Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000572.1 Hibiscus syriacus cultivar Beakdansim tig00001120_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2399138
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:1104 original size:54 final size:54
Alignment explanation
Indices: 1022--1129 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1012 TTTATAAACT
1022 GTAAATATAATTCATGTAATGGACTAACACTTGATTTTTGTACTCTAGTTTTTG
1 GTAAATATAATTCATGTAATGGACTAACACTTGATTTTTGTACTCTAGTTTTTG
1076 GTAAATATAATTCATGTAATGGACTAACACTTGATTTTTGTACTCTAGTTTTTG
1 GTAAATATAATTCATGTAATGGACTAACACTTGATTTTTGTACTCTAGTTTTTG
1130 ATAAGAGAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (54 bp):
GTAAATATAATTCATGTAATGGACTAACACTTGATTTTTGTACTCTAGTTTTTG
Found at i:5128 original size:2 final size:2
Alignment explanation
Indices: 5116--5197 Score: 146
Period size: 2 Copynumber: 41.0 Consensus size: 2
5106 AGCATATGAC
* *
5116 AT AT TT AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5198 CTCAAATTCG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9066 original size:21 final size:22
Alignment explanation
Indices: 9032--9072 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
9022 GAGATCGTTG
9032 GTATAGTTTGTTTT-TTTCTCT
1 GTATAGTTTGTTTTGTTTCTCT
* *
9053 GTATATTTTTTTTTGTTTCT
1 GTATAGTTTGTTTTGTTTCT
9073 GTCTCTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.10, C:0.07, G:0.12, T:0.71
Consensus pattern (22 bp):
GTATAGTTTGTTTTGTTTCTCT
Found at i:9565 original size:9 final size:10
Alignment explanation
Indices: 9544--9683 Score: 128
Period size: 9 Copynumber: 15.2 Consensus size: 10
9534 ATTATGTATT
*
9544 TAATATAT-T
1 TAATATATAA
9553 TAATATA-AA
1 TAATATATAA
9562 TAATA-ATAA
1 TAATATATAA
9571 TAATA-ATAA
1 TAATATATAA
*
9580 TGATA-ATAA
1 TAATATATAA
*
9589 TAATAATATGA
1 TAAT-ATATAA
9600 TAATA-ATAA
1 TAATATATAA
9609 TAATA-ATAA
1 TAATATATAA
*
9618 TGATA-ATAA
1 TAATATATAA
9627 TAATA-ATAA
1 TAATATATAA
9636 TAATA-ATAA
1 TAATATATAA
9645 TAATAT-TAA
1 TAATATATAA
9654 TAATGATAT-A
1 TAAT-ATATAA
9664 TAATA-ATAA
1 TAATATATAA
9673 TAATA-ATAA
1 TAATATATAA
9682 TA
1 TA
9684 TGGATAAAAC
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
8 3 0.03
9 96 0.83
10 9 0.08
11 8 0.07
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (10 bp):
TAATATATAA
Found at i:9568 original size:3 final size:3
Alignment explanation
Indices: 9560--9683 Score: 187
Period size: 3 Copynumber: 41.3 Consensus size: 3
9550 ATTTAATATA
* *
9560 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT -AT GAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
9607 AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
9655 AAT GAT ATAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT A
9684 TGGATAAAAC
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
2 2 0.02
3 105 0.95
4 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:10194 original size:119 final size:119
Alignment explanation
Indices: 9832--10356 Score: 840
Period size: 119 Copynumber: 4.5 Consensus size: 119
9822 TTCTCCAGAT
* ** * *
9832 GAGTTCTTCTCATTACGAACT-TT-CTGCTGGGGATAATGTTCCATCAAA-TGATGAATTCAAGC
1 GAGTTCTTCTCATTATGAACTCTTCCT-CTGGAAATGATGATCCATCAAATTGATGAATTCAAGC
* *
9894 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTCCTTCCTTCTTCAGAT---
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
* * *
9946 GAGTTCTTCTCATTATGAAC-CTT-CTCTGGTAATGTTGATCCATC-AAGTGATGAATTCAAGC-
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
10007 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
10060 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
10125 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
66 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
10179 GAGTTCTTCTCATTATGAACTCTTCC-CTTGGAAATGATGATCCATCAAATTGATGAATTCAAAC
1 GAGTTCTTCTCATTATGAACTCTTCCTC-TGGAAATGATGATCCATCAAATTGATGAATTCAAGC
10243 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
65 AAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
*
10298 GAATTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATT
1 GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATT
10357 TGAATCTTTG
Statistics
Matches: 386, Mismatches: 13, Indels: 19
0.92 0.03 0.05
Matches are distributed among these distances:
111 15 0.04
112 35 0.09
113 28 0.07
114 43 0.11
115 3 0.01
116 19 0.05
117 16 0.04
118 35 0.09
119 191 0.49
120 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.36
Consensus pattern (119 bp):
GAGTTCTTCTCATTATGAACTCTTCCTCTGGAAATGATGATCCATCAAATTGATGAATTCAAGCA
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAC
Found at i:11154 original size:100 final size:101
Alignment explanation
Indices: 10981--12086 Score: 1804
Period size: 100 Copynumber: 11.0 Consensus size: 101
10971 CTTGATTCTG
* *
10981 TCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATGTTCTGTCCAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11046 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATGTT
11081 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11146 GATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
* *
11184 GTCTAACCAGATCAGATACCTCAAAGAACACTTTCAGAAGATGCTATGTTCTGTCCAACCAGATC
1 -TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATC
11249 AGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT
65 AGATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
11288 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11353 G--AACTCAAAGAACACTTCCAGAAGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
11389 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11454 GATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
11492 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11557 GATAACTCAAAG-A-ACTTCCAG-AGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
*
11592 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11656 GATAACTCAAAG-ACACTTCCAGAAGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
11693 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-T-CAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
*
11756 GATAACTC-AAGAACGCTTCCAGAAGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
*
11793 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
11857 -AT-ACTC-AAGAACACTTCCAGAAGATG--ATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
*
11890 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
*
11954 GATAACTCAAAGAACGCTTCCAGAAGATGCTATGTTCT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTATG-T-T
*
11992 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-TCTAACCAGATCA
1 TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
12056 GATAACTCAAAGAACACTTCC--AAGATGCTAT
66 GATAACTCAAAGAACACTTCCAGAAGATGCTAT
12087 TGAGCACATA
Statistics
Matches: 978, Mismatches: 13, Indels: 30
0.96 0.01 0.03
Matches are distributed among these distances:
97 71 0.07
98 2 0.00
99 55 0.06
100 295 0.30
101 185 0.19
102 92 0.09
103 177 0.18
104 101 0.10
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (101 bp):
TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAGATGCTATGTT
Found at i:11316 original size:51 final size:51
Alignment explanation
Indices: 10968--12086 Score: 1916
Period size: 51 Copynumber: 22.1 Consensus size: 51
10958 TCTAAACTCA
* *
10968 ATGCT-TGATTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAA
1 ATGCTATG-TTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11020 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11072 ATGCTATG---TTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11120 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
11172 ATGCTATGTTCTGTCTAACCAGATCAGATACCTCAAAGAACACTTTCAGAAG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11224 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11276 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11327 ATGCTATGTTCTGTCCAACCAGATCAG--AACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11377 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11428 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11480 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11531 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAG-A-ACTTCCAG-AG
1 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11580 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11631 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAG-ACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11681 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11732 ATGCTATGTTCTTC-AACCAGATCAGATAACTC-AAGAACGCTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11781 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11832 ATGCTATGTTCTTCTAACCAGATCA-AT-ACTC-AAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11880 ATG--ATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
11929 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACGCTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
11980 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
12031 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCC--AAG
1 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
12080 ATGCTAT
1 ATGCTAT
12087 TGAGCACATA
Statistics
Matches: 1024, Mismatches: 22, Indels: 45
0.94 0.02 0.04
Matches are distributed among these distances:
46 20 0.02
47 2 0.00
48 94 0.09
49 93 0.09
50 139 0.14
51 385 0.38
52 289 0.28
53 2 0.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (51 bp):
ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:13031 original size:6 final size:5
Alignment explanation
Indices: 13014--13081 Score: 61
Period size: 5 Copynumber: 13.8 Consensus size: 5
13004 GACCCCTCTT
* * *
13014 TTTTC TTTT- TTTCC TTTTC TTTTT TTTTC TTTTC TTTT- TTTCTT TTTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTT-TC TTTTC
*
13063 TTTTTC TTTT- TTCTC TTTT
1 -TTTTC TTTTC TTTTC TTTT
13082 TTTCTTCTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
4 9 0.18
5 34 0.67
6 8 0.16
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTTC
Found at i:13037 original size:15 final size:15
Alignment explanation
Indices: 13014--13085 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
13004 GACCCCTCTT
13014 TTTTC-TTTTTTTCC
1 TTTTCTTTTTTTTCC
*
13028 TTTTCTTTTTTTTTC
1 TTTTCTTTTTTTTCC
13043 TTTTC-TTTTTTT-C
1 TTTTCTTTTTTTTCC
* *
13056 TTTT-TTCTTTTTCTT
1 TTTTCTTTTTTTTC-C
13071 TTTTCTCTTTTTTTC
1 TTTTCT-TTTTTTTC
13086 TTCTTCAAGC
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
13 11 0.23
14 12 0.25
15 17 0.35
16 1 0.02
17 7 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTTTTCC
Found at i:13038 original size:13 final size:13
Alignment explanation
Indices: 13014--13081 Score: 63
Period size: 13 Copynumber: 5.3 Consensus size: 13
13004 GACCCCTCTT
13014 TTTTCTTTTTTTCC
1 TTTTC-TTTTTTCC
13028 TTTTC-TTTTT--
1 TTTTCTTTTTTCC
*
13038 TTTTCTTTTCTT-T
1 TTTTCTTTT-TTCC
*
13051 TTTTCTTTTTTCT
1 TTTTCTTTTTTCC
13064 TTTTCTTTTTTCTC
1 TTTTCTTTTTTC-C
13078 TTTT
1 TTTT
13082 TTTCTTCTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
10 5 0.10
11 3 0.06
12 9 0.19
13 22 0.46
14 9 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTTTCC
Found at i:13062 original size:30 final size:30
Alignment explanation
Indices: 13012--13087 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
13002 TTGACCCCTC
*
13012 TTTTTTCTTTTTTTC-CTTTTCTTTTT-TT
1 TTTTTTCTTTTTTTCTTTTTTCTTTTTCTT
13040 TTCTTTTCTTTTTTTCTTTTTTCTTTTTCTT
1 TT-TTTTCTTTTTTTCTTTTTTCTTTTTCTT
*
13071 TTTTCTCTTTTTTTCTT
1 TTTTTTCTTTTTTTCTT
13088 CTTCAAGCAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 2 0.05
29 13 0.30
30 24 0.56
31 4 0.09
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (30 bp):
TTTTTTCTTTTTTTCTTTTTTCTTTTTCTT
Found at i:13089 original size:13 final size:12
Alignment explanation
Indices: 13012--13089 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 12
13002 TTGACCCCTC
13012 TTTTTTCT-TTT
1 TTTTTTCTCTTT
13023 TTTCCTTT-TCTTT
1 TTT--TTTCTCTTT
13036 TTTTTTCT-TTT
1 TTTTTTCTCTTT
13047 CTTTTTT-TCTTT
1 -TTTTTTCTCTTT
* *
13059 TTTCTT-T-TTC
1 TTTTTTCTCTTT
13069 TTTTTTCTCTTT
1 TTTTTTCTCTTT
13081 TTTTCTTCT
1 TTTT-TTCT
13090 TCAAGCATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 7 0.13
11 17 0.31
12 17 0.31
13 13 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTCTCTTT
Found at i:13089 original size:20 final size:18
Alignment explanation
Indices: 13010--13090 Score: 67
Period size: 20 Copynumber: 4.2 Consensus size: 18
13000 CCTTGACCCC
*
13010 TCTTTTTTCTTTTTTTCCTTT
1 TCTTTTTT-TTTTTTT--TCT
*
13031 TCTTTTTTTTTCTTTTCT
1 TCTTTTTTTTTTTTTTCT
13049 T-TTTTTCTTTTTTCTTT-T
1 TCTTTTT-TTTTTT-TTTCT
13067 TCTTTTTTCTCTTTTTTTCT
1 TCTTTTTT-T-TTTTTTTCT
13087 TCTT
1 TCTT
13091 CAAGCATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
17 5 0.10
18 11 0.22
19 12 0.24
20 15 0.29
21 8 0.16
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TCTTTTTTTTTTTTTTCT
Found at i:23628 original size:17 final size:17
Alignment explanation
Indices: 23589--23631 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
23579 AATACTTGCA
23589 AATAAAACATATAAATAT
1 AATAAAA-ATATAAATAT
*
23607 TATAAAAATA-ATAATAT
1 AATAAAAATATA-AATAT
23624 AATAAAAA
1 AATAAAAA
23632 AAATTTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 15 0.68
18 6 0.27
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAAATATAAATAT
Found at i:25747 original size:3 final size:3
Alignment explanation
Indices: 25739--25854 Score: 196
Period size: 3 Copynumber: 38.7 Consensus size: 3
25729 TAATATAAAT
* *
25739 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
25787 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25835 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
25855 TGGATAAAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 105 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28279 original size:17 final size:17
Alignment explanation
Indices: 28257--28291 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28247 CATTTTTCTC
*
28257 ACTTGTGTTGCATATTA
1 ACTTGTGGTGCATATTA
*
28274 ACTTGTGGTGCATGTTA
1 ACTTGTGGTGCATATTA
28291 A
1 A
28292 ACTAAAGTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.11, G:0.23, T:0.43
Consensus pattern (17 bp):
ACTTGTGGTGCATATTA
Found at i:31154 original size:25 final size:25
Alignment explanation
Indices: 31125--31184 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
31115 ATTAATTTTT
31125 ATTTAAATATTCGAATTACGAATAA
1 ATTTAAATATTCGAATTACGAATAA
31150 ATTTAAATATTCGAATTACGAATAA
1 ATTTAAATATTCGAATTACGAATAA
31175 ATTTAGAATA
1 ATTTA-AATA
31185 ATTGATTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 30 0.88
26 4 0.12
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTTAAATATTCGAATTACGAATAA
Found at i:36774 original size:21 final size:20
Alignment explanation
Indices: 36750--36798 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
36740 GATTTAATAC
*
36750 TATTACAATATTTTTTAGAAA
1 TATTACAATATATTTTA-AAA
**
36771 TATTATTATATATTTTAAAA
1 TATTACAATATATTTTAAAA
36791 TA-TACAAT
1 TATTACAAT
36799 TATGGAACTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 4 0.17
20 5 0.22
21 14 0.61
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (20 bp):
TATTACAATATATTTTAAAA
Found at i:37227 original size:19 final size:19
Alignment explanation
Indices: 37203--37246 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
37193 ATTTTGGAAG
37203 TCCACAACATAAATCGTCA
1 TCCACAACATAAATCGTCA
37222 TCCACAACATAAATCGTCA
1 TCCACAACATAAATCGTCA
37241 TCCACA
1 TCCACA
37247 TGTACATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.34, G:0.05, T:0.20
Consensus pattern (19 bp):
TCCACAACATAAATCGTCA
Found at i:47466 original size:136 final size:136
Alignment explanation
Indices: 47280--47547 Score: 457
Period size: 136 Copynumber: 2.0 Consensus size: 136
47270 TCAGCTTCTT
*
47280 GGTTATACCATTAAGAGATTCATAAGTGGATGATTTCATTCACTGCTGCCATCTTATTCA-TAGC
1 GGTTATACCATTAAGAGATTCATAAGTGGATAATTTCATTCACTGCTGCCATCTTATTCATTA-C
* * *
47344 GCTTCACCTCTAAGTTAGTTAAACGTGCAGTGAAGACATAGAAAGAAATCCTCCATATGTACCTC
65 GCTTCACCTCTAAGTTAGTTAAAAGTGCAGTGAAGAAAGAGAAAGAAATCCTCCATATGTACCTC
47409 TCTATTC
130 TCTATTC
* *
47416 GGTTATACCATTAAGAGATTCATAAGTGGGTAATTTCATTCACTGCTGCCATCTTATTCATTATG
1 GGTTATACCATTAAGAGATTCATAAGTGGATAATTTCATTCACTGCTGCCATCTTATTCATTACG
*
47481 CTTCACCTCTAAGTTAGTTAAAAGTGCAGTGAAGAAAGAGAAAGAAATTCTCCATATGTACCTCT
66 CTTCACCTCTAAGTTAGTTAAAAGTGCAGTGAAGAAAGAGAAAGAAATCCTCCATATGTACCTCT
47546 CT
131 CT
47548 CTTTGTCGGG
Statistics
Matches: 124, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
136 122 0.98
137 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (136 bp):
GGTTATACCATTAAGAGATTCATAAGTGGATAATTTCATTCACTGCTGCCATCTTATTCATTACG
CTTCACCTCTAAGTTAGTTAAAAGTGCAGTGAAGAAAGAGAAAGAAATCCTCCATATGTACCTCT
CTATTC
Found at i:56489 original size:17 final size:19
Alignment explanation
Indices: 56455--56490 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
56445 TTAAAGTTAG
56455 TTTAAATGTATCATTATTT
1 TTTAAATGTATCATTATTT
56474 TTTAAAT-TAT-ATTATTT
1 TTTAAATGTATCATTATTT
56491 GTATTAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 3 0.18
19 7 0.41
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTAAATGTATCATTATTT
Found at i:59354 original size:21 final size:22
Alignment explanation
Indices: 59313--59354 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
59303 TTTTTAAAAA
*
59313 ATAATTATTTATATGAAATTGG
1 ATAATTATTTATATAAAATTGG
*
59335 ATAATTTTTTAT-TAAAATTG
1 ATAATTATTTATATAAAATTG
59355 AAAATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
ATAATTATTTATATAAAATTGG
Found at i:75580 original size:180 final size:182
Alignment explanation
Indices: 75168--75630 Score: 680
Period size: 180 Copynumber: 2.6 Consensus size: 182
75158 TAAAAATGTG
* * * * **
75168 TCGATCCAAAATGATATAACAGGTAAAACTATGACAAAACCGATATTGAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGATATCAAAATGATAAAACCGGTA
* * * * *
75233 AAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCGTGAATTTA
66 AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
* *
75298 AAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTAAAAAATATA
131 AAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTAAAAAAAATA
*
75350 TCGATCCAAAACGATATACCAGGTAAAAATATGATAAAATCGATATCAAAATGATAAAACCGGTA
1 TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGATATCAAAATGATAAAACCGGTA
* *
75415 AAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTTGTGAATTTA
66 AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
** * ** *
75479 AAAGAGAATTATTTTTAGCGCCTATAATGTGTCGATAC-TTTAAAAAAAATA
131 AAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTAAAAAAAATA
* *
75530 TCGAT-CAACAACGATATAACATGTAAAAATATGATAAAATCGGTATCAAAATGATAAAACCGGT
1 TCGATCCAA-AACGATATAACAGGTAAAAATATGATAAAATCGATATCAAAATGATAAAACCGGT
75594 AAAACGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAAACGATACCGGATATATTGAAAGTGTCGATACTTT
75631 CGTAAGTACG
Statistics
Matches: 255, Mismatches: 25, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
179 3 0.01
180 105 0.41
181 58 0.23
182 89 0.35
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
TCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGATATCAAAATGATAAAACCGGTA
AAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTCGTGAATTTA
AAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTTAAAAAAAATA
Found at i:76085 original size:19 final size:19
Alignment explanation
Indices: 76061--76109 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
76051 AATGTAGGGT
76061 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
76080 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
76099 TAATTTTGTAT
1 TAATTTTGTAT
76110 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:76120 original size:18 final size:19
Alignment explanation
Indices: 76061--76121 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 19
76051 AATGTAGGGT
* *
76061 TAATTTTGTATAAGATTTA
1 TAATTTTGTATATGATATA
*
76080 TAATTTTGTATATGATTTA
1 TAATTTTGTATATGATATA
*
76099 TAATTTTGTATGTGA-ATA
1 TAATTTTGTATATGATATA
76117 TAATT
1 TAATT
76122 ATGAATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
18 7 0.18
19 32 0.82
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATATGATATA
Found at i:76986 original size:183 final size:183
Alignment explanation
Indices: 76645--77230 Score: 971
Period size: 183 Copynumber: 3.2 Consensus size: 183
76635 ACAAGTTTTC
*
76645 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACATT-T
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
76709 TCAAAAAGTGTCG--ATTGAAAAAATATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
66 T-AAAAAGTGTCGACATT---TACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
*
76772 ATATAATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
127 ATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
76829 ACACTTTTTAATATTGTGTCGGTACTTTATGTTCATAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* *
76894 TAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGGTAATTTTGTAATAT
66 TAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
* *
76959 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAATCAATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
77012 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
77077 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 TAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
* *
77142 AACCGGTAAAAAATATACTGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGT-ATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
77196 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCA
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
77231 TAATTATAAT
Statistics
Matches: 377, Mismatches: 21, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
183 225 0.60
184 147 0.39
185 2 0.01
186 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
TAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:77321 original size:120 final size:121
Alignment explanation
Indices: 77107--77350 Score: 409
Period size: 120 Copynumber: 2.0 Consensus size: 121
77097 ACATCGGAAC
*
77107 CCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAAAAATATACTGGTTTTATGAG
1 CCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAAAAATATACCGGTTTTATGAG
*
77172 CGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * * * *
77228 CCATAATTATAATGTACTAGATAATTTTGTAATATAACTGGT-ATAAGTATACCGGTTTTATTAG
1 CCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAAAAATATACCGGTTTTATGAG
*
77292 CGAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
77348 CCA
1 CCA
77351 GAATGGAAGA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
120 75 0.65
121 40 0.35
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (121 bp):
CCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTAAAAAATATACCGGTTTTATGAG
CGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:79110 original size:23 final size:23
Alignment explanation
Indices: 79060--79104 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
79050 TGCCTATTTT
* *
79060 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
79083 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
79105 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:80310 original size:29 final size:28
Alignment explanation
Indices: 80255--80310 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
80245 ATAAATAAAA
* * *
80255 TTAAAATTTAATAATTATATTATAAATT
1 TTAAAATTTAATAATTAAAATACAAATT
*
80283 TTAAAATTTTAGTAATTAAAATACAAAT
1 TTAAAA-TTTAATAATTAAAATACAAAT
80311 GGCTTAAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (28 bp):
TTAAAATTTAATAATTAAAATACAAATT
Found at i:81021 original size:33 final size:33
Alignment explanation
Indices: 80983--81055 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
80973 TTTTGTTCGG
80983 GTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
* *
81016 GTCGGG-TTTTTTAAGTGTGATATTCGGGTTGG
1 GTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
81048 GTCGGGTT
1 GTCGGGTT
81056 CGGGTTTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 30 0.81
33 7 0.19
ACGTcount: A:0.12, C:0.08, G:0.37, T:0.42
Consensus pattern (33 bp):
GTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:85680 original size:78 final size:78
Alignment explanation
Indices: 85549--85704 Score: 294
Period size: 78 Copynumber: 2.0 Consensus size: 78
85539 CCGGCAAGGG
*
85549 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCGGTGGTCCTTCTCCCCT
1 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
85614 CTGCAACAAAGTC
66 CTGCAACAAAGTC
85627 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
1 GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
*
85692 CTGCAAGAAAGTC
66 CTGCAACAAAGTC
85705 AGGTCTTCCT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.13, C:0.30, G:0.22, T:0.35
Consensus pattern (78 bp):
GCCTTTCCTGCTTATTTTAGCTGCTGGGTCTGCAACACTTGGTGTCTCAGTGGTCCTTCTCCCCT
CTGCAACAAAGTC
Found at i:87548 original size:14 final size:16
Alignment explanation
Indices: 87524--87556 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
87514 CACGTGTCTT
87524 ATAATAAATATT-TAA
1 ATAATAAATATTATAA
87539 ATAA-AAATATTATAA
1 ATAATAAATATTATAA
87554 ATA
1 ATA
87557 GTTATCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAATAAATATTATAA
Found at i:89720 original size:16 final size:16
Alignment explanation
Indices: 89696--89744 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
89686 AATATTTTAA
89696 TTTTAATATAATATTC
1 TTTTAATATAATATTC
* *
89712 TTTTTATATATATAATC
1 TTTTAATATA-ATATTC
89729 TTTTAATTATAATATT
1 TTTTAA-TATAATATT
89745 TATTATGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.33
17 14 0.52
18 4 0.15
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTAATATAATATTC
Found at i:90190 original size:15 final size:15
Alignment explanation
Indices: 90166--90208 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
90156 ACATCATTAA
*
90166 ATTAATTTATAAAAC
1 ATTAAATTATAAAAC
*
90181 ATTAAATTATAAAAT
1 ATTAAATTATAAAAC
*
90196 ACTAAATGTATAA
1 ATTAAAT-TATAA
90209 TTACAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (15 bp):
ATTAAATTATAAAAC
Found at i:91192 original size:27 final size:27
Alignment explanation
Indices: 91149--91200 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
91139 CATATATAAT
91149 TTATAATATAATTAATAATAAATAACC
1 TTATAATATAATTAATAATAAATAACC
* *
91176 TTATAAT-TACTTAAATATTAAATAA
1 TTATAATATAATT-AATAATAAATAA
91201 TTGAATAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (27 bp):
TTATAATATAATTAATAATAAATAACC
Found at i:92636 original size:20 final size:19
Alignment explanation
Indices: 92590--92640 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
92580 TTTATAGAGA
92590 TTTTAT-TATAATAT--TC
1 TTTTATATATAATATAATC
92606 TTTTATATATATATATAATC
1 TTTTATATATA-ATATAATC
92626 TTTTA-ATTATAATAT
1 TTTTATA-TATAATAT
92641 TTTATGTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.20
17 4 0.13
18 4 0.13
19 5 0.17
20 11 0.37
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTATATATAATATAATC
Found at i:93499 original size:18 final size:19
Alignment explanation
Indices: 93463--93501 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
93453 TTTAGATGTG
93463 TTTGATACATGATATAATTA
1 TTTGATACATGA-ATAATTA
93483 TTTGATACATG-ATAATTA
1 TTTGATACATGAATAATTA
93501 T
1 T
93502 ATAAATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.46
Consensus pattern (19 bp):
TTTGATACATGAATAATTA
Found at i:95840 original size:17 final size:15
Alignment explanation
Indices: 95804--95844 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
95794 TTGTTAAAAT
*
95804 TGAATGGTTTAGCAC
1 TGAATGATTTAGCAC
95819 TGAATGATTTAGCAGTC
1 TGAATGATTTAGCA--C
95836 TGAATGATT
1 TGAATGATT
95845 AAGAGGCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.57
17 10 0.43
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (15 bp):
TGAATGATTTAGCAC
Found at i:97710 original size:41 final size:40
Alignment explanation
Indices: 97655--98053 Score: 409
Period size: 41 Copynumber: 9.8 Consensus size: 40
97645 CAAAATACTA
* *
97655 TACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGAATCG
1 TACTTTAGTGGCGTTT-TATACAAACGCCGCTATAGAATCG
* * *
97696 TAATGTAGTGGCGTTTTTATACAAACGCCGCTATA-AACTAG
1 TACTTTAGTGGCG-TTTTATACAAACGCCGCTATAGAA-TCG
* *
97737 TATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACA-CG
1 TACTTTAGTGGCG-TTTTATACAAACGCCGCTATAGA-ATCG
* * *
97778 TACTTTA-TGGCGTTTTAATACCAAACGACGCTATAGACTCA
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCCGCTATAGAATCG
* *
97819 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGC-GTTTTATACAAACGCCGCTATAGA-ATCG
* *
97860 TACTTTTGTGGCATTTTAATACCAAACGCCGCTATAG-A-CG
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCCGCTATAGAATCG
*
97900 TACTTT-GTGGCGTTTTAATACCAAACGCCGCTATAGATTCG
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCCGCTATAGAATCG
*
97941 TACTTTAGTGGCGTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGA-ATCG
* * * *
97981 TACTTTTGTGGCATTTAATAACAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTAT-ACAAACGCCGCTATAGAATCG
98022 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTT-ATA-CAAACGCCGC
98054 AATTGTCATA
Statistics
Matches: 304, Mismatches: 34, Indels: 39
0.81 0.09 0.10
Matches are distributed among these distances:
39 33 0.11
40 56 0.18
41 163 0.54
42 47 0.15
43 5 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (40 bp):
TACTTTAGTGGCGTTTTATACAAACGCCGCTATAGAATCG
Found at i:97803 original size:82 final size:83
Alignment explanation
Indices: 97636--98053 Score: 482
Period size: 81 Copynumber: 5.1 Consensus size: 83
97626 CGTTTTTGAA
* * * * * * *
97636 CAAACGCCGCAAAATACTA-TACTTTAGTGGCGTTTGTATAAAAACGCCGCTAAAGA-ATCGTAA
1 CAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CGTAC
* *
97699 TGTAGTGGCGTTTTTATA-
65 TTTAGTGGCGTTTTAATAC
* * *
97717 CAAACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACACGTACT
1 CAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACT
97782 TTA-TGGCGTTTTAATAC
66 TTAGTGGCGTTTTAATAC
* * *
97799 CAAACGACGCTATAGACTCA-TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTAC
1 CAAACGCCGCTATAGACT-AGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTAC
* *
97863 TTTTGTGGCATTTTAATAC
65 TTTAGTGGCGTTTTAATAC
* **
97882 CAAACGCCGCTATAGAC--GTACTTT-GTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTAC
1 CAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACACGTAC
*
97944 TTTAGTGGCGTTTT-ACA-
65 TTTAGTGGCGTTTTAATAC
* * * *
97961 CAAACGCCGCTATAGAC-ACGTACTTTTGTGGC-ATTTAATAACAAACGCCGCTATAGACTCGTA
1 CAAACGCCGCTATAGACTA-GTACTTTAGTGGCGTTTTTAT-ACAAACGCCGCTATAGACACGTA
98024 CTTTAGTGGCGTTTTAATAC
64 CTTTAGTGGCGTTTTAATAC
98044 CAAACGCCGC
1 CAAACGCCGC
98054 AATTGTCATA
Statistics
Matches: 293, Mismatches: 31, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.06
80 13 0.04
81 116 0.40
82 106 0.36
83 41 0.14
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (83 bp):
CAAACGCCGCTATAGACTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACT
TTAGTGGCGTTTTAATAC
Found at i:100214 original size:20 final size:20
Alignment explanation
Indices: 100189--100244 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
100179 TGATTTATTA
**
100189 TTATGGATTCATTTTTCTTG
1 TTATGGATTCAAGTTTCTTG
* *
100209 TTATGGATTTAAGTTTGTTG
1 TTATGGATTCAAGTTTCTTG
100229 TTATGGATGTCAAGTT
1 TTATGGAT-TCAAGTT
100245 ATTGGAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 24 0.80
21 6 0.20
ACGTcount: A:0.20, C:0.05, G:0.21, T:0.54
Consensus pattern (20 bp):
TTATGGATTCAAGTTTCTTG
Found at i:100417 original size:40 final size:40
Alignment explanation
Indices: 100372--100509 Score: 134
Period size: 43 Copynumber: 3.3 Consensus size: 40
100362 TTTGTATCTT
* *
100372 AAAACGCCGCTATATACCAGATTTTGCGGTGTTTGTGGGA
1 AAAACGCCGCTATATACCAGATATTGCGGCGTTTGTGGGA
* *
100412 AAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTGT-GGA
1 AAAACGCCGCTATATA-CCAGA--TATTGCGGCGTTTGTGGGA
* ** *
100454 CAAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTGTGGAA
1 -AAAACGCCGCT--ATAT-ACCAGATATTGCGGCGTTTGTGGGA
100498 AAAACGCCGCTA
1 AAAACGCCGCTA
100510 AATCTCAACA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
40 15 0.19
41 5 0.06
42 3 0.04
43 50 0.62
44 2 0.03
45 4 0.05
46 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (40 bp):
AAAACGCCGCTATATACCAGATATTGCGGCGTTTGTGGGA
Found at i:100450 original size:43 final size:42
Alignment explanation
Indices: 100395--100617 Score: 272
Period size: 43 Copynumber: 5.3 Consensus size: 42
100385 ATACCAGATT
* *
100395 TTGCGGTGTTTGTGGGAAAAACGCCGCTAAATATCAAGACCTA
1 TTGCGGCGTTTGT-GGAAAAACGCCGCTAAATATCAACACCTA
100438 TTGCGGCGTTTGTGGACAAAACGCCGCTAAATATCAACACCTA
1 TTGCGGCGTTTGTGGA-AAAACGCCGCTAAATATCAACACCTA
*
100481 TTGCGGCGTTTGTGGAAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTGG-AAAAACGCCGCTAAATATCAACACCTA
* * *
100524 TTGCGGC-ATTGTTGGAAAAA-GCCACCAAATATCAACACCTA
1 TTGCGGCGTTTG-TGGAAAAACGCCGCTAAATATCAACACCTA
** * ***
100565 TTGC-GCGTTTGTCCAACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTGGAA-AAACGCCGCTAAATATCAACACCTA
100607 TTGCGGCGTTT
1 TTGCGGCGTTT
100618 TTGTTACCAA
Statistics
Matches: 157, Mismatches: 16, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
40 5 0.03
41 28 0.18
42 30 0.19
43 93 0.59
44 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (42 bp):
TTGCGGCGTTTGTGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:100606 original size:83 final size:86
Alignment explanation
Indices: 100411--100613 Score: 261
Period size: 83 Copynumber: 2.4 Consensus size: 86
100401 TGTTTGTGGG
* * * *
100411 AAAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTGTGGACAAAACGCCGCTAAATATCAAC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTGTGGACAAAACGCCACCAAATATCAAC
**
100476 ACCTATTGCGGCGTTTGTGGA
66 ACCTATTGCGGCGTTTGTCCA
*
100497 AAAAACGCCGCTAAATCTCAACACCTATTGCGGCA-TTGTTGGA-AAAA-GCCACCAAATATCAA
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTG-TGGACAAAACGCCACCAAATATCAA
100559 CACCTATTGC-GCGTTTGTCCA
65 CACCTATTGCGGCGTTTGTCCA
* * ***
100580 ACAAACGCCGCTATATATCGTTACCTATTGCGGC
1 AAAAACGCCGCTAAATATCAACACCTATTGCGGC
100614 GTTTTTGTTA
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
83 37 0.36
84 23 0.22
85 7 0.07
86 36 0.35
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (86 bp):
AAAAACGCCGCTAAATATCAACACCTATTGCGGCATTTGTGGACAAAACGCCACCAAATATCAAC
ACCTATTGCGGCGTTTGTCCA
Found at i:101429 original size:18 final size:18
Alignment explanation
Indices: 101408--101447 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
101398 CCGAAGGAGG
101408 TGAACGACAGAAGAAGGA
1 TGAACGACAGAAGAAGGA
* *
101426 TGAACGACCGAAGGAGGA
1 TGAACGACAGAAGAAGGA
101444 TGAA
1 TGAA
101448 TCGATTGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.35, T:0.07
Consensus pattern (18 bp):
TGAACGACAGAAGAAGGA
Found at i:106370 original size:58 final size:59
Alignment explanation
Indices: 106299--106409 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 59
106289 GACGATACCA
* *
106299 AAATAAAACAAAAAATAAACATTAGATATGATTTT-CAACAAATGAAAGTTTAGGTATC
1 AAATAAAACAAAAAATAAACATTAGATATGATTTTAAAACAAATAAAAGTTTAGGTATC
* * *
106357 AAATAAAATAAAAAATAAATATTAGATATGATTTTAAAATAAATAAAAGTTTA
1 AAATAAAACAAAAAATAAACATTAGATATGATTTTAAAACAAATAAAAGTTTA
106410 TGTAGTAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 33 0.70
59 14 0.30
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.30
Consensus pattern (59 bp):
AAATAAAACAAAAAATAAACATTAGATATGATTTTAAAACAAATAAAAGTTTAGGTATC
Found at i:120144 original size:83 final size:83
Alignment explanation
Indices: 120005--120191 Score: 329
Period size: 83 Copynumber: 2.3 Consensus size: 83
119995 GAGATTTTGA
120005 AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
1 AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
120070 ATAAGAGAGAATACAAGG
66 ATAAGAGAGAATACAAGG
* * *
120088 AGATTGTATCAGGGTTGAAATGTTCTAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAGTT
1 AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
120153 ATAAGAGAGAATACAAGG
66 ATAAGAGAGAATACAAGG
* *
120171 AGATTGTCTTAGGGTTTAAAT
1 AGATTGTATTAGGGTTGAAAT
120192 CATTTAATGA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 98 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (83 bp):
AGATTGTATTAGGGTTGAAATGTTCCAATAAGATAGGTTTCTTTTGAGTATAAACTCTAACAATT
ATAAGAGAGAATACAAGG
Found at i:120289 original size:36 final size:32
Alignment explanation
Indices: 120244--120338 Score: 124
Period size: 36 Copynumber: 2.9 Consensus size: 32
120234 TATTGTTCGA
120244 AATAATAAGAATAAAATATATTTTTTAAGTTAAGAT
1 AATAATAAGAATAAAATATATTTTTTAAGTT----T
120280 AATAATAAGAATAAAATATA-TTTTTAA-TTT
1 AATAATAAGAATAAAATATATTTTTTAAGTTT
120310 AAT-ATAAGAATAAAATATATTTTTATAAG
1 AATAATAAGAATAAAATATATTTTT-TAAG
120339 AATAAAATAT
Statistics
Matches: 56, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
29 16 0.29
30 8 0.14
31 3 0.05
34 2 0.04
35 7 0.12
36 20 0.36
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (32 bp):
AATAATAAGAATAAAATATATTTTTTAAGTTT
Found at i:120322 original size:29 final size:32
Alignment explanation
Indices: 120244--120334 Score: 125
Period size: 29 Copynumber: 2.8 Consensus size: 32
120234 TATTGTTCGA
120244 AATAATAAGAATAAAATATATTTTTTAAGTTAAGAT
1 AATAATAAGAATAAAATATA-TTTTTAAGTT---AT
120280 AATAATAAGAATAAAATATATTTTTAA-TT-T
1 AATAATAAGAATAAAATATATTTTTAAGTTAT
120310 AAT-ATAAGAATAAAATATATTTTTA
1 AATAATAAGAATAAAATATATTTTTA
120335 TAAGAATAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
29 22 0.40
30 4 0.07
34 2 0.04
35 7 0.13
36 20 0.36
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (32 bp):
AATAATAAGAATAAAATATATTTTTAAGTTAT
Found at i:120322 original size:35 final size:36
Alignment explanation
Indices: 120247--120326 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
120237 TGTTCGAAAT
*
120247 AATAAGAATAAAATATATTTTTTAAGTTAAGATAAT
1 AATAAGAATAAAATATATTTTTTAAGTTAAGATAAG
* *
120283 AATAAGAATAAAATATA-TTTTTAATTTAATATAAG
1 AATAAGAATAAAATATATTTTTTAAGTTAAGATAAG
120318 AATAA-AATA
1 AATAAGAATA
120327 TATTTTTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
34 4 0.10
35 20 0.49
36 17 0.41
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (36 bp):
AATAAGAATAAAATATATTTTTTAAGTTAAGATAAG
Found at i:120543 original size:29 final size:29
Alignment explanation
Indices: 120506--120588 Score: 98
Period size: 29 Copynumber: 2.8 Consensus size: 29
120496 AATAAAAACA
120506 AAATATATTTAATAAATTAAGACAAAAATT
1 AAATATATTTAATAAATTAAGACAAAAA-T
* *
120536 AAA-ATATTTAATAAGTTAAAACAAAAAT
1 AAATATATTTAATAAATTAAGACAAAAAT
*
120564 AAATATAATTTTAA-AATTTAAGACA
1 AAATAT-A-TTTAATAAATTAAGACA
120589 TATAACATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.09
29 24 0.52
30 13 0.28
31 5 0.11
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.33
Consensus pattern (29 bp):
AAATATATTTAATAAATTAAGACAAAAAT
Found at i:121337 original size:19 final size:19
Alignment explanation
Indices: 121300--121337 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
121290 TTTTGGGTGG
*
121300 GATCAAATCAAATTTAAAT
1 GATCAAATCAAATTCAAAT
121319 GATCAAATTCAAA-TCAAAT
1 GATCAAA-TCAAATTCAAAT
121338 AGAAAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (19 bp):
GATCAAATCAAATTCAAAT
Found at i:124903 original size:18 final size:19
Alignment explanation
Indices: 124882--124922 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
124872 TTTTTAATAT
124882 TTTTGTA-TTTATGATACG
1 TTTTGTATTTTATGATACG
* *
124900 TTTTTTATTTTTTGATACG
1 TTTTGTATTTTATGATACG
124919 TTTT
1 TTTT
124923 TTTATATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.17, C:0.05, G:0.12, T:0.66
Consensus pattern (19 bp):
TTTTGTATTTTATGATACG
Found at i:128094 original size:189 final size:189
Alignment explanation
Indices: 127774--128145 Score: 654
Period size: 189 Copynumber: 2.0 Consensus size: 189
127764 AGGGGTTATC
127774 CTAAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGGCTACTTTCCAA
1 CTAAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGGCTACTTTCCAA
* * * *
127839 ATTGCACTTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCATTTCAGTGTGCCACTTGGGAG
66 ATTGCACCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAG
* *
127904 GTGATGCTTTGTCCGGAATAAAGGACTCATTTCTTGTTTCCTGCTCTAGAAGCTTTACA
131 GTGATGCTTTGTCCGGAATAAAGGACTCAATTCTTGTTTCCTGCTCTAAAAGCTTTACA
* *
127963 CTAAGTAAAGACATCATTTCATCTTTCATTACTGGGACTTTACTTCCATAGGGGCTACTTTCCAT
1 CTAAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGGCTACTTTCCAA
*
128028 ATTGCCCCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAG
66 ATTGCACCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAG
*
128093 GTGATGCTTTGTCCGGAATAAAGGGCTCAATTCTTGTTTCCTGCTCTAAAAGC
131 GTGATGCTTTGTCCGGAATAAAGGACTCAATTCTTGTTTCCTGCTCTAAAAGC
128146 CTGCAAAATC
Statistics
Matches: 173, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
189 173 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (189 bp):
CTAAGTAAAGACATCATTTCATCTTTCATGACTGGGACTTTACTTCCATAGGGGCTACTTTCCAA
ATTGCACCTATCATTTTTCATTGGACTTGAAGATCTCAAAAGCAGTTCAGTGTGCAACTCGGGAG
GTGATGCTTTGTCCGGAATAAAGGACTCAATTCTTGTTTCCTGCTCTAAAAGCTTTACA
Found at i:140125 original size:24 final size:24
Alignment explanation
Indices: 140098--140143 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
140088 TGTTAGGAGG
140098 ATAAA-TCACTAAAATTGTAAGGGA
1 ATAAACTCA-TAAAATTGTAAGGGA
* *
140122 ATAAACTTATAAAATTTTAAGG
1 ATAAACTCATAAAATTGTAAGG
140144 ATGAAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 17 0.89
25 2 0.11
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (24 bp):
ATAAACTCATAAAATTGTAAGGGA
Found at i:147761 original size:26 final size:26
Alignment explanation
Indices: 147725--147781 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
147715 AGCTCGATTT
*
147725 GACTCGAAAACTCTGAAATGGAGTTC
1 GACTCGAAAACTCTGAAATGGAATTC
*
147751 GACTTGAAAACTCTGAAATGGAATTC
1 GACTCGAAAACTCTGAAATGGAATTC
147777 GACTC
1 GACTC
147782 AACTCGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (26 bp):
GACTCGAAAACTCTGAAATGGAATTC
Found at i:147794 original size:31 final size:29
Alignment explanation
Indices: 147726--147794 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 29
147716 GCTCGATTTG
*
147726 ACTCGAAAACTCTGAAATGGAGTTCGACT
1 ACTCGAAAACTCTGAAATGGAATTCGACT
147755 --T-GAAAACTCTGAAATGGAATTCGACT
1 ACTCGAAAACTCTGAAATGGAATTCGACT
147781 CAACTCGAAAACTC
1 --ACTCGAAAACTC
147795 GCGAGACTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
26 24 0.71
27 1 0.03
30 1 0.03
31 8 0.24
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.23
Consensus pattern (29 bp):
ACTCGAAAACTCTGAAATGGAATTCGACT
Found at i:151139 original size:25 final size:25
Alignment explanation
Indices: 151111--151178 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 25
151101 TTTTTTTTTC
151111 ATTTTTCT-TTGAGTTATAT-TATATT
1 ATTTTTCTATT-A-TTATATATATATT
151136 ATTTTTCTATTATTATATATATATAT
1 ATTTTTCTATTATTATATATATAT-T
* *
151162 ATATATTATATTATTAT
1 AT-TTTTCTATTATTAT
151179 TATTTTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 6 0.16
25 14 0.38
26 5 0.14
27 12 0.32
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (25 bp):
ATTTTTCTATTATTATATATATATT
Found at i:151373 original size:20 final size:20
Alignment explanation
Indices: 151348--151398 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
151338 CTATTTAGTA
151348 TTTTATTATTATACATACAT
1 TTTTATTATTATACATACAT
* *
151368 TTTTA-TATATATATATATAT
1 TTTTATTAT-TATACATACAT
151388 TTTTAATTATT
1 TTTT-ATTATT
151399 TTATTTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 3 0.12
20 18 0.69
21 2 0.08
22 3 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTATTATTATACATACAT
Found at i:151419 original size:22 final size:21
Alignment explanation
Indices: 151383--151443 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
151373 TATATATATA
* *
151383 TATATTTTTAATTATTTT-ATT
1 TATATATTTATTTATTTTCA-T
151404 TATACTATTTATTTATTTTCAT
1 TATA-TATTTATTTATTTTCAT
*
151426 TATATTTTTAATTTATTT
1 TATATATTT-ATTTATTT
151444 GTTCTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 8 0.24
22 25 0.74
23 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
TATATATTTATTTATTTTCAT
Found at i:151439 original size:26 final size:27
Alignment explanation
Indices: 151410--151461 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
151400 TATTTATACT
151410 ATTTATTTATT-TTCATTA-TATTTTTA
1 ATTTATTTATTCTT-ATTATTATTTTTA
*
151436 ATTTATTTGTTCTTATTATTATTTTT
1 ATTTATTTATTCTTATTATTATTTTT
151462 CTTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 14 0.61
27 9 0.39
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (27 bp):
ATTTATTTATTCTTATTATTATTTTTA
Found at i:152123 original size:16 final size:16
Alignment explanation
Indices: 152078--152123 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
152068 ACACTGGTAT
152078 TTTTTATAAAAAAAATA
1 TTTTTAT-AAAAAAATA
152095 TTATTTA-AAAAAAATA
1 TT-TTTATAAAAAAATA
152111 TTTTTATATAAAA
1 TTTTTATA-AAAA
152124 TTTAGAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 4 0.15
16 12 0.46
17 6 0.23
18 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTTATAAAAAAATA
Found at i:161446 original size:20 final size:21
Alignment explanation
Indices: 161421--161471 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
161411 ACTAGTGTGG
*
161421 AAATTACTCAAT-GGTAAAAT
1 AAATTACTCAATCAGTAAAAT
*
161441 AAATTATTCAATCAGTAAAAT
1 AAATTACTCAATCAGTAAAAT
* *
161462 GAATTTCTCA
1 AAATTACTCA
161472 TGCAATTCAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (21 bp):
AAATTACTCAATCAGTAAAAT
Found at i:171894 original size:19 final size:19
Alignment explanation
Indices: 171870--171906 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
171860 TTATTTTGAA
171870 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
171889 TTTTTCACTATCGCAACA
1 TTTTTCACTATCGCAACA
171907 ACACGTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.05, T:0.38
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:171955 original size:19 final size:19
Alignment explanation
Indices: 171871--171956 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 19
171861 TATTTTGAAT
* *
171871 TTTTCACTATCGCAACACT
1 TTTTAACTATCGCAACACA
*
171890 TTTTCACTATCGCAACAACA
1 TTTTAACTATCGCAAC-ACA
* *
171910 CGTTTTTCAAACTCTCGCAATACA
1 ---TTTT--AACTATCGCAACACA
*
171934 TTTTAACTATCGCAACATA
1 TTTTAACTATCGCAACACA
171953 TTTT
1 TTTT
171957 TCAAAATCGC
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
19 32 0.59
20 2 0.04
21 4 0.07
23 4 0.07
24 3 0.06
25 9 0.17
ACGTcount: A:0.30, C:0.27, G:0.06, T:0.37
Consensus pattern (19 bp):
TTTTAACTATCGCAACACA
Found at i:172166 original size:19 final size:19
Alignment explanation
Indices: 172122--172166 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
172112 TATTTTCTCT
*
172122 TATAATTATTATATTTGTA
1 TATAATTTTTATATTTGTA
172141 T-TAATTTTTATATTT-TA
1 TATAATTTTTATATTTGTA
172158 TAATAATTT
1 T-ATAATTT
172167 ATACACATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 7 0.30
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATAATTTTTATATTTGTA
Found at i:174105 original size:15 final size:14
Alignment explanation
Indices: 174086--174126 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
174076 GCAAATAAAA
174086 TTATAATTAATATT
1 TTATAATTAATATT
174100 TATATAATT-ATATT
1 T-TATAATTAATATT
*
174114 TT-TAATAAATATT
1 TTATAATTAATATT
174127 ACAATACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 4 0.17
13 6 0.25
14 7 0.29
15 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATAATTAATATT
Found at i:175030 original size:22 final size:22
Alignment explanation
Indices: 175005--175051 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
174995 CATGCCATAA
*
175005 AAAATAAGA-AAAATTGTGTCAT
1 AAAA-AAGAGAAAAGTGTGTCAT
*
175027 AAAAAAGAGTAAAGTGTGTCAT
1 AAAAAAGAGAAAAGTGTGTCAT
175049 AAA
1 AAA
175052 TGTAAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.55, C:0.04, G:0.17, T:0.23
Consensus pattern (22 bp):
AAAAAAGAGAAAAGTGTGTCAT
Found at i:175761 original size:28 final size:29
Alignment explanation
Indices: 175706--175763 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
175696 TGTTTGTTGA
*** *
175706 AGAAATTATATTATATTTTTTTATTAAAT
1 AGAAATTATATTATATTTTAAAAATAAAT
175735 AGAAA-TATATTATATTTTAAAAATAAAT
1 AGAAATTATATTATATTTTAAAAATAAAT
175763 A
1 A
175764 TCAAATTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 20 0.80
29 5 0.20
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (29 bp):
AGAAATTATATTATATTTTAAAAATAAAT
Found at i:176306 original size:2 final size:2
Alignment explanation
Indices: 176299--176344 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
176289 ATTAATTCAA
176299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176341 AT AT
1 AT AT
176345 GAATCAAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:184514 original size:3 final size:3
Alignment explanation
Indices: 184506--184531 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
184496 ACTTTTACTT
184506 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
184532 TTCATTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:187337 original size:33 final size:33
Alignment explanation
Indices: 187295--187361 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
187285 AATAAGACTC
187295 ATAGAAAGATCATTTTCAACAATGAACAAATGA
1 ATAGAAAGATCATTTTCAACAATGAACAAATGA
**
187328 ATAGAAAGATCATTTTCAAGGATGAACAAATGA
1 ATAGAAAGATCATTTTCAACAATGAACAAATGA
187361 A
1 A
187362 AAACCTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.24
Consensus pattern (33 bp):
ATAGAAAGATCATTTTCAACAATGAACAAATGA
Found at i:191251 original size:45 final size:43
Alignment explanation
Indices: 191196--191279 Score: 105
Period size: 45 Copynumber: 1.9 Consensus size: 43
191186 CTATTATTTA
* * *
191196 ATTTTTATTTTAATCTTTTAATTATTATTTTCTGAAAATCATTAT
1 ATTTTAATTTTAATCTTTTAATT-TT-TTTTATAAAAATCATTAT
* *
191241 ATTTTAATTTTATTTTTTTAATTTTTTTTATAAAAATCA
1 ATTTTAATTTTAATCTTTTAATTTTTTTTATAAAAATCA
191280 ACATAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 12 0.35
44 2 0.06
45 20 0.59
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (43 bp):
ATTTTAATTTTAATCTTTTAATTTTTTTTATAAAAATCATTAT
Found at i:192044 original size:2 final size:2
Alignment explanation
Indices: 192037--192065 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
192027 CCAAATTCAT
192037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
192066 TAGTTGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:201347 original size:14 final size:14
Alignment explanation
Indices: 201324--201356 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
201314 AAAAAAGCTA
*
201324 TTTT-TTTGTTCAC
1 TTTTATTTGTTAAC
201337 TTTTATTTGTTAAC
1 TTTTATTTGTTAAC
201351 TTTTAT
1 TTTTAT
201357 ATTTACTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.15, C:0.09, G:0.06, T:0.70
Consensus pattern (14 bp):
TTTTATTTGTTAAC
Found at i:201688 original size:16 final size:16
Alignment explanation
Indices: 201667--201697 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
201657 TATTTATTCT
201667 CTCTCATACATAAACA
1 CTCTCATACATAAACA
201683 CTCTCATACATAAAC
1 CTCTCATACATAAAC
201698 GTATCTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (16 bp):
CTCTCATACATAAACA
Found at i:203702 original size:60 final size:60
Alignment explanation
Indices: 203532--203703 Score: 190
Period size: 60 Copynumber: 2.9 Consensus size: 60
203522 GTCCCTTAAC
* *
203532 TATAA-GATATTGTTTTGTTGAGT-TCTTTAACTATTAAAAGTTACAAAATGATCATCTGAT
1 TATAAGGA-ATTGTTTTGTTGAGTCT-TTTGACTATTAAAAGTTACAAAATGGTCATCTGAT
** * * * * *
203592 CGTAGGGAGTTGCTTTTG-TGAGTCTCTTGACTATTAAAGGTTACAAAATGGT-TTCCTGAT
1 TATAAGGAATTG-TTTTGTTGAGTCTTTTGACTATTAAAAGTTACAAAATGGTCAT-CTGAT
*
203652 TATAAGGAATTGTTTTGTTGAGTCTTTTGATTATTAAAAGTTACAAAATGGT
1 TATAAGGAATTGTTTTGTTGAGTCTTTTGACTATTAAAAGTTACAAAATGGT
203704 AACCCAATTA
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
59 6 0.07
60 77 0.85
61 8 0.09
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (60 bp):
TATAAGGAATTGTTTTGTTGAGTCTTTTGACTATTAAAAGTTACAAAATGGTCATCTGAT
Found at i:208537 original size:16 final size:16
Alignment explanation
Indices: 208516--208567 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
208506 AAAGTAATTT
208516 TAAAAATATATCATAA
1 TAAAAATATATCATAA
*
208532 TAAAAATA-AT--T-T
1 TAAAAATATATCATAA
208544 TAAAAATATATCATAA
1 TAAAAATATATCATAA
208560 TAAAAATA
1 TAAAAATA
208568 ATTTTAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 8 0.27
13 3 0.10
15 3 0.10
16 16 0.53
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAAATATATCATAA
Found at i:208596 original size:31 final size:28
Alignment explanation
Indices: 208504--208576 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
208494 GTGTTAACCC
*
208504 TAAAAGTAATTTTAAAAATATATCATAA
1 TAAAAATAATTTTAAAAATATATCATAA
208532 TAAAAATAATTTTAAAAATATATCATAA
1 TAAAAATAATTTTAAAAATATATCATAA
208560 TAAAAATAATTTTAAAA
1 TAAAAATAATTTTAAAA
208577 TAGATATATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (28 bp):
TAAAAATAATTTTAAAAATATATCATAA
Found at i:212554 original size:55 final size:56
Alignment explanation
Indices: 212450--212563 Score: 212
Period size: 55 Copynumber: 2.1 Consensus size: 56
212440 TAATTAAAAA
212450 ATATTTTATTTATTGATTTGTTTTTTTTTAATTATAATAAAATATAATTTTATTAT
1 ATATTTTATTTATTGATTTGTTTTTTTTTAATTATAATAAAATATAATTTTATTAT
*
212506 ATATTTTATTTATTGATTTG-TTTTTTTTAATTATAATCAAATATAATTTTATTAT
1 ATATTTTATTTATTGATTTGTTTTTTTTTAATTATAATAAAATATAATTTTATTAT
212561 ATA
1 ATA
212564 CTACCATAAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
55 37 0.65
56 20 0.35
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (56 bp):
ATATTTTATTTATTGATTTGTTTTTTTTTAATTATAATAAAATATAATTTTATTAT
Found at i:219060 original size:2 final size:2
Alignment explanation
Indices: 219011--219041 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
219001 GAAATAAACA
219011 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
219042 TTCACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:226032 original size:13 final size:13
Alignment explanation
Indices: 226014--226051 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
226004 CAACCCGACA
226014 CGACCCGTTGACC
1 CGACCCGTTGACC
226027 CGACCCGTTGACC
1 CGACCCGTTGACC
*
226040 CGGCCCGTTGAC
1 CGACCCGTTGAC
226052 AGTTGACCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.13, C:0.45, G:0.26, T:0.16
Consensus pattern (13 bp):
CGACCCGTTGACC
Found at i:226107 original size:29 final size:29
Alignment explanation
Indices: 226062--226117 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
226052 AGTTGACCGG
*
226062 GTGCTATTCTGGTAATTATTTGGAAAAGA
1 GTGCTATTCTGGAAATTATTTGGAAAAGA
*
226091 GTGCTATTCTGGAAATTATTTTGAAAA
1 GTGCTATTCTGGAAATTATTTGGAAAA
226118 TGGTGTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.07, G:0.21, T:0.39
Consensus pattern (29 bp):
GTGCTATTCTGGAAATTATTTGGAAAAGA
Found at i:226127 original size:29 final size:28
Alignment explanation
Indices: 226061--226127 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 28
226051 CAGTTGACCG
*
226061 GGTGCTATTCTGGTAATTATTTGGAAAA
1 GGTGCTATTCTGGAAATTATTTGGAAAA
*
226089 GAGTGCTATTCTGGAAATTATTTTGAAAA
1 G-GTGCTATTCTGGAAATTATTTGGAAAA
*
226118 TGGTGTTATT
1 -GGTGCTATT
226128 TTCATAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 32 0.94
30 1 0.03
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (28 bp):
GGTGCTATTCTGGAAATTATTTGGAAAA
Found at i:226160 original size:25 final size:26
Alignment explanation
Indices: 226124--226175 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
226114 AAAATGGTGT
226124 TATTTTCATAA-TTTTTTTAAAAAAA
1 TATTTTCATAATTTTTTTTAAAAAAA
*
226149 TATTTTCCTAATTTTTTTTAAAAAAA
1 TATTTTCATAATTTTTTTTAAAAAAA
226175 T
1 T
226176 GATATTTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTTTCATAATTTTTTTTAAAAAAA
Found at i:226189 original size:29 final size:29
Alignment explanation
Indices: 226135--226224 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
226125 ATTTTCATAA
**
226135 TTTTTTT-AAAAAA--ATATTTTCCTAAT
1 TTTTTTTAAAAAAATGATATTTTAGTAAT
226161 TTTTTTTAAAAAAATGATATTTTAGTAAT
1 TTTTTTTAAAAAAATGATATTTTAGTAAT
* * ***
226190 TATTTTGAAAATGGTGATA-TTTAGTAAT
1 TTTTTTTAAAAAAATGATATTTTAGTAAT
226218 TTTTTTT
1 TTTTTTT
226225 TGAAAATGAT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
26 7 0.13
27 6 0.12
28 14 0.27
29 25 0.48
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (29 bp):
TTTTTTTAAAAAAATGATATTTTAGTAAT
Found at i:226228 original size:30 final size:28
Alignment explanation
Indices: 226171--226241 Score: 83
Period size: 30 Copynumber: 2.5 Consensus size: 28
226161 TTTTTTTAAA
226171 AAAATGAT-AT-TTTAGTAATTATTTTG
1 AAAATGATGATATTTAGTAATTATTTTG
* *
226197 AAAATGGTGATATTTAGTAATTTTTTTTTG
1 AAAATGATGATATTTAGTAA--TTATTTTG
*
226227 AAAATGATGCTATTT
1 AAAATGATGATATTT
226242 TCGTAAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 7 0.19
27 2 0.05
28 8 0.22
30 20 0.54
ACGTcount: A:0.35, C:0.01, G:0.14, T:0.49
Consensus pattern (28 bp):
AAAATGATGATATTTAGTAATTATTTTG
Found at i:230451 original size:16 final size:16
Alignment explanation
Indices: 230432--230484 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
230422 CCATAACCCC
230432 TATCACACATATATCA
1 TATCACACATATATCA
** * *
230448 TATCATGCACACATCA
1 TATCACACATATATCA
230464 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
230482 TAT
1 TAT
230485 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:230840 original size:23 final size:23
Alignment explanation
Indices: 230814--230882 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
230804 CACCACAGCT
*
230814 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
* * *
230837 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTACACCGAAGTGCCA
*
230860 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTACACCGAAGTGCCA
230883 TATAATAACG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCA
Found at i:231077 original size:103 final size:103
Alignment explanation
Indices: 230898--231108 Score: 359
Period size: 103 Copynumber: 2.0 Consensus size: 103
230888 TAACGTCCAT
* *
230898 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
230963 GACTTCACACATGCTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATACTCCAAAGAATACATATATGTCCCG
* *
231001 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAATGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
231066 GACTTTACACATATTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATACTCCAAAGAATACATATATGTCCCG
231104 AAGGA
1 AAGGA
231109 TCGCGTAGAC
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATACTCCAAAGAATACATATATGTCCCG
Found at i:236598 original size:29 final size:29
Alignment explanation
Indices: 236422--236605 Score: 112
Period size: 29 Copynumber: 6.5 Consensus size: 29
236412 GTTGATCGGG
* *
236422 TGCTATTCTAGTAATTATTTGGAAAAGTG-
1 TGCTATTTTAGTAATTATTTTGAAAA-TGA
* * * *
236451 TGTTATTCTGGTAATTATTTTGAAAATGG
1 TGCTATTTTAGTAATTATTTTGAAAATGA
* * * * *
236480 TTCTATTTTTGTAAATATTTTTTAAAAAGA
1 TGCTATTTTAGTAATTA-TTTTGAAAATGA
* * **
236510 T--AATTTT--TAATT-TTTTTAAAAAAA
1 TGCTATTTTAGTAATTATTTTGAAAATGA
*
236534 TGGTATTTTAGTAATTATTTTGAAAAT-A
1 TGCTATTTTAGTAATTATTTTGAAAATGA
* * *
236562 GTGATATTTTGGTAATTTTTTTGAAAATGA
1 -TGCTATTTTAGTAATTATTTTGAAAATGA
*
236592 TGCTATTTTCGTAA
1 TGCTATTTTAGTAA
236606 AATGATTGTT
Statistics
Matches: 124, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
24 12 0.10
26 9 0.07
28 13 0.10
29 79 0.64
30 11 0.09
ACGTcount: A:0.33, C:0.03, G:0.14, T:0.49
Consensus pattern (29 bp):
TGCTATTTTAGTAATTATTTTGAAAATGA
Found at i:238619 original size:39 final size:40
Alignment explanation
Indices: 238534--238620 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
238524 GTCCTATCAT
* *
238534 TCTAAATTCTTAATTTCTTAAATTATTTTCACCACAACAT
1 TCTAAATTCTTAATTTCTTAAATTATTATCACCACAACAA
* * *
238574 TTTAAATTGTTAATTTCTTAAATTA-TATCACCCCAACAA
1 TCTAAATTCTTAATTTCTTAAATTATTATCACCACAACAA
238613 TCTAAATT
1 TCTAAATT
238621 ATATCTCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
39 18 0.44
40 23 0.56
ACGTcount: A:0.37, C:0.18, G:0.01, T:0.44
Consensus pattern (40 bp):
TCTAAATTCTTAATTTCTTAAATTATTATCACCACAACAA
Found at i:238800 original size:22 final size:21
Alignment explanation
Indices: 238762--238803 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
238752 AACCTTTAAA
*
238762 TTTTAAAAACAATATAATTTT
1 TTTTAAAAACAAAATAATTTT
*
238783 TTTTAAAAATTAAAATAATTT
1 TTTTAAAAA-CAAAATAATTT
238804 AAAATCAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
TTTTAAAAACAAAATAATTTT
Found at i:239468 original size:32 final size:31
Alignment explanation
Indices: 239426--239488 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
239416 TGTATATGGA
*
239426 TTATATTTATATCTATTTTA-ATTGTAATTAT
1 TTATATTTATAT-TATATTATATTGTAATTAT
*
239457 TTATATATTATATTATATTATATTGTGATTAT
1 TTATAT-TTATATTATATTATATTGTAATTAT
239489 AAATACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 12 0.43
32 16 0.57
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (31 bp):
TTATATTTATATTATATTATATTGTAATTAT
Found at i:254623 original size:10 final size:9
Alignment explanation
Indices: 254604--254628 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
254594 CATATGGAAG
254604 AAAAATAAA
1 AAAAATAAA
254613 AAAAATAAA
1 AAAAATAAA
254622 AAAAATA
1 AAAAATA
254629 TTTTTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAATAAA
Found at i:257115 original size:84 final size:84
Alignment explanation
Indices: 256974--257143 Score: 340
Period size: 84 Copynumber: 2.0 Consensus size: 84
256964 CTTTCTTTCC
256974 TTCTATTATTCAATTTTAATTTCTGTTGTTGCTATATTGCAGAAAGTGCAGTTTCTGTAGACAGA
1 TTCTATTATTCAATTTTAATTTCTGTTGTTGCTATATTGCAGAAAGTGCAGTTTCTGTAGACAGA
257039 GGAGGCAATTATGATACGG
66 GGAGGCAATTATGATACGG
257058 TTCTATTATTCAATTTTAATTTCTGTTGTTGCTATATTGCAGAAAGTGCAGTTTCTGTAGACAGA
1 TTCTATTATTCAATTTTAATTTCTGTTGTTGCTATATTGCAGAAAGTGCAGTTTCTGTAGACAGA
257123 GGAGGCAATTATGATACGG
66 GGAGGCAATTATGATACGG
257142 TT
1 TT
257144 TGTACTCCTT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 86 1.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (84 bp):
TTCTATTATTCAATTTTAATTTCTGTTGTTGCTATATTGCAGAAAGTGCAGTTTCTGTAGACAGA
GGAGGCAATTATGATACGG
Found at i:265667 original size:17 final size:17
Alignment explanation
Indices: 265624--265774 Score: 142
Period size: 18 Copynumber: 8.6 Consensus size: 17
265614 TTTGTTTCTA
* *
265624 ATAACTGTAAAACATATG
1 ATAACTGT-AAATATCTG
*
265642 ATATCTGTAAATATCTG
1 ATAACTGTAAATATCTG
*
265659 ATAAATGT-AATCATCTG
1 ATAACTGTAAAT-ATCTG
* *
265676 ATAAATGAAAATCATCTG
1 ATAACTGTAAAT-ATCTG
265694 ATAACTGTAAATATCTG
1 ATAACTGTAAATATCTG
* *
265711 ATAACTGAAAATAATTTG
1 ATAACTGTAAAT-ATCTG
* *
265729 ATAATTGTAAATATCTA
1 ATAACTGTAAATATCTG
* *
265746 ATAACGGTGAAATGTCTG
1 ATAACTGT-AAATATCTG
265764 ATAACTGTAAA
1 ATAACTGTAAA
265775 CATTTAGAAT
Statistics
Matches: 110, Mismatches: 19, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
16 3 0.03
17 53 0.48
18 54 0.49
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (17 bp):
ATAACTGTAAATATCTG
Found at i:265690 original size:18 final size:17
Alignment explanation
Indices: 265650--265749 Score: 94
Period size: 17 Copynumber: 5.8 Consensus size: 17
265640 TGATATCTGT
265650 AAATATCTGATAAATG-
1 AAATATCTGATAAATGA
*
265666 TAATCATCTGATAAATGA
1 AAAT-ATCTGATAAATGA
* *
265684 AAATCATCTGATAACTGT
1 AAAT-ATCTGATAAATGA
*
265702 AAATATCTGATAACTGA
1 AAATATCTGATAAATGA
* * *
265719 AAATAATTTGATAATTGT
1 AAAT-ATCTGATAAATGA
*
265737 AAATATCTAATAA
1 AAATATCTGATAA
265750 CGGTGAAATG
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
16 3 0.04
17 35 0.49
18 33 0.46
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (17 bp):
AAATATCTGATAAATGA
Found at i:265773 original size:35 final size:35
Alignment explanation
Indices: 265650--265774 Score: 123
Period size: 35 Copynumber: 3.6 Consensus size: 35
265640 TGATATCTGT
* * *
265650 AAAT-ATCTGATAAATGT-AATCATCTGATAAATGA
1 AAATAATCTGATAACTGTAAAT-ATCTAATAACTGA
* *
265684 AAATCATCTGATAACTGTAAATATCTGATAACTGA
1 AAATAATCTGATAACTGTAAATATCTAATAACTGA
* *
265719 AAATAATTTGATAATTGTAAATATCTAATAACGGTG-
1 AAATAATCTGATAACTGTAAATATCTAATAAC--TGA
*
265755 AAAT-GTCTGATAACTGTAAA
1 AAATAATCTGATAACTGTAAA
265775 CATTTAGAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
34 4 0.05
35 65 0.83
36 7 0.09
37 2 0.03
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (35 bp):
AAATAATCTGATAACTGTAAATATCTAATAACTGA
Found at i:266304 original size:18 final size:18
Alignment explanation
Indices: 266281--266320 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
266271 ATTTTAAACG
266281 AATCTAGATTGACATACA
1 AATCTAGATTGACATACA
*
266299 AATCTAGATTGACATACG
1 AATCTAGATTGACATACA
266317 AATC
1 AATC
266321 AACGATGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (18 bp):
AATCTAGATTGACATACA
Found at i:274165 original size:2 final size:2
Alignment explanation
Indices: 274158--274183 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
274148 ATCCAATCTA
274158 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
274184 TTAGGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:274573 original size:21 final size:21
Alignment explanation
Indices: 274549--274600 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
274539 AAAAATTATG
*
274549 TTTTAAGTAAAAATGATAACA
1 TTTTAAGTAAAAATAATAACA
* *
274570 TTTTAGGTAAAAATAATAATA
1 TTTTAAGTAAAAATAATAACA
274591 TTTTAAGTAA
1 TTTTAAGTAA
274601 CTTTTTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAGTAAAAATAATAACA
Found at i:275721 original size:36 final size:36
Alignment explanation
Indices: 275668--275863 Score: 293
Period size: 36 Copynumber: 5.4 Consensus size: 36
275658 GTGCGATACA
** *
275668 TCCTTCCGTTCAACTTGAATCGGAAGTGTTGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
* *
275704 TCCTTCCGTTCGTCTTGAATAGGAAGTGCTGATGAT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
275740 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
* * *
275776 TCATTCCGTTCGTCTTGAATTGGAAGTTCTGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
* *
275812 TCCTTCCGTTCGACTTGAATCGGAAGTGCCGATGCT
1 TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
*
275848 TCCTTCCGTTCTTCTT
1 TCCTTCCGTTCGTCTT
275864 ATTCACAATA
Statistics
Matches: 143, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 143 1.00
ACGTcount: A:0.16, C:0.24, G:0.22, T:0.38
Consensus pattern (36 bp):
TCCTTCCGTTCGTCTTGAATCGGAAGTGCTGATGCT
Found at i:278268 original size:20 final size:20
Alignment explanation
Indices: 278239--278281 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
278229 ATTTCACCAC
* *
278239 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCAAA
*
278259 ATGCATCTATATGATCCAAA
1 ATGCAACTATATGATCCAAA
278279 ATG
1 ATG
278282 GGCTTTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAACTATATGATCCAAA
Found at i:281372 original size:29 final size:29
Alignment explanation
Indices: 281311--281384 Score: 76
Period size: 29 Copynumber: 2.5 Consensus size: 29
281301 GTCTGCAAAA
* ** *
281311 AAAATTAATTAAATAAAATATTTAGCAATT
1 AAAA-TAATTAAATAAAATATTAAAAAACT
*
281341 AAAATAATTAAATAAATTATTAAAAAACT
1 AAAATAATTAAATAAAATATTAAAAAACT
*
281370 AAATATAATAAAATA
1 AAA-ATAATTAAATA
281385 TACCTTAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 23 0.62
30 14 0.38
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATAATTAAATAAAATATTAAAAAACT
Found at i:282343 original size:16 final size:17
Alignment explanation
Indices: 282314--282345 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
282304 TGTTTTTATC
282314 TTTTGTTCAAGTTTTTG
1 TTTTGTTCAAGTTTTTG
282331 TTTTGTT-AAGTTTTT
1 TTTTGTTCAAGTTTTT
282346 AACATTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.12, C:0.03, G:0.16, T:0.69
Consensus pattern (17 bp):
TTTTGTTCAAGTTTTTG
Found at i:291048 original size:46 final size:47
Alignment explanation
Indices: 290992--291094 Score: 158
Period size: 47 Copynumber: 2.2 Consensus size: 47
290982 TTTTAAGTAA
* *
290992 TTTTTT-ACTGAAAATGTT-AAAAAAATAACATTTCT-AGTAGTGTAT
1 TTTTTTAACTGAAAATATTAAAAAAAATAACATTTCTGA-TAGCGTAT
291037 TTTTTTAACTGAAAATATTAAAAAAAATAACATTTCTGATAGCGTAT
1 TTTTTTAACTGAAAATATTAAAAAAAATAACATTTCTGATAGCGTAT
291084 TTTTTTAACTG
1 TTTTTTAACTG
291095 TATATTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 6 0.11
46 11 0.21
47 35 0.66
48 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.43
Consensus pattern (47 bp):
TTTTTTAACTGAAAATATTAAAAAAAATAACATTTCTGATAGCGTAT
Found at i:308989 original size:39 final size:42
Alignment explanation
Indices: 308912--309000 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 42
308902 TATTTTAGAT
*
308912 ATTATAATAAATATATTAAATCGATTTAAAAAATTAAATA-TA
1 ATTAT-ATAAATATATTAAATCGAATTAAAAAATTAAATATTA
* ** *
308954 ATTATATAAATATATT-TATC-AATTAAATTATTAAATATTG
1 ATTATATAAATATATTAAATCGAATTAAAAAATTAAATATTA
308994 ATTATAT
1 ATTATAT
309001 TAAAATTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 14 0.34
40 11 0.27
41 11 0.27
42 5 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (42 bp):
ATTATATAAATATATTAAATCGAATTAAAAAATTAAATATTA
Found at i:309050 original size:20 final size:21
Alignment explanation
Indices: 309022--309068 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
309012 CATACATATA
*
309022 TAATTAAAA-TCATT-TTACAT
1 TAATAAAAACTCATTATTAC-T
*
309042 TAATAAAAACTGATTATTACT
1 TAATAAAAACTCATTATTACT
309063 TAATAA
1 TAATAA
309069 TAATAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 8 0.35
21 11 0.48
22 4 0.17
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (21 bp):
TAATAAAAACTCATTATTACT
Found at i:313968 original size:15 final size:15
Alignment explanation
Indices: 313948--314015 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
313938 TTCCGAAAGA
*
313948 TGAATTACTGTAATT
1 TGAATTACTGAAATT
313963 TGAATTACTGAAATT
1 TGAATTACTGAAATT
*
313978 TGAATTACTAAAATT
1 TGAATTACTGAAATT
**
313993 TGAATTACTGAAAAA
1 TGAATTACTGAAATT
314008 TGAATTAC
1 TGAATTAC
314016 ATTTCTGGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 48 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (15 bp):
TGAATTACTGAAATT
Found at i:314056 original size:14 final size:14
Alignment explanation
Indices: 314017--314057 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
314007 ATGAATTACA
* *
314017 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
314031 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
314045 TTTCCGTAAAATG
1 TTTCCGGAAAATG
314058 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:314291 original size:31 final size:31
Alignment explanation
Indices: 314244--314306 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
314234 ATTAAATAGT
314244 ATTTTTATAATTTTATT-AATAAAAATATTA
1 ATTTTTATAATTTTATTAAATAAAAATATTA
*
314274 ATTTTTGTATATTTTATTGAAATAAAAATATTA
1 ATTTTTATA-ATTTTATT-AAATAAAAATATTA
314307 TAAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 8 0.28
31 8 0.28
33 13 0.45
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTTTTATAATTTTATTAAATAAAAATATTA
Found at i:314371 original size:23 final size:23
Alignment explanation
Indices: 314341--314385 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
314331 TATAGTGTTA
314341 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
314364 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
314386 AAATATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:314391 original size:23 final size:23
Alignment explanation
Indices: 314342--314404 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
314332 ATAGTGTTAT
**
314342 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
314365 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
*
314388 ATA-TATAAATAATATTA
1 ATATTTTAAA-AATATTA
314405 TTCATTATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:314433 original size:28 final size:27
Alignment explanation
Indices: 314380--314545 Score: 80
Period size: 29 Copynumber: 6.0 Consensus size: 27
314370 TTAAATATAT
314380 TTATTAAAATATATAAATAATATTATTCA
1 TTATT-AAATATATAAATAATATTATT-A
**
314409 TTATTAAATATATAAATTTTTTTATTATATA
1 TTATTAAATATATAAA---TAATATTAT-TA
314440 TTATTAAA-ATAATAATATAATATCT-TATA
1 TTATTAAATAT-ATAA-ATAATAT-TAT-TA
* * * *
314469 TTATTATA-ATATAATTGATTATTTTATA
1 TTATTAAATATATAAAT-AATATTAT-TA
314497 TATATTAAA-A-AT--ATAATATTATTA
1 T-TATTAAATATATAAATAATATTATTA
*
314521 TTA-TAAAT-TAATAAATAATAATATT
1 TTATTAAATAT-ATAAATAATATTATT
314546 TTGATGAAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 33
0.71 0.08 0.21
Matches are distributed among these distances:
22 4 0.04
23 2 0.02
24 5 0.05
25 6 0.05
26 11 0.10
27 2 0.02
28 26 0.24
29 29 0.26
30 3 0.03
31 20 0.18
32 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (27 bp):
TTATTAAATATATAAATAATATTATTA
Found at i:314490 original size:23 final size:24
Alignment explanation
Indices: 314451--314518 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 24
314441 TATTAAAATA
*
314451 ATAATATAATATCTTATATTAT-T
1 ATAATATAATATATTATATTATAT
*
314474 ATAATATAAT-TGATTATTTTATAT
1 ATAATATAATAT-ATTATATTATAT
* * *
314498 ATATTA-AAAATATAATATTAT
1 ATAATATAATATATTATATTAT
314519 TATTATAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.03
23 28 0.78
24 7 0.19
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
ATAATATAATATATTATATTATAT
Found at i:314501 original size:61 final size:59
Alignment explanation
Indices: 314366--314541 Score: 159
Period size: 60 Copynumber: 3.0 Consensus size: 59
314356 TTAATTAGTA
*
314366 TATTTTAAATATATTTATTAAAATATATAA-ATAATATTATTCATTATTAAATATATAAAT
1 TATTTTATATATA-TTATTAAAATA-ATAATATAATATTATTCATTATTAAATATATAAAT
* **
314426 TTTTTTATTATATATTATTAAAATAATAATATAATATCT-TAT-ATTATTATAATATAATTGAT
1 TATTTTA-TATATATTATTAAAATAATAATATAATAT-TAT-TCATTATTA-AATAT-ATAAAT
* ** *
314488 TATTTTATATATATTA--AAAAT-ATAATATTATTATTATAAATTAATAAATA-ATAA
1 TATTTTATATATATTATTAAAATAATAATA-TAATATTATTCATTATTAAATATATAA
314542 TATTTTGATG
Statistics
Matches: 97, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
56 2 0.02
58 11 0.11
59 21 0.22
60 32 0.33
61 21 0.22
62 10 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (59 bp):
TATTTTATATATATTATTAAAATAATAATATAATATTATTCATTATTAAATATATAAAT
Found at i:314776 original size:42 final size:42
Alignment explanation
Indices: 314718--314867 Score: 212
Period size: 42 Copynumber: 3.6 Consensus size: 42
314708 TACGTTCAGA
* * * *
314718 AAAACCAATTGCGTGAAACAAACACTGGAAAATATTTTCCGG
1 AAAACGAATTACGTGAAACAAACACTGGAAAACATTTTCTGG
*
314760 AAAACGAATTACGTGAAACAAACACGGGAAAACATTTTCTGG
1 AAAACGAATTACGTGAAACAAACACTGGAAAACATTTTCTGG
* *
314802 AAAACGAATTACGTGAAATAAATA-TGGGAAAACATTTTCTGG
1 AAAACGAATTACGTGAAACAAACACT-GGAAAACATTTTCTGG
*
314844 AAAACGAATTACATGAAACAAACA
1 AAAACGAATTACGTGAAACAAACA
314868 TAGGAATTCG
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
42 96 1.00
ACGTcount: A:0.47, C:0.15, G:0.17, T:0.21
Consensus pattern (42 bp):
AAAACGAATTACGTGAAACAAACACTGGAAAACATTTTCTGG
Found at i:314970 original size:20 final size:20
Alignment explanation
Indices: 314945--314982 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
314935 TTTGGTTCAC
314945 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
314965 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
314983 GGAATATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Done.