: 285076--285149 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
285066 ACATCTTTTT
285076 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
****
285096 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGCAA
285117 CATGTATCGATACATTGCAA
1 CATGTATCGATACATTGCAA
285137 CATGTATCGATAC
1 CATGTATCGATAC
285150 TTTGAATTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (20 bp):
CATGTATCGATACATTGCAA
Found at i:285113 original size:41 final size:41
Alignment explanation
Indices: 285056--285149 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
285046 CTGCCAAGAA
285056 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
285097 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
285138 ATGTATCGATAC
1 ATGTATCGATAC
285150 TTTGAATTGT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
Found at i:292234 original size:97 final size:97
Alignment explanation
Indices: 292068--292263 Score: 374
Period size: 97 Copynumber: 2.0 Consensus size: 97
292058 CTATATAATT
*
292068 AGAAGTTAGTTGCTTGTTAGTCTCGTTTAATCCCACTCTAATGGACAAATTGTTGAAATCAGATG
1 AGAAGTTAGTTGCTTGTTAGTCTCGTTTAATCCCACTCTAATGGACAAATTGTTGAAATCAGAGG
292133 TGTAGTGTTCAATCATTCTTCCTTTTTGCTTG
66 TGTAGTGTTCAATCATTCTTCCTTTTTGCTTG
292165 AGAAGTTAGTTGCTTGTTAGTCTCGTTTAATCCCACTCTAATGGACAAATTGTTGAAATCAGAGG
1 AGAAGTTAGTTGCTTGTTAGTCTCGTTTAATCCCACTCTAATGGACAAATTGTTGAAATCAGAGG
*
292230 TGTAGTGTTCAATCGTTCTTCCTTTTTGCTTG
66 TGTAGTGTTCAATCATTCTTCCTTTTTGCTTG
292262 AG
1 AG
292264 CAAATGAAAC
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 97 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.40
Consensus pattern (97 bp):
AGAAGTTAGTTGCTTGTTAGTCTCGTTTAATCCCACTCTAATGGACAAATTGTTGAAATCAGAGG
TGTAGTGTTCAATCATTCTTCCTTTTTGCTTG
Found at i:293154 original size:16 final size:16
Alignment explanation
Indices: 293130--293163 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
293120 CCTAAAGTAA
293130 AAACATTATCCTAAAC
1 AAACATTATCCTAAAC
*
293146 AAACTTTATCCTAAAC
1 AAACATTATCCTAAAC
293162 AA
1 AA
293164 TAATCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (16 bp):
AAACATTATCCTAAAC
Found at i:297915 original size:18 final size:18
Alignment explanation
Indices: 297890--297931 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
297880 ACCGAAAAGG
* *
297890 AAATAAAATTAATTTGTT
1 AAATAAAATCAATTCGTT
*
297908 ATATAAAATCAATTCGTT
1 AAATAAAATCAATTCGTT
297926 AAATAA
1 AAATAA
297932 TTTATTATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (18 bp):
AAATAAAATCAATTCGTT
Found at i:304269 original size:33 final size:33
Alignment explanation
Indices: 304225--304289 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
304215 TTAGAAACAA
*
304225 TGTATCGATACAAT-TCATCATGTATCGATACAT
1 TGTATCGATACAATAT-ACCATGTATCGATACAT
*
304258 TGTATCTATACAATATACCATGTATCGATACA
1 TGTATCGATACAATATACCATGTATCGATACA
304290 AATAGTGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATATACCATGTATCGATACAT
Found at i:304363 original size:19 final size:19
Alignment explanation
Indices: 304319--304374 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
304309 CTGCCAGTTT
**
304319 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
304339 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
304358 CATGTATCAATACAATG
1 CATGTATCGATACAATG
304375 TATCGATGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:312430 original size:20 final size:20
Alignment explanation
Indices: 312397--312436 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
312387 AAAGGTCAAA
312397 ACCTTGAAAAGTATCGATAC
1 ACCTTGAAAAGTATCGATAC
* *
312417 ACCTTTAAATGTATCGATAC
1 ACCTTGAAAAGTATCGATAC
312437 TGTGCAATCT
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:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (20 bp):
ACCTTGAAAAGTATCGATAC
Found at i:312485 original size:13 final size:13
Alignment explanation
Indices: 312467--312491 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312457 AGATTGCACA
312467 GTATCGATACATT
1 GTATCGATACATT
312480 GTATCGATACAT
1 GTATCGATACAT
312492 GACCAAATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:312504 original size:20 final size:21
Alignment explanation
Indices: 312479--312531 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
312469 ATCGATACAT
**
312479 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
312499 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
312520 TGTATCGATACA
1 TGTATCGATACA
312532 GGTCATTGGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACATGAAAAGAA
Found at i:312602 original size:13 final size:13
Alignment explanation
Indices: 312584--312609 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312574 ACACACAATA
312584 TGTATCGATACAT
1 TGTATCGATACAT
312597 TGTATCGATACAT
1 TGTATCGATACAT
312610 CATAGAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:312625 original size:33 final size:32
Alignment explanation
Indices: 312564--312631 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
312554 GTAGCCAAAT
312564 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAATATGTATCGATACA
*
312596 TTGTATCGATACATCATAGA-ATGTATCGATACA
1 TTGTATCGATACA-CACA-ATATGTATCGATACA
312629 TTG
1 TTG
312632 GCTTGTAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 19 0.58
34 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (32 bp):
TTGTATCGATACACACAATATGTATCGATACA
Found at i:314346 original size:33 final size:33
Alignment explanation
Indices: 314304--314366 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
314294 AGAAATAATG
*
314304 TATCGATACAAT-TCATCATGTATCGATACATTA
1 TATCGATACAATAT-ACCATGTATCGATACATTA
314337 TATCGATACAATATACCATGTATCGATACA
1 TATCGATACAATATACCATGTATCGATACA
314367 AACAGTGGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (33 bp):
TATCGATACAATATACCATGTATCGATACATTA
Found at i:314441 original size:19 final size:18
Alignment explanation
Indices: 314396--314451 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
314386 CTGCCAGTTT
*
314396 CATGTATCGATACAATTGT
1 CATGTATCGATACAA-TGA
314415 CTATGTATCGATACAATGAA
1 C-ATGTATCGATACAATG-A
*
314435 CATGTATCCATACAATG
1 CATGTATCGATACAATG
314452 TATCGATACA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (18 bp):
CATGTATCGATACAATGA
Found at i:315300 original size:15 final size:15
Alignment explanation
Indices: 315271--315308 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
315261 TTCATGTTTT
315271 ATTAA-CATCATTTC
1 ATTAATCATCATTTC
*
315285 ATTAATCATTATTTC
1 ATTAATCATCATTTC
*
315300 ATCAATCAT
1 ATTAATCAT
315309 AAAAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTAATCATCATTTC
Found at i:315383 original size:15 final size:17
Alignment explanation
Indices: 315349--315385 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
315339 GTAGGATGAA
*
315349 AAAAATTTAGAAAGATG
1 AAAAATTTAGAAAGAAG
315366 AAAAA-TTA-AAAGAAG
1 AAAAATTTAGAAAGAAG
315381 AAAAA
1 AAAAA
315386 AATGAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 11 0.58
16 3 0.16
17 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (17 bp):
AAAAATTTAGAAAGAAG
Found at i:317760 original size:15 final size:14
Alignment explanation
Indices: 317742--317816 Score: 57
Period size: 15 Copynumber: 5.2 Consensus size: 14
317732 TTGAACCAGA
317742 AAAGAAAAAGGAAAG
1 AAAGAAAAA-GAAAG
*
317757 AAAGAAGAAGAAA-
1 AAAGAAAAAGAAAG
317770 AAGAGAAAGAAGAAAG
1 AA-AGAAA-AAGAAAG
*
317786 -AA-AAAAAGAAAA
1 AAAGAAAAAGAAAG
*
317798 AAAGGAAAATAGAAGG
1 AAA-GAAAA-AGAAAG
317814 AAA
1 AAA
317817 TAGAGAAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
12 6 0.12
13 7 0.15
14 9 0.19
15 19 0.40
16 7 0.15
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.01
Consensus pattern (14 bp):
AAAGAAAAAGAAAG
Found at i:317764 original size:7 final size:7
Alignment explanation
Indices: 317754--317796 Score: 51
Period size: 6 Copynumber: 6.9 Consensus size: 7
317744 AGAAAAAGGA
317754 AAGAAAG
1 AAGAAAG
317761 AAG-AAG
1 AAGAAAG
317767 AA-AAAG
1 AAGAAAG
317773 -AGAAAG
1 AAGAAAG
317779 AAGAAAG
1 AAGAAAG
317786 AA-AAA-
1 AAGAAAG
317791 AAGAAA
1 AAGAAA
317797 AAAAGGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
5 3 0.09
6 18 0.56
7 11 0.34
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (7 bp):
AAGAAAG
Found at i:317785 original size:29 final size:27
Alignment explanation
Indices: 317744--317837 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 27
317734 GAACCAGAAA
317744 AGAAAAAGGAAAGAAAGAAGAAGAAAAAG
1 AGAAAAA-GAAAGAAA-AAGAAGAAAAAG
*
317773 AGAAAGAAGAAAGAAAAA-AAGAAAAAA
1 AGAAA-AAGAAAGAAAAAGAAGAAAAAG
*
317800 AGGAAAATAGAAGGAAATAGAGAAGAAAAAG
1 A-GAAAA-AGAAAGAAA-A-AGAAGAAAAAG
317831 AGAAAAA
1 AGAAAAA
317838 AAATGAGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
27 10 0.18
28 14 0.25
29 15 0.27
30 8 0.14
31 9 0.16
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (27 bp):
AGAAAAAGAAAGAAAAAGAAGAAAAAG
Found at i:317787 original size:11 final size:10
Alignment explanation
Indices: 317742--317831 Score: 66
Period size: 11 Copynumber: 9.1 Consensus size: 10
317732 TTGAACCAGA
317742 AAAGAAAAAGG
1 AAAGAAAAA-G
317753 AAAGAAAGAAG
1 AAAGAAA-AAG
317764 -AAGAAAAAG
1 AAAGAAAAAG
317773 --AGAAAGAAG
1 AAAGAAA-AAG
317782 AAAG-AAAA-
1 AAAGAAAAAG
317790 AAAGAAAAA-
1 AAAGAAAAAG
*
317799 AAGGAAAATAG
1 AAAGAAAA-AG
* *
317810 AAGGAAATAG
1 AAAGAAAAAG
317820 AGAAGAAAAAG
1 A-AAGAAAAAG
317831 A
1 A
317832 GAAAAAAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
8 9 0.13
9 19 0.28
10 12 0.18
11 25 0.37
12 2 0.03
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:318158 original size:3 final size:3
Alignment explanation
Indices: 318150--318199 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
318140 AGATTTTTTA
318150 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
318197 TAT
1 TAT
318200 GGCATGCTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:320379 original size:6 final size:7
Alignment explanation
Indices: 320361--320393 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
320351 TTCAACATTA
320361 AAAAAATT
1 AAAAAA-T
320369 AAAAAAT
1 AAAAAAT
320376 AAAAAAT
1 AAAAAAT
320383 AAAAAAT
1 AAAAAAT
320390 AAAA
1 AAAA
320394 TTTTAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:320948 original size:12 final size:12
Alignment explanation
Indices: 320933--320967 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
320923 GCAGCCATAC
320933 CAGCAACAACAA
1 CAGCAACAACAA
*
320945 CAGCAATAACAA
1 CAGCAACAACAA
*
320957 CAACAACAACA
1 CAGCAACAACA
320968 GTAACAGCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.60, C:0.31, G:0.06, T:0.03
Consensus pattern (12 bp):
CAGCAACAACAA
Found at i:320972 original size:18 final size:19
Alignment explanation
Indices: 320936--321022 Score: 54
Period size: 18 Copynumber: 4.6 Consensus size: 19
320926 GCCATACCAG
* *
320936 CAACAACAAC-AGCAATAA
1 CAACAACAACAACCAGTAA
320954 CAACAACAACAA-CAGTAA
1 CAACAACAACAACCAGTAA
* * * *
320972 CAGCAGCAGCAACCA-TAC
1 CAACAACAACAACCAGTAA
* * *
320990 CAACAATAACAAGCAGCAAA
1 CAACAACAACAACCAG-TAA
321010 CAACAAGCAACAA
1 CAACAA-CAACAA
321023 TAGCAAGTAA
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
18 36 0.71
19 3 0.06
20 7 0.14
21 5 0.10
ACGTcount: A:0.56, C:0.30, G:0.09, T:0.05
Consensus pattern (19 bp):
CAACAACAACAACCAGTAA
Found at i:321022 original size:27 final size:25
Alignment explanation
Indices: 320954--321029 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
320944 ACAGCAATAA
*
320954 CAACAACAACAACAGTAAC-AGCAG
1 CAACAACAACAACAATAACAAGCAG
*
320978 CAGCAACCATACCAACAATAACAAGCAG
1 CAACAA-CA-A-CAACAATAACAAGCAG
*
321006 CAAACAACAAGCAACAATAGCAAG
1 C-AACAACAA-CAACAATAACAAG
321030 TAAATAGCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
24 5 0.12
25 2 0.05
26 1 0.02
27 22 0.52
28 8 0.19
29 4 0.10
ACGTcount: A:0.54, C:0.29, G:0.12, T:0.05
Consensus pattern (25 bp):
CAACAACAACAACAATAACAAGCAG
Found at i:329906 original size:13 final size:13
Alignment explanation
Indices: 329888--329914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
329878 ATCTATTATG
329888 CTTTGTATCGATA
1 CTTTGTATCGATA
329901 CTTTGTATCGATA
1 CTTTGTATCGATA
329914 C
1 C
329915 ATGATCATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.19, G:0.15, T:0.44
Consensus pattern (13 bp):
CTTTGTATCGATA
Found at i:329946 original size:20 final size:19
Alignment explanation
Indices: 329903--329957 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
329893 TATCGATACT
329903 TTGTATCGATACATGATCA
1 TTGTATCGATACATGATCA
*
329922 TTGTATCGATTCATGCA-CAA
1 TTGTATCGATACATG-ATC-A
*
329942 TTGTATCAATACATGA
1 TTGTATCGATACATGA
329958 AACTGGCAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATGATCA
Found at i:338811 original size:20 final size:19
Alignment explanation
Indices: 338766--338822 Score: 89
Period size: 19 Copynumber: 2.9 Consensus size: 19
338756 GCTATCAATA
338766 CATTGTATCGATACATGAT
1 CATTGTATCGATACATGAT
338785 CATTGTATCGATACATGCA-
1 CATTGTATCGATACATG-AT
338804 CAATTGTATCGATACATGA
1 C-ATTGTATCGATACATGA
338823 AACTGGCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (19 bp):
CATTGTATCGATACATGAT
Found at i:338895 original size:33 final size:33
Alignment explanation
Indices: 338851--338915 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
338841 TACCACTATT
* * * *
338851 TGTATCGATACATGACACATTGTATCGATACAG
1 TGTATCAATACATAAAAAATTGTATCGATACAG
338884 TGTATCAATACATAAAAAATTGTATCGATACA
1 TGTATCAATACATAAAAAATTGTATCGATACA
338916 TTGTCCCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (33 bp):
TGTATCAATACATAAAAAATTGTATCGATACAG
Found at i:344988 original size:156 final size:154
Alignment explanation
Indices: 344799--345275 Score: 468
Period size: 156 Copynumber: 3.1 Consensus size: 154
344789 AGATCTACCA
* ** * *
344799 TCGACTTAGAAGTGCCCGATAATCCTAGAGGACTTAAAAAGGATTATAGATGGAATTAACTTATC
1 TCGACTTAGAAGTGCCTGATACCCCTAAAGGACTTAAAAAGGATTATAGATGG-ATTAACCTATC
*
344864 CTAAATACCCACCTTCGACATAAAAGCAGACCTAGTGACAAACTAAGACTTGATTCTAGAAAAAT
65 CTAAATACCCACCTTCGACATAAAAGCAGACCTAGTGACAACCTAAGACTTGATTCTA-AAAAAT
*
344929 TATAAAAATATCCC-TACGGGATACCTT
129 TATAAAAAT-TCCCTTAAGGGATA-CTT
* * *
344956 TC-ACTTAGAAGTGCCTAATACCCCTAAAGGACTTAAAAAGGATTATAAATGGGATGAACCTATC
1 TCGACTTAGAAGTGCCTGATACCCCTAAAGGACTTAAAAAGGATTATAGAT-GGATTAACCTATC
* * ** * *
345020 CTAAATA-CCACCTTC-AGCCTAAAAGCGGACCCGGTGACAACCTAGGACTCGATTCTAAAAAAT
65 CTAAATACCCACCTTCGA-CATAAAAGCAGACCTAGTGACAACCTAAGACTTGATTCTAAAAAAT
* * *
345083 TA-CAAAATGCCCTTAAGGGGTACTT
129 TATAAAAATTCCCTTAAGGGATACTT
* * * * * * *
345108 TCGACTTAAAAGT-ACTCGGTGCCCCTACAA-GACTTAAAAATGATTGTAGATGGGTTGAACCTA
1 TCGACTTAGAAGTGCCT-GATACCCCTA-AAGGACTTAAAAAGGATTATAGATGGATT-AACCTA
* * * * *
345171 TCCTAAATACCCACCTTTGACATAAAAGTAGA-CTTGATGATAACCTAAGACTTGATTTTAAAAA
63 TCCTAAATACCCACCTTCGACATAAAAGCAGACCTAG-TGACAACCTAAGACTTGATTCTAAAAA
* ** *
345235 ATTATGAAAATGTCCCCGATGGG-TACTT
127 ATTATAAAAAT-TCCCTTAAGGGATACTT
*
345263 TTGACTTAGAAGT
1 TCGACTTAGAAGT
345276 ACTCGGTACC
Statistics
Matches: 262, Mismatches: 46, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
152 13 0.05
153 63 0.24
154 54 0.21
155 63 0.24
156 65 0.25
157 4 0.02
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (154 bp):
TCGACTTAGAAGTGCCTGATACCCCTAAAGGACTTAAAAAGGATTATAGATGGATTAACCTATCC
TAAATACCCACCTTCGACATAAAAGCAGACCTAGTGACAACCTAAGACTTGATTCTAAAAAATTA
TAAAAATTCCCTTAAGGGATACTT
Found at i:345161 original size:153 final size:154
Alignment explanation
Indices: 344829--345293 Score: 501
Period size: 155 Copynumber: 3.0 Consensus size: 154
344819 AATCCTAGAG
* * *
344829 GACTTAAAAAGGATTATAGATGGAATTAACTTATCCTAAATACCCACCTTCGACATAAAAGCAGA
1 GACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGA
* * * * *
344894 CCTAGTGACAAACTAAGACTTGATTCTAGAAAAATTATAAAAATATCCCTACGGGATACCTTTC-
66 CCTGGTGACAACCTAAGACTTGATTCTA-AAAAATTATAAAAAT-GCCCTAAGGGGTA-CTTTCG
* **
344958 ACTTAGAAGTGC-CTAATACCCCTA-AA
128 ACTTAGAAGTACTC-GGTACCCCTACAA
* * *
344984 GGACTTAAAAAGGATTATAAATGGGATGAACCTATCCTAAATA-CCACCTTC-AGCCTAAAAGCG
1 -GACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGA-CATAAAAGCA
* * * *
345047 GACCCGGTGACAACCTAGGACTCGATTCTAAAAAATTA-CAAAATGCCCTTAAGGGGTACTTTCG
64 GACCTGGTGACAACCTAAGACTTGATTCTAAAAAATTATAAAAATGCCC-TAAGGGGTACTTTCG
* *
345111 ACTTAAAAGTACTCGGTGCCCCTACAA
128 ACTTAGAAGTACTCGGTACCCCTACAA
* * * * *
345138 GACTTAAAAATGATTGTAGATGGGTTGAACCTATCCTAAATACCCACCTTTGACATAAAAGTAGA
1 GACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGA
* * * * * ** * *
345203 CTTGATGATAACCTAAGACTTGATTTTAAAAAATTATGAAAATGTCCCCGATGGGTACTTTTGAC
66 CCTGGTGACAACCTAAGACTTGATTCTAAAAAATTATAAAAATG-CCCTAAGGGGTACTTTCGAC
*
345268 TTAGAAGTACTCGGTACCCTTACAA
130 TTAGAAGTACTCGGTACCCCTACAA
345293 G
1 G
345294 GCTCGAAAAA
Statistics
Matches: 257, Mismatches: 43, Indels: 19
0.81 0.13 0.06
Matches are distributed among these distances:
152 8 0.03
153 67 0.26
154 57 0.22
155 84 0.33
156 41 0.16
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.26
Consensus pattern (154 bp):
GACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCCACCTTCGACATAAAAGCAGA
CCTGGTGACAACCTAAGACTTGATTCTAAAAAATTATAAAAATGCCCTAAGGGGTACTTTCGACT
TAGAAGTACTCGGTACCCCTACAA
Found at i:347434 original size:164 final size:163
Alignment explanation
Indices: 347228--347532 Score: 355
Period size: 163 Copynumber: 1.9 Consensus size: 163
347218 AAATCTCCTT
* * * * * *
347228 AAAAACATTTACGGAATAGAAAACTAAGTTTTTTGGAAATAGAAGATTTTCAAAAAAAAAATTAA
1 AAAAACATTTACGGAATAGAAAACTAAGTATTTCGAAAATAGAAAAATTTCAAAAAAAAAATGAA
* * * * * *
347293 AAACT-TATGAAAATAAATGAATTTTTCAAAACTAGTTTACTATGA-ATTAAATGATGATAATTG
66 AAA-TGAATG-AAACAAATGAATTTTTCAAAACTAGTCTAATAT-ATATTAAATAATAATAATTG
347356 ATGAATTTTAAAAATTATAAACCAAGAATCACTCCC
128 ATGAATTTTAAAAATTATAAACCAAGAATCACTCCC
* * * * **
347392 AAAAACATTTATGGAGTAGAAAACTCTA-TATTTCGAAAATAGAAAAATTTGAAGGAAAAAATGA
1 AAAAACATTTACGGAATAGAAAACT-AAGTATTTCGAAAATAGAAAAATTTCAAAAAAAAAATGA
* * * *
347456 AAAATGAATGAAACGAATGAATTTTTCAAAACTGGTCTAATATATATTGAATAATAATATTTGAT
65 AAAATGAATGAAACAAATGAATTTTTCAAAACTAGTCTAATATATATTAAATAATAATAATTGAT
347521 GAATTTTAAAAA
130 GAATTTTAAAAA
347533 ATGAAAACCA
Statistics
Matches: 116, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
162 1 0.01
163 57 0.49
164 57 0.49
165 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.31
Consensus pattern (163 bp):
AAAAACATTTACGGAATAGAAAACTAAGTATTTCGAAAATAGAAAAATTTCAAAAAAAAAATGAA
AAATGAATGAAACAAATGAATTTTTCAAAACTAGTCTAATATATATTAAATAATAATAATTGATG
AATTTTAAAAATTATAAACCAAGAATCACTCCC
Found at i:347468 original size:19 final size:21
Alignment explanation
Indices: 347427--347468 Score: 52
Period size: 19 Copynumber: 2.0 Consensus size: 21
347417 CTATATTTCG
347427 AAAATAGAAAAATTTGAAGGAA
1 AAAATAGAAAAA-TTGAAGGAA
*
347449 AAAAT-GAAAAA-TGAATGAA
1 AAAATAGAAAAATTGAAGGAA
347468 A
1 A
347469 CGAATGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (21 bp):
AAAATAGAAAAATTGAAGGAA
Found at i:349069 original size:30 final size:30
Alignment explanation
Indices: 349033--349122 Score: 153
Period size: 30 Copynumber: 3.0 Consensus size: 30
349023 ATTAAGGCTC
*
349033 TCGTTTAAAAAATTTTATCCCCCTTGATAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
349063 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
* *
349093 TCGTTTAAAAGATTTTCTCTCCCTTGATAA
1 TCGTTTAAAAAATTTTCTCCCCCTTGATAA
349123 AAATTTATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (30 bp):
TCGTTTAAAAAATTTTCTCCCCCTTGATAA
Found at i:349494 original size:33 final size:33
Alignment explanation
Indices: 349446--349512 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
349436 AAGTGCACCA
*
349446 AAGTGCTCATCCATGTGCTGTGAGAGTGAAGTG
1 AAGTGCTCATCCATGTGCTGTGAAAGTGAAGTG
*
349479 AAGTGCTCA-CTCATGTGTTGTGAAAGTGAAGTG
1 AAGTGCTCATC-CATGTGCTGTGAAAGTGAAGTG
349512 A
1 A
349513 TCAACTCTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 1 0.03
33 30 0.97
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.28
Consensus pattern (33 bp):
AAGTGCTCATCCATGTGCTGTGAAAGTGAAGTG
Found at i:350865 original size:21 final size:21
Alignment explanation
Indices: 350826--350874 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
350816 TTTGTTGATG
*
350826 ATTTTG-ATGAAAAATGAAGT
1 ATTTTGAATGAAAAATGAAGA
350846 ATTTTGAAGTGAAAAA-GAAGA
1 ATTTTGAA-TGAAAAATGAAGA
*
350867 AATTTGAA
1 ATTTTGAA
350875 AAAGATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 12 0.48
22 7 0.28
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (21 bp):
ATTTTGAATGAAAAATGAAGA
Found at i:351012 original size:13 final size:13
Alignment explanation
Indices: 350993--351032 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
350983 ATAGTAACTC
350993 ATGTATCGATACA
1 ATGTATCGATACA
*
351006 TTGTATCGATACA
1 ATGTATCGATACA
351019 ATGTATCGATACA
1 ATGTATCGATACA
351032 A
1 A
351033 AGAATATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:356815 original size:19 final size:19
Alignment explanation
Indices: 356772--356826 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
356762 TGCCAGTTTA
* **
356772 ATGTATCAATACAATTGTGC
1 ATGTATCGATACAA-TGAAC
356792 ATGTATCGATACAATGAAC
1 ATGTATCGATACAATGAAC
*
356811 ATGTATCGATATAATG
1 ATGTATCGATACAATG
356827 TATCGATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACAATGAAC
Found at i:356833 original size:32 final size:33
Alignment explanation
Indices: 356792--356854 Score: 94
Period size: 32 Copynumber: 1.9 Consensus size: 33
356782 ACAATTGTGC
*
356792 ATGTATCGATACAATG-A-ACATGTATCGATATA
1 ATGTATCGATACAAAGCATA-ATGTATCGATATA
356824 ATGTATCGATACAAAGCATAATGTATCGATA
1 ATGTATCGATACAAAGCATAATGTATCGATA
356855 CATCTGGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.54
33 12 0.43
34 1 0.04
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGCATAATGTATCGATATA
Found at i:359657 original size:13 final size:13
Alignment explanation
Indices: 359639--359664 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
359629 AATTTTGGGA
359639 TGTATCGATACAT
1 TGTATCGATACAT
359652 TGTATCGATACAT
1 TGTATCGATACAT
359665 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:359771 original size:20 final size:19
Alignment explanation
Indices: 359724--359778 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
359714 GCCAATCACC
*
359724 TGTATCGATACATTCTTTGTA
1 TGTATCGATACA-T-TTGGTA
*
359745 AGTATCGATACATTTGGTCA
1 TGTATCGATACATTTGGT-A
359765 TGTATCGATACATT
1 TGTATCGATACATT
359779 GTATCGATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.13
20 15 0.50
21 11 0.37
ACGTcount: A:0.27, C:0.15, G:0.16, T:0.42
Consensus pattern (19 bp):
TGTATCGATACATTTGGTA
Found at i:359821 original size:20 final size:19
Alignment explanation
Indices: 359798--359836 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
359788 CTGTGCATTA
359798 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
359818 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
359837 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:360382 original size:16 final size:16
Alignment explanation
Indices: 360361--360391 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
360351 CCTTAATAAA
360361 GCAATTTAACAATTTT
1 GCAATTTAACAATTTT
360377 GCAATTTAACAATTT
1 GCAATTTAACAATTT
360392 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (16 bp):
GCAATTTAACAATTTT
Found at i:362086 original size:20 final size:21
Alignment explanation
Indices: 362056--362097 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
362046 CTGGTTTTGT
362056 TGATGATTTTG-A-TGAAAAA
1 TGATGATTTTGAAGTGAAAAA
362075 TGATGTATTTTGAAGTGAAAAA
1 TGATG-ATTTTGAAGTGAAAAA
362097 T
1 T
362098 AAGGAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 1 0.05
22 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.21, T:0.38
Consensus pattern (21 bp):
TGATGATTTTGAAGTGAAAAA
Found at i:364830 original size:13 final size:13
Alignment explanation
Indices: 364814--364838 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
364804 GGTAAAAAGG
364814 AAAAAATAAAAAT
1 AAAAAATAAAAAT
364827 AAAAAATAAAAA
1 AAAAAATAAAAA
364839 AAATTTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:364837 original size:19 final size:20
Alignment explanation
Indices: 364815--364860 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
364805 GTAAAAAGGA
364815 AAAAATAAAAAT-AAAAAAT
1 AAAAATAAAAATAAAAAAAT
**
364834 AAAAA-AAATTTAAAAAAAT
1 AAAAATAAAAATAAAAAAAT
364853 AGAAAATA
1 A-AAAATA
364861 CATTTTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 4 0.18
19 13 0.59
20 4 0.18
21 1 0.05
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAAATAAAAATAAAAAAAT
Found at i:364991 original size:19 final size:19
Alignment explanation
Indices: 364967--365061 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
364957 AAATCGTAAA
364967 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
364986 TGTATCGATAC--AA-TG-
1 TGTATCGATACATAAGTGT
365001 TG--TCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
365018 TGTATCGATAC--AA-TG-
1 TGTATCGATACATAAGTGT
*
365033 TG--TCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
365050 TGTATCGATACA
1 TGTATCGATACA
365062 ATGTATCGCT
Statistics
Matches: 63, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 14 0.22
15 8 0.13
16 7 0.11
17 8 0.13
19 26 0.41
ACGTcount: A:0.32, C:0.13, G:0.20, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:365007 original size:32 final size:32
Alignment explanation
Indices: 364965--365065 Score: 184
Period size: 32 Copynumber: 3.2 Consensus size: 32
364955 ACAAATCGTA
*
364965 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTGTCGATACATAAGTGTTGTATCGATAC
364997 AATGTGTCGATACATAAGTGTTGTATCGATAC
1 AATGTGTCGATACATAAGTGTTGTATCGATAC
*
365029 AATGTGTCGATACATAAGTTTTGTATCGATAC
1 AATGTGTCGATACATAAGTGTTGTATCGATAC
365061 AATGT
1 AATGT
365066 ATCGCTATGA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 67 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.36
Consensus pattern (32 bp):
AATGTGTCGATACATAAGTGTTGTATCGATAC
Found at i:365008 original size:13 final size:13
Alignment explanation
Indices: 364990--365042 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 13
364980 AAGTGTTGTA
364990 TCGATACAATGTG
1 TCGATACAATGTG
365003 TCGATACATAAGTGTTG
1 TCGATAC--AA-TG-TG
365020 TATCGATACAATGTG
1 --TCGATACAATGTG
365035 TCGATACA
1 TCGATACA
365043 TAAGTTTTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
13 15 0.44
15 4 0.12
16 4 0.12
17 4 0.12
19 7 0.21
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (13 bp):
TCGATACAATGTG
Found at i:365132 original size:13 final size:13
Alignment explanation
Indices: 365114--365139 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
365104 ATTAAGGAAA
365114 TGTATCGATACAT
1 TGTATCGATACAT
365127 TGTATCGATACAT
1 TGTATCGATACAT
365140 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:367561 original size:52 final size:52
Alignment explanation
Indices: 367504--367627 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 52
367494 CAATTATTCA
* *
367504 TAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTT-
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTT--TTG
*
367556 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTTG
1 TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTTG
* *
367608 CAATCGAGGATACTCCAACC
1 TAATCGGGGATACTCCAACC
367628 TCGTTATTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
51 2 0.03
52 48 0.75
53 14 0.22
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (52 bp):
TAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAAACACCAATTTTTTG
Found at i:367789 original size:79 final size:79
Alignment explanation
Indices: 367645--367844 Score: 231
Period size: 79 Copynumber: 2.5 Consensus size: 79
367635 TTCATCGGGA
** * * *
367645 ATACTCCAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATT
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATT
* **
367710 TCTCATAATTAGGG
66 TCTCACAACCAGGG
* * * * *
367724 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCTCGATTTTATTTCC-TAATCATCGAT
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATCGAT
* *
367788 TTTTCACAACCGGGG
65 TTCTCACAACCAGGG
**
367803 ATACTCCAACCCCGTTATTTTTAAGGGGATACTCCAACCCCG
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
367845 TTATTATCTC
Statistics
Matches: 101, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 3 0.03
79 98 0.97
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.30
Consensus pattern (79 bp):
ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATCGATT
TCTCACAACCAGGG
Found at i:372568 original size:13 final size:13
Alignment explanation
Indices: 372550--372575 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
372540 AATTTTGGGA
372550 TGTATCGATACAT
1 TGTATCGATACAT
372563 TGTATCGATACAT
1 TGTATCGATACAT
372576 CTTGTCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:372732 original size:20 final size:19
Alignment explanation
Indices: 372709--372747 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
372699 CTGTGCATTA
372709 TGTATCGATACATTTGAAGG
1 TGTATCGATACATTT-AAGG
372729 TGTATCGATACATTTAAGG
1 TGTATCGATACATTTAAGG
372748 GTTTTGACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (19 bp):
TGTATCGATACATTTAAGG
Found at i:373228 original size:87 final size:87
Alignment explanation
Indices: 373119--373317 Score: 240
Period size: 87 Copynumber: 2.3 Consensus size: 87
373109 ATATTTAGGA
*
373119 ACAAAGGGAAAATTCAATTTTTTT-GAAAAATAAGGTTGGAGTATCCCCTCGAA-AGAATGAAGA
1 ACAAA-GGAAAATTCAATTTTTTTGGAAAAATAAGATTGGAGTATCCCCTCGAAGA-AATG-AGA
*
373182 TGGAGTTTACCAAGGATAAAATTAT
63 TGGAGTTTACCAAGGACAAAATTAT
* * * * * * *
373207 ACGAAGGAAAATTCAATTTTTTTGGTAAAATGAGATTGGAGTATCCCTTTGGAGAAATGGGATGG
1 ACAAAGGAAAATTCAATTTTTTTGGAAAAATAAGATTGGAGTATCCCCTCGAAGAAATGAGATGG
**
373272 AGTTTTTCAAGGACAAAATTAT
66 AGTTTACCAAGGACAAAATTAT
*
373294 ACAAAGGAAAATTTAAATTTTTTT
1 ACAAAGGAAAA-TTCAATTTTTTT
373318 AGAACGGAGT
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
87 52 0.55
88 42 0.44
89 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.31
Consensus pattern (87 bp):
ACAAAGGAAAATTCAATTTTTTTGGAAAAATAAGATTGGAGTATCCCCTCGAAGAAATGAGATGG
AGTTTACCAAGGACAAAATTAT
Found at i:374699 original size:31 final size:31
Alignment explanation
Indices: 374664--374730 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
374654 AACCAATATC
*
374664 AGCATGCAAACACACAAAGGTGACATTTATT
1 AGCATGCAAACAAACAAAGGTGACATTTATT
*
374695 AGCATGCAAACAAACAAAGGTGACATTTTTT
1 AGCATGCAAACAAACAAAGGTGACATTTATT
374726 A-CATG
1 AGCATG
374731 GAAATGGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (31 bp):
AGCATGCAAACAAACAAAGGTGACATTTATT
Found at i:378746 original size:52 final size:51
Alignment explanation
Indices: 378668--378816 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
378658 CGAAATATGA
378668 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTAGGC
* * * *
378720 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTAGGC
**
378772 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
378817 ATGTATTGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.95
53 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTAGGC
Found at i:378907 original size:33 final size:33
Alignment explanation
Indices: 378870--378936 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
378860 AGTAGCTTAA
378870 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
378903 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
378936 A
1 A
378937 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:378910 original size:13 final size:13
Alignment explanation
Indices: 378892--378916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378882 CAAAAAAATA
378892 TGTATCGATACAT
1 TGTATCGATACAT
378905 TGTATCGATACA
1 TGTATCGATACA
378917 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:381094 original size:20 final size:19
Alignment explanation
Indices: 381047--381104 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
381037 TTTGTATCGA
*
381047 GACATTGTATCGATACATT
1 GACATTGTATCGATACATG
**
381066 TTCATTGTATCGATACATG
1 GACATTGTATCGATACATG
381085 GACAATTGTATCGATACATG
1 GAC-ATTGTATCGATACATG
381105 AAATTGGCAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (19 bp):
GACATTGTATCGATACATG
Found at i:382519 original size:3 final size:3
Alignment explanation
Indices: 382497--382534 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
382487 AACCATCAAA
*
382497 GAT GAT GAA GAT GA- GAAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT G-AT GAT GAT GAT GAT GAT GAT GA
382535 CTTGGATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 29 0.94
4 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.34, T:0.26
Consensus pattern (3 bp):
GAT
Found at i:387022 original size:20 final size:20
Alignment explanation
Indices: 386997--387034 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
386987 GAAATTTTTC
386997 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
387017 AGAATGTATCGATACATT
1 AGAATGTATCGATACATT
387035 TGGAAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:387073 original size:20 final size:20
Alignment explanation
Indices: 387048--387145 Score: 62
Period size: 20 Copynumber: 5.6 Consensus size: 20
387038 AAAACTTAGA
387048 TGTATCGATACAATATTCTT
1 TGTATCGATACAATATTCTT
*
387068 TGTATC----C-ATA--CAT
1 TGTATCGATACAATATTCTT
*
387081 TGTATCGATACAATATTTTT
1 TGTATCGATACAATATTCTT
*
387101 TGTATC----C-ATA--CAT
1 TGTATCGATACAATATTCTT
387114 TGTATCGATACAATATTCTT
1 TGTATCGATACAATATTCTT
*
387134 TGTATCCATACA
1 TGTATCGATACA
387146 TTGTATCGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 28
0.62 0.08 0.30
Matches are distributed among these distances:
13 15 0.26
15 6 0.11
16 2 0.04
17 2 0.04
18 6 0.11
20 26 0.46
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (20 bp):
TGTATCGATACAATATTCTT
Found at i:387090 original size:33 final size:33
Alignment explanation
Indices: 387048--387159 Score: 215
Period size: 33 Copynumber: 3.4 Consensus size: 33
387038 AAAACTTAGA
387048 TGTATCGATACAATATTCTTTGTATCCATACAT
1 TGTATCGATACAATATTCTTTGTATCCATACAT
*
387081 TGTATCGATACAATATTTTTTGTATCCATACAT
1 TGTATCGATACAATATTCTTTGTATCCATACAT
387114 TGTATCGATACAATATTCTTTGTATCCATACAT
1 TGTATCGATACAATATTCTTTGTATCCATACAT
387147 TGTATCGATACAA
1 TGTATCGATACAA
387160 GGGTTACTAT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATATTCTTTGTATCCATACAT
Found at i:387305 original size:21 final size:21
Alignment explanation
Indices: 387267--387306 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
387257 ATCAAATTTT
* *
387267 CTTCAAATTTCTTATTTTTCA
1 CTTCAAAATACTTATTTTTCA
*
387288 CTTCAAAATACTTCTTTTT
1 CTTCAAAATACTTATTTTT
387307 TTATCAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (21 bp):
CTTCAAAATACTTATTTTTCA
Found at i:389159 original size:20 final size:19
Alignment explanation
Indices: 389109--389165 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
389099 TTGTATCGAT
* *
389109 ACATTGTATTGATACATGT
1 ACATTGTATCGATACATGG
* *
389128 TCATTATATCGATACATGG
1 ACATTGTATCGATACATGG
389147 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
389166 AAACTGGCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:389232 original size:33 final size:33
Alignment explanation
Indices: 389195--389259 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
389185 TACCATTGTT
*
389195 TGTATCAATACATGGC-ACATTGTATCGATACAA
1 TGTATCAATACATGACGA-ATTGTATCGATACAA
** *
389228 TGTATTGATACATGACGAATTGTATTGATACA
1 TGTATCAATACATGACGAATTGTATCGATACA
389260 TTGCTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 26 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCAATACATGACGAATTGTATCGATACAA
Found at i:390328 original size:97 final size:97
Alignment explanation
Indices: 390076--390339 Score: 350
Period size: 97 Copynumber: 2.7 Consensus size: 97
390066 ATAAGCGAAG
* * * * * ** *
390076 ATAAGATTTAAACCTTGACAAGTTTAAAAATAAGGTTGGAGTATCCCCTCGGAAGAATAAGGTTA
1 ATAAGATTTAAATCTTGACAAGTTTAAAAACAAGGTTGGAGTATCTCCTCGAAAAAATGGGGTTG
* * * *
390141 GATTATCTTCATGGATGACAAATTAAGCAAAA
66 GAGTAACTCCATGGATGACAAATTAAGAAAAA
* ** * *
390173 TTAAGATTTAAATCTTGACAAGTTTAAAAACGGGGTTAGAGTATCTCCTCAAAAAAATGGGGTTG
1 ATAAGATTTAAATCTTGACAAGTTTAAAAACAAGGTTGGAGTATCTCCTCGAAAAAATGGGGTTG
390238 GAGTAAC-CCAATGGATGACAAATTAAGAAAAA
66 GAGTAACTCC-ATGGATGACAAATTAAGAAAAA
*
390270 ATAAGATTTAAATCTTGACAAGTTTAAAAACAAGGTTGGAATATCTCCTCGAAAAAATGGGGTTG
1 ATAAGATTTAAATCTTGACAAGTTTAAAAACAAGGTTGGAGTATCTCCTCGAAAAAATGGGGTTG
390335 GAGTA
66 GAGTA
390340 TTCTGTTGAA
Statistics
Matches: 143, Mismatches: 23, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
96 1 0.01
97 142 0.99
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (97 bp):
ATAAGATTTAAATCTTGACAAGTTTAAAAACAAGGTTGGAGTATCTCCTCGAAAAAATGGGGTTG
GAGTAACTCCATGGATGACAAATTAAGAAAAA
Found at i:392839 original size:20 final size:20
Alignment explanation
Indices: 392816--392862 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
392806 CATTTCAGAC
392816 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
*
392836 ATGTATCGATATATTCACTT
1 ATGTATCGATACATTCACTT
392856 ATTGTAT
1 A-TGTAT
392863 TAATACAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:395886 original size:15 final size:16
Alignment explanation
Indices: 395866--395903 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
395856 TAAATTTTGA
395866 TTCAAGTTTAA-CTTT
1 TTCAAGTTTAAGCTTT
395881 TTCAAGTTTAAGCTTT
1 TTCAAGTTTAAGCTTT
395897 TTCAAGT
1 TTCAAGT
395904 AAAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.26, C:0.13, G:0.11, T:0.50
Consensus pattern (16 bp):
TTCAAGTTTAAGCTTT
Done.