Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold53
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: 4419549
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.31
Warning! 41486 characters in sequence are not A, C, G, or T
File 2 of 28
Found at i:244495 original size:8 final size:8
Alignment explanation
Indices: 244482--244573 Score: 76
Period size: 8 Copynumber: 10.9 Consensus size: 8
244472 TTTTTGATGA
244482 TTTTATTT
1 TTTTATTT
244490 TTTTATTT
1 TTTTATTT
*
244498 CTTTGATTT
1 -TTTTATTT
* *
244507 CTTTAATT
1 TTTTATTT
*
244515 TTTGATTT
1 TTTTATTT
244523 TTTTGATTTTT
1 TTTT-A--TTT
244534 TTTTATTT
1 TTTTATTT
*
244542 TTTGATTT
1 TTTTATTT
*
244550 TTTTAAATT
1 TTTT-ATTT
*
244559 TTTAATTT
1 TTTTATTT
244567 TTTTATT
1 TTTTATT
244574 ATATCAAATC
Statistics
Matches: 65, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
8 43 0.66
9 14 0.22
10 1 0.02
11 7 0.11
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:244508 original size:9 final size:8
Alignment explanation
Indices: 244472--244552 Score: 58
Period size: 8 Copynumber: 9.6 Consensus size: 8
244462 CTAATTTTTA
244472 TTTTTGAT
1 TTTTTGAT
*
244480 GATTTT-AT
1 -TTTTTGAT
*
244488 TTTTTTAT
1 TTTTTGAT
244496 TTCTTTGAT
1 TT-TTTGAT
*
244505 TTCTTT-AA
1 TT-TTTGAT
244513 TTTTTGATT
1 TTTTTGA-T
244522 TTTTTGATTT
1 TTTTTGA--T
*
244532 TTTTTTAT
1 TTTTTGAT
244540 TTTTTGAT
1 TTTTTGAT
244548 TTTTT
1 TTTTT
244553 TAAATTTTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
7 7 0.12
8 23 0.38
9 22 0.37
10 8 0.13
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.77
Consensus pattern (8 bp):
TTTTTGAT
Found at i:244511 original size:25 final size:24
Alignment explanation
Indices: 244472--244569 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 24
244462 CTAATTTTTA
* *
244472 TTTTTGATGATTTTATTTTTTTATT
1 TTTTTGAT-TTTTTATTTTTTGATT
* *
244497 TCTTTGATTTCTTTAATTTTTGATT
1 TTTTTGATTT-TTTATTTTTTGATT
244522 TTTTTGATTTTTTTTTATTTTTTGATT
1 TTTTTGA---TTTTTTATTTTTTGATT
* *
244549 TTTTTAAATTTTTAATTTTTT
1 TTTTT-GATTTTTTATTTTTT
244570 TATTATATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
24 1 0.02
25 37 0.62
27 18 0.30
28 4 0.07
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.76
Consensus pattern (24 bp):
TTTTTGATTTTTTATTTTTTGATT
Found at i:244548 original size:43 final size:45
Alignment explanation
Indices: 244487--244570 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 45
244477 GATGATTTTA
*
244487 TTTTTTTATTTCTTTGATTTCTTT-AATTTTTGATTTTTTTGATT
1 TTTTTTTATTTCTTTGATTTCTTTAAATTTTTAATTTTTTTGATT
*
244531 TTTTTTTATTT-TTTGATTTTTTTAAATTTTTAATTTTTTT
1 TTTTTTTATTTCTTTGATTTCTTTAAATTTTTAATTTTTTT
244571 ATTATATCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 11 0.30
44 26 0.70
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.77
Consensus pattern (45 bp):
TTTTTTTATTTCTTTGATTTCTTTAAATTTTTAATTTTTTTGATT
Found at i:244553 original size:9 final size:9
Alignment explanation
Indices: 244472--244553 Score: 66
Period size: 9 Copynumber: 9.6 Consensus size: 9
244462 CTAATTTTTA
*
244472 TTTTTGATG
1 TTTTTGATT
*
244481 ATTTT-ATT
1 TTTTTGATT
244489 TTTTT-ATT
1 TTTTTGATT
*
244497 TCTTTGATT
1 TTTTTGATT
* *
244506 TCTTT-A-A
1 TTTTTGATT
244513 TTTTTGATT
1 TTTTTGATT
244522 TTTTTGATT
1 TTTTTGATT
*
244531 TTTTT-TTAT
1 TTTTTGAT-T
244540 TTTTTGATT
1 TTTTTGATT
244549 TTTTT
1 TTTTT
244554 AAATTTTTAA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
7 4 0.07
8 16 0.27
9 38 0.64
10 1 0.02
ACGTcount: A:0.13, C:0.02, G:0.07, T:0.77
Consensus pattern (9 bp):
TTTTTGATT
Found at i:244559 original size:18 final size:18
Alignment explanation
Indices: 244521--244571 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
244511 AATTTTTGAT
**
244521 TTTTTTGATTTTTTTTTA
1 TTTTTTGATTTTTTTAAA
244539 TTTTTTGATTTTTTTAAA
1 TTTTTTGATTTTTTTAAA
*
244557 -TTTTTAATTTTTTTA
1 TTTTTTGATTTTTTTA
244572 TTATATCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.18, C:0.00, G:0.04, T:0.78
Consensus pattern (18 bp):
TTTTTTGATTTTTTTAAA
Found at i:244570 original size:10 final size:10
Alignment explanation
Indices: 244513--244553 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
244503 ATTTCTTTAA
244513 TTTTTGA-TT
1 TTTTTGATTT
244522 TTTTTGATTT
1 TTTTTGATTT
*
244532 TTTTT--TAT
1 TTTTTGATTT
244540 TTTTTGATTT
1 TTTTTGATTT
244550 TTTT
1 TTTT
244554 AAATTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
8 7 0.26
9 7 0.26
10 13 0.48
ACGTcount: A:0.10, C:0.00, G:0.07, T:0.83
Consensus pattern (10 bp):
TTTTTGATTT
Found at i:246937 original size:52 final size:51
Alignment explanation
Indices: 246874--246989 Score: 142
Period size: 52 Copynumber: 2.3 Consensus size: 51
246864 TTGAAAAACA
* * * *
246874 GGGTTGAAGTATCCTCGATTATGAAAAATCAATATTTTGGAAACAAAAATCG
1 GGGTTGGAGTATCCACGATGATGAAAAATCAATATTTTAGAAAC-AAAATCG
* *** *
246926 GGGTTGGAGTATCCACGATGGTGAAAAATTGGTATTTTAGAAACAAAGTCG
1 GGGTTGGAGTATCCACGATGATGAAAAATCAATATTTTAGAAACAAAATCG
246977 GGGTTGGAGTATC
1 GGGTTGGAGTATC
246990 TCCTCAAAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
51 19 0.35
52 36 0.65
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.28
Consensus pattern (51 bp):
GGGTTGGAGTATCCACGATGATGAAAAATCAATATTTTAGAAACAAAATCG
Found at i:247175 original size:79 final size:78
Alignment explanation
Indices: 246975--247192 Score: 244
Period size: 78 Copynumber: 2.8 Consensus size: 78
246965 GAAACAAAGT
* * * *
246975 CGGGGTTGGAGTATCTCCTCAAAAATAACG-GGATTAGAGTATCCCTGATTGTGGAAAATCGATG
1 CGGGGTTGGAGTATCTCTTCAGAAATAACGAGG-TTGGAGTATCCCCGATTGTGGAAAATCGATG
**
247039 TTATGGAAATAAAA
65 TTATCAAAATAAAA
* * ** *
247053 TGGGGTTAGAGTATC-CTTTTGAAAATAACGAGGTTGGAGTATCCCCGATAGTGGAAAATCGATG
1 CGGGGTTGGAGTATCTCTTCAG-AAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAATCGATG
247117 TT-TCAAAAGTAAAA
65 TTATCAAAA-TAAAA
* * * *
247131 CCGGGGTTGGATTATCTCTTCAGAAATAATGAGGTTGGAATATCCCCGATTGTGAAAAATCG
1 -CGGGGTTGGAGTATCTCTTCAGAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAATCG
247193 GTACTTTGTT
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
77 6 0.05
78 56 0.49
79 49 0.43
80 4 0.03
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (78 bp):
CGGGGTTGGAGTATCTCTTCAGAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAAATCGATGT
TATCAAAATAAAA
Found at i:248829 original size:15 final size:15
Alignment explanation
Indices: 248809--248846 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
248799 TGTATCTTTC
248809 TTTCATTGC-ATGCCA
1 TTTCATTGCTAT-CCA
*
248824 TTTCATTACTATCCA
1 TTTCATTGCTATCCA
248839 TTTCATTG
1 TTTCATTG
248847 TTGTCCCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.21, C:0.24, G:0.08, T:0.47
Consensus pattern (15 bp):
TTTCATTGCTATCCA
Found at i:249008 original size:7 final size:7
Alignment explanation
Indices: 248998--249023 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
248988 TTTTTTTGTT
248998 TTTTTAA
1 TTTTTAA
249005 TTTTTAA
1 TTTTTAA
249012 TTTTTAA
1 TTTTTAA
249019 TTTTT
1 TTTTT
249024 TTGATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:249039 original size:18 final size:17
Alignment explanation
Indices: 249012--249059 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 17
249002 TAATTTTTAA
*
249012 TTTTTAATTTTTTTGAT
1 TTTTTGATTTTTTTGAT
249029 CTTTTTGATTTTTTTGAT
1 -TTTTTGATTTTTTTGAT
249047 TTCTTTGATTTTT
1 TT-TTTGATTTTT
249060 AATTTTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 2 0.07
18 26 0.93
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.75
Consensus pattern (17 bp):
TTTTTGATTTTTTTGAT
Found at i:249040 original size:7 final size:8
Alignment explanation
Indices: 248997--249068 Score: 51
Period size: 9 Copynumber: 8.9 Consensus size: 8
248987 TTTTTTTTGT
248997 TTTTTTAA
1 TTTTTTAA
249005 -TTTTTAA
1 TTTTTTAA
249012 -TTTTTAA
1 TTTTTTAA
*
249019 TTTTTTTGA
1 -TTTTTTAA
*
249028 TCTTTTTGAT
1 T-TTTTT-AA
*
249038 TTTTTTGA
1 TTTTTTAA
*
249046 TTTCTTTGA
1 TTT-TTTAA
249055 -TTTTTAA
1 TTTTTTAA
249062 TTTTTTA
1 TTTTTTA
249069 TGTCAAAAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
7 18 0.35
8 12 0.23
9 21 0.40
10 1 0.02
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (8 bp):
TTTTTTAA
Found at i:249058 original size:16 final size:16
Alignment explanation
Indices: 248989--249059 Score: 56
Period size: 18 Copynumber: 4.3 Consensus size: 16
248979 ATCATCATTT
*
248989 TTTTTTG-TTTTTTTA
1 TTTTTTGATTTTTTGA
* * *
249004 ATTTTT-AATTTTTAA
1 TTTTTTGATTTTTTGA
249019 TTTTTTTGATCTTTTTGA
1 -TTTTTTGAT-TTTTTGA
249037 TTTTTTTGATTTCTTTGA
1 -TTTTTTGATTT-TTTGA
249055 TTTTT
1 TTTTT
249060 AATTTTTTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 11 0.24
16 5 0.11
17 8 0.18
18 21 0.47
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTTTGATTTTTTGA
Found at i:249402 original size:30 final size:33
Alignment explanation
Indices: 249368--249463 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 33
249358 CCTTATAATG
249368 CTATC-TTTCAAGGCTAAGATAGAAACC-TC-C
1 CTATCTTTTCAAGGCTAAGATAGAAACCTTCTC
*
249398 CTATCTTTTCACGGGCTAAGATA-AAACCTTTCTC
1 CTATCTTTTCA-AGGCTAAGATAGAAACC-TTCTC
249432 CTTATCTTTTTCAAAGGCTAAGATAG-AACCTT
1 C-TATC-TTTTC-AAGGCTAAGATAGAAACCTT
249464 ACAATCACTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
30 5 0.09
31 10 0.18
32 10 0.18
33 2 0.04
34 2 0.04
35 6 0.11
36 19 0.35
37 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.33
Consensus pattern (33 bp):
CTATCTTTTCAAGGCTAAGATAGAAACCTTCTC
Found at i:260423 original size:20 final size:20
Alignment explanation
Indices: 260398--260437 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
260388 AGCCTTTGAT
*
260398 CATGCATTTTTAATATGTTC
1 CATGCATTTTTAACATGTTC
260418 CATGCATTTTTAACATGTTC
1 CATGCATTTTTAACATGTTC
260438 AACATTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (20 bp):
CATGCATTTTTAACATGTTC
Found at i:264911 original size:12 final size:11
Alignment explanation
Indices: 264889--264964 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
264879 AGAGAAAGAA
*
264889 GAGAGAGGAGG
1 GAGATAGGAGG
264900 GATGATAGGAGG
1 GA-GATAGGAGG
*
264912 AGAGACAGGA--
1 -GAGATAGGAGG
*
264922 GAGATAGTA--
1 GAGATAGGAGG
264931 GAGATAGGAGG
1 GAGATAGGAGG
264942 GATGATAGGAGG
1 GA-GATAGGAGG
*
264954 AGAGACAGGAG
1 -GAGATAGGAG
264965 AGGTAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:264940 original size:42 final size:42
Alignment explanation
Indices: 264879--264997 Score: 175
Period size: 42 Copynumber: 2.8 Consensus size: 42
264869 TAGCCCTCAA
* *
264879 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
*
264921 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* * * *
264963 AGAGGTAATAGAGAGAGGAGGGATGACAGAAGGAG
1 AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAG
264998 GAGAGAAGAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGTAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:268254 original size:15 final size:14
Alignment explanation
Indices: 268217--268255 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
268207 AGAATACAAA
268217 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
268231 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
268247 AAAAAAAAA
1 AAAAAAAAA
268256 AAACCAGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Found at i:269027 original size:12 final size:11
Alignment explanation
Indices: 269005--269080 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
268995 AGAGAAAGAA
*
269005 GAGAGAGGAGG
1 GAGATAGGAGG
269016 GATGATAGGAGG
1 GA-GATAGGAGG
*
269028 AGAGACAGGA--
1 -GAGATAGGAGG
*
269038 GAGATAGTA--
1 GAGATAGGAGG
269047 GAGATAGGAGG
1 GAGATAGGAGG
269058 GATGATAGGAGG
1 GA-GATAGGAGG
*
269070 AGAGACAGGAG
1 -GAGATAGGAG
269081 AGATAACAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:269056 original size:42 final size:42
Alignment explanation
Indices: 268995--269113 Score: 195
Period size: 42 Copynumber: 2.8 Consensus size: 42
268985 TAGCCCTCAA
*
268995 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
* *
269037 AGAGATAGTAGAGATAGGAGGGATGATAGGAGGAGAGACAGG
1 AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
269079 AGAGATA-ACAGAGAGAGGAGGGATGATAGGAGGAG
1 AGAGATAGA-AGAGAGAGGAGGGATGATAGGAGGAG
269114 GAGAGAAGAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (42 bp):
AGAGATAGAAGAGAGAGGAGGGATGATAGGAGGAGAGACAGG
Found at i:281929 original size:42 final size:42
Alignment explanation
Indices: 281874--281992 Score: 193
Period size: 42 Copynumber: 2.8 Consensus size: 42
281864 TTCTTCTCTC
* *
281874 CTCCTCCTGTCATCCCTCCTCTCTCTATTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
*
281916 CTCCTCCTATCATCCCTCCTATCTCTACTATCTCTCCTGTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
* *
281958 CTCCTCCTATCATCCCTCCTCTCTCTTCTTTCTCT
1 CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCT
281993 TTGAGGGCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.08, C:0.46, G:0.03, T:0.43
Consensus pattern (42 bp):
CTCCTCCTATCATCCCTCCTCTCTCTACTATCTCTCCTGTCT
Found at i:281933 original size:12 final size:11
Alignment explanation
Indices: 281907--281982 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
281897 TCTATTATCT
*
281907 CTCCTGTCTCTC
1 CTCCTATCTC-C
281919 CTCCTATCATCC
1 CTCCTATC-TCC
281931 CTCCTATCT--
1 CTCCTATCTCC
*
281940 CTACTATCT--
1 CTCCTATCTCC
*
281949 CTCCTGTCTCTC
1 CTCCTATCTC-C
281961 CTCCTATCATCC
1 CTCCTATC-TCC
*
281973 CTCCTCTCTC
1 CTCCTATCTC
281983 TTCTTTCTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 3 0.06
12 31 0.58
13 4 0.08
ACGTcount: A:0.09, C:0.49, G:0.03, T:0.39
Consensus pattern (11 bp):
CTCCTATCTCC
Found at i:281934 original size:24 final size:24
Alignment explanation
Indices: 281898--281983 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
281888 CCTCCTCTCT
* *
281898 CTATTATCTCTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
* *
281922 CTATCATCCCTCC--TATCT-CTA
1 CTATCATCCCTCCTGTCTCTCCTC
281943 CTATC-T--CTCCTGTCTCTCCTC
1 CTATCATCCCTCCTGTCTCTCCTC
*
281964 CTATCATCCCTCCTCTCTCT
1 CTATCATCCCTCCTGTCTCT
281984 TCTTTCTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 4 0.08
20 5 0.10
21 14 0.29
22 5 0.10
24 21 0.43
ACGTcount: A:0.10, C:0.45, G:0.02, T:0.42
Consensus pattern (24 bp):
CTATCATCCCTCCTGTCTCTCCTC
Found at i:281958 original size:18 final size:18
Alignment explanation
Indices: 281889--281959 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
281879 CCTGTCATCC
* *
281889 CTCCTCTCTCTATTATCT
1 CTCCTGTCTCTACTATCT
*
281907 CTCCTGTCTCTCCTCCTATCAT
1 CTCCTG--TCT-CTACTATC-T
*
281929 CCCTCCTATCTCTACTATCT
1 --CTCCTGTCTCTACTATCT
281949 CTCCTGTCTCT
1 CTCCTGTCTCT
281960 CCTCCTATCA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
18 15 0.37
20 4 0.10
21 13 0.32
22 4 0.10
24 5 0.12
ACGTcount: A:0.10, C:0.44, G:0.03, T:0.44
Consensus pattern (18 bp):
CTCCTGTCTCTACTATCT
Found at i:287541 original size:15 final size:15
Alignment explanation
Indices: 287521--287565 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
287511 GTTCTGCCAA
287521 ATCCACCACAAAATC
1 ATCCACCACAAAATC
** *
287536 ATCCACCACCTAATT
1 ATCCACCACAAAATC
*
287551 ACCCACCACAAAATC
1 ATCCACCACAAAATC
287566 GTCGATACAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (15 bp):
ATCCACCACAAAATC
Found at i:293514 original size:10 final size:10
Alignment explanation
Indices: 293512--293596 Score: 91
Period size: 10 Copynumber: 8.2 Consensus size: 10
293502 AAAAAAAACC
293512 AAACCAAAACA
1 AAACCAAAA-A
*
293523 AAAAC-AAAA
1 AAACCAAAAA
293532 AAACCAAAAA
1 AAACCAAAAA
293542 AAACCAAAAAAA
1 AAACC--AAAAA
**
293554 AAAAAACAAAA
1 AAACCA-AAAA
*
293565 AAACAAAAAA
1 AAACCAAAAA
293575 AAACCAAAAA
1 AAACCAAAAA
293585 AAACCAAAAA
1 AAACCAAAAA
293595 AA
1 AA
293597 CAAATTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
9 5 0.08
10 38 0.59
11 13 0.20
12 8 0.12
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (10 bp):
AAACCAAAAA
Found at i:293526 original size:1 final size:1
Alignment explanation
Indices: 293517--293625 Score: 56
Period size: 1 Copynumber: 109.0 Consensus size: 1
293507 AAACCAAACC
* * ** ** * * **
293517 AAAACAAAAACAAAAAAACCAAAAAAAACCAAAAAAAAAAAAACAAAAAAACAAAAAAAAACCAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * ** * * *
293582 AAAAAACCAAAAAAACAAATTAAAAAAACAAACAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
293626 GAAGGGTCCA
Statistics
Matches: 82, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:293531 original size:25 final size:22
Alignment explanation
Indices: 293502--293624 Score: 108
Period size: 23 Copynumber: 5.4 Consensus size: 22
293492 CCTTTGTACC
293502 AAAAAAAACCAAACCAAAACAAAA
1 AAAAAAAACCAAA--AAAACAAAA
293526 ACAAAAAAACCAAAAAAAACCAAAA
1 A-AAAAAAACC-AAAAAAA-CAAAA
*
293551 AAAAAAAAACAAAAAAAC---A
1 AAAAAAAACCAAAAAAACAAAA
*
293570 AAAAAAAACCAAAAAAAACCAAA
1 AAAAAAAACC-AAAAAAACAAAA
* **
293593 AAAACAAATTAAAAAAACAAACA
1 AAAAAAAACCAAAAAAACAAA-A
293616 AACAAAAAA
1 AA-AAAAAA
293625 AGAAGGGTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
19 10 0.12
20 8 0.10
22 11 0.13
23 18 0.22
24 18 0.22
25 15 0.18
26 3 0.04
ACGTcount: A:0.82, C:0.16, G:0.00, T:0.02
Consensus pattern (22 bp):
AAAAAAAACCAAAAAAACAAAA
Found at i:293535 original size:8 final size:8
Alignment explanation
Indices: 293522--293625 Score: 81
Period size: 8 Copynumber: 12.6 Consensus size: 8
293512 AAACCAAAAC
293522 AAAAACAA
1 AAAAACAA
293530 AAAAACCAAA
1 AAAAA-C-AA
*
293540 AAAAACCA
1 AAAAACAA
293548 AAAAA-AA
1 AAAAACAA
293555 AAAAACAA
1 AAAAACAA
293563 AAAAACAA
1 AAAAACAA
293571 AAAAA-AA
1 AAAAACAA
293578 CCAAAAA-AA
1 --AAAAACAA
293587 ACCAAAA-AA
1 A--AAAACAA
**
293596 ACAAATTAA
1 A-AAAACAA
293605 AAAAACAA
1 AAAAACAA
*
293613 ACAAACAA
1 AAAAACAA
293621 AAAAA
1 AAAAA
293626 GAAGGGTCCA
Statistics
Matches: 81, Mismatches: 7, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
7 9 0.11
8 46 0.57
9 19 0.23
10 7 0.09
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (8 bp):
AAAAACAA
Found at i:293575 original size:43 final size:44
Alignment explanation
Indices: 293499--293624 Score: 159
Period size: 43 Copynumber: 2.8 Consensus size: 44
293489 CATCCTTTGT
* *
293499 ACCAAAAAAAACCAAACCAAAACAAA-AACAAAAAAACCAAAAAAA
1 ACCAAAAAAAA-AAAAACAAAACAAACAA-AAAAAAACCAAAAAAA
293544 ACCAAAAAAAAAAAAACAAAA-AAACAAAAAAAAACCAAAAAAA
1 ACCAAAAAAAAAAAAACAAAACAAACAAAAAAAAACCAAAAAAA
293587 ACCAAAAAAACAAATTAAA-AAAACAAACAAACAAAAAA
1 ACCAAAAAAA-AAA--AAACAAAACAAACAAA-AAAAAA
293625 AGAAGGGTCC
Statistics
Matches: 73, Mismatches: 2, Indels: 10
0.86 0.02 0.12
Matches are distributed among these distances:
43 29 0.40
44 13 0.18
45 15 0.21
46 10 0.14
47 6 0.08
ACGTcount: A:0.81, C:0.17, G:0.00, T:0.02
Consensus pattern (44 bp):
ACCAAAAAAAAAAAAACAAAACAAACAAAAAAAAACCAAAAAAA
Found at i:293609 original size:33 final size:34
Alignment explanation
Indices: 293502--293594 Score: 143
Period size: 33 Copynumber: 2.7 Consensus size: 34
293492 CCTTTGTACC
* *
293502 AAAAAAAACCAAACCAAAACAAAAACAAAAAAACC
1 AAAAAAAACCAAA-AAAAACAAAAACAAAAAAACA
293537 AAAAAAAACCAAAAAAAA-AAAAACAAAAAAACA
1 AAAAAAAACCAAAAAAAACAAAAACAAAAAAACA
293570 AAAAAAAACCAAAAAAAACCAAAAA
1 AAAAAAAACCAAAAAAAA-CAAAAA
293595 AACAAATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
33 32 0.59
34 4 0.07
35 18 0.33
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (34 bp):
AAAAAAAACCAAAAAAAACAAAAACAAAAAAACA
Found at i:294874 original size:26 final size:27
Alignment explanation
Indices: 294802--294874 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 27
294792 CAAGAAATGG
*
294802 TTGTCAAGAAATTATCATCAAAAACTT
1 TTGTCAAGAAATTTTCATCAAAAACTT
* * *
294829 TTGACAAG-AATGCTT-GTCAAAAAC-T
1 TTGTCAAGAAAT-TTTCATCAAAAACTT
294854 TTGTCAAGAAATTTTCATCAA
1 TTGTCAAGAAATTTTCATCAA
294875 TACGACCCTT
Statistics
Matches: 36, Mismatches: 7, Indels: 7
0.72 0.14 0.14
Matches are distributed among these distances:
25 10 0.28
26 18 0.50
27 8 0.22
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (27 bp):
TTGTCAAGAAATTTTCATCAAAAACTT
Found at i:294959 original size:28 final size:28
Alignment explanation
Indices: 294884--295431 Score: 638
Period size: 28 Copynumber: 19.4 Consensus size: 28
294874 ATACGACCCT
294884 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
294912 TTCTCAAAGCCCATAAGTCAGTGGCATCC
1 TT-TCAAAGCCCACAAGTCAGTGGCATCC
* *
294941 TTTCAAAGCCCACATGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
294969 TTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
294997 TTTCAAAGCCTACATGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
295025 TTTTAAAGTCCACATGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
295053 TTTCAAAGCCCATATGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
295081 TTTCAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
295109 TTTCAAAGCCTC-CATGTCAGTGGCATTC
1 TTTCAAAGCC-CACAAGTCAGTGGCATCC
*
295137 TTTCAAAGCCCACATGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
295165 TCTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * * *
295193 TTTCAAAGCCCATAAGTTAGGGGCACCCC
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
** *
295222 TTT--AAGCCCACACAAGTTGGTGGCAACC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCC
* *
295250 TCTCTCAAAGCCCACAAGTTAGTGGCACCC
1 T-T-TCAAAGCCCACAAGTCAGTGGCATCC
* *
295280 TTTCAAAGCCCACAAGTCAGCGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
295308 TTTCAAAGCCCATAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
295336 TTTCGAAGCCCACAAGTTAGTGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
295363 TTTTCAAAGCCCACAAGTTAATGGCA-CC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
295391 TTTTCAAAGCCTACAAGTTAGTGGCACCC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCC
295420 TTTCAAAGCCCA
1 TTTCAAAGCCCA
295432 TATAAGTTGG
Statistics
Matches: 458, Mismatches: 50, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
27 6 0.01
28 380 0.83
29 49 0.11
30 18 0.04
31 2 0.00
32 3 0.01
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:294995 original size:56 final size:56
Alignment explanation
Indices: 294884--295525 Score: 648
Period size: 56 Copynumber: 11.2 Consensus size: 56
294874 ATACGACCCT
* *
294884 TTTCAAAGCCCACAAGTCAGTGGCATCCTTCTCAAAGCCCATAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTT-TCAAAGCCCACAAGTTAGTGGCATCC
* * *
294941 TTTCAAAGCCCACATGTCAATGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
* * * * * *
294997 TTTCAAAGCCTACATGTCAATGGCATCCTTTTAAAGTCCACATGTTAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
* * * *
295053 TTTCAAAGCCCATATGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
* * * *
295109 TTTCAAAGCCTC-CATGTCAGTGGCATTCTTTCAAAGCCCACATGTCAGTGGCATCC
1 TTTCAAAGCC-CACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
* * * *
295165 TCTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCATAAGTTAGGGGCACCCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-TCC
** * *
295222 TTT--AAGCCCACACAAGTTGGTGGCAACCTCTCTCAAAGCCCACAAGTTAGTGGCACCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCCT-T-TCAAAGCCCACAAGTTAGTGGCATCC
* * * *
295280 TTTCAAAGCCCACAAGTCAGCGGCACCCTTTCAAAGCCCATAAGTTAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
* * *
295336 TTTCGAAGCCCACAAGTTAGTGGCA-CCTTTTCAAAGCCCACAAGTTAATGGCA-CC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTTAGTGGCATCC
* * * * * *
295391 TTTTCAAAGCCTACAAGTTAGTGGCACCCTTTCAAAGCCCATATAAGTTGGTGGCAACC
1 -TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCC--ACAAGTTAGTGGCATCC
* * * * *
295450 TTCTCTAAAGCCTACACAGGTC-GATGGCAACCCTTTTAAAGCCCACACAAGTTGGTGGCAACC
1 TT-TC-AAAGCC--CACAAGTCAG-TGGC-ATCCTTTCAAAG-CC-CACAAGTTAGTGGCATCC
295513 TTCTCTAAAGCCC
1 TT-TC-AAAGCCC
295526 GCACAAGTTG
Statistics
Matches: 508, Mismatches: 54, Indels: 42
0.84 0.09 0.07
Matches are distributed among these distances:
55 8 0.02
56 324 0.64
57 52 0.10
58 35 0.07
59 27 0.05
60 9 0.02
61 2 0.00
62 9 0.02
63 39 0.08
64 2 0.00
65 1 0.00
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (56 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCC
Found at i:295498 original size:31 final size:32
Alignment explanation
Indices: 295412--295533 Score: 117
Period size: 32 Copynumber: 3.9 Consensus size: 32
295402 TACAAGTTAG
* * * * *
295412 TGGCACCCTT-TC-AAAGCCCATATAAGTTGG
1 TGGCAACCTTCTCTAAAGCCCACACAAGTCGA
* *
295442 TGGCAACCTTCTCTAAAGCCTACACAGGTCGA
1 TGGCAACCTTCTCTAAAGCCCACACAAGTCGA
* *
295474 TGGCAACCCTT-T-TAAAGCCCACACAAGTTGG
1 TGGCAA-CCTTCTCTAAAGCCCACACAAGTCGA
*
295505 TGGCAACCTTCTCTAAAGCCCGCACAAGT
1 TGGCAACCTTCTCTAAAGCCCACACAAGT
295534 TGGTGCCAAC
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
30 13 0.17
31 24 0.32
32 34 0.45
33 4 0.05
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (32 bp):
TGGCAACCTTCTCTAAAGCCCACACAAGTCGA
Found at i:298211 original size:34 final size:34
Alignment explanation
Indices: 298168--298235 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
298158 GAAACATGGC
298168 ATTTTGGTCACACATATGACATCAAGTCATCAAA
1 ATTTTGGTCACACATATGACATCAAGTCATCAAA
298202 ATTTTGGTCACACATATGACATCAAGTCATCAAA
1 ATTTTGGTCACACATATGACATCAAGTCATCAAA
298236 GCAAACTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (34 bp):
ATTTTGGTCACACATATGACATCAAGTCATCAAA
Found at i:299088 original size:20 final size:20
Alignment explanation
Indices: 299063--299179 Score: 117
Period size: 20 Copynumber: 5.8 Consensus size: 20
299053 ACATCTGGGT
299063 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
299083 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*** *
299103 TCCATTTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
299123 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
*** * *
299143 TCCATTTATCAATACATTGA
1 AGAATGTATCGATACATTGA
* *
299163 AAAATGTATTGATACAT
1 AGAATGTATCGATACAT
299180 CTGGGTAAAA
Statistics
Matches: 74, Mismatches: 23, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:299124 original size:40 final size:40
Alignment explanation
Indices: 299069--299179 Score: 195
Period size: 40 Copynumber: 2.8 Consensus size: 40
299059 GGGTAGAATG
299069 TATCGATACATTGAAGAATGTATCGATACATTCATCCATT
1 TATCGATACATTGAAGAATGTATCGATACATTCATCCATT
299109 TATCGATACATTGAAGAATGTATCGATACATTCATCCATT
1 TATCGATACATTGAAGAATGTATCGATACATTCATCCATT
* * *
299149 TATCAATACATTGAAAAATGTATTGATACAT
1 TATCGATACATTGAAGAATGTATCGATACAT
299180 CTGGGTAAAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 68 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (40 bp):
TATCGATACATTGAAGAATGTATCGATACATTCATCCATT
Found at i:299975 original size:33 final size:32
Alignment explanation
Indices: 299930--300000 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
299920 CCAGCGACAT
*
299930 TGGG-TTTAGA-AAGGTTGCCACCAACTTCTG
1 TGGGATTTAGAGAAAGTTGCCACCAACTTCTG
* * * *
299960 TGGGCTTTAGAGAAAGTTGCCATCGACTTGTG
1 TGGGATTTAGAGAAAGTTGCCACCAACTTCTG
299992 TGGGATTTA
1 TGGGATTTA
300001 AAAGGATGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 4 0.12
31 6 0.18
32 24 0.71
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (32 bp):
TGGGATTTAGAGAAAGTTGCCACCAACTTCTG
Found at i:300440 original size:172 final size:170
Alignment explanation
Indices: 299990--300759 Score: 904
Period size: 172 Copynumber: 4.6 Consensus size: 170
299980 CATCGACTTG
* * * * * **
299990 TGTGGGATTTAAAAGGATGCCACTGACTTGTGGGTTTTGAGAAGGTGCCT-CTGACTTGTGGGCT
1 TGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGTTACTACTGACTTGTGGGCT
* * * * ** * *
300054 TTGAAGA-GATGCCACTGACTTGT-GGACTTTGAAAGGATGCCACTGACTCATGGGCTTTG-GAA
66 TTGAAAAGGGTGCCATTGACTTGTAGG-CTTTGAAAGGGTGCCACTGACTTGTGGGCTATGAAAA
** * * * *
300116 GGATGCCACTGACTCATG-GCTTTGGAAGGATGCCACTGACT
130 GG-TGCCACTGACTTGTGAGCTATGAAAAGATGTCACTGACT
* * *
300157 TGTGGGGTTTGAAAA-GGTGCCACTAACTTATGGGCTTTGAAAAGG-TGCTACTGACTTGTGGGC
1 TGTGGGCTTT-AAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGTTACTACTGACTTGTGGGC
* * *
300220 TTTGAAAA-GGTGCCACTGACTTGTGGGCTATGCAAA-GGTGCCACTGACTTGTGGGCTATGAAA
65 TTTGAAAAGGGTGCCATTGACTTGTAGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTATGAAA
*
300283 AGGTGCCACTGACTTGTGAGCTATGAAAAGATGTCATTGACT
129 AGGTGCCACTGACTTGTGAGCTATGAAAAGATGTCACTGACT
*
300325 TGTGGGCTTTATAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTACTACT-AGCTTATGG
1 TGTGGGCTTTA-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAG-GTTACTACTGA-CTTGTGG
300389 GCTTTGAAAAGGGTGCCATTGACTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTATGAA
63 GCTTTGAAAAGGGTGCCATTGACTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTATGAA
*
300454 AAGGTGCCACTGACTTGTGAGCTATGAAAAGGTGTCACTGACT
128 AAGGTGCCACTGACTTGTGAGCTATGAAAAGATGTCACTGACT
*
300497 TGTGGGCTTTATAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGAGTTACTACT-AGCTTATGG
1 TGTGGGCTTTA-AAAGGGTGCCACTAACTTGTGGGCTTTGAAAAG-GTTACTACTGA-CTTGTGG
* * *
300561 GCTTTGAAAAGGGTGCCATTGACTCGTAGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTGAA
63 GCTTTGAAAAGGGTGCCATTGACTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTATGAA
* * * * * *
300626 ACGAT--TACTGACTTGTGGGCTTTGAAAGGATGTCACTGACT
128 AAGGTGCCACTGACTTGTGAGCTATGAAAAGATGTCACTGACT
* * * * * *
300667 TGTGGGCTTTGAAAGGGTACCACTGACTTGTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCT
1 TGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGTTACTACTGACTTGTGGGCT
* * *
300731 TTG-AAAGGATGCCATTGATTTGTGGGCTT
66 TTGAAAAGGGTGCCATTGACTTGTAGGCTT
300760 GGAAGAGATG
Statistics
Matches: 536, Mismatches: 53, Indels: 29
0.87 0.09 0.05
Matches are distributed among these distances:
166 24 0.04
167 125 0.23
168 48 0.09
169 54 0.10
170 43 0.08
171 25 0.05
172 217 0.40
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (170 bp):
TGTGGGCTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGAAAAGGTTACTACTGACTTGTGGGCT
TTGAAAAGGGTGCCATTGACTTGTAGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTATGAAAAG
GTGCCACTGACTTGTGAGCTATGAAAAGATGTCACTGACT
Found at i:300769 original size:28 final size:28
Alignment explanation
Indices: 299990--300759 Score: 758
Period size: 28 Copynumber: 27.3 Consensus size: 28
299980 CATCGACTTG
* *
299990 TGTGGGATTTAAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
300018 TGTGGGTTTTGAGAAGG-TGCCTCTGACT
1 TGTGGGCTTTGA-AAGGATGCCACTGACT
300046 TGTGGGCTTTG-AAGAGATGCCACTGACT
1 TGTGGGCTTTGAAAG-GATGCCACTGACT
*
300074 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** *
300102 CATGGGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
** *
300130 CAT-GGCTTTGGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
300157 TGTGGGGTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
300185 TATGGGCTTTGAAAAGG-TGCTACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
300213 TGTGGGCTTTGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
300241 TGTGGGCTATGCAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
300269 TGTGGGCTATGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * * * *
300297 TGTGAGCTATGAAAAGATGTCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
300325 TGTGGGCTTTATAAAGGGTGCCACTAACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* * *
300354 TGTGGGCTTTGAAAAGAGTTACTACT-AGCT
1 TGTGGGCTTTG-AAAG-GATGCCACTGA-CT
* * *
300384 TATGGGCTTTGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
300413 TGTAGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
300441 TGTGGGCTATGAAAAGG-TGCCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
300469 TGTGAGCTATGAAAAGG-TGTCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * *
300497 TGTGGGCTTTATAAAGGGTGCCACTAACT
1 TGTGGGCTTT-GAAAGGATGCCACTGACT
* * *
300526 TGTGGGCTTTGAAAAGAGTTACTACT-AGCT
1 TGTGGGCTTTG-AAAG-GATGCCACTGA-CT
* * *
300556 TATGGGCTTTGAAAAGGGTGCCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* * * *
300585 CGTAGGCTTTGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
300613 TGTGGGCTTTGAAACGAT--TACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
300639 TGTGGGCTTTGAAAGGATGTCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
300667 TGTGGGCTTTGAAAGGGTACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
300695 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
300723 TGTGGGCTTTGAAAGGATGCCATTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
300751 TGTGGGCTT
1 TGTGGGCTT
300760 GGAAGAGATG
Statistics
Matches: 636, Mismatches: 85, Indels: 42
0.83 0.11 0.06
Matches are distributed among these distances:
26 27 0.04
27 30 0.05
28 433 0.68
29 98 0.15
30 48 0.08
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:302035 original size:12 final size:11
Alignment explanation
Indices: 302011--302090 Score: 69
Period size: 11 Copynumber: 7.5 Consensus size: 11
302001 TCTGAACCCC
*
302011 TTTTTTGTTTT
1 TTTTTTGTGTT
302022 TTTGTTTGTGTT
1 TTT-TTTGTGTT
302034 TTTTTT-TG-T
1 TTTTTTGTGTT
*
302043 TTTTTTATGTT
1 TTTTTTGTGTT
*
302054 TTTTTGGTGTT
1 TTTTTTGTGTT
*
302065 TTTTTCT-TGGT
1 TTTTT-TGTGTT
*
302076 TTTTTTCT-TT
1 TTTTTTGTGTT
302086 TTTTT
1 TTTTT
302091 GGTACGAAGG
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.12
10 11 0.19
11 30 0.52
12 10 0.17
ACGTcount: A:0.01, C:0.03, G:0.14, T:0.82
Consensus pattern (11 bp):
TTTTTTGTGTT
Found at i:302046 original size:31 final size:32
Alignment explanation
Indices: 302012--302093 Score: 98
Period size: 30 Copynumber: 2.6 Consensus size: 32
302002 CTGAACCCCT
*
302012 TTTTTGTTTTTTTGTTT-GTGTTTTTTT-TT-G
1 TTTTT-TTTTTTTTTTTGGTGTTTTTTTCTTGG
*
302042 TTTTTTTATGTTTTTTTGGTGTTTTTTTCTTGG
1 TTTTTTT-TTTTTTTTTGGTGTTTTTTTCTTGG
*
302075 TTTTTTTCTTTTTTTTGGT
1 TTTTTTTTTTTTTTTTGGT
302094 ACGAAGGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 2 0.05
30 12 0.27
31 10 0.23
32 12 0.27
33 8 0.18
ACGTcount: A:0.01, C:0.02, G:0.16, T:0.80
Consensus pattern (32 bp):
TTTTTTTTTTTTTTTTGGTGTTTTTTTCTTGG
Found at i:302090 original size:32 final size:29
Alignment explanation
Indices: 302011--302093 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 29
302001 TCTGAACCCC
*
302011 TTTTTTGTTTTTTTGTTTGTGTTTTTTTTTG
1 TTTTTT-TTTTTTT-TTGGTGTTTTTTTTTG
302042 TTTTTTTATGTTTTTTTGGTGTTTTTTTCTTGG
1 TTTTTTT-T-TTTTTTTGGTGTTTTTTT-TT-G
302075 TTTTTTTCTTTTTTTTGGT
1 TTTTTTT-TTTTTTTTGGT
302094 ACGAAGGAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
30 1 0.02
31 19 0.41
32 17 0.37
33 9 0.20
ACGTcount: A:0.01, C:0.02, G:0.16, T:0.81
Consensus pattern (29 bp):
TTTTTTTTTTTTTTTGGTGTTTTTTTTTG
Found at i:302090 original size:33 final size:31
Alignment explanation
Indices: 302011--302090 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 31
302001 TCTGAACCCC
* *
302011 TTTTTTGTTTTTTTGTTTGTGTTTTTTTTTGT
1 TTTTTTATTTTTTT-TTGGTGTTTTTTTTTGT
*
302043 TTTTTTATGTTTTTTTGGTGTTTTTTTCTTGGT
1 TTTTTTATTTTTTTTTGGTGTTTTTTT-TT-GT
*
302076 TTTTTTCTTTTTTTT
1 TTTTTTATTTTTTTT
302091 GGTACGAAGG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
31 12 0.29
32 14 0.34
33 15 0.37
ACGTcount: A:0.01, C:0.03, G:0.14, T:0.82
Consensus pattern (31 bp):
TTTTTTATTTTTTTTTGGTGTTTTTTTTTGT
Found at i:305196 original size:43 final size:43
Alignment explanation
Indices: 305148--305231 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
305138 TTTTAACTAG
* * *
305148 ATGTATCAATACATTGAACAATGTATCGATACATCTAGGTAGA
1 ATGTATCAATACATTCAACAATGTATCAATAAATCTAGGTAGA
* * *
305191 ATGTATCGATACATTCATCCATGTATCAATAAATCTAGGTA
1 ATGTATCAATACATTCAACAATGTATCAATAAATCTAGGTA
305232 AAAAAACAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (43 bp):
ATGTATCAATACATTCAACAATGTATCAATAAATCTAGGTAGA
Found at i:311835 original size:13 final size:13
Alignment explanation
Indices: 311817--311847 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
311807 ACAATTCATC
311817 ATGTATCGATACA
1 ATGTATCGATACA
311830 ATGTATCGATACA
1 ATGTATCGATACA
*
311843 TTGTA
1 ATGTA
311848 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:311835 original size:33 final size:33
Alignment explanation
Indices: 311797--311863 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
311787 GTTACAAGCT
*
311797 ATGTATCGATACAATT-CATCATGTATCGATACA
1 ATGTATCGATAC-ATTGCACCATGTATCGATACA
*
311830 ATGTATCGATACATTGTACCATGTATCGATACA
1 ATGTATCGATACATTGCACCATGTATCGATACA
311863 A
1 A
311864 ACAGTGGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 28 0.90
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACATTGCACCATGTATCGATACA
Found at i:311936 original size:19 final size:20
Alignment explanation
Indices: 311892--311943 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
311882 CTGCCAATCT
**
311892 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
311912 CATGTATCGATACAATT-AA
1 CATGTATCGATACAATTGAA
311931 CATGTATCGATAC
1 CATGTATCGATAC
311944 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:313618 original size:51 final size:51
Alignment explanation
Indices: 313562--313678 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
313552 GAAAATAATT
*
313562 GGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAGGCCG
1 GGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAAGCCG
* * * * *
313613 GGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAAAGCCT
1 GGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAAGCCG
313664 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
313679 CTCGGAAATA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (51 bp):
GGGTTGGAGTATCCCTAATTATGAGAAATCAATATTTTAGAAATAAAGCCG
Found at i:313674 original size:130 final size:127
Alignment explanation
Indices: 313372--313707 Score: 334
Period size: 130 Copynumber: 2.6 Consensus size: 127
313362 ACATCTCCCG
* *
313372 ATGAGAAATTTAATATTTTGGAGATAATAACGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTT
1 ATGAGAAA--TAATATTTTGGAAATAA-AACTGGGTTGGAGTATCCCC-TGAAAATAACGGGGTT
* * * *
313437 GGAGTAACCCCGATTGTGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTGAAGTGTCCCCGAT
62 GGAGTATCCCCAATTATGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTGAAGTATCCCCGAT
313502 T
127 T
* *** * * * **
313503 AT-AGAAAATAGATGTTTCAAAAATAAAATTAGGATTTGAGTATCCCCGTGAAAATAATTGGGTT
1 ATGAG-AAATA-ATATTTTGGAAATAAAACT-GGGTTGGAGTATCCCC-TGAAAATAACGGGGTT
* * ** *
313567 GGAGTATCCCTAATTATGAGAAATCAAT-ATTTTAGAAATAAGGCCGGGGTTGAAGTATCCCTGA
62 GGAGTATCCCCAATTATGAAAAATCAATGA-TTTAGAAATAAGGCAAGGGTTGAAGTATCCCCGA
313631 TT
126 TT
* * * *
313633 GTGAGAAATCAATATTTTGGAAATAAAGCCTGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTA
1 ATGAGAAAT-AATATTTTGGAAATAAA-ACTGGGTTGGAGTATCCCCT-GAAAATAACGGGGTTG
313698 GAGTATCCCC
63 GAGTATCCCC
313708 GATGAAATAA
Statistics
Matches: 162, Mismatches: 35, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
129 6 0.04
130 147 0.91
131 9 0.06
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (127 bp):
ATGAGAAATAATATTTTGGAAATAAAACTGGGTTGGAGTATCCCCTGAAAATAACGGGGTTGGAG
TATCCCCAATTATGAAAAATCAATGATTTAGAAATAAGGCAAGGGTTGAAGTATCCCCGATT
Found at i:313701 original size:28 final size:28
Alignment explanation
Indices: 313664--313733 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
313654 AATAAAGCCT
**
313664 GGGTTGGAGTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
* *
313692 GGGTTAGAGTATCCCCGATGAAATAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
*
313720 AGGTTGGAGTATCC
1 GGGTTGGAGTATCC
313734 TCCATTGTGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGGAAATAACG
Found at i:313863 original size:79 final size:79
Alignment explanation
Indices: 313773--314071 Score: 390
Period size: 79 Copynumber: 3.8 Consensus size: 79
313763 TAAAATCGGA
* * * * *
313773 GTTGGAATATCCCCGATTATGGAGAATT-AGTGTTTCAGAAATAAAACCGGGGTTTGAGTATCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGA-TGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
313837 CTCGAAAATAACGGG
65 CTCGAAAATAACGGG
* *
313852 GTTGGAGTATCCCCAATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGCTGGAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
*
313917 TCGAAAATAACGAG
66 TCGAAAATAACGGG
* *
313931 GTTAGAGTATCCCCGA-TA--AAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
313993 TCGAAAATAACGGG
66 TCGAAAATAACGGG
* * * * * * * * *
314007 GTTGGAGTATCCCCGATTGTGAAAAGTCGGTGTTTTGGAAATAAAATCGGAGTAGAAGTATCCCC
1 GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
314072 GATTATGGAA
Statistics
Matches: 192, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
76 70 0.36
77 1 0.01
78 2 0.01
79 118 0.61
80 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (79 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCC
TCGAAAATAACGGG
Found at i:313914 original size:288 final size:286
Alignment explanation
Indices: 313397--313915 Score: 663
Period size: 288 Copynumber: 1.8 Consensus size: 286
313387 TTTTGGAGAT
* * *
313397 AATAACGGGGTTGGAGTATCCCCTTGAAAATAACGGGGTTGGAGTAACCCCGATTGTGAAAAATC
1 AATAACGGGGTTAGAGTATCCCCATGAAAATAACGAGGTTGGAGTAACCCCGATTGTGAAAAATC
*
313462 AATGATTTAGAAATAAGGCAAGGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCAAAAAT
66 AATGATTTAGAAATAA-G-AAGGGTTGAAGTATCCCCGATTATAGAAAATAGATGTTTCAAAAAT
** ** * *
313527 AAAATTAGGATTTGAGTATCCCCGTGAAAATAATTGGGTTGGAGTATCCCTAATTATGAGAAATC
129 AAAACCAGGATTTGAGTATCCCCGTGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATC
** *
313592 AATATTTTAGAAATAAGGCCGGGGTTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAAT
194 AATATTTTAGAAATAAAACCGGGGCTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAAT
313657 AAAGCCTGGGTTGGAGTATCCCCTCGGA
259 AAAGCCTGGGTTGGAGTATCCCCTCGGA
*
313685 AATAACGGGGTTAGAGTATCCCCGATG-AAATAACGAGGTTGGAGTATCCTCC-ATTGTGAAAAA
1 AATAACGGGGTTAGAGTATCCCC-ATGAAAATAACGAGGTTGGAGTAACC-CCGATTGTGAAAAA
* * * * * *
313748 TTAGTGTTTTGGAAATAA-AATCGGAGTTGGAA-TATCCCCGATTATGGAGAATTAG-TGTTTCA
64 TCAATGATTTAGAAATAAGAA--GG-GTT-GAAGTATCCCCGATTATAGA-AAATAGATGTTTCA
* * *
313810 GAAATAAAACCGGGGTTTGAGTATCCCC-TCGAAAATAACGGGGTTGGAGTATCCCCAATTATGA
124 AAAATAAAACCAGGATTTGAGTATCCCCGT-GAAAATAACGGGGTTGGAGTATCCCCAATTATGA
** * *
313874 AAAATTGATGTTTTAGAAATAAAACCGGGGCTGGAGTATCCC
188 AAAATCAATATTTTAGAAATAAAACCGGGGCTGAAGTATCCC
313916 CTCGAAAATA
Statistics
Matches: 196, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
285 2 0.01
287 3 0.02
288 179 0.91
289 12 0.06
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (286 bp):
AATAACGGGGTTAGAGTATCCCCATGAAAATAACGAGGTTGGAGTAACCCCGATTGTGAAAAATC
AATGATTTAGAAATAAGAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATGTTTCAAAAATAA
AACCAGGATTTGAGTATCCCCGTGAAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAA
TATTTTAGAAATAAAACCGGGGCTGAAGTATCCCTGATTGTGAGAAATCAATATTTTGGAAATAA
AGCCTGGGTTGGAGTATCCCCTCGGA
Found at i:313985 original size:76 final size:77
Alignment explanation
Indices: 313803--314023 Score: 354
Period size: 76 Copynumber: 2.9 Consensus size: 77
313793 GGAGAATTAG
* * *
313803 TGTTTCAGAAATAAAACCGGGGTTTGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAA
1 TGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
313868 TTATGAAAAATTGA
66 -TA-GAAAAATTGA
* * *
313882 TGTTTTAGAAATAAAACCGGGGCTGGAGTATCCCCTCGAAAATAACGAGGTTAGAGTATCCCCGA
1 TGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
313947 TA-AAAAATTGA
66 TAGAAAAATTGA
*
313958 TGTTTTAGAAATAAAACCGGGGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
1 TGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
314023 T
66 T
314024 TGTGAAAAGT
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
76 71 0.54
78 2 0.02
79 59 0.45
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (77 bp):
TGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA
TAGAAAAATTGA
Found at i:314165 original size:51 final size:51
Alignment explanation
Indices: 314007--314175 Score: 209
Period size: 51 Copynumber: 3.3 Consensus size: 51
313997 AAATAACGGG
*
314007 GTTGGAGTATCCCCGATT-GTGAAAAGTCGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAG-GAAAAATCGGTGTTTTGGAAATAAAATCGGA
* * * *
314058 GTAGAAGTATCCCCGATTATGG-AAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTA-GGAAAAATCGGTGTTTTGGAAATAAAATCGGA
* * * *
314109 GTTGGAGTATCCCCGATTAGGAAAAATTGATGTTTTGGAAATGAAACTGGGA
1 GTTGGAGTATCCCCGATTAGGAAAAATCGGTGTTTTGGAAAT-AAAATCGGA
314161 -TTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
314176 AATGAAAAAT
Statistics
Matches: 102, Mismatches: 12, Indels: 8
0.84 0.10 0.07
Matches are distributed among these distances:
50 2 0.02
51 91 0.89
52 8 0.08
53 1 0.01
ACGTcount: A:0.32, C:0.12, G:0.28, T:0.28
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTAGGAAAAATCGGTGTTTTGGAAATAAAATCGGA
Found at i:316493 original size:13 final size:13
Alignment explanation
Indices: 316475--316509 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
316465 TGTAAAAATA
316475 TATCGATACAATG
1 TATCGATACAATG
316488 TATCGATACAATG
1 TATCGATACAATG
316501 TATCGATAC
1 TATCGATAC
316510 GAGGATCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:317014 original size:21 final size:21
Alignment explanation
Indices: 316988--317032 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
316978 AAAAATTTTC
316988 CCCCTTAATT-AAAGCAATTCT
1 CCCCTT-ATTGAAAGCAATTCT
*
317009 CCCCTTTTTGAAAGCAATTCT
1 CCCCTTATTGAAAGCAATTCT
317030 CCC
1 CCC
317033 ATTTTTGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (21 bp):
CCCCTTATTGAAAGCAATTCT
Found at i:317037 original size:21 final size:21
Alignment explanation
Indices: 316998--317039 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
316988 CCCCTTAATT
*
316998 AAAGCAATTCTCCCCTTTTTG
1 AAAGCAATTCTCCCATTTTTG
317019 AAAGCAATTCTCCCATTTTTG
1 AAAGCAATTCTCCCATTTTTG
317040 TAAAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAGCAATTCTCCCATTTTTG
Found at i:318342 original size:41 final size:40
Alignment explanation
Indices: 318231--318344 Score: 124
Period size: 41 Copynumber: 2.8 Consensus size: 40
318221 AATGGAAGGG
* * * *
318231 GTGTCCCACTTTTTGAGGACAAAGG-AAAAGAGAATGAAA
1 GTGTCCTACTTCTTGAGGACAAAGGAAAAAGAAAAGGAAA
* *
318270 -TAGGTCTTACTCCTTGAGGACAAAGGAAAAAAGAAAAGGAAA
1 GT--GTCCTACTTCTTGAGGACAAAGG-AAAAAGAAAAGGAAA
318312 GTGTCCTACTTCTTGAGGACAAAGTGAAAAAGA
1 GTGTCCTACTTCTTGAGGACAAAG-GAAAAAGA
318345 GTACATCCTG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
38 1 0.02
40 19 0.31
41 27 0.44
42 13 0.21
43 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (40 bp):
GTGTCCTACTTCTTGAGGACAAAGGAAAAAGAAAAGGAAA
Found at i:318441 original size:42 final size:43
Alignment explanation
Indices: 318387--318546 Score: 182
Period size: 42 Copynumber: 3.7 Consensus size: 43
318377 AAGAAAAACG
*
318387 AAATGTGTCCTGCTCTTTGAGGAC-AAAAGAAAGAGGAAAATA
1 AAATGCGTCCTGCTCTTTGAGGACAAAAAGAAAGAGGAAAATA
* *
318429 AAATGCGTCCTGCTCTTTGAGGACAAAAGAGAAAAGAAGG-GAATG
1 AAATGCGTCCTGCTCTTTGAGGACAAAA-AG-AAAG-AGGAAAATA
** * *
318474 AAGGGTGTCCTGCTCTTTGAGGAC-AAAAGAAAAAGGAAAATA
1 AAATGCGTCCTGCTCTTTGAGGACAAAAAGAAAGAGGAAAATA
* *
318516 AAGTGCATCCTGCTCTTTGAGGACTAAAAAG
1 AAATGCGTCCTGCTCTTTGAGGAC-AAAAAG
318547 TGCCACCAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.03
42 50 0.51
43 5 0.05
44 10 0.10
45 28 0.28
46 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (43 bp):
AAATGCGTCCTGCTCTTTGAGGACAAAAAGAAAGAGGAAAATA
Found at i:318672 original size:121 final size:122
Alignment explanation
Indices: 318520--318781 Score: 353
Period size: 121 Copynumber: 2.2 Consensus size: 122
318510 AAAATAAAGT
318520 GCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGGAAAAAG-T
1 GCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTG-AAAGGAAAAAGAT
* * * *
318584 CCTATTTTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA
65 CCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTGCAAAGAGAAA
* * * *
318641 GCATCTTGCTCTTTTAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGAAAAGGCA
1 GCATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAAG-A
*
318705 TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTT--AAA-AG---
64 TCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTGCAAAGAGAAA
318758 GCATCCTGCTCTTTGAGGACTAAA
1 GCATCCTGCTCTTTGAGGACTAAA
318782 GGGTGAAAGG
Statistics
Matches: 126, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
116 2 0.02
117 20 0.16
120 12 0.10
121 46 0.37
122 19 0.15
123 27 0.21
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (122 bp):
GCATCCTGCTCTTTGAGGACTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGAAAAAGATC
CTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTGCAAAGAGAAA
Found at i:318677 original size:61 final size:61
Alignment explanation
Indices: 318520--318779 Score: 317
Period size: 61 Copynumber: 4.4 Consensus size: 61
318510 AAAATAAAGT
*
318520 GCATCCTGCTCTTTGAGGACTA-AAAAGTGCCACCAACTCGTGTGGGCTTTGAAA-AGGAAA
1 GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGA-GAAA
* ** * *
318580 -AAGTCCTATTTTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGCAAAGAGAAA
1 GCA-TCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTG-AAAGAGAAA
* *
318641 GCATCTTGCTCTTTTAGGACTAGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAG-GAAAA
1 GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAG-AAA
*
318701 GGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTT-AAA-AG---
1 -GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAA
318758 GCATCCTGCTCTTTGAGGACTA
1 GCATCCTGCTCTTTGAGGACTA
318780 AAGGGTGAAA
Statistics
Matches: 174, Mismatches: 16, Indels: 24
0.81 0.07 0.11
Matches are distributed among these distances:
56 22 0.13
59 2 0.01
60 49 0.28
61 73 0.42
62 28 0.16
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (61 bp):
GCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGAGAAA
Found at i:318729 original size:28 final size:28
Alignment explanation
Indices: 318696--318779 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 28
318686 GCTTTGAAAG
318696 GAAAAGGCATCCTGCTCTTTGAGGACTA
1 GAAAAGGCATCCTGCTCTTTGAGGACTA
** * * * *
318724 GAAAAGTGCCA-CCAACT-TATGTGGGCTT
1 GAAAAG-G-CATCCTGCTCTTTGAGGACTA
*
318752 TAAAAGGCATCCTGCTCTTTGAGGACTA
1 GAAAAGGCATCCTGCTCTTTGAGGACTA
318780 AAGGGTGAAA
Statistics
Matches: 39, Mismatches: 13, Indels: 8
0.65 0.22 0.13
Matches are distributed among these distances:
26 2 0.05
27 5 0.13
28 25 0.64
29 5 0.13
30 2 0.05
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (28 bp):
GAAAAGGCATCCTGCTCTTTGAGGACTA
Found at i:318852 original size:94 final size:98
Alignment explanation
Indices: 318690--318881 Score: 268
Period size: 95 Copynumber: 2.0 Consensus size: 98
318680 GTGTGGGCTT
*
318690 TGAAAGGAAAAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTT-A
1 TGAAAGGAAAAGGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAA
318754 AA-AG-GCATCCTGCTCTTTGAGGACTAAAGGG
66 AAGAGAGCATCCTGCTCTTTGAGGACTAAAGGG
* ** *
318785 TGAAAGGAGAAA-GCGTCCTACTCTTTGAGGACT-GGGAAGTGCCACCAACTTGTGTGGGCTTTA
1 TGAAAGGA-AAAGGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTA
318848 AAAGGAGAAAGCATCCTGCTCTTTGAGGACTAAA
65 AAA-GAG--AGCATCCTGCTCTTTGAGGACTAAA
318882 AAAATGCCAC
Statistics
Matches: 85, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
94 26 0.31
95 30 0.35
96 3 0.04
97 2 0.02
100 24 0.28
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (98 bp):
TGAAAGGAAAAGGCATCCTACTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAA
AAGAGAGCATCCTGCTCTTTGAGGACTAAAGGG
Found at i:318995 original size:155 final size:154
Alignment explanation
Indices: 318635--319088 Score: 651
Period size: 155 Copynumber: 2.9 Consensus size: 154
318625 GCTTTGCAAA
* * * * * *
318635 GAGAAAGCATCTTGCTCTTTTAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGA-A
1 GAGAAAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGA
* * *
318699 AAGGCATCCTGCTCTTTGAGGACTAGAAAAGTGCCACCAACTTATGTGGGCTTTAAAAGGCATCC
66 AA-GCATCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT--AAGGCGTCC
* *
318764 TGCTCTTTGAGGACTAAAGGGTGAAAG
128 TGCTCTTTGAGGACTAAAAGGCGAAAG
* *
318791 GAGAAAGCGTCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGA
1 GAGAAAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGA
* *
318856 AAGCATCCTGCTCTTTGAGGACTAAAAAAATGCCACCAACTTGCGTGGGCTTTGAAGGCGTCCTG
66 AAGCATCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTT-AAGGCGTCCTG
318921 CTCTTTGAGGACTAAAAGGCGAAAG
130 CTCTTTGAGGACTAAAAGGCGAAAG
* *
318946 GAGAGAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCTCCAACTTGTGTGGGCTTTAAAAGGAGA
1 GAGAAAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGA
* * * *
319011 AAGCATCCTGCTCTTTGAGGACT-GAAAAATGCCACCAGCTAGTGTGGGCTTTAAGACGTGTCTT
66 AAGCATCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAG--GCGTCCT
319075 GCTCTTTGAGGACT
129 GCTCTTTGAGGACT
319089 GGAAAATGCC
Statistics
Matches: 269, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
153 3 0.01
154 25 0.09
155 136 0.51
156 102 0.38
157 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (154 bp):
GAGAAAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGA
AAGCATCCTGCTCTTTGAGGACTAGAAAAATGCCACCAACTTGTGTGGGCTTTAAGGCGTCCTGC
TCTTTGAGGACTAAAAGGCGAAAG
Found at i:319021 original size:61 final size:60
Alignment explanation
Indices: 318942--319154 Score: 224
Period size: 61 Copynumber: 3.6 Consensus size: 60
318932 CTAAAAGGCG
* * *
318942 AAAGGAGAGAGCGTCCTGCTCTTTGAGGACTAGGAAGTGCCTCCAACTTGTGTGGGCTTTA
1 AAAGGAGAAAGCGTCCTGCTCTTTGAGGACT-GGAAATGCCACCAACTTGTGTGGGCTTTA
* * * *
319003 AAAGGAGAAAGCATCCTGCTCTTTGAGGACTGAAAAATGCCACCAGCTAGTGTGGGCTTT-
1 AAAGGAGAAAGCGTCCTGCTCTTTGAGGACTG-GAAATGCCACCAACTTGTGTGGGCTTTA
* * *
319063 --A--AG-ACGTGTCTTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTA
1 AAAGGAGAAAGCGTCCTGCTCTTTGAGGACTGG-AAATGCCACCAACTTGTGTGGGCTTTA
* * *
319119 AATGGA-AAAGGCGTCCTGCTTTTTGAGGACTAGAAA
1 AAAGGAGAAA-GCGTCCTGCTCTTTGAGGACTGGAAA
319155 AGTGAAAGGA
Statistics
Matches: 123, Mismatches: 20, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
55 44 0.36
56 2 0.02
58 1 0.01
60 6 0.05
61 70 0.57
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (60 bp):
AAAGGAGAAAGCGTCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTA
Found at i:320138 original size:1 final size:1
Alignment explanation
Indices: 320132--320201 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
320122 CAGATTCTTC
* * * * * * * * * *
320132 TTTTTTTTTCTCTTTTTTCTTTGTTTTGTTTGTTTTTTTTTGTTTTTTTGTTGTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
320197 TTTTT
1 TTTTT
320202 AAAAAGAATG
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:320151 original size:22 final size:20
Alignment explanation
Indices: 320126--320201 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
320116 CTTAAGCAGA
*
320126 TTCTTCTTTTTTTTTCTCTTTT
1 TTCTT-TTTTTTTTTGT-TTTT
*
320148 TTCTTTGTTTTGTTTGTTTTT
1 TTCTTT-TTTTTTTTGTTTTT
320169 TT-TTGTTTTTTTGTTGTTTTT
1 TTCTT-TTTTTTT-TTGTTTTT
*
320190 TTGTTTTTTTTT
1 TTCTTTTTTTTT
320202 AAAAAGAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 7 0.15
21 25 0.53
22 15 0.32
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (20 bp):
TTCTTTTTTTTTTTGTTTTT
Found at i:320153 original size:19 final size:19
Alignment explanation
Indices: 320129--320199 Score: 76
Period size: 19 Copynumber: 3.7 Consensus size: 19
320119 AAGCAGATTC
320129 TTCTTT-TTTTTTCTCTTTT
1 TTCTTTGTTTTTT-TCTTTT
*
320148 TTCTTTGTTTTGTTTGTTTT
1 TTCTTTGTTTT-TTTCTTTT
*
320168 TT-TTTGTTTTTTTGTTGTT
1 TTCTTTGTTTTTTTCTT-TT
320187 TT-TTTGTTTTTTT
1 TTCTTTGTTTTTTT
320200 TTAAAAAGAA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
18 6 0.12
19 29 0.60
20 11 0.23
21 2 0.04
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.85
Consensus pattern (19 bp):
TTCTTTGTTTTTTTCTTTT
Found at i:320158 original size:10 final size:10
Alignment explanation
Indices: 320129--320197 Score: 56
Period size: 9 Copynumber: 7.2 Consensus size: 10
320119 AAGCAGATTC
*
320129 TTCTTTTTTT
1 TTCTTTGTTT
*
320139 TTCTCT-TTT
1 TTCTTTGTTT
320148 TTCTTTG-TT
1 TTCTTTGTTT
*
320157 TTGTTTGTTT
1 TTCTTTGTTT
*
320167 TTTTTTG-TT
1 TTCTTTGTTT
320176 TT-TTTGTTGT
1 TTCTTTGTT-T
*
320186 TTTTTTGTTT
1 TTCTTTGTTT
320196 TT
1 TT
320198 TTTTAAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
8 4 0.08
9 21 0.42
10 19 0.38
11 6 0.12
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (10 bp):
TTCTTTGTTT
Found at i:320170 original size:30 final size:29
Alignment explanation
Indices: 320134--320199 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
320124 GATTCTTCTT
320134 TTTTTTTCTCTTTTTTCT-TTGTTTTGTTTG
1 TTTTTTTCTCTTTTTT-TGTTGTTTT-TTTG
* *
320164 TTTTTTTTTGTTTTTTTGTTGTTTTTTTG
1 TTTTTTTCTCTTTTTTTGTTGTTTTTTTG
320193 TTTTTTT
1 TTTTTTT
320200 TTAAAAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 12 0.36
30 21 0.64
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.85
Consensus pattern (29 bp):
TTTTTTTCTCTTTTTTTGTTGTTTTTTTG
Found at i:320191 original size:11 final size:11
Alignment explanation
Indices: 320155--320201 Score: 71
Period size: 10 Copynumber: 4.4 Consensus size: 11
320145 TTTTTCTTTG
320155 TTTTGTTTGTTT
1 TTTTG-TTGTTT
320167 TTTT-TTGTTT
1 TTTTGTTGTTT
320177 TTTTGTTGTTT
1 TTTTGTTGTTT
320188 TTTTGTT-TTT
1 TTTTGTTGTTT
320198 TTTT
1 TTTT
320202 AAAAAGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 17 0.50
11 13 0.38
12 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (11 bp):
TTTTGTTGTTT
Found at i:320198 original size:9 final size:9
Alignment explanation
Indices: 320145--320200 Score: 60
Period size: 9 Copynumber: 5.9 Consensus size: 9
320135 TTTTTTCTCT
320145 TTTTTCTTTG
1 TTTTT-TTTG
*
320155 TTTTGTTTG
1 TTTTTTTTG
320164 TTTTTTTT-
1 TTTTTTTTG
320172 TGTTTTTTTG
1 T-TTTTTTTG
320182 TTGTTTTTTTG
1 -T-TTTTTTTG
320193 TTTTTTTT
1 TTTTTTTT
320201 TAAAAAGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 1 0.02
9 25 0.61
10 5 0.12
11 10 0.24
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.86
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:320200 original size:30 final size:32
Alignment explanation
Indices: 320132--320201 Score: 101
Period size: 29 Copynumber: 2.3 Consensus size: 32
320122 CAGATTCTTC
320132 TTTTTTTTTCTCTTTTTTCTTTGTTTTGTTTG
1 TTTTTTTTTCTCTTTTTTCTTTGTTTTGTTTG
* *
320164 TTTTTTTTTGT-TTTTTT-GTTGTTTT-TTTG
1 TTTTTTTTTCTCTTTTTTCTTTGTTTTGTTTG
320193 TTTTTTTTT
1 TTTTTTTTT
320202 AAAAAGAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 13 0.36
30 7 0.19
31 6 0.17
32 10 0.28
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (32 bp):
TTTTTTTTTCTCTTTTTTCTTTGTTTTGTTTG
Found at i:332666 original size:51 final size:51
Alignment explanation
Indices: 332610--332728 Score: 175
Period size: 51 Copynumber: 2.3 Consensus size: 51
332600 TGAAAATAAT
332610 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCC
* ** * * * *
332661 GGGGTTGAAGTATCCCTGATTGTGAGAAATCGATATTTTGGAAATAATGCC
1 GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCC
332712 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
332729 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (51 bp):
GGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTAGAAATAAGGCC
Found at i:332706 original size:130 final size:130
Alignment explanation
Indices: 332459--332756 Score: 341
Period size: 130 Copynumber: 2.3 Consensus size: 130
332449 AACGGGGTTG
* * * *
332459 GAGTATCCCCTCGAAAATAACGGGGTTAGAGTATCCCCGATTATGAAAAATCGATGATTTAGAAA
1 GAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTAGAAA
* * **
332524 TAAGGCAAGGGTTGAAGTGTCCCCGATTATAGAAAATAGATGTTTCCAAAATAAAATTAGGATTA
66 TAAGGCAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATATTTCCAAAATAAAACCAGGATTA
*
332589 GAGTATCCCCGT-GAAAATAATGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTTAGA
1 GAGTATCCCC-TCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGA-TTTAGA
** * * * *** ** * *
332652 AATAAGGCCGGGGTTGAAGTATCCCTGATTGT-GAGAAATCGATATTTTGGAAATAATGCCGGGG
64 AATAAGGCAAGGGTTGAAGTATCCCCGATTATAGA-AAATAGATATTTCCAAAATAAAACCAGGA
*
332716 TTG
128 TTA
*
332719 GAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCCCC
1 GAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCC
332757 GATGAAATAA
Statistics
Matches: 141, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
129 4 0.03
130 136 0.96
131 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.27
Consensus pattern (130 bp):
GAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCAATTATGAAAAATCAATGATTTAGAAA
TAAGGCAAGGGTTGAAGTATCCCCGATTATAGAAAATAGATATTTCCAAAATAAAACCAGGATTA
Found at i:332747 original size:28 final size:28
Alignment explanation
Indices: 332713--332781 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
332703 AATAATGCCG
*
332713 GGGTTGGAGTATCCCCTCGA-AAATAATA
1 GGGTTGGAGTATCCCC-CGAGAAATAACA
332741 GGGTTGGAGTAT-CCCCGATGAAATAACA
1 GGGTTGGAGTATCCCCCGA-GAAATAACA
*
332769 AGGTTGGAGTATC
1 GGGTTGGAGTATC
332782 TTCGATTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 30 0.83
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCCGAGAAATAACA
Found at i:332960 original size:79 final size:78
Alignment explanation
Indices: 332846--333072 Score: 336
Period size: 76 Copynumber: 2.9 Consensus size: 78
332836 GATTGTGGAG
* * *
332846 AATTGGTGTTTTAGAAATAAAACCGGGGTTCGAGTATCCCCTTGAAAATAACAGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTAT
332911 CCCCGATTATGAAA
66 CCCCGA-TATGAAA
*
332925 AATTGATGTTTTAGAAATAAAACCGGGGCTGGAGTA-CTCCCTCGAAAATAAC-GGAGTTGGAGT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATC-CCCTCGAAAATAACAGG-GTTGGAGT
332988 ATCCCCG--ATGAAA
64 ATCCCCGATATGAAA
* *
333001 AATTGATGTTTTAGAAATAAAACCGTGGTTGGAGTGTCCCCTCGAAAATAACAGGGTTGGAGTAT
1 AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTAT
*
333066 GCCCGAT
66 CCCCGAT
333073 CGTGGAAAGT
Statistics
Matches: 134, Mismatches: 8, Indels: 13
0.86 0.05 0.08
Matches are distributed among these distances:
76 67 0.50
77 3 0.02
78 3 0.02
79 61 0.46
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (78 bp):
AATTGATGTTTTAGAAATAAAACCGGGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTAT
CCCCGATATGAAA
Found at i:333169 original size:51 final size:51
Alignment explanation
Indices: 333056--333176 Score: 161
Period size: 51 Copynumber: 2.4 Consensus size: 51
333046 AAATAACAGG
* ** * *
333056 GTTGGAGTATGCCCGATCGTGGAAAGTCGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTAGAAATAAAATCGGA
* * *
333107 GTTGAAATATCCCCGATTATGGAAAATGGGTGTTTTAGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTAGAAATAAAATCGGA
*
333158 GTTGGAGTATCCTCGATTA
1 GTTGGAGTATCCCCGATTA
333177 AGAAATTGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.31, C:0.12, G:0.28, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATGGAAAATCGGTGTTTTAGAAATAAAATCGGA
Found at i:335548 original size:20 final size:19
Alignment explanation
Indices: 335523--335592 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 19
335513 TGCCTGAATA
* *
335523 TATCGATGCATTGTAAAATG
1 TATCGATACAATG-AAAATG
*
335543 TATCGATACAATGAGCAATG
1 TATCGATACAATGA-AAATG
335563 TATCGATACAATGCAAAATG
1 TATCGATACAATG-AAAATG
335583 TATCGATACA
1 TATCGATACA
335593 TCTGGGTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (19 bp):
TATCGATACAATGAAAATG
Found at i:337955 original size:13 final size:12
Alignment explanation
Indices: 337936--337974 Score: 60
Period size: 13 Copynumber: 3.1 Consensus size: 12
337926 ATAGTACCCA
337936 ATGTATCGATAC
1 ATGTATCGATAC
337948 AGTGTATCGATACC
1 A-TGTATCGATA-C
337962 ATGTATCGATAC
1 ATGTATCGATAC
337974 A
1 A
337975 AGAAATATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 20 0.80
14 2 0.08
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (12 bp):
ATGTATCGATAC
Found at i:343171 original size:20 final size:21
Alignment explanation
Indices: 343127--343180 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
343117 GTTAGAAGCA
343127 ATGTATCGATACAATTCATCT
1 ATGTATCGATACAATTCATCT
*
343148 -TGTATTGATACAATGT-A-CT
1 ATGTATCGATACAAT-TCATCT
343167 ATGTATCGATACAA
1 ATGTATCGATACAA
343181 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (21 bp):
ATGTATCGATACAATTCATCT
Found at i:343253 original size:20 final size:20
Alignment explanation
Indices: 343210--343257 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
343200 ATGCCAGTTT
**
343210 CATGTATCAATACAATTGTC
1 CATGTATCAATACAATTGAA
343230 CATGTATCAATACGAA-TGAA
1 CATGTATCAATAC-AATTGAA
343250 CATGTATC
1 CATGTATC
343258 GATATAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (20 bp):
CATGTATCAATACAATTGAA
Found at i:345236 original size:13 final size:13
Alignment explanation
Indices: 345218--345242 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
345208 AGATTGCACA
345218 GTATCGATACATT
1 GTATCGATACATT
345231 GTATCGATACAT
1 GTATCGATACAT
345243 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:345294 original size:19 final size:20
Alignment explanation
Indices: 345230--345322 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
345220 ATCGATACAT
* *
345230 TGTATCGATACATGACCAAA
1 TGTATCGATACATCACAAAA
* * *
345250 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATCACAA-AA
*
345271 TGTATCGATACA-CACAATA
1 TGTATCGATACATCACAAAA
* *
345290 TGTATCAATACATCCCAAAA
1 TGTATCGATACATCACAAAA
345310 TGTATCGATACAT
1 TGTATCGATACAT
345323 TGGCTTGTAA
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
19 12 0.20
20 35 0.58
21 13 0.22
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATCACAAAA
Found at i:349071 original size:199 final size:199
Alignment explanation
Indices: 348725--349132 Score: 764
Period size: 199 Copynumber: 2.1 Consensus size: 199
348715 AGATGAAGCT
348725 TTAGAA-AAATTCATCACGTTTTGTAAAATAGTTCAAAATGAAAAGGGTTACTCCTTATCTAGTA
1 TTAGAAGAAATTCATCACGTTTTGTAAAATAGTTCAAAATGAAAAGGGTTACTCCTTATCTAGTA
*
348789 TAAGAAGTGATCACGGAATAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGAAAACGGT
66 TAAGAAGTGATCACAGAATAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGAAAACGGT
*
348854 ATTAGCCATAATTTCTCTGTTCCTAGAACTCCTCAACAAAACGGAGTCGTTGAGAGGAAAAATCG
131 ATTAGCCATAATTTCTCTGCTCCTAGAACTCCTCAACAAAACGGAGTCGTTGAGAGGAAAAATCG
348919 AACA
196 AACA
348923 TTAGAAGAAATTCATCACGTTTTGTAAAATAGTTCAAAATGAAAAGGGTTACTCCTTATCTAGTA
1 TTAGAAGAAATTCATCACGTTTTGTAAAATAGTTCAAAATGAAAAGGGTTACTCCTTATCTAGTA
*
348988 TAAGAAGTGATCACAGAATAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGAAAATGGT
66 TAAGAAGTGATCACAGAATAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGAAAACGGT
349053 ATTAGCCATAATTTCTCTGCTCCTAGAACTCCTCAACAAAACGGAGTCGTTGAGAGGAAAAATCG
131 ATTAGCCATAATTTCTCTGCTCCTAGAACTCCTCAACAAAACGGAGTCGTTGAGAGGAAAAATCG
*
349118 GACA
196 AACA
*
349122 TTGGAAGAAAT
1 TTAGAAGAAAT
349133 GGCTAGAACC
Statistics
Matches: 204, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
198 6 0.03
199 198 0.97
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (199 bp):
TTAGAAGAAATTCATCACGTTTTGTAAAATAGTTCAAAATGAAAAGGGTTACTCCTTATCTAGTA
TAAGAAGTGATCACAGAATAGAATTTGAAAACCTTGGTTTTGATAAATTTTGTAATGAAAACGGT
ATTAGCCATAATTTCTCTGCTCCTAGAACTCCTCAACAAAACGGAGTCGTTGAGAGGAAAAATCG
AACA
Found at i:351683 original size:13 final size:13
Alignment explanation
Indices: 351665--351689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
351655 CAGCATTCTC
351665 TGTATCGATACAG
1 TGTATCGATACAG
351678 TGTATCGATACA
1 TGTATCGATACA
351690 AGGGGATTAT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:352155 original size:20 final size:21
Alignment explanation
Indices: 352123--352174 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
352113 CCCCTAGGCA
* *
352123 GCACCCACCAGGTTGCGACC-G
1 GCACCC-CCAGGTCGCAACCGG
352144 GCACCCCCAGGTCGCAACCGG
1 GCACCCCCAGGTCGCAACCGG
352165 GCAACCCCCA
1 GC-ACCCCCA
352175 TACTAGCAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 11 0.41
21 9 0.33
22 7 0.26
ACGTcount: A:0.21, C:0.48, G:0.25, T:0.06
Consensus pattern (21 bp):
GCACCCCCAGGTCGCAACCGG
Found at i:353568 original size:22 final size:22
Alignment explanation
Indices: 353542--353584 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
353532 CGAAAGTGTT
353542 AAATTATTTT-ACTAAGGGGGAG
1 AAATT-TTTTGACTAAGGGGGAG
*
353564 AAATTTTTTGATTAAGGGGGA
1 AAATTTTTTGACTAAGGGGGA
353585 AAGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (22 bp):
AAATTTTTTGACTAAGGGGGAG
Found at i:354178 original size:20 final size:21
Alignment explanation
Indices: 354153--354205 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
354143 ATCAATACAT
**
354153 TGTATCGATACATGACCA-AA
1 TGTATCGATACATGAAAAGAA
*
354173 TGTATCGATACTTGAAAAGAA
1 TGTATCGATACATGAAAAGAA
354194 TGTATCGATACA
1 TGTATCGATACA
354206 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:354275 original size:13 final size:13
Alignment explanation
Indices: 354257--354282 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
354247 ACACACAATA
354257 TGTATCGATACAT
1 TGTATCGATACAT
354270 TGTATCGATACAT
1 TGTATCGATACAT
354283 CCCAAAATGT
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:354298 original size:33 final size:32
Alignment explanation
Indices: 354237--354304 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
354227 GTAGCCAAAT
*
354237 TTGTATCGATACACACAATATGTATCGATACA
1 TTGTATCGATACACACAAAATGTATCGATACA
*
354269 TTGTATCGATACATCCCAAAATGTATCGATACA
1 TTGTATCGATACA-CACAAAATGTATCGATACA
354302 TTG
1 TTG
354305 GCTTGTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGTATCGATACACACAAAATGTATCGATACA
Found at i:356481 original size:13 final size:13
Alignment explanation
Indices: 356463--356488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
356453 ACATTATTCC
356463 ATGTATCGATACA
1 ATGTATCGATACA
356476 ATGTATCGATACA
1 ATGTATCGATACA
356489 TGGATCTTTG
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:356501 original size:33 final size:33
Alignment explanation
Indices: 356442--356508 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
356432 CTGCCAAGGA
*
356442 AATGTATCGATACATTATTCCATGTATCGATAC
1 AATGTATCGATACATGATTCCATGTATCGATAC
**
356475 AATGTATCGATACATGGA-TCTTTGTATCGATAC
1 AATGTATCGATACAT-GATTCCATGTATCGATAC
356508 A
1 A
356509 TTTGGGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (33 bp):
AATGTATCGATACATGATTCCATGTATCGATAC
Found at i:357802 original size:80 final size:79
Alignment explanation
Indices: 357667--357823 Score: 203
Period size: 80 Copynumber: 2.0 Consensus size: 79
357657 ATATTTCCCG
* ** *
357667 ATGAGAAATTTAATATTTTGCAGATAATAACGGGGTTGGAGTGTCCCCTTGAAAATAACGGGGCT
1 ATGAGAAATTTAATATTTT-CAGATAATAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGCT
357732 GGAGTATCCCCGGTT
65 GGAGTATCCCCGGTT
357747 ATGAGAAA-TTAATATTTT-AGA-AATAAAGCCGAGGGTTGGAGTATCCCCTCAAAAATAACAGG
1 ATGAGAAATTTAATATTTTCAGATAAT-AA--CG-GGGTTGGAGTATCCCCTCAAAAATAACAGG
*
357809 GTTGGAGTATCCCCG
62 GCTGGAGTATCCCCG
357824 ATGATTAACG
Statistics
Matches: 68, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
76 3 0.04
77 5 0.07
79 12 0.18
80 48 0.71
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (79 bp):
ATGAGAAATTTAATATTTTCAGATAATAACGGGGTTGGAGTATCCCCTCAAAAATAACAGGGCTG
GAGTATCCCCGGTT
Found at i:357840 original size:27 final size:27
Alignment explanation
Indices: 357778--357855 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
357768 AATAAAGCCG
* **
357778 AGGGTTGGAGTATCCCCTCAAAAATAAC
1 AGGGTTGGAGTATCCCC-GATGAATAAC
*
357806 AGGGTTGGAGTATCCCCGATGATTAAC
1 AGGGTTGGAGTATCCCCGATGAATAAC
* *
357833 GGGGTTGGAGTATCCCTGATGAA
1 AGGGTTGGAGTATCCCCGATGAA
357856 AAATTGATGT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 26 0.60
28 17 0.40
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (27 bp):
AGGGTTGGAGTATCCCCGATGAATAAC
Found at i:357926 original size:51 final size:51
Alignment explanation
Indices: 357855--357952 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 51
357845 TCCCTGATGA
357855 AAAATTGATGTTTTAGAAATAAAATCGGAGTT-GGAGTATCCCCGATTATAG
1 AAAATTGATGTTTTAGAAATAAAATCGGAGTTGGGA-TATCCCCGATTATAG
*
357906 AAAATT-AGTGTTTT-GAAAATAAAATCGGAGTTGGGATATCCTCGATT
1 AAAATTGA-TGTTTTAG-AAATAAAATCGGAGTTGGGATATCCCCGATT
357953 GCGGAGAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
50 2 0.05
51 38 0.88
52 3 0.07
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (51 bp):
AAAATTGATGTTTTAGAAATAAAATCGGAGTTGGGATATCCCCGATTATAG
Found at i:360338 original size:34 final size:33
Alignment explanation
Indices: 360295--360359 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
360285 AACTTCCTAG
* *
360295 ATGTATCGATACAAAGAATAGATGTATTGATATA
1 ATGTATCGATACAAAGAA-AAATGTATCGATATA
*
360329 ATGTATCGATACACAGAAAAATGTATCGATA
1 ATGTATCGATACAAAGAAAAATGTATCGATA
360360 CATTTCCTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 11 0.39
34 17 0.61
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATATA
Found at i:360417 original size:19 final size:18
Alignment explanation
Indices: 360393--360519 Score: 113
Period size: 19 Copynumber: 7.7 Consensus size: 18
360383 AGCGATACAT
360393 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
360412 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
360425 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
360444 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
360457 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
360476 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
360489 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
360508 TGTATCGATACA
1 TGTATCGATACA
360520 TTGTATCGAT
Statistics
Matches: 90, Mismatches: 0, Indels: 36
0.71 0.00 0.29
Matches are distributed among these distances:
13 33 0.37
14 3 0.03
16 6 0.07
18 3 0.03
19 45 0.50
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:360426 original size:32 final size:32
Alignment explanation
Indices: 360385--360533 Score: 289
Period size: 32 Copynumber: 4.7 Consensus size: 32
360375 AGCTTCCTAG
*
360385 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
360417 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
360449 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
360481 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
360513 CGATACATTGTATCGATACAA
1 CGATACATTGTATCGATACAA
360534 AATCGCTGAA
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 116 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:360597 original size:21 final size:21
Alignment explanation
Indices: 360571--360647 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
360561 GTTGGGACCC
* *
360571 TGTATCGATACATTTGTA-GAA
1 TGTATCGATACA-TTCTACAAA
*
360592 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCTACAAA
*
360613 TATATCGATACATTCTACAAA
1 TGTATCGATACATTCTACAAA
360634 TGTATCGATACATT
1 TGTATCGATACATT
360648 TGGATAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (21 bp):
TGTATCGATACATTCTACAAA
Found at i:363036 original size:51 final size:51
Alignment explanation
Indices: 362980--363428 Score: 314
Period size: 51 Copynumber: 8.6 Consensus size: 51
362970 TTAAGTTCCT
362980 CAATTTTTCATAATCGAGGG-TACTCCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTTCATAATCG-GGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
* *
363031 TAATTTTTCATAATCGGGGGTACTCCAACCCCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* * * ** * *
363082 CAATTTTCCTTTAATCGGGGATACTCCAACTCCAATTTTAATTCCAAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGGTTTT-ATTTC-TAAAACAC
* * * * ***** * *
363136 CAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGT-TTT-ATTTCTAAAACAC
** * * **** * * * * *
363189 CAACCCCGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTTCCAAAATAT
1 CAA---TTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
** * * * *
363243 TGATCTCTCATAATCGGGGATACTCCAACTCCGATTTTATTTTCTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACAC
* * * * *
363295 TAATTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* *
363346 CAATTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* *
363397 CAA-TTTTCACAATCGGGAATACTCCAACCCCG
1 CAATTTTTCATAATCGGGGATACTCCAACCCCG
363429 TTAATCATCG
Statistics
Matches: 309, Mismatches: 77, Indels: 25
0.75 0.19 0.06
Matches are distributed among these distances:
50 32 0.10
51 135 0.44
52 67 0.22
53 29 0.09
54 25 0.08
55 2 0.01
56 19 0.06
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
Found at i:363176 original size:31 final size:28
Alignment explanation
Indices: 363148--363224 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
363138 ATTTTTCACA
*
363148 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
* **
363176 ATCGGGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
363204 --CGAGGGGATACTCCAACCCCG
1 ATCGA--GGATACTCCAACCCCG
363225 GCTCTATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
28 40 0.95
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:363336 original size:103 final size:101
Alignment explanation
Indices: 362984--363428 Score: 288
Period size: 103 Copynumber: 4.3 Consensus size: 101
362974 GTTCCTCAAT
* ** * * * * * *
362984 TTTTCATAATCGAGGG-TACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCATAATCGG
1 TTTTCACAATCG-GGGATACTCCAACCCCGACTCTATTTCCAAAACACCAATTCTCCACAATCGG
* *
363048 GGGTACTCCAACCCCGGTTTTATTTTCAAAACACCAA
65 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAA
* * * * * * *
363085 TTTTC-CTTTAATCGGGGATACTCCAACTCCAATTTTAATTCCAAAAAACACCAATTTTTCACAA
1 TTTTCAC---AATCGGGGATACTCCAACCCCGACTCTATTTCC--AAAACACCAATTCTCCACAA
* * * ***** * *
363149 TCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAA
61 TCGGGGATACTCCAACCCCG--ATTTTATTTTCAAAACACCAA
** * * * *** *
363192 CCCCGTT-AC-CTCCGAGGGGATACTCCAACCCCGGCTCTATTTCCAAAATATTGA-TCTCTCAT
1 ---TTTTCACAAT-C--GGGGATACTCCAACCCCGACTCTATTTCCAAAACACCAATTCTC-CAC
* *
363254 AATCGGGGATACTCCAACTCCGATTTTATTTTCTAAAACACTAA
59 AATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAA
* * * * *
363298 TTTTCCACAATCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCCACAATCGG
1 TTTT-CACAATCGGGGATACTCCAACCCCGACTCTATTTCCAAAACACCAATTCTCCACAATCGG
*
363363 GGATACTCCAACCCCGGTTTTATTTTCAAAACACCAA
65 GGATACTCCAACCCCGATTTTATTTTCAAAACACCAA
*
363400 TTTTCACAATCGGGAATACTCCAACCCCG
1 TTTTCACAATCGGGGATACTCCAACCCCG
363429 TTAATCATCG
Statistics
Matches: 256, Mismatches: 67, Indels: 42
0.70 0.18 0.12
Matches are distributed among these distances:
101 28 0.11
102 16 0.06
103 89 0.35
104 3 0.01
105 44 0.17
106 10 0.04
107 40 0.16
109 23 0.09
110 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (101 bp):
TTTTCACAATCGGGGATACTCCAACCCCGACTCTATTTCCAAAACACCAATTCTCCACAATCGGG
GATACTCCAACCCCGATTTTATTTTCAAAACACCAA
Found at i:363445 original size:27 final size:28
Alignment explanation
Indices: 363408--363483 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 28
363398 AATTTTCACA
*
363408 ATCGGGAATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
363435 ATCGGGGATACTCCAACCCCTTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
363463 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
363484 GTTTTATTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:363485 original size:105 final size:107
Alignment explanation
Indices: 363361--363561 Score: 275
Period size: 105 Copynumber: 1.9 Consensus size: 107
363351 TTCCACAATC
*
363361 GGGGATACTCCAACCCCGGTTTTATT-TTCAAAACACCAATTT-TCACAATCGG-GAATACTCCA
1 GGGGATACTCCAACCCCGGTTTTATTCCT-AAAACACCAATTTCTCACAATCGGAG-ATACTCCA
**
363423 ACCCCGTTA-ATCATCGGGGATACTCCAACCCCTTTATTTCCGA
64 ACCCCGTTATATCAGAGGGGATACTCCAACCCCTTTATTTCCGA
* ***
363466 GGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTGATTTCTCACAATCGGAGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTCCTAAAACACCAATTTCTCACAATCGGAGATACTCCAAC
* *
363531 CCCGTTATTTCCGAGGGGATACTCCAACCCC
66 CCCGTTATATCAGAGGGGATACTCCAACCCC
363562 GGCTTTATTC
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
105 35 0.42
106 28 0.34
107 20 0.24
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (107 bp):
GGGGATACTCCAACCCCGGTTTTATTCCTAAAACACCAATTTCTCACAATCGGAGATACTCCAAC
CCCGTTATATCAGAGGGGATACTCCAACCCCTTTATTTCCGA
Found at i:363526 original size:259 final size:262
Alignment explanation
Indices: 363000--363534 Score: 776
Period size: 259 Copynumber: 2.0 Consensus size: 262
362990 TAATCGAGGG
* * * * *
363000 TACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTTCATAATCGGGGGTACTCCAACCCCGG
1 TACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATCGGGGATACTCCAACCCCGA
** *
363065 TTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTCCAATTTTAATTCCAAA
66 TTTTATTTTCAAAACACCAATTTTCCTACAATCGGGGATACTCCAACCCCAATTTTAATTCC-AA
* *
363130 AAACACCAATTTTTCACAATCGAGGATACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCC
130 AAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCGGGGATACTCCAACCC
*
363195 CGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTTCCAAAATATTGATCTCTCATAATCGG
195 CGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTTCCAAAATATTGATCTCTCACAATCGG
*
363260 GGA
260 AGA
* *
363263 TACTCCAACTCCGATTTTATTTTCTAAAACACTAATTTTCCACAATCGGGGATACTCCAACTCCG
1 TACTCCAACCCCGATTTTA-TTTCTAAAACACTAATTTTCCACAATCGGGGATACTCCAACCCCG
** * *
363328 ATTTTATTTTCAAAACACCAATTTTCC-ACAATCGGGGATACTCCAACCCCGGTTTTATTTTC-A
65 ATTTTATTTTCAAAACACCAATTTTCCTACAATCGGGGATACTCCAACCCCAATTTTAATTCCAA
363391 AAACACCAA-TTTTCACAATCG-GGAATACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACC
130 AAACACCAATTTTTCACAATCGAGG-ATACTCCAACCCCGTTATATCATCGGGGATACTCCAACC
* ** * * *
363453 CCTTTATTTCCGAGGGGATACTCCAACCCCGGTTTTA-TTCCTAAAATATTGATTTCTCACAATC
194 CCGTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTTCC-AAAATATTGATCTCTCACAATC
363517 GGAGA
258 GGAGA
363522 TACTCCAACCCCG
1 TACTCCAACCCCG
363535 TTATTTCCGA
Statistics
Matches: 244, Mismatches: 25, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
258 4 0.02
259 90 0.37
260 28 0.11
261 10 0.04
263 45 0.18
264 67 0.27
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (262 bp):
TACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATCGGGGATACTCCAACCCCGA
TTTTATTTTCAAAACACCAATTTTCCTACAATCGGGGATACTCCAACCCCAATTTTAATTCCAAA
AACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTATATCATCGGGGATACTCCAACCCC
GTTACCTCCGAGGGGATACTCCAACCCCGGCTCTATTTCCAAAATATTGATCTCTCACAATCGGA
GA
Found at i:363746 original size:79 final size:78
Alignment explanation
Indices: 363439--363720 Score: 449
Period size: 79 Copynumber: 3.6 Consensus size: 78
363429 TTAATCATCG
*
363439 GGGATACTCCAACCCCTTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTG
1 GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTG
363504 ATTTCTCACAATC
66 ATTTCTCACAATC
*
363517 GGAGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCTAAAATATT
1 GG-GATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATT
363582 GATTTCTCACAATC
65 GATTTCTCACAATC
* *
363596 GAGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATT
1 G-GGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATT
* *
363661 GATTTCTCATAATTA
65 GATTTCTCACAA-TC
* *
363676 GGGATACTCCAACCCCATTATTTTC-ACGGGGATACTCCAACCCCG
1 GGGATACTCCAACCCCGTTATTTCCGA-GGGGATACTCCAACCCCG
363721 ATCTATTTTT
Statistics
Matches: 192, Mismatches: 8, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
78 3 0.02
79 186 0.97
80 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (78 bp):
GGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGGTTTTATTCCTAAAATATTG
ATTTCTCACAATC
Found at i:368216 original size:52 final size:52
Alignment explanation
Indices: 368138--368499 Score: 190
Period size: 52 Copynumber: 6.6 Consensus size: 52
368128 ATATCTCACT
* *
368138 AAAGGTGTCAATATGCTGATTCAAGGCCAACAATATTGGGCTT-AAGAAAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAG-AAGAA
* * * * * *
368190 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTGAAAGATGATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGAAGA-A
* * * * *
368243 AGGATGAGTAGAATGCTAATGTGCCGATTCAAGGCCAATGAA-ATTGGGCTTAAAAATAGGAAAA
1 A--A--AG--G--TGCCAATATGCTGATTCAAGGCCAA-CAATATTGGACTT---AA-A-G---A
368307 AGAATGA
49 AG-A--A
* * * * * *
368314 TAAAAGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGAC
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGAAGAA
* * * ** ** * *
368367 AAATGTGCCAATGTGCTGATTCAAAGCCAATGACGTTGGACTTAAAGATGAG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGAAGAA
* *
368419 AAAGGCGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT-AAGAAAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAG-AAGAA
* * *
368471 AAAAGTGCCAATCTGCTGATTTAAGGCCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCA
368500 GTGACATGGG
Statistics
Matches: 234, Mismatches: 52, Indels: 48
0.70 0.16 0.14
Matches are distributed among these distances:
51 3 0.01
52 144 0.62
53 5 0.02
55 2 0.01
56 2 0.01
57 2 0.01
59 2 0.01
60 1 0.00
61 31 0.13
62 1 0.00
63 1 0.00
64 30 0.13
65 1 0.00
66 2 0.01
68 1 0.00
69 2 0.01
70 2 0.01
71 1 0.00
72 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGAAGAA
Found at i:368500 original size:52 final size:52
Alignment explanation
Indices: 368305--368514 Score: 215
Period size: 52 Copynumber: 4.0 Consensus size: 52
368295 AAAATAGGAA
* *
368305 AAAGAATGATAAAAGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTT
1 AAAG-ATGAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * * ** **
368358 AAAGATGACAAATGTGCCAATGTGCTGATTCAAAGCCAATGACGTTGGACTT
1 AAAGATGAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
368410 AAAGATGAGAAAGGCGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT
1 AAAGATGAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * * * *
368462 -AAGAAAGAAAAAAGTGCCAATCTGCTGATTTAAGGCCAGTGACATGGGACTT
1 AAAG-ATGAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
368514 A
1 A
368515 GAAAGAGATA
Statistics
Matches: 126, Mismatches: 29, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
51 3 0.02
52 119 0.94
53 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (52 bp):
AAAGATGAAAAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:368512 original size:104 final size:104
Alignment explanation
Indices: 368321--368514 Score: 273
Period size: 104 Copynumber: 1.9 Consensus size: 104
368311 TGATAAAAGT
* * * * * *
368321 GCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGATGACAAATGTGCCAATGTGCTGA
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGAAGAAAAAAGTGCCAATCTGCTGA
* *
368386 TTCAAAGCCAATGACGTTGGACTTAAAGATGAGAAAGGC
66 TTCAAAGCCAATGACATGGGACTTAAAGATGAGAAAGGC
368425 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTT-AAGAAAGAAAAAAGTGCCAATCTGCTG
1 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG-AAGAAAAAAGTGCCAATCTGCTG
* * *
368489 ATTTAAGGCCAGTGACATGGGACTTA
65 ATTCAAAGCCAATGACATGGGACTTA
368515 GAAAGAGATA
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 3 0.04
104 75 0.96
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (104 bp):
GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGAAGAAAAAAGTGCCAATCTGCTGA
TTCAAAGCCAATGACATGGGACTTAAAGATGAGAAAGGC
Found at i:368667 original size:64 final size:63
Alignment explanation
Indices: 368582--368829 Score: 284
Period size: 64 Copynumber: 3.9 Consensus size: 63
368572 TAGAAAGAGA
* * ** *
368582 TGCCACCAACTTGTGTGGGCTTTTGAGAGGGGTTGCCATCGCCTTGTGTAGGCTTTGAAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGA-AGGGGTTGCCACCAACTTGTGTGGGCTTTGAAAAGGT
* *
368646 TGCCACCGACTTGTGTGGGCTTTGGAAGGGGGTGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAGGGGTTGCCACCAACTTGTGTGGGCTTTGAA-AAGGT
* * * * *
368710 TGCCACTGACTTGTGTGGGC-TTTGAAGAAGGTTGCCACCAACTTATGTGGGTTTTGAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTTGAAG-GGGTTGCCACCAACTTGTGTGGGCTTTGA-AAAGGT
* * * *
368774 TGCCACCGACTTATGTAGGC-TTTGAAAAAGGGTTGCCACCAGCTTGTGTGGGCTTT
1 TGCCACCGACTTGTGTGGGCTTTTG--AAGGGGTTGCCACCAACTTGTGTGGGCTTT
368830 AAAGAAGAAG
Statistics
Matches: 157, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
63 33 0.21
64 98 0.62
65 24 0.15
66 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (63 bp):
TGCCACCGACTTGTGTGGGCTTTTGAAGGGGTTGCCACCAACTTGTGTGGGCTTTGAAAAGGT
Found at i:368690 original size:32 final size:31
Alignment explanation
Indices: 368582--368829 Score: 244
Period size: 32 Copynumber: 7.7 Consensus size: 31
368572 TAGAAAGAGA
368582 TGCCACCAACTTGTGTGGGCTTTTGAGAGGGGT
1 TGCCACCAACTTGTGTGGGC-TTTGA-AGGGGT
* ** * **
368615 TGCCATCGCCTTGTGTAGGCTTTGAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAGGGGT
* *
368646 TGCCACCGACTTGTGTGGGCTTTGGAAGGGGG
1 TGCCACCAACTTGTGTGGGCTTT-GAAGGGGT
*
368678 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAG-GGGT
** *
368710 TGCCACTGACTTGTGTGGGCTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTGAAG-GGGT
* * *
368742 TGCCACCAACTTATGTGGGTTTTGAGAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTGA-AGGGGT
* * * *
368774 TGCCACCGACTTATGTAGGCTTTGAAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTG--AAGGGGT
*
368807 TGCCACCAGCTTGTGTGGGCTTT
1 TGCCACCAACTTGTGTGGGCTTT
368830 AAAGAAGAAG
Statistics
Matches: 180, Mismatches: 30, Indels: 10
0.82 0.14 0.05
Matches are distributed among these distances:
31 28 0.16
32 109 0.61
33 42 0.23
34 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.30
Consensus pattern (31 bp):
TGCCACCAACTTGTGTGGGCTTTGAAGGGGT
Found at i:368747 original size:96 final size:96
Alignment explanation
Indices: 368582--368836 Score: 304
Period size: 96 Copynumber: 2.6 Consensus size: 96
368572 TAGAAAGAGA
* * *
368582 TGCCACCAACTTGTGTGGGCTTTTG-AGAGGGGTTGCCA-TCGCCTTGTGTAGGCTTTGAA-AAG
1 TGCCACCAACTTGTGTGGGC-TTTGAAGA-AGGTTGCCACT-GACTTGTGTGGGCTTTGAAGAAG
* *
368644 GTTGCCACCGACTTGTGTGGGCTTTG-GAAGGGGG
63 GTTGCCACCAACTTATGTGGGCTTTGAGAA-GGGG
368678 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACTGACTTGTGTGGGCTTTGAAGAAGGTT
1 TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACTGACTTGTGTGGGCTTTGAAGAAGGTT
* *
368743 GCCACCAACTTATGTGGGTTTTGAGAAGGGT
66 GCCACCAACTTATGTGGGCTTTGAGAAGGGG
* * * * * *
368774 TGCCACCGACTTATGTAGGCTTTGAAAAAGGGTTGCCAC-CAGCTTGTGTGGGCTTTAAAGAAG
1 TGCCACCAACTTGTGTGGGCTTTGAAGAA-GGTTGCCACTGA-CTTGTGTGGGCTTTGAAGAAG
368837 AAGTTGAATC
Statistics
Matches: 140, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
95 29 0.21
96 79 0.56
97 32 0.23
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (96 bp):
TGCCACCAACTTGTGTGGGCTTTGAAGAAGGTTGCCACTGACTTGTGTGGGCTTTGAAGAAGGTT
GCCACCAACTTATGTGGGCTTTGAGAAGGGG
Found at i:370017 original size:21 final size:20
Alignment explanation
Indices: 369952--370017 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 20
369942 GTTGTTTTTC
*
369952 TTTTTGATTTTGCTTTTGCATT
1 TTTTTCATTTT-CTTTTGC-TT
*
369974 TTTTTCTATTTTCTTCTT-ATT
1 TTTTTC-ATTTTCTT-TTGCTT
369995 TTTTTCATTTTCTTTGTGCTT
1 TTTTTCATTTTCTTT-TGCTT
370016 TT
1 TT
370018 GCTTTTGACT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.03
20 9 0.24
21 12 0.32
22 8 0.22
23 7 0.19
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.73
Consensus pattern (20 bp):
TTTTTCATTTTCTTTTGCTT
Found at i:370488 original size:19 final size:19
Alignment explanation
Indices: 370464--370523 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
370454 AAATGTGATG
370464 GACAAAGAATAAAGGTGAA
1 GACAAAGAATAAAGGTGAA
* * *
370483 GAC-AA-AA-ACATGT-ATG
1 GACAAAGAATAAAGGTGA-A
370499 GACAAAGAATAAAGGTGAA
1 GACAAAGAATAAAGGTGAA
370518 GACAAA
1 GACAAA
370524 AACATGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
15 1 0.03
16 7 0.23
17 4 0.13
18 4 0.13
19 13 0.43
20 1 0.03
ACGTcount: A:0.57, C:0.08, G:0.23, T:0.12
Consensus pattern (19 bp):
GACAAAGAATAAAGGTGAA
Found at i:370500 original size:35 final size:35
Alignment explanation
Indices: 370456--370539 Score: 150
Period size: 35 Copynumber: 2.4 Consensus size: 35
370446 AATAGGTAAA
370456 ATGTGATGGACAAAGAATAAAGGTGAAGACAAAAAC
1 ATGT-ATGGACAAAGAATAAAGGTGAAGACAAAAAC
370492 ATGTATGGACAAAGAATAAAGGTGAAGACAAAAAC
1 ATGTATGGACAAAGAATAAAGGTGAAGACAAAAAC
*
370527 ATGTATAGACAAA
1 ATGTATGGACAAA
370540 AGTTGAATAG
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
35 43 0.91
36 4 0.09
ACGTcount: A:0.54, C:0.08, G:0.23, T:0.15
Consensus pattern (35 bp):
ATGTATGGACAAAGAATAAAGGTGAAGACAAAAAC
Found at i:377360 original size:15 final size:14
Alignment explanation
Indices: 377323--377361 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
377313 CAAGAATACA
377323 AAAAAAAAAGAAAG
1 AAAAAAAAAGAAAG
*
377337 AATACAAAAAGAAAGG
1 AA-AAAAAAAGAAA-G
377353 AAAAAAAAA
1 AAAAAAAAA
377362 CCAGTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 2 0.10
15 16 0.76
16 3 0.14
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGAAAG
Done.