Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008024.1 Hibiscus syriacus cultivar Beakdansim tig00110499_pilon, whole genome shotgun sequence
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: 1023309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:16236 original size:17 final size:17
Alignment explanation
Indices: 16214--16353 Score: 127
Period size: 17 Copynumber: 8.1 Consensus size: 17
16204 AATTAAGAGT
*
16214 TAGTTTAATAAATGAAC
1 TAGTTTAATGAATGAAC
* *
16231 TAGTTTGATGAATGAAA
1 TAGTTTAATGAATGAAC
*
16248 TAGTTTAATTAATGAAC
1 TAGTTTAATGAATGAAC
* * *
16265 TAACTTTATTTAATGAAC
1 T-AGTTTAATGAATGAAC
* * **
16283 TTGTAATCTTGAATGAAC
1 TAGT-TTAATGAATGAAC
*
16301 TAGTTTGATGAATGAAC
1 TAGTTTAATGAATGAAC
*
16318 TAGTTTAATGAATAAAC
1 TAGTTTAATGAATGAAC
* *
16335 AAGTTTAATCAATGAAC
1 TAGTTTAATGAATGAAC
16352 TA
1 TA
16354 CTTAGTTAAA
Statistics
Matches: 98, Mismatches: 23, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
17 70 0.71
18 28 0.29
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.37
Consensus pattern (17 bp):
TAGTTTAATGAATGAAC
Found at i:16895 original size:2 final size:2
Alignment explanation
Indices: 16888--16933 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
16878 GAAGGGATAA
16888 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16930 AT AT
1 AT AT
16934 GAATGTAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23892 original size:15 final size:16
Alignment explanation
Indices: 23852--23894 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
23842 AATGTTTTAA
*
23852 TATAGTTATTTTCATC
1 TATAGTTATTATCATC
23868 TATA-TATATTAT-ATC
1 TATAGT-TATTATCATC
23883 TATAGTTATTAT
1 TATAGTTATTAT
23895 GATGATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (16 bp):
TATAGTTATTATCATC
Found at i:25173 original size:22 final size:21
Alignment explanation
Indices: 25136--25176 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
25126 CCATCTCCAT
25136 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
25157 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
25177 TTTTCGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:25499 original size:18 final size:19
Alignment explanation
Indices: 25475--25540 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
25465 AATTGGAGTG
*
25475 CAAAAAGAAAGAAAAAGAT
1 CAAAAAGAAAGAAAAAAAT
25494 -AAAAAG-AAGAAAAAAAT
1 CAAAAAGAAAGAAAAAAAT
*
25511 CAAAAA-AGAAGAAAAGAAAA
1 CAAAAAGA-AAGAAAA-AAAT
*
25531 GAAAAAGAAA
1 CAAAAAGAAA
25541 TTCAAAAGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 10 0.26
18 11 0.28
19 7 0.18
20 10 0.26
21 1 0.03
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
CAAAAAGAAAGAAAAAAAT
Found at i:25503 original size:11 final size:10
Alignment explanation
Indices: 25479--25536 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
25469 GGAGTGCAAA
25479 AAGAAAGAAA-
1 AAGAAA-AAAG
25489 AAGATAAAAAG
1 AAGA-AAAAAG
25500 AAGAAAAAA-
1 AAGAAAAAAG
**
25509 ATCAAAAAAG
1 AAGAAAAAAG
25519 AAGAAAAGAA-
1 AAGAAAA-AAG
25529 AAGAAAAA
1 AAGAAAAA
25537 GAAATTCAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 8 0.20
10 24 0.60
11 8 0.20
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.03
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:25503 original size:17 final size:18
Alignment explanation
Indices: 25476--25539 Score: 69
Period size: 19 Copynumber: 3.4 Consensus size: 18
25466 ATTGGAGTGC
*
25476 AAAAAGAAAGAAAAAGAT-
1 AAAAAG-AAGAAAAAAATA
25494 AAAAAGAAGAAAAAAATCA
1 AAAAAGAAGAAAAAAAT-A
25513 AAAAAGAAGAAAAGAAA-A
1 AAAAAGAAGAAAA-AAATA
25531 GAAAAAGAA
1 -AAAAAGAA
25540 ATTCAAAAGA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 10 0.24
18 7 0.17
19 21 0.51
20 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.03
Consensus pattern (18 bp):
AAAAAGAAGAAAAAAATA
Found at i:29056 original size:16 final size:15
Alignment explanation
Indices: 29035--29076 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
29025 TGTGACCTTT
29035 CATGAATGATGCTGCC
1 CATGAA-GATGCTGCC
* *
29051 CATGAAGATACTTCC
1 CATGAAGATGCTGCC
29066 CATGAAGATGC
1 CATGAAGATGC
29077 ATTTCCATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 17 0.74
16 6 0.26
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (15 bp):
CATGAAGATGCTGCC
Found at i:29745 original size:26 final size:25
Alignment explanation
Indices: 29701--29750 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
29691 TGAGATACAA
*
29701 CAACACCACCATCTCCATTTCATCAT
1 CAACACCACCAACTCCATTT-ATCAT
* *
29727 CAACACCATCAACTTCATTTATCA
1 CAACACCACCAACTCCATTTATCA
29751 AGACCATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (25 bp):
CAACACCACCAACTCCATTTATCAT
Found at i:34350 original size:22 final size:21
Alignment explanation
Indices: 34318--34358 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
34308 CCATCTCCAT
34318 TTCATCATCAACG-CCATCAAC
1 TTCATCATCAA-GACCATCAAC
34339 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAAGACCATCA
34359 TTTTCGCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.34, C:0.37, G:0.05, T:0.24
Consensus pattern (21 bp):
TTCATCATCAAGACCATCAAC
Found at i:38894 original size:22 final size:21
Alignment explanation
Indices: 38857--38897 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38847 CCATCTCCTT
38857 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
38878 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
38898 TTTTCGCAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:39219 original size:18 final size:19
Alignment explanation
Indices: 39196--39247 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 19
39186 AATTGTAGTG
*
39196 CAAAAAGAAAGAAAAAGA-
1 CAAAAAGAAAGAAAAAAAT
39214 CAAAAAG-AAGAAAAAAAT
1 CAAAAAGAAAGAAAAAAAT
39232 CAGAAAAGAAAGAAAA
1 CA-AAAAGAAAGAAAA
39248 GAAAAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 9 0.30
18 9 0.30
19 5 0.17
20 7 0.23
ACGTcount: A:0.77, C:0.06, G:0.15, T:0.02
Consensus pattern (19 bp):
CAAAAAGAAAGAAAAAAAT
Found at i:39245 original size:9 final size:9
Alignment explanation
Indices: 39198--39257 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 9
39188 TTGTAGTGCA
39198 AAAAGAAAG
1 AAAAGAAAG
*
39207 AAAAAGACA-
1 -AAAAGAAAG
39216 AAAAG-AAG
1 AAAAGAAAG
*
39224 AAAAAAATCAG
1 AAAAGAA--AG
39235 AAAAGAAAG
1 AAAAGAAAG
39244 AAAAGAAAAG
1 AAAAG-AAAG
39254 AAAA
1 AAAA
39258 ACAATTTCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 1 0.02
8 9 0.22
9 8 0.20
10 15 0.37
11 8 0.20
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:39255 original size:19 final size:18
Alignment explanation
Indices: 39198--39257 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
39188 TTGTAGTGCA
*
39198 AAAAGAAAGAAAAAGACA-
1 AAAAGAAAGAAAAA-AAAG
39216 AAAAG-AAGAAAAAAATCAG
1 AAAAGAAAGAAAAAAA--AG
39235 AAAAGAAAGAAAAGAAAAG
1 AAAAGAAAGAAAA-AAAAG
39254 AAAA
1 AAAA
39258 ACAATTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
16 1 0.03
17 8 0.22
18 6 0.17
19 11 0.31
20 7 0.19
21 3 0.08
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAGAAAGAAAAAAAAG
Found at i:44975 original size:22 final size:22
Alignment explanation
Indices: 44949--44997 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
44939 TTTACTATGC
44949 AAAGATACTCACCACCTTCCTA
1 AAAGATACTCACCACCTTCCTA
44971 AAAGATACTCACCACCTTCCTA
1 AAAGATACTCACCACCTTCCTA
*
44993 GAAGA
1 AAAGA
44998 ACAACCAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.33, G:0.08, T:0.20
Consensus pattern (22 bp):
AAAGATACTCACCACCTTCCTA
Found at i:48524 original size:22 final size:21
Alignment explanation
Indices: 48487--48527 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
48477 CCATCTCCAT
48487 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
48508 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
48528 TATCCGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:51580 original size:13 final size:13
Alignment explanation
Indices: 51562--51622 Score: 51
Period size: 13 Copynumber: 4.9 Consensus size: 13
51552 ATATAGGCGT
51562 AATATGGTGATGG
1 AATATGGTGATGG
51575 AATATGGTGAT-G
1 AATATGGTGATGG
*
51587 -ATATAGGCG-T-G
1 AATAT-GGTGATGG
51598 -ATAATGGTGATGG
1 AAT-ATGGTGATGG
*
51611 ACTATGGTGATG
1 AATATGGTGATG
51623 ATATAGGCGT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 11 0.28
12 7 0.17
13 21 0.52
14 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.36, T:0.31
Consensus pattern (13 bp):
AATATGGTGATGG
Found at i:51604 original size:23 final size:23
Alignment explanation
Indices: 51576--51682 Score: 80
Period size: 23 Copynumber: 4.5 Consensus size: 23
51566 TGGTGATGGA
51576 ATATGGTGATGATATAGGCG-TG
1 ATATGGTGATGATATAGGCGATG
*
51598 ATAATGGTGATGGACTAT-GGTGATG
1 AT-ATGGTGAT-GA-TATAGGCGATG
* *
51623 ATATAGGCG-TGATA-ATGGAGATGG
1 ATAT-GGTGATGATATA-GGCGAT-G
51647 ACTATGGTGATGATATAGGCG-TG
1 A-TATGGTGATGATATAGGCGATG
51670 ATAATGGTGATGA
1 AT-ATGGTGATGA
51683 ACAGATTGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
22 5 0.07
23 27 0.40
24 14 0.21
25 21 0.31
26 1 0.01
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (23 bp):
ATATGGTGATGATATAGGCGATG
Found at i:51617 original size:36 final size:36
Alignment explanation
Indices: 51544--51681 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
51534 ATTTATAAGT
* * *
51544 TGGTGATAATATAGGCGTAAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
51579 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
51615 TGGTGATGATATAGGCGTGATAATGGAGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
51651 TGGTGATGATATAGGCGTGATAATGGTGATG
1 TGGTGATGATATAGGCGTGATAATGGTGATG
51682 AACAGATTGT
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 19 0.20
36 78 0.80
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:51658 original size:13 final size:11
Alignment explanation
Indices: 51563--51682 Score: 75
Period size: 11 Copynumber: 10.1 Consensus size: 11
51553 TATAGGCGTA
51563 ATATGGTGATGG
1 ATATGGTGAT-G
51575 AATATGGTGATG
1 -ATATGGTGATG
*
51587 ATATAGGCG-TG
1 ATAT-GGTGATG
51598 ATAATGGTGATGG
1 AT-ATGGTGAT-G
51611 ACTATGGTGATG
1 A-TATGGTGATG
*
51623 ATATAGGCG-TG
1 ATAT-GGTGATG
*
51634 ATAATGGAGATGG
1 AT-ATGGTGAT-G
51647 ACTATGGTGATG
1 A-TATGGTGATG
*
51659 ATATAGGCG-TG
1 ATAT-GGTGATG
51670 ATAATGGTGATG
1 AT-ATGGTGATG
51682 A
1 A
51683 ACAGATTGTA
Statistics
Matches: 87, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
11 31 0.36
12 25 0.29
13 29 0.33
14 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.36, T:0.30
Consensus pattern (11 bp):
ATATGGTGATG
Found at i:55691 original size:17 final size:17
Alignment explanation
Indices: 55669--55701 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55659 GTAGGAGTCT
55669 TTTTCTT-TTCTCTTTTA
1 TTTTCTTCTT-TCTTTTA
55686 TTTTCTTCTTTCTTTT
1 TTTTCTTCTTTCTTTT
55702 TCTCTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTA
Found at i:56136 original size:13 final size:12
Alignment explanation
Indices: 56117--56238 Score: 64
Period size: 11 Copynumber: 10.2 Consensus size: 12
56107 ATATAGGCGT
56117 GATATGGTGATG
1 GATATGGTGATG
56129 GAATATGGTGAT-
1 G-ATATGGTGATG
*
56141 GATATAGGCG-T-
1 GATAT-GGTGATG
56152 GATAATGGTGATG
1 GAT-ATGGTGATG
56165 GACTATGGTGAT-
1 GA-TATGGTGATG
*
56177 GATATAGGCG-T-
1 GATAT-GGTGATG
*
56188 GATAATGGAGATG
1 GAT-ATGGTGATG
56201 GACTATGGTGAT-
1 GA-TATGGTGATG
*
56213 GATATAGGCG-T-
1 GATAT-GGTGATG
56224 GATAATGGTGATG
1 GAT-ATGGTGATG
56237 GA
1 GA
56239 CAAATTGTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 29
0.71 0.06 0.23
Matches are distributed among these distances:
11 31 0.35
12 24 0.27
13 31 0.35
14 2 0.02
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:56161 original size:23 final size:23
Alignment explanation
Indices: 56131--56236 Score: 78
Period size: 23 Copynumber: 4.5 Consensus size: 23
56121 TGGTGATGGA
56131 ATATGGTGATGATATAGGCG-TG
1 ATATGGTGATGATATAGGCGATG
*
56153 ATAATGGTGATGGACTAT-GGTGATG
1 AT-ATGGTGAT-GA-TATAGGCGATG
* *
56178 ATATAGGCG-TGATA-ATGGAGATGG
1 ATAT-GGTGATGATATA-GGCGAT-G
56202 ACTATGGTGATGATATAGGCG-TG
1 A-TATGGTGATGATATAGGCGATG
56225 ATAATGGTGATG
1 AT-ATGGTGATG
56237 GACAAATTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
22 5 0.07
23 26 0.39
24 14 0.21
25 21 0.31
26 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (23 bp):
ATATGGTGATGATATAGGCGATG
Found at i:56172 original size:36 final size:36
Alignment explanation
Indices: 56107--56239 Score: 241
Period size: 36 Copynumber: 3.7 Consensus size: 36
56097 GTTGATGTTA
*
56107 ATATAGGCGTGAT-ATGGTGATGGAATATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
56142 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
*
56178 ATATAGGCGTGATAATGGAGATGGACTATGGTGATG
1 ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
56214 ATATAGGCGTGATAATGGTGATGGAC
1 ATATAGGCGTGATAATGGTGATGGAC
56240 AAATTGTATC
Statistics
Matches: 94, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 13 0.14
36 81 0.86
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.29
Consensus pattern (36 bp):
ATATAGGCGTGATAATGGTGATGGACTATGGTGATG
Found at i:62337 original size:29 final size:30
Alignment explanation
Indices: 62302--62362 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
62292 TGGCTTTGCT
62302 TTCTTTT-TGAAATTCTTCTT-TTCTTTT-TC
1 TTCTTTTCT-AAATT-TTCTTCTTCTTTTGTC
*
62331 TTCTTTTCTAAATTTTTTTCTTCTTTTGTC
1 TTCTTTTCTAAATTTTCTTCTTCTTTTGTC
62361 TT
1 TT
62363 TGAACTCCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 4 0.14
29 19 0.68
30 5 0.18
ACGTcount: A:0.10, C:0.16, G:0.03, T:0.70
Consensus pattern (30 bp):
TTCTTTTCTAAATTTTCTTCTTCTTTTGTC
Found at i:67879 original size:15 final size:15
Alignment explanation
Indices: 67845--67882 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
67835 AATATGGAAG
67845 AAGAAATGAAATGAT
1 AAGAAATGAAATGAT
*
67860 AAGAATTGAAATGGAT
1 AAGAAATGAAAT-GAT
67876 -AGAAATG
1 AAGAAATG
67883 TTATCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.21
Consensus pattern (15 bp):
AAGAAATGAAATGAT
Found at i:71670 original size:11 final size:11
Alignment explanation
Indices: 71654--71678 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
71644 AAAAATTTTG
71654 AATATTAAAAA
1 AATATTAAAAA
71665 AATATTAAAAA
1 AATATTAAAAA
71676 AAT
1 AAT
71679 TACAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATATTAAAAA
Found at i:78807 original size:13 final size:13
Alignment explanation
Indices: 78769--78856 Score: 76
Period size: 13 Copynumber: 6.8 Consensus size: 13
78759 ATAGGCGTGA
*
78769 ATGGTGAT-AGAG
1 ATGGTGATGAAAG
78781 AATGGTGATGGAAAG
1 -ATGGTGAT-GAAAG
78796 ATGGTGATGAAAAG
1 ATGGTGATG-AAAG
** *
78810 ATGGTGATGTTAT
1 ATGGTGATGAAAG
78823 A-GGTG-TGAAA-
1 ATGGTGATGAAAG
*
78833 ATGGTGATGGAAG
1 ATGGTGATGAAAG
78846 ATGGTGATGAA
1 ATGGTGATGAA
78857 CATATAGTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
10 1 0.02
11 7 0.11
12 8 0.13
13 21 0.34
14 21 0.34
15 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (13 bp):
ATGGTGATGAAAG
Found at i:84744 original size:17 final size:17
Alignment explanation
Indices: 84704--84774 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
84694 TTCATGCATT
*
84704 TAGTTCATTGAA-TAAAGT
1 TAGTTCATT-AATTAAA-C
84722 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
84739 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
84756 TAGTTTATTTATTAAAC
1 TAGTTCATTAATTAAAC
84773 TA
1 TA
84775 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:85141 original size:17 final size:17
Alignment explanation
Indices: 85102--85134 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
85092 GTATGTTGTT
*
85102 CATTAAAGCATGTATTG
1 CATTTAAGCATGTATTG
85119 CATTTAAGCATGTATT
1 CATTTAAGCATGTATT
85135 TTATTTAGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (17 bp):
CATTTAAGCATGTATTG
Found at i:85168 original size:17 final size:17
Alignment explanation
Indices: 85148--85206 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
85138 TTTAGGGAAG
85148 TAGTTCATTTATGCATC
1 TAGTTCATTTATGCATC
* *
85165 TAGTT-ATTTAAT-AAAC
1 TAGTTCATTT-ATGCATC
* * *
85181 TAATTCATTCATGCATT
1 TAGTTCATTTATGCATC
85198 TAGTTCATT
1 TAGTTCATT
85207 GAATAAAGTT
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
16 12 0.39
17 19 0.61
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (17 bp):
TAGTTCATTTATGCATC
Found at i:85220 original size:18 final size:18
Alignment explanation
Indices: 85197--85242 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
85187 ATTCATGCAT
85197 TTAGTTCATTGAATAAAG
1 TTAGTTCATTGAATAAAG
*
85215 TTAGTTCATTGAATAATG
1 TTAGTTCATTGAATAAAG
*
85233 TTATTTCATT
1 TTAGTTCATT
85243 AATCAAACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.48
Consensus pattern (18 bp):
TTAGTTCATTGAATAAAG
Found at i:89192 original size:13 final size:13
Alignment explanation
Indices: 89158--89194 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
89148 ACTACTTAAA
*
89158 CCATCACCATCTT
1 CCATCACCTTCTT
89171 CCATCACCTTCTT
1 CCATCACCTTCTT
89184 CCATCACCTTC
1 CCATCACCTTC
89195 ATGCCAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.19, C:0.49, G:0.00, T:0.32
Consensus pattern (13 bp):
CCATCACCTTCTT
Found at i:89930 original size:17 final size:16
Alignment explanation
Indices: 89906--89939 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
89896 CTATCTTACC
89906 TTTAACCATATCCATT
1 TTTAACCATATCCATT
89922 TTTATACCATATCCATT
1 TTTA-ACCATATCCATT
89939 T
1 T
89940 CCTTTAGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAACCATATCCATT
Found at i:93621 original size:22 final size:22
Alignment explanation
Indices: 93596--93646 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
93586 GATATTTAAG
93596 CATATTAGGATAGTTTTATAAT
1 CATATTAGGATAGTTTTATAAT
93618 CATATTAGGATAGTTTTATAAT
1 CATATTAGGATAGTTTTATAAT
93640 CATATTA
1 CATATTA
93647 AACATGATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (22 bp):
CATATTAGGATAGTTTTATAAT
Found at i:94594 original size:16 final size:16
Alignment explanation
Indices: 94573--94605 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
94563 GAATATTTCA
94573 TTTGTAATCAGACCAT
1 TTTGTAATCAGACCAT
94589 TTTGTAATCAGACCAT
1 TTTGTAATCAGACCAT
94605 T
1 T
94606 CGGCCATGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (16 bp):
TTTGTAATCAGACCAT
Found at i:100304 original size:22 final size:21
Alignment explanation
Indices: 100279--100331 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 21
100269 TCATCTTGAA
*
100279 AAAAAAAGAATTCTGAAAATTT
1 AAAAAAAGAATTATGAAAA-TT
*
100301 AAAAAAAAAATTATGAAAATT
1 AAAAAAAGAATTATGAAAATT
100322 AAAAAAAGAA
1 AAAAAAAGAA
100332 AAGAAACGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.21
Consensus pattern (21 bp):
AAAAAAAGAATTATGAAAATT
Found at i:112833 original size:32 final size:32
Alignment explanation
Indices: 112788--112862 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
112778 ATTCATCTTG
112788 AAAAAAAAGAATTCCGAAAATTAAAACAAAAAC
1 AAAAAAAAGAATTCCGAAAATTAAAA-AAAAAC
* *
112821 AAAAACAA-AATTCTGAAAATTAAAAAAAAGA-
1 AAAAAAAAGAATTCCGAAAATTAAAAAAAA-AC
*
112852 AAAGAAAAGAA
1 AAAAAAAAGAA
112863 ACGTTCTGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
31 10 0.28
32 19 0.53
33 7 0.19
ACGTcount: A:0.72, C:0.08, G:0.08, T:0.12
Consensus pattern (32 bp):
AAAAAAAAGAATTCCGAAAATTAAAAAAAAAC
Found at i:122580 original size:19 final size:19
Alignment explanation
Indices: 122539--122591 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
122529 GAAACCCCTT
*
122539 TGAAAATACATGATTTTTGA
1 TGAAAATACATGA-TTTTAA
122559 TGAAAATACATGATTTTAA
1 TGAAAATACATGATTTTAA
* *
122578 TGAAGACACATGAT
1 TGAAAATACATGAT
122592 CTTGGCCGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.34
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:125063 original size:16 final size:16
Alignment explanation
Indices: 125042--125082 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
125032 TAACAATAAC
125042 TTCATAACT-TCATACA
1 TTCATAACTATCAT-CA
125058 TTCATAA-TATCATCA
1 TTCATAACTATCATCA
125073 -TCATAACTAT
1 TTCATAACTAT
125083 AATTATAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.26
15 6 0.26
16 11 0.48
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (16 bp):
TTCATAACTATCATCA
Found at i:127926 original size:17 final size:17
Alignment explanation
Indices: 127904--127936 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
127894 GTAGGAGTCT
127904 TTTTCTT-TTCTCTTTTA
1 TTTTCTTCTT-TCTTTTA
127921 TTTTCTTCTTTCTTTT
1 TTTTCTTCTTTCTTTT
127937 TCTCTTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTCTTCTTTCTTTTA
Found at i:128151 original size:15 final size:15
Alignment explanation
Indices: 128131--128161 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
128121 AATTAAAAGT
*
128131 GAATAGAATTGGAAA
1 GAATAGAAATGGAAA
128146 GAATAGAAATGGAAA
1 GAATAGAAATGGAAA
128161 G
1 G
128162 GAATGTTATC
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:0.55, C:0.00, G:0.29, T:0.16
Consensus pattern (15 bp):
GAATAGAAATGGAAA
Found at i:135528 original size:19 final size:20
Alignment explanation
Indices: 135487--135529 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
135477 GAAACCCCTT
*
135487 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
*
135507 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
135526 TGAA
1 TGAA
135530 GACACATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.12, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:142757 original size:15 final size:15
Alignment explanation
Indices: 142721--142764 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
142711 TTAAATGGAA
142721 ATAAGAAATGAAAT-
1 ATAAGAAATGAAATG
*
142735 AAAAGAAATGAAATG
1 ATAAGAAATGAAATG
142750 ATAAGAAATGAAATG
1 ATAAGAAATGAAATG
142765 GATAGAGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (15 bp):
ATAAGAAATGAAATG
Found at i:147786 original size:11 final size:12
Alignment explanation
Indices: 147757--147791 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
147747 TTTGGTGCTG
147757 GAAACAAGATAA
1 GAAACAAGATAA
*
147769 GAAACAAGATTA
1 GAAACAAGATAA
147781 -AAACAAGATAA
1 GAAACAAGATAA
147792 ATAAAAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.66, C:0.09, G:0.14, T:0.11
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:152669 original size:16 final size:16
Alignment explanation
Indices: 152648--152687 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
152638 AAAGCAAAGG
152648 AAATGAAGTAAAGAGA
1 AAATGAAGTAAAGAGA
152664 AAATGAAGTAAAGAGA
1 AAATGAAGTAAAGAGA
152680 AAATGAAG
1 AAATGAAG
152688 ATAACTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.25, T:0.12
Consensus pattern (16 bp):
AAATGAAGTAAAGAGA
Found at i:171105 original size:20 final size:20
Alignment explanation
Indices: 171067--171105 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
171057 ACAAAGAACA
* *
171067 AGTATCGATACTATCCCTAT
1 AGTATCGATAATATACCTAT
*
171087 AGTATCGATAATGTACCTA
1 AGTATCGATAATATACCTA
171106 ACGAAGTCAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (20 bp):
AGTATCGATAATATACCTAT
Found at i:175772 original size:19 final size:17
Alignment explanation
Indices: 175730--175779 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
175720 AATTGGAGTG
*
175730 CAAAAAGAAAGAAAAAGA
1 CAAAAAG-AAGAAAAACA
175748 CAAAAAGAAGAAAAACA
1 CAAAAAGAAGAAAAACA
175765 TCAGAAAAGAAGAAA
1 -CA-AAAAGAAGAAA
175780 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 9 0.31
18 9 0.31
19 11 0.38
ACGTcount: A:0.74, C:0.08, G:0.16, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAGAAAAACA
Found at i:175784 original size:12 final size:11
Alignment explanation
Indices: 175731--175807 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
175721 ATTGGAGTGC
175731 AAAAAG-AAAG
1 AAAAAGAAAAG
175741 AAAAAGACAAA-
1 AAAAAGA-AAAG
*
175752 AAGAAGAAAA-
1 AAAAAGAAAAG
**
175762 ACATCAGAAAAG
1 A-AAAAGAAAAG
175774 AAGAAAGAAAAG
1 AA-AAAGAAAAG
*
175786 AAAAATAAAAG
1 AAAAAGAAAAG
175797 TCAAAAAGAAA
1 --AAAAAGAAA
175808 GCAAGCCAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
10 10 0.19
11 22 0.42
12 13 0.25
13 8 0.15
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:178592 original size:24 final size:24
Alignment explanation
Indices: 178565--178616 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
178555 CGTTCATTTA
*
178565 CGTTTGTGAACGTTCGGTTATGTT
1 CGTTTATGAACGTTCGGTTATGTT
**
178589 CGTTTATGTTCGTTCGGTTATGTT
1 CGTTTATGAACGTTCGGTTATGTT
178613 CGTT
1 CGTT
178617 CATTTATGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.13, G:0.27, T:0.50
Consensus pattern (24 bp):
CGTTTATGAACGTTCGGTTATGTT
Found at i:178603 original size:14 final size:14
Alignment explanation
Indices: 178586--178626 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
178576 GTTCGGTTAT
178586 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
*
178600 GTTCGGTTATGTTC
1 GTTCGTTTATGTTC
*
178614 GTTCATTTATGTT
1 GTTCGTTTATGTT
178627 TAACCCAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:179253 original size:16 final size:16
Alignment explanation
Indices: 179233--179294 Score: 92
Period size: 16 Copynumber: 4.0 Consensus size: 16
179223 GTTAGCTTAA
179233 GTTCGTGTTCATTTAT
1 GTTCGTGTTCATTTAT
* *
179249 ATTCGTGTTCGTTTAT
1 GTTCGTGTTCATTTAT
179265 GTTCGTGTTCATTTAT
1 GTTCGTGTTCATTTAT
179281 GTTCGT-TT-ATTTAT
1 GTTCGTGTTCATTTAT
179295 TAAATGAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.14
15 2 0.05
16 34 0.81
ACGTcount: A:0.13, C:0.11, G:0.18, T:0.58
Consensus pattern (16 bp):
GTTCGTGTTCATTTAT
Found at i:183436 original size:16 final size:16
Alignment explanation
Indices: 183411--183472 Score: 58
Period size: 16 Copynumber: 4.0 Consensus size: 16
183401 TCCCGTAATC
*
183411 ACAAAATACAAAAAAT
1 ACAAATTACAAAAAAT
*
183427 ACAAATTACATAAAAT
1 ACAAATTACAAAAAAT
* *
183443 ATAAA--ACAAATAAT
1 ACAAATTACAAAAAAT
183457 AC-AATATACAAAAAAT
1 ACAAAT-TACAAAAAAT
183473 GTAAACATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 2 0.06
14 8 0.22
16 26 0.72
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.19
Consensus pattern (16 bp):
ACAAATTACAAAAAAT
Found at i:183458 original size:30 final size:30
Alignment explanation
Indices: 183418--183477 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
183408 ATCACAAAAT
*
183418 ACAAAAAATACAA-ATTACATAAAATATAAA
1 ACAAAAAATACAATA-TACAAAAAATATAAA
* *
183448 ACAAATAATACAATATACAAAAAATGTAAA
1 ACAAAAAATACAATATACAAAAAATATAAA
183478 CATTTACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.68, C:0.10, G:0.02, T:0.20
Consensus pattern (30 bp):
ACAAAAAATACAATATACAAAAAATATAAA
Found at i:186351 original size:54 final size:54
Alignment explanation
Indices: 186287--186404 Score: 121
Period size: 54 Copynumber: 2.2 Consensus size: 54
186277 AACGGTGCAT
* * * *
186287 TTTCAGCACTAAATGTG-AAACCTATTGTATTCATAATGTGTTTATGAATGACCA
1 TTTCGGCACTAAATGTGCAAACC-ATGGAATTCATAATGAGTTTATGAATGACCA
** * * ** *
186341 TTTCGGCACTATGTGTGCAATCCATGGAATTCATAATGAGTTTGTGAATTTCTA
1 TTTCGGCACTAAATGTGCAAACCATGGAATTCATAATGAGTTTATGAATGACCA
186395 TTTCGGCACT
1 TTTCGGCACT
186405 TCGGTGCAAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
54 48 0.92
55 4 0.08
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (54 bp):
TTTCGGCACTAAATGTGCAAACCATGGAATTCATAATGAGTTTATGAATGACCA
Found at i:196449 original size:29 final size:30
Alignment explanation
Indices: 196410--196466 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
196400 AAAATTTTGG
196410 TTAGTGACCAAAATATAAAATTT-GAAAGT
1 TTAGTGACCAAAATATAAAATTTAGAAAGT
* * *
196439 TTAGTGGCCAAAGTATAAAGTTTAGAAA
1 TTAGTGACCAAAATATAAAATTTAGAAA
196467 AGCTTAGGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.30
Consensus pattern (30 bp):
TTAGTGACCAAAATATAAAATTTAGAAAGT
Found at i:196507 original size:30 final size:30
Alignment explanation
Indices: 196448--196530 Score: 78
Period size: 30 Copynumber: 2.7 Consensus size: 30
196438 TTTAGTGGCC
* *
196448 AAAGTATAAAGTTTAGAAAAGCTTAGGGACTAA
1 AAAGTAT-AATTTTA-AAAAGTTTAGGGAC-AA
* * *
196481 AAAG-GTAATTTTAAAAAGTTTGGGGACCA
1 AAAGTATAATTTTAAAAAGTTTAGGGACAA
*
196510 AAAGTATAATTTTCAAAAGTT
1 AAAGTATAATTTTAAAAAGTT
196531 AGGTTTTGAA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
29 5 0.12
30 26 0.62
31 6 0.14
32 1 0.02
33 4 0.10
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.29
Consensus pattern (30 bp):
AAAGTATAATTTTAAAAAGTTTAGGGACAA
Found at i:204548 original size:24 final size:25
Alignment explanation
Indices: 204520--204570 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
204510 TATGTGGTTC
204520 ATATCATGTTAATAT-TAGTAAGAA
1 ATATCATGTTAATATGTAGTAAGAA
*
204544 ATATCATGTTAATATGTGGTAAGAA
1 ATATCATGTTAATATGTAGTAAGAA
204569 AT
1 AT
204571 TATAGGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (25 bp):
ATATCATGTTAATATGTAGTAAGAA
Found at i:206005 original size:2 final size:2
Alignment explanation
Indices: 205998--206061 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
205988 AATAATAAGA
205998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
206040 AT AT A- AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
206062 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:206228 original size:8 final size:8
Alignment explanation
Indices: 206201--206234 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
206191 GACAGGGAAA
206201 AAAATAAT
1 AAAATAAT
206209 AAATATAAT
1 AAA-ATAAT
*
206218 AAAAGAAT
1 AAAATAAT
206226 AAAATAAT
1 AAAATAAT
206234 A
1 A
206235 CATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (8 bp):
AAAATAAT
Found at i:206299 original size:27 final size:28
Alignment explanation
Indices: 206237--206299 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
206227 AAATAATACA
* * *
206237 TAAATATATATAAATGAAAATGTTAAAT
1 TAAATAAATATAAAAGAAAATGATAAAT
206265 TAAATAAATATAAAAGAAAAT-ATAAAT
1 TAAATAAATATAAAAGAAAATGATAAAT
*
206292 TAAGTAAA
1 TAAATAAA
206300 AAAGACTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.30
Consensus pattern (28 bp):
TAAATAAATATAAAAGAAAATGATAAAT
Found at i:221197 original size:55 final size:55
Alignment explanation
Indices: 221124--221477 Score: 347
Period size: 55 Copynumber: 6.6 Consensus size: 55
221114 GTGTTTTTTT
* * *
221124 AGAAACTAAGTCTGATTTTCGGAAGTTTCTTAATGATTTTTAAATGAGCTTTCAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAA
* * * **
221179 AGAAACTATGTCTTATTTTCAGAGGTTTCTTG--GCA-TCGT---T-AGCTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATG-ATTTTTAAATGAGCTTTTAA
*
221228 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAA
* * * *
221283 ATAAACTAAGTCAT-ATTTTCAGAAGTTTCTTGACGATTTTCAAATAAG--TTTAA
1 AGAAACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAA
* * * ** * *
221336 AAAAACTAAGTAT-AGTTTCAGAAGTTTCTTGACAATTTTTAAATTAGTTTTTAA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAA
* * * *
221390 AGAAACAAAGT-TCGATTTTC-GAAAGTTTCTTGATTATTTTTAAATGATCTTTCAA
1 AGAAACTAAGTCT-GATTTTCAG-AAGTTTCTTGATGATTTTTAAATGAGCTTTTAA
* *
221445 AGAAACTAAGTCTGATTTTTAGAGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
221478 CATGATGAAT
Statistics
Matches: 247, Mismatches: 36, Indels: 32
0.78 0.11 0.10
Matches are distributed among these distances:
49 37 0.15
50 2 0.01
51 3 0.01
52 31 0.13
53 19 0.08
54 17 0.07
55 135 0.55
56 3 0.01
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (55 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAA
Found at i:221304 original size:104 final size:106
Alignment explanation
Indices: 221124--221477 Score: 351
Period size: 104 Copynumber: 3.3 Consensus size: 106
221114 GTGTTTTTTT
* * * * *
221124 AGAAACTAAGTCTGATTTTCGGAAGTTTCTTAATGATTTTTAAATGAGCTTTCAAAGAAACTATG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
* * * **
221189 TCTTATTTTCAGAGGTTTCTTGGC-ATCGTT-AGCT-TTTAA
66 TCATATTTTCAGAAGTTTCTTGACGAT-GTTCAAATATTTAA
*
221228 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAATAAACTAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
*
221293 TCATATTTTCAGAAGTTTCTTGACGATTTTCAAATAAGTTTAA
66 TCATATTTTCAGAAGTTTCTTGACGATGTTCAAAT-A-TTTAA
* * * ** * *
221336 AAAAACTAAGTAT-AGTTTCAGAAGTTTCTTGACAATTTTTAAATTAGTTTTTAAAGAAACAAAG
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
* ** * *
221400 TTC-GATTTTC-GAAAGTTTCTTGATTATTTTTAAATGATCTTTCAA
66 -TCATATTTTCAG-AAGTTTCTTGACGATGTTCAAAT-A--TTT-AA
* *
221445 AGAAACTAAGTCTGATTTTTAGAGGTTTCTTGA
1 AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
221478 CATGATGAAT
Statistics
Matches: 209, Mismatches: 31, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
104 82 0.39
105 4 0.02
106 1 0.00
107 72 0.34
108 21 0.10
109 13 0.06
110 16 0.08
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (106 bp):
AGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAAGAAACTAAG
TCATATTTTCAGAAGTTTCTTGACGATGTTCAAATATTTAA
Found at i:221379 original size:107 final size:108
Alignment explanation
Indices: 221223--221479 Score: 286
Period size: 107 Copynumber: 2.4 Consensus size: 108
221213 ATCGTTAGCT
* * * ** *
221223 TTTAAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGTTTTTAAATAAA
1 TTTAAAAAAACTAAGTATGAGTTTCAGAAGTTTCTTGACAATTTTTAAATGAGTTTTTAAAGAAA
* *
221288 CTAAG-TCATATTTTC-AGAAGTTTCTTGACGATTTTCAAATAAG
66 CAAAGTTC-GATTTTCGA-AAGTTTCTTGACGATTTTCAAATAAG
*
221331 TTTAAAAAAACTAAGTAT-AGTTTCAGAAGTTTCTTGACAATTTTTAAATTAGTTTTTAAAGAAA
1 TTTAAAAAAACTAAGTATGAGTTTCAGAAGTTTCTTGACAATTTTTAAATGAGTTTTTAAAGAAA
** * **
221395 CAAAGTTCGATTTTCGAAAGTTTCTTGATTATTTTTAAATGATC
66 CAAAGTTCGATTTTCGAAAGTTTCTTGACGATTTTCAAAT-AAG
* * * * *
221439 TTTCAAAGAAACTAAGTCTGATTTTTAGAGGTTTCTTGACA
1 TTT-AAAAAAACTAAGTATGAGTTTCAGAAGTTTCTTGACA
221480 TGATGAATTT
Statistics
Matches: 125, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
107 71 0.57
108 23 0.18
109 13 0.10
110 18 0.14
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (108 bp):
TTTAAAAAAACTAAGTATGAGTTTCAGAAGTTTCTTGACAATTTTTAAATGAGTTTTTAAAGAAA
CAAAGTTCGATTTTCGAAAGTTTCTTGACGATTTTCAAATAAG
Found at i:221675 original size:54 final size:53
Alignment explanation
Indices: 221524--221679 Score: 231
Period size: 53 Copynumber: 2.9 Consensus size: 53
221514 GGCTTCTTGA
*
221524 CAAATGAAATTTAAAGAAGCTAATCCTAATTTTTAGGGGTTTCTTGATGTTTT
1 CAAATGAATTTTAAAGAAGCTAATCCTAATTTTTAGGGGTTTCTTGATGTTTT
* * * * *
221577 CAAATGAATTTAAAAGAAGTTAAGCCTGATTTTCAGGGGTTTCTTGATGTTTT
1 CAAATGAATTTTAAAGAAGCTAATCCTAATTTTTAGGGGTTTCTTGATGTTTT
* *
221630 CAAATGGATTTTTAAAGAAGCTAATCCTAATTTTTAGGGGGTTCTTGATG
1 CAAAT-GAATTTTAAAGAAGCTAATCCTAATTTTTAGGGGTTTCTTGATG
221680 ATAATTGTAA
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 52 0.58
54 37 0.42
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (53 bp):
CAAATGAATTTTAAAGAAGCTAATCCTAATTTTTAGGGGTTTCTTGATGTTTT
Found at i:222462 original size:90 final size:90
Alignment explanation
Indices: 222310--222485 Score: 282
Period size: 90 Copynumber: 2.0 Consensus size: 90
222300 TAGCATACCC
* * *
222310 TTTTATAGCCAAGTTACCCTAATTATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATAATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATT
* *
222375 TAATT-AATTGGAATTTAATAATCA
66 TAATTAAATTGAAATTAAATAATCA
*
222399 TTTTATATCCAAGTTACCCTAATAATATTACGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATAATATTA-GGATTTTATTATTTCAAATTAATTAAATCTATAT
222464 TTAATTAAATTGAAATTAAATA
65 TTAATTAAATTGAAATTAAATA
222486 TTCGGGATTA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 28 0.35
90 38 0.48
91 13 0.16
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATAATATTAGGATTTTATTATTTCAAATTAATTAAATCTATATT
TAATTAAATTGAAATTAAATAATCA
Found at i:228894 original size:90 final size:90
Alignment explanation
Indices: 228740--228915 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 90
228730 CAGCACACCC
** * *
228740 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTTATTATTTCAAACTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGAATTTTATTATTTAAAACTAATTAAATATATAT
* *
228805 TTAATTAATTGGAATTTAATAATCA
66 TTAATTAATTGAAATTAAATAATCA
* *
228830 TTTTATATCCAAGTTACCCTAATCATATTAGGAATTTTATTATTTAAAATTAATTAAATATATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGAATTTTATTATTTAAAACTAATTAAATATATAT
228895 TTAATTAATTGAAATTAAATA
66 TTAATTAATTGAAATTAAATA
228916 TTCAGGATTA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (90 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGAATTTTATTATTTAAAACTAATTAAATATATAT
TTAATTAATTGAAATTAAATAATCA
Found at i:229956 original size:42 final size:40
Alignment explanation
Indices: 229907--230025 Score: 121
Period size: 41 Copynumber: 2.9 Consensus size: 40
229897 TAACAGTAAG
*
229907 TCCTTCGGGCCATCAGTAAGTCTTTCAAGCATGATGCTTAAA
1 TCCTTCGGGCCATCA-TAAGTCTTTCAAGCATGATG-ATAAA
* * * * * *
229949 TTCTTCGGGTCATCTATAAGTCTTTCTAGTAAGATGATAAG
1 TCCTTCGGGCCATC-ATAAGTCTTTCAAGCATGATGATAAA
* *
229990 TCCTTCGGGCCGTCCATAAGACTTTCAAGCATGATG
1 TCCTTCGGGCCAT-CATAAGTCTTTCAAGCATGATG
230026 TATTTAAAAG
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
41 30 0.49
42 30 0.49
43 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
TCCTTCGGGCCATCATAAGTCTTTCAAGCATGATGATAAA
Found at i:230563 original size:100 final size:101
Alignment explanation
Indices: 230389--230609 Score: 363
Period size: 100 Copynumber: 2.2 Consensus size: 101
230379 AGGGAGAATA
* *
230389 AGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCGCATATAGAGTTGAATCAATA
1 AGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTCGATTCATCGCATATAGAGTTGAATCAACA
* *
230454 ACACCTCACTCGAGGGATCAATATTTTC-ATTGGAG
66 ACACCTCACTCGAGGGATCAACATTTTCAATGGGAG
* * * *
230489 GGTTCATAATGAGAATAACTTGTTAAACCTTAGCTCGATTCATCGCATATGGAGTTGAATCAGCA
1 AGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTCGATTCATCGCATATAGAGTTGAATCAACA
230554 ACACCTCACTCGAGGGATCAACATTTTCAATGGGAG
66 ACACCTCACTCGAGGGATCAACATTTTCAATGGGAG
230590 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
230610 CATCCGATAA
Statistics
Matches: 110, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 86 0.78
101 24 0.22
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (101 bp):
AGTTCATAATGAGAAGAACTTGTTAAACCTTAGCTCGATTCATCGCATATAGAGTTGAATCAACA
ACACCTCACTCGAGGGATCAACATTTTCAATGGGAG
Found at i:231288 original size:17 final size:16
Alignment explanation
Indices: 231266--231303 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
231256 GAATCAAATT
231266 AATTAGATATTATTTA
1 AATTAGATATTATTTA
231282 CAATTAGATATTATTTA
1 -AATTAGATATTATTTA
231299 AATTA
1 AATTA
231304 ATTGTAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (16 bp):
AATTAGATATTATTTA
Found at i:233016 original size:2 final size:2
Alignment explanation
Indices: 233009--233061 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
232999 AAGTATTTAT
233009 TA TA TA TA TA TA TA TA TA -A TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
233049 TA T- TA TA -A TA TA T
1 TA TA TA TA TA TA TA T
233062 GTATGTTCCA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 4 0.09
2 43 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:237406 original size:11 final size:11
Alignment explanation
Indices: 237390--237421 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
237380 TAAAACCATA
237390 TTTTTCAAAAG
1 TTTTTCAAAAG
237401 TTTTTCAAAAG
1 TTTTTCAAAAG
237412 TTTTTCAAAA
1 TTTTTCAAAA
237422 ACTTTGCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (11 bp):
TTTTTCAAAAG
Found at i:243607 original size:29 final size:29
Alignment explanation
Indices: 243565--243632 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
243555 TACAAGCCTC
* * *
243565 TGAAAAATTGGGGATCATTTCGTAAGTTT
1 TGAAAAATTGGGGATAAATTCGTAAATTT
* *
243594 TGAAAAGTTTGGGATAAATTCGTAAATTT
1 TGAAAAATTGGGGATAAATTCGTAAATTT
*
243623 TGGAAAATTG
1 TGAAAAATTG
243633 ATGAAGAACC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (29 bp):
TGAAAAATTGGGGATAAATTCGTAAATTT
Found at i:245685 original size:48 final size:45
Alignment explanation
Indices: 245587--245800 Score: 232
Period size: 48 Copynumber: 4.6 Consensus size: 45
245577 GTAACCATGC
** *
245587 AAATAAGCTTATGAGCTTACAGAATAATGGCAAGTGTATTGG-AA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGTAA
* * *
245631 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGGTAA
* **
245679 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTG--GTAA
* * *
245726 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTAA
1 AAATAAGCTTATGAGCTTATGGAA--T-AATGGCAAGTATATTGGTAA
*
245774 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
245801 AAGGTAAGAA
Statistics
Matches: 141, Mismatches: 20, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
44 21 0.15
45 16 0.11
46 3 0.02
47 38 0.27
48 48 0.34
49 1 0.01
50 14 0.10
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGGTAA
Found at i:245697 original size:92 final size:93
Alignment explanation
Indices: 245587--245792 Score: 360
Period size: 95 Copynumber: 2.2 Consensus size: 93
245577 GTAACCATGC
* *
245587 AAATAAGCTTATGAGCTTACAGAATAATGGCAAGTGTATTG-GAAAAATAAGCTTACGAGCTTAT
1 AAATAAGCTTATGAGCTTACAGAATAATGGCAAGTATATTGAAAAAAATAAGCTTACGAGCTTAT
245651 GGAATTTAAATGGTAAGTATTTTGGTAA
66 GGAATTTAAATGGTAAGTATTTTGGTAA
*
245679 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAAAAAATAAGCTTACGAGCTT
1 AAATAAGCTTATGAGCTTACAGAATAATGGCAAGTATATTG--AAAAAAATAAGCTTACGAGCTT
245744 ATGGAATTTAAATGGTAAGTATTTTGGTAA
64 ATGGAATTTAAATGGTAAGTATTTTGGTAA
245774 AAATAAGCTTATGAGCTTA
1 AAATAAGCTTATGAGCTTA
245793 TGGGATAAAA
Statistics
Matches: 108, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
92 39 0.36
95 69 0.64
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (93 bp):
AAATAAGCTTATGAGCTTACAGAATAATGGCAAGTATATTGAAAAAAATAAGCTTACGAGCTTAT
GGAATTTAAATGGTAAGTATTTTGGTAA
Found at i:250973 original size:29 final size:31
Alignment explanation
Indices: 250931--251004 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
250921 ATATATATCG
*
250931 TTATACCATTGAACTTCCA-TTTT-TTTCAA
1 TTATACCATTGAACTTCAATTTTTGTTTCAA
* *
250960 TTATACCACTGAACTTTAATTTTTGTTTCAA
1 TTATACCATTGAACTTCAATTTTTGTTTCAA
250991 TTATACCATTGAAC
1 TTATACCATTGAAC
251005 CGCTAAATTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 16 0.41
30 4 0.10
31 19 0.49
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.46
Consensus pattern (31 bp):
TTATACCATTGAACTTCAATTTTTGTTTCAA
Found at i:251160 original size:29 final size:31
Alignment explanation
Indices: 251109--251167 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
251099 GACCTCTTAG
251109 TATAATTGAAACAGAAATCAAAGTTTAGTGC
1 TATAATTGAAACAGAAATCAAAGTTTAGTGC
* *
251140 TATAATTGGAA-A-AAATGAAAGTTTAGTG
1 TATAATTGAAACAGAAATCAAAGTTTAGTG
251168 AGATAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 15 0.58
30 1 0.04
31 10 0.38
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.31
Consensus pattern (31 bp):
TATAATTGAAACAGAAATCAAAGTTTAGTGC
Found at i:256629 original size:56 final size:53
Alignment explanation
Indices: 256536--256653 Score: 182
Period size: 56 Copynumber: 2.2 Consensus size: 53
256526 ACCCACGTAG
256536 TGAGTTTTTGTTCTTTGTTTAATTGTTATGCTTATAGTACTTGTGTGTGTTCT
1 TGAGTTTTTGTTCTTTGTTTAATTGTTATGCTTATAGTACTTGTGTGTGTTCT
* *
256589 TGAGTTTTTGTTCTTTGTTTGTTAATTGTTATGCTTATAGTGCTTGTGTTTGTTCT
1 TGAGTTTTTGTTCTTTG--T-TTAATTGTTATGCTTATAGTACTTGTGTGTGTTCT
*
256645 TGATTTTTT
1 TGAGTTTTT
256654 TATATTGATT
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
53 17 0.29
55 1 0.02
56 41 0.69
ACGTcount: A:0.12, C:0.07, G:0.20, T:0.61
Consensus pattern (53 bp):
TGAGTTTTTGTTCTTTGTTTAATTGTTATGCTTATAGTACTTGTGTGTGTTCT
Found at i:259124 original size:42 final size:42
Alignment explanation
Indices: 259067--259195 Score: 197
Period size: 42 Copynumber: 3.1 Consensus size: 42
259057 TGATGTTGAT
*
259067 TTTA-TTTAGACTTATTGAGAATTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGAATTAATAGTGTTATGGTGTTA
* * * *
259108 TTTATTTTAAACTTATTGAGATTTAATGGTGTTATGATGTTA
1 TTTATTTTAGACTTATTGAGAATTAATAGTGTTATGGTGTTA
*
259150 TTTATTTTAGACTTATTGAGACTTAATAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATTGAGAATTAATAGTGTTATGGTGTTA
259192 TTTA
1 TTTA
259196 AAGGTGTAGC
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
41 4 0.05
42 74 0.95
ACGTcount: A:0.27, C:0.03, G:0.18, T:0.52
Consensus pattern (42 bp):
TTTATTTTAGACTTATTGAGAATTAATAGTGTTATGGTGTTA
Found at i:270396 original size:17 final size:18
Alignment explanation
Indices: 270374--270414 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
270364 TTGTTGGAAA
*
270374 TTTCTTTCTTTTTG-GCT
1 TTTCTTTCTTGTTGTGCT
270391 TTTC-TTCTTGTTGTGCT
1 TTTCTTTCTTGTTGTGCT
270408 TTTCTTT
1 TTTCTTT
270415 TTTATTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 8 0.38
17 11 0.52
18 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.12, T:0.71
Consensus pattern (18 bp):
TTTCTTTCTTGTTGTGCT
Found at i:275690 original size:13 final size:13
Alignment explanation
Indices: 275672--275703 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
275662 TAATGAAACC
275672 TCAAATTTTCCCA
1 TCAAATTTTCCCA
275685 TCAAATTTTCCCA
1 TCAAATTTTCCCA
275698 TCAAAT
1 TCAAAT
275704 GCACTAACAA
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:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (13 bp):
TCAAATTTTCCCA
Found at i:278812 original size:2 final size:2
Alignment explanation
Indices: 278805--278850 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
278795 TCGATCATAC
278805 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
278847 AT AT
1 AT AT
278851 CATTTGGTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:279390 original size:33 final size:33
Alignment explanation
Indices: 279353--279440 Score: 149
Period size: 33 Copynumber: 2.7 Consensus size: 33
279343 CATATCAAGG
279353 CAATTCGAATGATACTCTTCATGCATCAACATA
1 CAATTCGAATGATACTCTTCATGCATCAACATA
* *
279386 CAATTCGAATGATACTCTTCATGTATCAACATG
1 CAATTCGAATGATACTCTTCATGCATCAACATA
*
279419 CAATTCGAATTATACTCTTCAT
1 CAATTCGAATGATACTCTTCAT
279441 ACAATAATCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (33 bp):
CAATTCGAATGATACTCTTCATGCATCAACATA
Found at i:282014 original size:63 final size:63
Alignment explanation
Indices: 281894--282014 Score: 154
Period size: 63 Copynumber: 1.9 Consensus size: 63
281884 CAAATAAATG
* * *
281894 AACATCGAATGCAATTAGTGCATCGATGCATAAGGAGTGCATCGATTCACCCCTTAAGATGAA
1 AACATCGAATGCAATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACACCTTAAGATGAA
* * * * *
281957 AACATCGAATGGAATTTGTGTACCGATGCAT-AGATAGTGCATCGATGCACACGTTAAG
1 AACATCGAATGCAATTAGTGCACCGATGCATAAG-GAGTGCATCGATGCACACCTTAAG
282015 GGATGCATCG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
62 2 0.04
63 47 0.96
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (63 bp):
AACATCGAATGCAATTAGTGCACCGATGCATAAGGAGTGCATCGATGCACACCTTAAGATGAA
Found at i:282026 original size:24 final size:24
Alignment explanation
Indices: 281994--282042 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
281984 GCATAGATAG
281994 TGCATCGATGCACACGTTAAGGGA
1 TGCATCGATGCACACGTTAAGGGA
282018 TGCATCGATGCACACGTTAAGGGA
1 TGCATCGATGCACACGTTAAGGGA
282042 T
1 T
282043 TAATCGATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (24 bp):
TGCATCGATGCACACGTTAAGGGA
Found at i:282048 original size:24 final size:24
Alignment explanation
Indices: 281997--282050 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
281987 TAGATAGTGC
*
281997 ATCGATGCACACGTTAAGGGATGC
1 ATCGATGCACACGTTAAGGGATGA
*
282021 ATCGATGCACACGTTAAGGGATTA
1 ATCGATGCACACGTTAAGGGATGA
282045 ATCGAT
1 ATCGAT
282051 ACACTGTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (24 bp):
ATCGATGCACACGTTAAGGGATGA
Found at i:283287 original size:21 final size:21
Alignment explanation
Indices: 283253--283293 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
283243 GAAATTTTAG
*
283253 TGCATCGATTCACTATAGCAA
1 TGCATCGATGCACTATAGCAA
* *
283274 TGCATTGATGCACTGTAGCA
1 TGCATCGATGCACTATAGCA
283294 CTGTTCACGG
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:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCACTATAGCAA
Found at i:288966 original size:29 final size:30
Alignment explanation
Indices: 288879--288966 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 30
288869 GGGCCGAATT
*
288879 AACTTTT-TAAAA-TTACATTTTTGTCCCTA
1 AACTTTTCTAAAATTTACA-TTTTGTCACTA
* * * *
288908 AACTTTTCTAAAGTTTATACTTTGCCACTA
1 AACTTTTCTAAAATTTACATTTTGTCACTA
288938 AAC-TTTC-AAAATTTACATTTTGGTCACTA
1 AACTTTTCTAAAATTTACATTTT-GTCACTA
288967 GACGAAATTT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
28 11 0.23
29 17 0.36
30 15 0.32
31 4 0.09
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (30 bp):
AACTTTTCTAAAATTTACATTTTGTCACTA
Found at i:314106 original size:56 final size:56
Alignment explanation
Indices: 314021--314429 Score: 649
Period size: 56 Copynumber: 7.3 Consensus size: 56
314011 TTCTTACTTT
*
314021 TTAG-TTTTGCAAACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
314076 TTAGTTTTTGCACAGAAAGTGCCCATACGGAAATTCATAAACGCATTATAAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
314132 TTAGTTTTTGTACACAAAGTGCTCATATGGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* **
314188 TTAGTTTTTGCACATAAAGTGCCCATACGGAAATTTGTAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
314244 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
314300 TTATTTTTTGCACACAAATTGCCCATACAGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* * *
314356 TTAGTTTTTGCAAATAAAGTGCCCATACAGAAATTCATAAACTCATTATGAATTTC
1 TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
* *
314412 ATAGTTTTTACACACAAA
1 TTAGTTTTTGCACACAAA
314430 TAGTGTCATT
Statistics
Matches: 323, Mismatches: 30, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
55 4 0.01
56 319 0.99
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (56 bp):
TTAGTTTTTGCACACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTC
Found at i:319770 original size:24 final size:25
Alignment explanation
Indices: 319743--319802 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
319733 TCTTAATTCT
*
319743 TATACATAATTATTC-GATCATA-CA
1 TATACATAATCATTCAG-TCATACCA
*
319767 TATATATAAATCATTCAGTCATACCA
1 TATACAT-AATCATTCAGTCATACCA
319793 TATAACATAA
1 TAT-ACATAA
319803 CAAACAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 6 0.21
25 12 0.41
26 8 0.28
27 3 0.10
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (25 bp):
TATACATAATCATTCAGTCATACCA
Found at i:323451 original size:21 final size:21
Alignment explanation
Indices: 323425--323495 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 21
323415 GTAGACATTG
323425 TTAATAATTAATTGTTTGCTA
1 TTAATAATTAATTGTTTGCTA
*
323446 TTAATAATTTGAACACTTATTTTTG-TA
1 TTAATAA-TT--A-A--T-TGTTTGCTA
323473 TTAATAATTAATTGTTTGCTA
1 TTAATAATTAATTGTTTGCTA
323494 TT
1 TT
323496 TTGTTTGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 16
0.69 0.03 0.28
Matches are distributed among these distances:
20 5 0.12
21 12 0.30
22 2 0.05
23 1 0.03
24 2 0.05
25 1 0.03
26 2 0.05
27 10 0.25
28 5 0.12
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (21 bp):
TTAATAATTAATTGTTTGCTA
Found at i:324438 original size:2 final size:2
Alignment explanation
Indices: 324431--324458 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
324421 TAAAAACTTT
324431 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
324459 ACTACTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:325108 original size:42 final size:41
Alignment explanation
Indices: 324977--325125 Score: 124
Period size: 42 Copynumber: 3.6 Consensus size: 41
324967 AATTAATGAT
* * * * **
324977 CCTAAGTTTTCAATCCCACTTTGCACTTTTATAA-TTGAAC
1 CCTAATTTTTCAATCTCACTTTTCACCTTTATAATTTGGGC
* * *
325017 TCCTAATTTTTCAATATTAC-TTTCTACCTTTATTA-TTGAGGC
1 -CCTAATTTTTCAATCTCACTTTTC-ACCTTTATAATTTG-GGC
*
325059 CCTTAATTTTTTAATCTCACTTTTCACCTTTATAATTTGGGC
1 CC-TAATTTTTCAATCTCACTTTTCACCTTTATAATTTGGGC
*
325101 CTCTAATTTTCTCAATCTCAGTTTT
1 C-CTAATTTT-TCAATCTCACTTTT
325126 ACTTATATAC
Statistics
Matches: 86, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
40 3 0.03
41 28 0.33
42 35 0.41
43 20 0.23
ACGTcount: A:0.23, C:0.22, G:0.07, T:0.48
Consensus pattern (41 bp):
CCTAATTTTTCAATCTCACTTTTCACCTTTATAATTTGGGC
Found at i:325568 original size:27 final size:27
Alignment explanation
Indices: 325512--325568 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
325502 TTCATAAAGA
* *
325512 TAAGACATGGTCACTTTCGTTGTTAAT
1 TAAGACATAGTCACTTTCATTGTTAAT
* * *
325539 TAAGATATAGTCACTTTCATTTTTATT
1 TAAGACATAGTCACTTTCATTGTTAAT
325566 TAA
1 TAA
325569 TTAATATGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (27 bp):
TAAGACATAGTCACTTTCATTGTTAAT
Found at i:325719 original size:27 final size:27
Alignment explanation
Indices: 325689--325771 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
325679 TTAGTCATAC
* *
325689 TTTTAAATAAAATTTAA-AGTAAAATAT
1 TTTTAAA-AAAAGTTAATAATAAAATAT
*
325716 TTTTAAAATAAGTTAATAATAAAATAT
1 TTTTAAAAAAAGTTAATAATAAAATAT
* *
325743 ATTT--AATAAGTTAAT-ATAAAATAT
1 TTTTAAAAAAAGTTAATAATAAAATAT
325767 ATTTT
1 -TTTT
325772 TTAAGTTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
24 9 0.18
25 14 0.29
26 7 0.14
27 19 0.39
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (27 bp):
TTTTAAAAAAAGTTAATAATAAAATAT
Found at i:325738 original size:16 final size:17
Alignment explanation
Indices: 325719--325751 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
325709 AAAATATTTT
325719 TAAAATA-AGTTAATAA
1 TAAAATATAGTTAATAA
*
325735 TAAAATATATTTAATAA
1 TAAAATATAGTTAATAA
325752 GTTAATATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAAAATATAGTTAATAA
Found at i:325766 original size:24 final size:24
Alignment explanation
Indices: 325708--325784 Score: 100
Period size: 24 Copynumber: 3.1 Consensus size: 24
325698 AAATTTAAAG
*
325708 TAAAATATTTTTAAAATAAGTTAATAA
1 TAAAATATATTT--AATAAGTTAAT-A
325735 TAAAATATATTTAATAAGTTAATA
1 TAAAATATATTTAATAAGTTAATA
**
325759 TAAAATATATTTTTTAAGTTAATA
1 TAAAATATATTTAATAAGTTAATA
325783 TA
1 TA
325785 TATAAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 25 0.53
25 11 0.23
27 11 0.23
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (24 bp):
TAAAATATATTTAATAAGTTAATA
Found at i:325774 original size:27 final size:28
Alignment explanation
Indices: 325708--325775 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 28
325698 AAATTTAAAG
**
325708 TAAAATAT-TTTTAAAATAAGTTAATAA
1 TAAAATATATTTTTTAATAAGTTAATAA
325735 TAAAATATA---TTTAATAAGTTAAT-A
1 TAAAATATATTTTTTAATAAGTTAATAA
325759 TAAAATATATTTTTTAA
1 TAAAATATATTTTTTAA
325776 GTTAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
24 10 0.29
25 12 0.34
27 13 0.37
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (28 bp):
TAAAATATATTTTTTAATAAGTTAATAA
Found at i:330388 original size:49 final size:49
Alignment explanation
Indices: 330333--330433 Score: 202
Period size: 49 Copynumber: 2.1 Consensus size: 49
330323 ATCGAACTTC
330333 TTTTTAAATGATTGTCATGTTAGCAAGTTTAAGAAAGATATCAAGATAA
1 TTTTTAAATGATTGTCATGTTAGCAAGTTTAAGAAAGATATCAAGATAA
330382 TTTTTAAATGATTGTCATGTTAGCAAGTTTAAGAAAGATATCAAGATAA
1 TTTTTAAATGATTGTCATGTTAGCAAGTTTAAGAAAGATATCAAGATAA
330431 TTT
1 TTT
330434 CGAAGGAAGT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.39
Consensus pattern (49 bp):
TTTTTAAATGATTGTCATGTTAGCAAGTTTAAGAAAGATATCAAGATAA
Found at i:332485 original size:24 final size:24
Alignment explanation
Indices: 332453--332522 Score: 113
Period size: 24 Copynumber: 2.9 Consensus size: 24
332443 TCGAGGGTTT
332453 TACGCGGTCCTTCGGGACAAATTC
1 TACGCGGTCCTTCGGGACAAATTC
*
332477 TACGTGGTCCTTCGGGACAAATTC
1 TACGCGGTCCTTCGGGACAAATTC
* *
332501 TATGCGGTCCTTCGGTACAAAT
1 TACGCGGTCCTTCGGGACAAAT
332523 CTATATGGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (24 bp):
TACGCGGTCCTTCGGGACAAATTC
Found at i:334782 original size:55 final size:55
Alignment explanation
Indices: 334455--335124 Score: 948
Period size: 55 Copynumber: 12.1 Consensus size: 55
334445 TCATTATACT
* *
334455 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGACACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
334510 TGCAAAAGCTAAGAAATTCTTAATAAGTTTATGAATTTACGTACGGGCACTTTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
334566 TGCAAAAGCTAGGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACATTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
*
334622 TGC-AAACTATA-AAATTCATAATAAGTTTATGAATTTCCGTATGGCCACTTTGTG
1 TGCAAAACTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * *
334676 TGCAAAAGCTAAAAAAATCATAATAAGTTTATGAATTTCCGTTTGGGCACTTTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * * *
334732 TGCAAAACTAAGAAATTCATAAAAAATTTATGAATTTTCGTATGGTCACTTTATG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* ** *
334787 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTTTGTATGGGCACGTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
334842 TACAAAAGCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATTTGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
334898 TGCAAAACTAAGAAATTCATAATAAGTTTATAAATTTCCATATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
334953 TGCAAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
335008 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTTTG
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* * * * * * **
335063 TGTAAAAGTTAAGAAAATCATATTAAGTTTATGAATTACCGTATTGGCACTACGTG
1 TGCAAAA-CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
335119 TGCAAA
1 TGCAAA
335125 CTATAGAGTT
Statistics
Matches: 550, Mismatches: 58, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
54 47 0.09
55 263 0.48
56 240 0.44
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (55 bp):
TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:334805 original size:166 final size:167
Alignment explanation
Indices: 334455--335124 Score: 972
Period size: 166 Copynumber: 4.0 Consensus size: 167
334445 TCATTATACT
* *
334455 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATAGACACTTTGTGTGCAAAAGCT
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
* * * *
334520 AAGAAATTCTTAATAAGTTTATGAATTTACGTACGGGCACTTTGTGTGCAAAAGCTAGGAAATTC
66 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCTAAGAAATTC
*
334585 ATAATAAGTTTATGAATTTCCGTATGGGCACATTGTG
131 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
*
334622 TGC-AAACTATA-AAATTCATAATAAGTTTATGAATTTCCGTATGGCCACTTTGTGTGCAAAAGC
1 TGCAAAACTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGC
* * *
334685 TAAAAAAATCATAATAAGTTTATGAATTTCCGTTTGGGCACTTTGTGTGCAAAA-CTAAGAAATT
65 TAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCTAAGAAATT
* * * * *
334749 CATAAAAAATTTATGAATTTTCGTATGGTCACTTTATG
130 CATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* ** * *
334787 TGCAAAACTAAGAAATTCATAATAAATTTATGAATTTTTGTATGGGCACGTTGTGTACAAAAGCT
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
*
334852 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCAATTTGTGTGCAAAA-CTAAGAAATTC
66 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCTAAGAAATTC
* *
334916 ATAATAAGTTTATAAATTTCCATATGGGCACTTTGTG
131 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
* *
334953 TGCAAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAA-CT
1 TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
* * * * *
335017 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTTTGTGTAAAAGTTAAGAAAATC
66 AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCTAAGAAATTC
* * * **
335082 ATATTAAGTTTATGAATTACCGTATTGGCACTACGTG
131 ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
335119 TGCAAA
1 TGCAAA
335125 CTATAGAGTT
Statistics
Matches: 449, Mismatches: 50, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
165 96 0.21
166 349 0.78
167 4 0.01
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (167 bp):
TGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCT
AAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTGTGCAAAAGCTAAGAAATTC
ATAATAAGTTTATGAATTTCCGTATGGGCACTTTGTG
Found at i:338783 original size:56 final size:55
Alignment explanation
Indices: 338586--338790 Score: 320
Period size: 55 Copynumber: 3.7 Consensus size: 55
338576 ATAGTCTTAT
*
338586 GAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTGCAAAACTAA
1 GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCAAAACTAA
* **
338641 GAAATTCATAATACGTTTATGAATTTTTGTATGGTTACTTTGTGTGCAAAACTAA
1 GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCAAAACTAA
* *
338696 GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTCTGTGTGTAAAACCTAA
1 GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCAAAA-CTAA
** *
338752 GAAATTCATAATAAGTTTATGAATTACTGTATTGGCACT
1 GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACT
338791 ACATGTACGA
Statistics
Matches: 137, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
55 97 0.71
56 40 0.29
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (55 bp):
GAAATTCATAATAAGTTTATGAATTTTTGTATGGGCACTTTGTGTGCAAAACTAA
Found at i:352511 original size:24 final size:24
Alignment explanation
Indices: 352467--352513 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
352457 ATAAAGAACC
*
352467 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
352491 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
352514 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:355836 original size:20 final size:19
Alignment explanation
Indices: 355788--355836 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
355778 AAGAAAGAGA
* *
355788 AAAGGTAAAATTTAAAATG
1 AAAGATAAAAATTAAAATG
*
355807 AAAGAGAAAAATTAATAATG
1 AAAGATAAAAATTAA-AATG
*
355827 AAATATAAAA
1 AAAGATAAAA
355837 GAAAAAGTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.22
Consensus pattern (19 bp):
AAAGATAAAAATTAAAATG
Found at i:358417 original size:14 final size:14
Alignment explanation
Indices: 358398--358425 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
358388 ATCCATGAAG
358398 ATCTCCAGAAAATC
1 ATCTCCAGAAAATC
358412 ATCTCCAGAAAATC
1 ATCTCCAGAAAATC
358426 CTCAACCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (14 bp):
ATCTCCAGAAAATC
Found at i:361812 original size:18 final size:18
Alignment explanation
Indices: 361789--361824 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
361779 CAAGTAAACT
361789 ATACAAAA-AAATATAAAA
1 ATACAAAACAAA-ATAAAA
361807 ATACAAAACAAAATAAAA
1 ATACAAAACAAAATAAAA
361825 TGCTCTGGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (18 bp):
ATACAAAACAAAATAAAA
Found at i:362760 original size:24 final size:24
Alignment explanation
Indices: 362716--362762 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
362706 ATAAAGAACC
*
362716 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
362740 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
362763 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:372437 original size:20 final size:20
Alignment explanation
Indices: 372412--372463 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
372402 ATGTGCTGAT
* * *
372412 AAACCATATTTTTTTGTTGG
1 AAACCAAATTTTTTGGTCGG
*
372432 AAACCAGA-TTTTTGGTCGG
1 AAACCAAATTTTTTGGTCGG
372451 AAACCAAATTTTT
1 AAACCAAATTTTT
372464 GGGTGTAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (20 bp):
AAACCAAATTTTTTGGTCGG
Found at i:384338 original size:19 final size:19
Alignment explanation
Indices: 384313--384399 Score: 95
Period size: 19 Copynumber: 4.6 Consensus size: 19
384303 TTTGGTCGGA
*
384313 AACCAGATTTTAGGTTAGT
1 AACCAGATTTTAGGTTGGT
* * *
384332 AATCAGATTTTTGGTTGGA
1 AACCAGATTTTAGGTTGGT
*
384351 AACCAGATTTTAGATTGGT
1 AACCAGATTTTAGGTTGGT
* *
384370 AGCCAGATTTTAGATTGG-
1 AACCAGATTTTAGGTTGGT
384388 AAGCCAGATTTT
1 AA-CCAGATTTT
384400 TGGGTGTAAG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 1 0.02
19 56 0.98
ACGTcount: A:0.30, C:0.10, G:0.23, T:0.37
Consensus pattern (19 bp):
AACCAGATTTTAGGTTGGT
Found at i:384352 original size:38 final size:38
Alignment explanation
Indices: 384300--384399 Score: 128
Period size: 38 Copynumber: 2.6 Consensus size: 38
384290 TGAGAAACTA
* * *
384300 ATTTTTGGTCGGAAACCAGATTTTAGGTTAGTAATCAG
1 ATTTTTGGTTGGAAACCAGATTTTAGATTAGTAACCAG
* *
384338 ATTTTTGGTTGGAAACCAGATTTTAGATTGGTAGCCAG
1 ATTTTTGGTTGGAAACCAGATTTTAGATTAGTAACCAG
* * *
384376 ATTTTAGATTGGAAGCCAGATTTT
1 ATTTTTGGTTGGAAACCAGATTTT
384400 TGGGTGTAAG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.28, C:0.10, G:0.24, T:0.38
Consensus pattern (38 bp):
ATTTTTGGTTGGAAACCAGATTTTAGATTAGTAACCAG
Found at i:387471 original size:90 final size:90
Alignment explanation
Indices: 387364--387531 Score: 300
Period size: 90 Copynumber: 1.9 Consensus size: 90
387354 TATTTATTTT
**
387364 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCTAATATGATTAGGGTAACT
387429 TGGATATAAAAGGATTATTAAATTC
66 TGGATATAAAAGGATTATTAAATTC
*
387454 CAATTAATTAAATATAGATTTAATTATTTTGAAATAATAAAAAACCTAATATGATTAGGGTAACT
1 CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCTAATATGATTAGGGTAACT
*
387519 TGGCTATAAAAGG
66 TGGATATAAAAGG
387532 GTGTCCTAGG
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (90 bp):
CAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAAACCTAATATGATTAGGGTAACT
TGGATATAAAAGGATTATTAAATTC
Found at i:390551 original size:21 final size:20
Alignment explanation
Indices: 390511--390549 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
390501 AACAGTACTC
390511 GTAGGGGGAATCGATTCCCT
1 GTAGGGGGAATCGATTCCCT
*
390531 GTAGGGGGAATCGGTTCCC
1 GTAGGGGGAATCGATTCCC
390550 CTTTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.38, T:0.23
Consensus pattern (20 bp):
GTAGGGGGAATCGATTCCCT
Found at i:390988 original size:45 final size:45
Alignment explanation
Indices: 390919--391043 Score: 153
Period size: 45 Copynumber: 2.8 Consensus size: 45
390909 ATTCAATATT
390919 TTACCATTTATTAACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
1 TTACCATTTA-T-ACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * **
390966 TTACCATTTATCCCATAAGCTCGTAAGCTTATCTTACCATTATAC
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
* * * *
391011 TTGCCA-TTATTCTATAAGCTCGTGAGCTTATTT
1 TTACCATTTATACCATAAGCTCGTAAGCTTATTT
391044 ACATGGTTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
44 23 0.33
45 35 0.51
46 1 0.01
47 10 0.14
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
TTACCATTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATAC
Found at i:401028 original size:58 final size:63
Alignment explanation
Indices: 400957--401077 Score: 155
Period size: 65 Copynumber: 2.0 Consensus size: 63
400947 AATAGAAGAG
400957 CTAAGCCGTATCTGT-G-A-G-CTATTATGTAATG-AAACTTTTTGTT-TCAATGGAAGTTGAA
1 CTAAGCCGTATCTGTAGAATGACTATTATGTAATGAAAACTTTTTGTTAT-AATGGAAGTTGAA
* *
401015 CTAAGCCTTATCTGTAGAAATGAATTATTATGTAATGAAAACTTTTTGTTATAATGGAAGTTG
1 CTAAGCCGTATCTGTAG-AATG-ACTATTATGTAATGAAAACTTTTTGTTATAATGGAAGTTG
401078 TTCTATGACA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
58 14 0.26
59 1 0.02
61 1 0.02
62 1 0.02
64 12 0.23
65 23 0.43
66 1 0.02
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (63 bp):
CTAAGCCGTATCTGTAGAATGACTATTATGTAATGAAAACTTTTTGTTATAATGGAAGTTGAA
Found at i:408489 original size:15 final size:15
Alignment explanation
Indices: 408455--408542 Score: 124
Period size: 15 Copynumber: 5.8 Consensus size: 15
408445 ATGCTGGAAG
408455 AAAAAATGAATGAATG-
1 AAAAAATGAA--AATGA
408471 AAAAAATGAAAATGA
1 AAAAAATGAAAATGA
408486 AAAAAATGAAAATGA
1 AAAAAATGAAAATGA
**
408501 AAAAAATGAAAAAAA
1 AAAAAATGAAAATGA
*
408516 AAAAAATGAAAAAGA
1 AAAAAATGAAAATGA
408531 AAAAAATGAAAA
1 AAAAAATGAAAA
408543 AAAGAGAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.06
15 54 0.79
16 10 0.15
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.11
Consensus pattern (15 bp):
AAAAAATGAAAATGA
Found at i:408493 original size:9 final size:9
Alignment explanation
Indices: 408479--408565 Score: 75
Period size: 9 Copynumber: 10.4 Consensus size: 9
408469 TGAAAAAATG
408479 AAAATGAAA
1 AAAATGAAA
408488 AAAATG---
1 AAAATGAAA
408494 AAAATGAAA
1 AAAATGAAA
408503 AAAATG-AA
1 AAAATGAAA
408511 AAAA--AAA
1 AAAATGAAA
408518 AAAATG--A
1 AAAATGAAA
408525 AAAA-GAAA
1 AAAATGAAA
408533 AAAATGAAA
1 AAAATGAAA
*
408542 AAAAGAGAAAA
1 AAAA-TG-AAA
*
408553 AAAAAGAAA
1 AAAATGAAA
408562 AAAA
1 AAAA
408566 AAGAAAAGAA
Statistics
Matches: 66, Mismatches: 1, Indels: 22
0.74 0.01 0.25
Matches are distributed among these distances:
6 7 0.11
7 11 0.17
8 11 0.17
9 27 0.41
10 3 0.05
11 7 0.11
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (9 bp):
AAAATGAAA
Found at i:408511 original size:24 final size:22
Alignment explanation
Indices: 408473--408542 Score: 90
Period size: 24 Copynumber: 3.2 Consensus size: 22
408463 AATGAATGAA
408473 AAAATG-AAAATGAAAAAAATG
1 AAAATGAAAAATGAAAAAAATG
**
408494 AAAATGAAAAAAATGAAAAAAAAA
1 AAAATG--AAAAATGAAAAAAATG
408518 AAAATGAAAAA-GAAAAAAATG
1 AAAATGAAAAATGAAAAAAATG
408539 AAAA
1 AAAA
408543 AAAGAGAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 18 0.43
22 5 0.12
24 19 0.45
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (22 bp):
AAAATGAAAAATGAAAAAAATG
Found at i:408515 original size:10 final size:10
Alignment explanation
Indices: 408500--408580 Score: 94
Period size: 10 Copynumber: 8.0 Consensus size: 10
408490 AATGAAAATG
*
408500 AAAAAAATGA
1 AAAAAAAAGA
408510 AAAAAAAA-A
1 AAAAAAAAGA
408519 AAATGAAAAAG-
1 AAA--AAAAAGA
*
408530 AAAAAAATGA
1 AAAAAAAAGA
*
408540 AAAAAAGAGA
1 AAAAAAAAGA
408550 AAAAAAAAGA
1 AAAAAAAAGA
408560 AAAAAAAAGA
1 AAAAAAAAGA
408570 AAAGAAAAAGA
1 AAA-AAAAAGA
408581 GGGTTCGAGA
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
9 9 0.15
10 37 0.61
11 15 0.25
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:408543 original size:15 final size:15
Alignment explanation
Indices: 408471--408578 Score: 125
Period size: 15 Copynumber: 7.3 Consensus size: 15
408461 TGAATGAATG
*
408471 AAAAAATGAAAATGA
1 AAAAAATGAAAAAGA
*
408486 AAAAAATGAAAATGA
1 AAAAAATGAAAAAGA
*
408501 AAAAAATGAAAAAAA
1 AAAAAATGAAAAAGA
408516 AAAAAATGAAAAAGA
1 AAAAAATGAAAAAGA
408531 AAAAAATGAAAAA-A
1 AAAAAATGAAAAAGA
408545 AGAGAAAA--AAAAAGA
1 A-A-AAAATGAAAAAGA
*
408560 AAAAAA-AAGAAAAGA
1 AAAAAATGA-AAAAGA
408575 AAAA
1 AAAA
408579 GAGGGTTCGA
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.05
14 9 0.11
15 68 0.80
16 4 0.05
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAAATGAAAAAGA
Done.