Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008111.1 Hibiscus syriacus cultivar Beakdansim tig00110647_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: 1666726
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
File 6 of 9
Found at i:1093093 original size:81 final size:81
Alignment explanation
Indices: 1092988--1093161 Score: 226
Period size: 81 Copynumber: 2.2 Consensus size: 81
1092978 CATGGGACGT
* * * *
1092988 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGAGGGAT-CAACATGGGATG
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGATGCAACATGGGACG
1093051 TGGGAATGCATGGGGGA
66 TGGGAATGCAT-GGGGA
* * *** *
1093068 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGGGGATGGTGCATTGGACG
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGATGCAACATGGGACG
*
1093133 TGGGAATGCATGGGGT
66 TGGGAATGCATGGGGA
1093149 GGGAATGCATGGG
1 GGGAATGCATGGG
1093162 GAGGGGATGG
Statistics
Matches: 80, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 12 0.15
81 50 0.62
82 18 0.22
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (81 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGATGCAACATGGGACG
TGGGAATGCATGGGGA
Found at i:1093115 original size:49 final size:47
Alignment explanation
Indices: 1092978--1093170 Score: 214
Period size: 49 Copynumber: 4.0 Consensus size: 47
1092968 ATGCAATCAA
* * * *
1092978 CATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATG
1 CATGGGACGTGGGAATGCAT-GGGGTGGGAATGCATGGGGAGGGGATG
* *
1093026 CATGGG--GAGGG-ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATG
1 CATGGGACGTGGGAAT--GCATGGG--GTGGGAATGCAT-GGGGAGGGGATG
1093075 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGG-GGGGATGGTG
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGA---TG
*
1093124 CATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGATG
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGATG
1093171 GTCACGGTGG
Statistics
Matches: 124, Mismatches: 9, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
45 2 0.02
46 12 0.10
47 9 0.07
48 28 0.23
49 56 0.45
50 11 0.09
51 4 0.03
52 2 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (47 bp):
CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGATG
Found at i:1093254 original size:32 final size:32
Alignment explanation
Indices: 1093213--1093276 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
1093203 AAGGTCCTGC
1093213 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1093245 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1 TGCATGCATGCGTTGCATCATAGCTCATAGCT
1093277 CAGAGATTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (32 bp):
TGCATGCATGCGTTGCATCATAGCTCATAGCT
Found at i:1093633 original size:21 final size:21
Alignment explanation
Indices: 1093585--1093633 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1093575 ACTAAAATCT
*
1093585 AGTTAATTAGTTTGTTAGTATA
1 AGTT-ATTAGTTTGTAAGTATA
* *
1093607 AATTATTAGTTTGTAAGTTTA
1 AGTTATTAGTTTGTAAGTATA
1093628 AGTTAT
1 AGTTAT
1093634 ATTATATTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (21 bp):
AGTTATTAGTTTGTAAGTATA
Found at i:1093643 original size:28 final size:28
Alignment explanation
Indices: 1093610--1093670 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
1093600 TAGTATAAAT
*
1093610 TATTAGTTTGTAAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
*
1093638 TATTAGTTTATTAGTTTAAGTTATATTA
1 TATTAGTTTATAAGTTTAAGTTATATTA
1093666 TATTA
1 TATTA
1093671 TATAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (28 bp):
TATTAGTTTATAAGTTTAAGTTATATTA
Found at i:1093727 original size:40 final size:44
Alignment explanation
Indices: 1093632--1093739 Score: 125
Period size: 47 Copynumber: 2.5 Consensus size: 44
1093622 AGTTTAAGTT
1093632 ATATTATATTAGTTTATTAGTTTAAGTTATATTATATTATATAAAA
1 ATATTA-ATTAGTTTATTAGTTTAAGTTATATTATA-TATATAAAA
*
1093678 ATTAGTTAATTAGTTTCTTAGTTTAAG-T-TATTA-A-ATATAAAA
1 A-TA-TTAATTAGTTTATTAGTTTAAGTTATATTATATATATAAAA
* *
1093720 ATATTAATTAATTTGTTAGT
1 ATATTAATTAGTTTATTAGT
1093740 GTCTTTAAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
40 15 0.26
41 2 0.04
42 9 0.16
44 1 0.02
45 5 0.09
46 2 0.04
47 20 0.35
48 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.08, T:0.51
Consensus pattern (44 bp):
ATATTAATTAGTTTATTAGTTTAAGTTATATTATATATATAAAA
Found at i:1094177 original size:16 final size:16
Alignment explanation
Indices: 1094156--1094212 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
1094146 TAATTTCCGT
1094156 TTTAAAAAATATTGTG
1 TTTAAAAAATATTGTG
*
1094172 TTTAAAAATATTTAGTGTTG
1 TTTAAAAA-A--TATTG-TG
*
1094192 TTTAAAAAATATTTTG
1 TTTAAAAAATATTGTG
1094208 TTTAA
1 TTTAA
1094213 TTTACATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 15 0.44
17 4 0.12
19 5 0.15
20 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (16 bp):
TTTAAAAAATATTGTG
Found at i:1094501 original size:26 final size:25
Alignment explanation
Indices: 1094472--1094530 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
1094462 AAATCATATT
*
1094472 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
1094498 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
1094524 ATTATTA
1 ATTATTA
1094531 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:1097904 original size:47 final size:46
Alignment explanation
Indices: 1097804--1097894 Score: 134
Period size: 44 Copynumber: 2.0 Consensus size: 46
1097794 CAACAAACAA
1097804 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
* *
1097851 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
1097894 A
1 A
1097895 ACTATATAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 11 0.26
44 13 0.31
45 5 0.12
46 6 0.14
47 7 0.17
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (46 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
Found at i:1097962 original size:41 final size:40
Alignment explanation
Indices: 1097825--1097962 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 40
1097815 CTATTTAACT
* *
1097825 AACACAAACTAATTAAATAATTTTTT-A-TATAACTAACTATT
1 AACATAAACTAATTAAAT-ATTTTTTAACTAT-A-TAACTATA
*
1097866 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATATTTTTTAACTATATAACTAT-A
* * *
1097910 AACATATACTAATTAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATATTTTTTAA-CTATATA-ACTATA
*
1097951 AACTTAAACTAA
1 AACATAAACTAA
1097963 CAATCATATA
Statistics
Matches: 80, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
41 33 0.41
42 6 0.08
43 21 0.26
44 17 0.21
45 3 0.04
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (40 bp):
AACATAAACTAATTAAATATTTTTTAACTATATAACTATA
Found at i:1098126 original size:4 final size:4
Alignment explanation
Indices: 1098099--1098155 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
1098089 TTTCGAATTC
* * **
1098099 TTCT TACT TTCCT TTC- TCCT TTCT TTCT TTCT TTCCT TTCT CCCT TTCT
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT
1098148 TTCT TTCT
1 TTCT TTCT
1098156 CGGCTGCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
3 2 0.05
4 32 0.76
5 8 0.19
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (4 bp):
TTCT
Found at i:1098132 original size:24 final size:25
Alignment explanation
Indices: 1098099--1098155 Score: 98
Period size: 24 Copynumber: 2.3 Consensus size: 25
1098089 TTTCGAATTC
*
1098099 TTCTTACTTTCCTTTCT-CCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
1098123 TTCTTTCTTTCCTTTCTCCCTTTCT
1 TTCTTTCTTTCCTTTCTCCCTTTCT
1098148 TTCTTTCT
1 TTCTTTCT
1098156 CGGCTGCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (25 bp):
TTCTTTCTTTCCTTTCTCCCTTTCT
Found at i:1098137 original size:17 final size:17
Alignment explanation
Indices: 1098115--1098156 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1098105 CTTTCCTTTC
**
1098115 TCCTTTCTTTCTTTCTT
1 TCCTTTCTCCCTTTCTT
1098132 TCCTTTCTCCCTTTCTT
1 TCCTTTCTCCCTTTCTT
1098149 T-CTTTCTC
1 TCCTTTCTC
1098157 GGCTGCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (17 bp):
TCCTTTCTCCCTTTCTT
Found at i:1098245 original size:25 final size:25
Alignment explanation
Indices: 1098217--1098268 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
1098207 TTTCTTTTAT
*
1098217 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
1098242 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
1098267 AA
1 AA
1098269 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:1098436 original size:26 final size:23
Alignment explanation
Indices: 1098379--1098438 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
1098369 ACACGTGAAG
1098379 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
1098402 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
*
1098425 GAATGGACGATGGG
1 GAATGGATGATGGG
1098439 AATGGCGCCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.08, G:0.45, T:0.23
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:1098477 original size:29 final size:29
Alignment explanation
Indices: 1098444--1098552 Score: 175
Period size: 29 Copynumber: 3.8 Consensus size: 29
1098434 ATGGGAATGG
1098444 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
1098473 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
*
1098502 CGCCGGGACTACATGGCGACCTACAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
* *
1098531 CGCCTAGG-CTGCATGGCGACCT
1 CGCC-GGGACTACATGGCGACCT
1098553 CTCTCCTATT
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
29 74 0.97
30 2 0.03
ACGTcount: A:0.22, C:0.30, G:0.31, T:0.17
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTATAAGGT
Found at i:1098584 original size:19 final size:19
Alignment explanation
Indices: 1098560--1098597 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1098550 CCTCTCTCCT
1098560 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
1098579 ATTCCACTGCATGGCCACC
1 ATTCCACTGCATGGCCACC
1098598 TCGCATGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (19 bp):
ATTCCACTGCATGGCCACC
Found at i:1098725 original size:55 final size:55
Alignment explanation
Indices: 1098660--1098770 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
1098650 GAACGACCTC
1098660 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1098715 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1098770 T
1 T
1098771 GGGGACCTCG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.16, C:0.34, G:0.22, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:1098747 original size:139 final size:139
Alignment explanation
Indices: 1098579--1098854 Score: 552
Period size: 139 Copynumber: 2.0 Consensus size: 139
1098569 CATGGCCACC
1098579 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1098644 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
1098709 TATGCATCT
131 TATGCATCT
1098718 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1 ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
1098783 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
66 TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
1098848 TATGCAT
131 TATGCAT
1098855 GGGGAGAACC
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.24
Consensus pattern (139 bp):
ATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCGCA
TGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCG
TATGCATCT
Found at i:1098752 original size:27 final size:27
Alignment explanation
Indices: 1098667--1098752 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1098657 CTCTCTATTC
1098667 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
* * * * ***
1098694 CACTCGTATGG-CTCGTATGCATCTATTC-
1 CACT-GCATGGCCACCT-CGCAT-GGCTCG
1098722 CACTGCATGGCCACCTCGCATGGCTCG
1 CACTGCATGGCCACCTCGCATGGCTCG
1098749 CACT
1 CACT
1098753 CGTATGGCTC
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
26 2 0.05
27 20 0.50
28 16 0.40
29 2 0.05
ACGTcount: A:0.16, C:0.37, G:0.22, T:0.24
Consensus pattern (27 bp):
CACTGCATGGCCACCTCGCATGGCTCG
Found at i:1098779 original size:41 final size:41
Alignment explanation
Indices: 1098725--1098856 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
1098715 TCTATTCCAC
1098725 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
1098766 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
1098808 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1098850 TGCATGG
1 TGCATGG
1098857 GGAGAACCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:1100019 original size:8 final size:8
Alignment explanation
Indices: 1100006--1100046 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
1099996 CTATGGCATT
1100006 TGCATCAA
1 TGCATCAA
1100014 TGCATCAA
1 TGCATCAA
1100022 TGCATCAA
1 TGCATCAA
1100030 TGCATCAA
1 TGCATCAA
1100038 TGCATCAA
1 TGCATCAA
1100046 T
1 T
1100047 CAGGGGGCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (8 bp):
TGCATCAA
Found at i:1103101 original size:33 final size:33
Alignment explanation
Indices: 1103059--1103125 Score: 118
Period size: 33 Copynumber: 2.0 Consensus size: 33
1103049 AATGATCTGT
1103059 ACTTGATTAATCTCC-ATTTCAACTTAAAGATTG
1 ACTTGATTAATCTCCTA-TTCAACTTAAAGATTG
1103092 ACTTGATTAATCTCCTATTCAACTTAAAGATTG
1 ACTTGATTAATCTCCTATTCAACTTAAAGATTG
1103125 A
1 A
1103126 TTTACAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (33 bp):
ACTTGATTAATCTCCTATTCAACTTAAAGATTG
Found at i:1104139 original size:32 final size:31
Alignment explanation
Indices: 1104098--1104189 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
1104088 AATATTAAAA
* * *
1104098 ATTATAAAATGATCATTAATTTTTATCAAATT
1 ATTATAAAATAATCATTAA-ATTTATCAAACT
*
1104130 ATTATAAAATAATTATTAAATTTATCAAACT
1 ATTATAAAATAATCATTAAATTTATCAAACT
* * * *
1104161 GTTATAAAACAATCTTTAAACTTATCAAA
1 ATTATAAAATAATCATTAAATTTATCAAA
1104190 ATTTATCATT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
31 34 0.67
32 17 0.33
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (31 bp):
ATTATAAAATAATCATTAAATTTATCAAACT
Found at i:1105878 original size:2 final size:2
Alignment explanation
Indices: 1105871--1105915 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1105861 TAAACCAGTA
1105871 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
1105913 AT A
1 AT A
1105916 GATGTATAAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1109202 original size:14 final size:14
Alignment explanation
Indices: 1109165--1109207 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1109155 GTTAGAGAAC
*
1109165 CGTTTGTTTATCTT
1 CGTTTGTTTATGTT
**
1109179 CGTTCATTTATGTT
1 CGTTTGTTTATGTT
1109193 CGTTTGTTTATGTT
1 CGTTTGTTTATGTT
1109207 C
1 C
1109208 TTCAGACTCG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.09, C:0.14, G:0.16, T:0.60
Consensus pattern (14 bp):
CGTTTGTTTATGTT
Found at i:1113643 original size:20 final size:21
Alignment explanation
Indices: 1113618--1113710 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1113608 TTTTCCCAAT
*
1113618 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1113638 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1113659 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1113679 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1113700 TCGCAATGCGA
1 TCGCAATGCGA
1113711 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1113663 original size:41 final size:41
Alignment explanation
Indices: 1113618--1113710 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1113608 TTTTCCCAAT
1113618 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1113659 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1113700 TCGCAATGCGA
1 TCGCAATGCGA
1113711 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1113723 original size:41 final size:41
Alignment explanation
Indices: 1113637--1113771 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1113627 GAATAAGTAA
** *
1113637 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1113678 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
1113719 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1113760 TTCGCAACGCGA
1 ATCGCAACGCGA
1113772 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1113724 original size:20 final size:20
Alignment explanation
Indices: 1113699--1113812 Score: 99
Period size: 20 Copynumber: 5.7 Consensus size: 20
1113689 AATTGGGAAA
1113699 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTTACT
* *
1113719 ATCGCAATGCGATA-ATACAAA
1 ATCGCAATGCGATACTTAC--T
* *
1113740 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTTACT
* * *
1113760 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTTACT
*
1113780 TTCGCAATGCGAT--TTACAT
1 ATCGCAATGCGATACTTAC-T
1113799 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
1113813 TTTCAAAGCG
Statistics
Matches: 77, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
18 3 0.04
19 4 0.05
20 55 0.71
21 12 0.16
22 3 0.04
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTTACT
Found at i:1114008 original size:22 final size:22
Alignment explanation
Indices: 1113980--1114023 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1113970 CACTCTCTCA
*
1113980 CCCATCTCTGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1114002 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1114024 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1115578 original size:18 final size:18
Alignment explanation
Indices: 1115557--1115601 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1115547 TCCACTTCGG
* *
1115557 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
1115575 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
1115593 GAGCCATCA
1 GAGCCATCA
1115602 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:1116145 original size:14 final size:14
Alignment explanation
Indices: 1116126--1116183 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1116116 ATGCGAAATG
1116126 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1116140 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
1116156 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1116172 AAAATCGCAACG
1 AAAATCGCAACG
1116184 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1116168 original size:32 final size:33
Alignment explanation
Indices: 1116110--1116200 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
1116100 GGAAATGGCT
*
1116110 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1116143 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1116175 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1116201 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1116194 original size:19 final size:19
Alignment explanation
Indices: 1116072--1116205 Score: 92
Period size: 19 Copynumber: 7.6 Consensus size: 19
1116062 TAGTTTACTT
* **
1116072 TCGCAACACGAAATGACTA
1 TCGCAACGCGAAATGAAAA
***
1116091 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
1116111 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1116130 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1116144 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
1116162 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
1116176 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1116195 TCGCAATGCGA
1 TCGCAACGCGA
1116206 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 35 0.38
20 17 0.18
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1116236 original size:14 final size:14
Alignment explanation
Indices: 1116217--1116274 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1116207 TTGTGTTTCG
1116217 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1116231 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1116247 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
1116263 CGTTGCGATTTT
1 CGTTGCGATTTT
1116275 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1116251 original size:32 final size:33
Alignment explanation
Indices: 1116212--1116290 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
1116202 GCGATTTGTG
1116212 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1116244 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
1116277 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1116291 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:1116289 original size:19 final size:17
Alignment explanation
Indices: 1116212--1116290 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 17
1116202 GCGATTTGTG
1116212 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
1116228 TGTCG-TTGCGATTTCA
1 TTTCGCTTGCGATTTCA
1116244 TTTCGCGTTGCGATTT--
1 TTTCGC-TTGCGATTTCA
*
1116260 TGTCG-TTGCGATTTTCA
1 TTTCGCTTGCGA-TTTCA
1116277 TTTCGCATTGCGAT
1 TTTCGC-TTGCGAT
1116291 AGCCATTTCC
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
14 15 0.30
15 3 0.06
16 12 0.24
17 4 0.08
18 10 0.20
19 6 0.12
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (17 bp):
TTTCGCTTGCGATTTCA
Found at i:1116309 original size:20 final size:19
Alignment explanation
Indices: 1116275--1116328 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
1116265 TTGCGATTTT
*
1116275 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
* *
1116294 CATTTCCGTGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1116314 CATTTCGCGTTGCGA
1 CATTTCGCGTTGCGA
1116329 ATTTAAGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1119020 original size:39 final size:38
Alignment explanation
Indices: 1118977--1119127 Score: 168
Period size: 39 Copynumber: 4.1 Consensus size: 38
1118967 TCTTTTGGTT
* * *
1118977 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAATGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** * *
1119016 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
1119049 GAAATGAAAATCGCAACCGCGAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
1119088 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
1119126 GA
1 GA
1119128 TTTTGGTTTC
Statistics
Matches: 93, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
33 25 0.27
34 2 0.02
35 1 0.01
38 23 0.25
39 42 0.45
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1119028 original size:19 final size:19
Alignment explanation
Indices: 1118977--1119127 Score: 168
Period size: 19 Copynumber: 8.1 Consensus size: 19
1118967 TCTTTTGGTT
*
1118977 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
1118996 GATAATGAGAATCGCAATGC
1 GA-AATGAAAATCGCAACGC
** *
1119016 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1119034 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1119049 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1119069 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1119088 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1119107 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1119126 GA
1 GA
1119128 TTTTGGTTTC
Statistics
Matches: 112, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
14 10 0.09
15 2 0.02
18 2 0.02
19 64 0.57
20 34 0.30
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1119145 original size:19 final size:19
Alignment explanation
Indices: 1119123--1119170 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1119113 AAAATCGCAA
*
1119123 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
1119142 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
1119162 TGCGATTTT
1 TGCGATTTT
1119171 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:1119781 original size:20 final size:20
Alignment explanation
Indices: 1119688--1119781 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1119678 GATTATGTAA
* *
1119688 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
1119708 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
1119728 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
1119749 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
1119769 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
1119782 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:1119799 original size:21 final size:21
Alignment explanation
Indices: 1119770--1119862 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
1119760 ATAGTAAGTA
1119770 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1119791 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1119811 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
1119832 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
1119852 TCGCATTGCGA
1 TCGCATTGCGA
1119863 ATTGGTAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:1119800 original size:41 final size:41
Alignment explanation
Indices: 1119709--1119843 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1119699 AAAGTCAGTA
* * * ** *
1119709 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-GTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
*
1119749 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
1119791 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
1119832 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1119844 TTACTTATTC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 4 0.05
41 75 0.93
42 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:1119844 original size:41 final size:41
Alignment explanation
Indices: 1119770--1119862 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1119760 ATAGTAAGTA
1119770 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1119811 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1119852 TCGCATTGCGA
1 TCGCATTGCGA
1119863 ATTGGTAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1126909 original size:35 final size:35
Alignment explanation
Indices: 1126863--1126937 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
1126853 AAAATACTTC
*
1126863 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
* * *
1126898 AATTTGGGGTTTAGAATGTGATTAAAGTGTTTTGG
1 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
1126933 AATTT
1 AATTT
1126938 TGAACATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
Found at i:1128478 original size:28 final size:28
Alignment explanation
Indices: 1128428--1128501 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
1128418 AACTGGTATT
1128428 ACCTGACCTGTTTTCAACCTGACCTGTTATGA
1 ACCTGACCTGTTTT----CTGACCTGTTATGA
* * * *
1128460 ACCTGACTTGTTTTCTGACTTGTTTTTA
1 ACCTGACCTGTTTTCTGACCTGTTATGA
1128488 ACCTGACCTGTTTT
1 ACCTGACCTGTTTT
1128502 TAACTTGATC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 24 0.65
32 13 0.35
ACGTcount: A:0.18, C:0.24, G:0.15, T:0.43
Consensus pattern (28 bp):
ACCTGACCTGTTTTCTGACCTGTTATGA
Found at i:1128514 original size:16 final size:16
Alignment explanation
Indices: 1128428--1128505 Score: 83
Period size: 16 Copynumber: 5.1 Consensus size: 16
1128418 AACTGGTATT
*
1128428 ACCTGACCTGTTTTCA
1 ACCTGACCTGTTTTTA
* *
1128444 ACCTGACCTGTTATGA
1 ACCTGACCTGTTTTTA
*
1128460 ACCTGACTTG-TTTT-
1 ACCTGACCTGTTTTTA
*
1128474 --CTGACTTGTTTTTA
1 ACCTGACCTGTTTTTA
1128488 ACCTGACCTGTTTTTA
1 ACCTGACCTGTTTTTA
1128504 AC
1 AC
1128506 TTGATCTGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
12 8 0.15
13 4 0.08
15 2 0.04
16 38 0.73
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.42
Consensus pattern (16 bp):
ACCTGACCTGTTTTTA
Found at i:1131884 original size:28 final size:28
Alignment explanation
Indices: 1131796--1131893 Score: 72
Period size: 28 Copynumber: 3.3 Consensus size: 28
1131786 TGATTTAATA
* *
1131796 TATTAATTTAAGCTTCATATTTCAACTT
1 TATTAATTTAAGCTTCATATTTAAAATT
* * * *
1131824 TTTTAATTTAATCCAAATTTA-ATGTTATAATT
1 TATTAATTTAA-GC---TTCATAT-TTAAAATT
1131856 TATTAATTTAAGCTTCATATTTAAAATT
1 TATTAATTTAAGCTTCATATTTAAAATT
*
1131884 TGTTCAATTT
1 TATT-AATTT
1131894 GATCCTTATA
Statistics
Matches: 52, Mismatches: 11, Indels: 13
0.68 0.14 0.17
Matches are distributed among these distances:
28 23 0.44
29 8 0.15
31 3 0.06
32 18 0.35
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (28 bp):
TATTAATTTAAGCTTCATATTTAAAATT
Found at i:1132008 original size:33 final size:33
Alignment explanation
Indices: 1131964--1132191 Score: 144
Period size: 33 Copynumber: 7.5 Consensus size: 33
1131954 ATATAATATA
*
1131964 TAAATACTATATAGTTTATATATACTAATGAAC
1 TAAATAATATATAGTTTATATATACTAATGAAC
*
1131997 TAAATAATATATAG-TT-TGTATAC------AC
1 TAAATAATATATAGTTTATATATACTAATGAAC
* * * *
1132022 CATATACTATATAGGTTATATATACTAATGAAC
1 TAAATAATATATAGTTTATATATACTAATGAAC
*
1132055 TATATAATATATAGTTTATATATACT-AT--A-
1 TAAATAATATATAGTTTATATATACTAATGAAC
1132084 T-AAT--T-TATA---TATAGTA-----ATGAAC
1 TAAATAATATATAGTTTATA-TATACTAATGAAC
*
1132106 TATATAATATATAGTTTATATATACTAATGAAC
1 TAAATAATATATAGTTTATATATACTAATGAAC
* *
1132139 TATATATATTATATAGTTTATATATACTAATAAAC
1 TA-A-ATAATATATAGTTTATATATACTAATGAAC
* * *
1132174 TATATAATGTATATTTTA
1 TAAATAATATATAGTTTA
1132192 GGATTTAGGG
Statistics
Matches: 151, Mismatches: 18, Indels: 52
0.68 0.08 0.24
Matches are distributed among these distances:
19 2 0.01
21 1 0.01
22 5 0.03
23 4 0.03
25 18 0.12
26 7 0.05
27 6 0.04
28 4 0.03
29 5 0.03
30 1 0.01
31 6 0.04
32 4 0.03
33 58 0.38
35 30 0.20
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.43
Consensus pattern (33 bp):
TAAATAATATATAGTTTATATATACTAATGAAC
Found at i:1132041 original size:58 final size:53
Alignment explanation
Indices: 1131962--1132132 Score: 226
Period size: 51 Copynumber: 3.2 Consensus size: 53
1131952 ATATATAATA
*
1131962 TATAA-ATACTATATAGTTTATATATACTAATGAACTAAATAATATATAGTTT
1 TATAATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTT
*
1132014 GTATACACCATATACTATATAGGTTATATATACTAATGAACTATATAATATATAG-TT
1 -TAT--A--ATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTT
* *
1132071 TAT-ATATACTATATAATTTATATATAGTAATGAACTATATAATATATAG-TT
1 TATAATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTT
1132122 TAT-ATATACTA
1 TATAATATACTA
1132133 ATGAACTATA
Statistics
Matches: 108, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
51 56 0.52
53 3 0.03
55 1 0.01
56 3 0.03
57 3 0.03
58 42 0.39
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (53 bp):
TATAATATACTATATAGTTTATATATACTAATGAACTATATAATATATAGTTT
Found at i:1132110 original size:35 final size:34
Alignment explanation
Indices: 1132071--1132179 Score: 166
Period size: 35 Copynumber: 3.2 Consensus size: 34
1132061 ATATATAGTT
* *
1132071 TATATATACTATATAATTTATATATAGTAATGAAC
1 TATATATA-TATATAGTTTATATATACTAATGAAC
1132106 TATATA-ATATATAGTTTATATATACTAATGAAC
1 TATATATATATATAGTTTATATATACTAATGAAC
*
1132139 TATATATATTATATAGTTTATATATACTAATAAAC
1 TATATATA-TATATAGTTTATATATACTAATGAAC
1132174 TATATA
1 TATATA
1132180 ATGTATATTT
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
33 30 0.43
34 2 0.03
35 37 0.54
ACGTcount: A:0.46, C:0.06, G:0.05, T:0.44
Consensus pattern (34 bp):
TATATATATATATAGTTTATATATACTAATGAAC
Found at i:1132162 original size:51 final size:51
Alignment explanation
Indices: 1132023--1132146 Score: 182
Period size: 51 Copynumber: 2.5 Consensus size: 51
1132013 TGTATACACC
* *
1132023 ATATACTATATAGGT-TATATATACTAATGAACTATATAATATATAGTTTAT
1 ATATACTATATA-ATCTATATATAGTAATGAACTATATAATATATAGTTTAT
*
1132074 ATATACTATATAATTTATATATAGTAATGAACTATATAATATATAGTTTAT
1 ATATACTATATAATCTATATATAGTAATGAACTATATAATATATAGTTTAT
1132125 ATATACTA-ATGAA-CTATATATA
1 ATATACTATAT-AATCTATATATA
1132147 TTATATAGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
50 11 0.16
51 57 0.84
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (51 bp):
ATATACTATATAATCTATATATAGTAATGAACTATATAATATATAGTTTAT
Found at i:1132252 original size:2 final size:2
Alignment explanation
Indices: 1132235--1132307 Score: 55
Period size: 2 Copynumber: 36.0 Consensus size: 2
1132225 ATATGTAAAT
*
1132235 TA TA T- TA TA TA GTA TA TA TA GTT TA TA TA TA TA T- TA TA TA GTA
1 TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA
*
1132278 TA TA AA TA TCA -A CTA TA -A TA TA TA TA TA TA
1 TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA TA
1132308 GGTCACATGT
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
1 4 0.07
2 47 0.81
3 7 0.12
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1132254 original size:9 final size:9
Alignment explanation
Indices: 1132240--1132281 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
1132230 TAAATTATAT
1132240 TATATAGTA
1 TATATAGTA
1132249 TATATAGTTTA
1 TATATAG--TA
1132260 TATATA-TA
1 TATATAGTA
1132268 TTATATAGTA
1 -TATATAGTA
1132278 TATA
1 TATA
1132282 AATATCAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 2 0.07
9 17 0.59
10 2 0.07
11 8 0.28
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (9 bp):
TATATAGTA
Found at i:1132265 original size:20 final size:20
Alignment explanation
Indices: 1132235--1132307 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
1132225 ATATGTAAAT
1132235 TATAT-TATATAGTATATATAG
1 TATATATATATA-T-TATATAG
*
1132256 TTTATATATATATTATATAG
1 TATATATATATATTATATAG
* *
1132276 TATATA-A-ATATCAACTATAA
1 TATATATATATAT-TA-TATAG
1132296 TATATATATATA
1 TATATATATATA
1132308 GGTCACATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 4 0.09
19 2 0.05
20 22 0.51
21 6 0.14
22 9 0.21
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (20 bp):
TATATATATATATTATATAG
Found at i:1132380 original size:18 final size:18
Alignment explanation
Indices: 1132357--1132463 Score: 110
Period size: 18 Copynumber: 5.7 Consensus size: 18
1132347 AGTTTATATA
1132357 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
1132375 TATAGTTCATATGTAAATATTAAC
1 TATAGTTCATATG----TA--AAC
*
1132399 TATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
*
1132417 TATAGTT-AGTATATAAAC
1 TATAGTTCA-TATGTAAAC
*
1132435 -ATAGTTTATATGTAAAC
1 TATAGTTCATATGTAAAC
1132452 TATAGTTCATAT
1 TATAGTTCATAT
1132464 ATATAGTATA
Statistics
Matches: 76, Mismatches: 4, Indels: 18
0.78 0.04 0.18
Matches are distributed among these distances:
17 15 0.20
18 42 0.55
20 2 0.03
22 2 0.03
24 15 0.20
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:1132394 original size:55 final size:53
Alignment explanation
Indices: 1132269--1132410 Score: 196
Period size: 53 Copynumber: 2.6 Consensus size: 53
1132259 ATATATATAT
* *
1132269 TATATAGTATATAAATATCAACTATAATATATATATATAGGTCACATGTAAAC
1 TATATAGTATATAAATATCAACTATAGTTTATATATATAGGTCACATGTAAAC
* *
1132322 TATATAGTATATAAATATCAACTATAGTTTATATATATAGTTCATATGTAAAC
1 TATATAGTATATAAATATCAACTATAGTTTATATATATAGGTCACATGTAAAC
* *
1132375 TATAGTTCA-TATGTAAATATTAACTATAGTTTATAT
1 TATA--T-AGTATATAAATATCAACTATAGTTTATAT
1132411 GTAAACTATA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
53 53 0.66
55 26 0.32
56 1 0.01
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (53 bp):
TATATAGTATATAAATATCAACTATAGTTTATATATATAGGTCACATGTAAAC
Found at i:1132410 original size:53 final size:52
Alignment explanation
Indices: 1132247--1132410 Score: 188
Period size: 53 Copynumber: 3.1 Consensus size: 52
1132237 TATTATATAG
* * * * *
1132247 TATATATAGTTTATATATATATTATATAGTATATAAATATCAACTATAATATA
1 TATATATAGTTCATATGTAAACTATATAGTATATAAATATCAACTATAGT-TA
* *
1132300 TATATATAGGTCACATGTAAACTATATAGTATATAAATATCAACTATAGTTTA
1 TATATATAGTTCATATGTAAACTATATAGTATATAAATATCAACTATAG-TTA
* *
1132353 TATATATAGTTCATATGTAAACTATAGTTCA-TATGTAAATATTAACTATAGTT-
1 TATATATAGTTCATATGTAAACTATA--T-AGTATATAAATATCAACTATAGTTA
1132406 TATAT
1 TATAT
1132411 GTAAACTATA
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
53 73 0.76
54 3 0.03
55 19 0.20
56 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (52 bp):
TATATATAGTTCATATGTAAACTATATAGTATATAAATATCAACTATAGTTA
Found at i:1132416 original size:42 final size:40
Alignment explanation
Indices: 1132357--1132468 Score: 144
Period size: 35 Copynumber: 2.9 Consensus size: 40
1132347 AGTTTATATA
* *
1132357 TATAGTTCATATGTAAACTATAGTTCATATGTAAATATTAAC
1 TATAGTTTATATGTAAACTATAGTTCATATGT--ATATAAAC
1132399 TATAGTTTATATGTAAACTATAG-T--TA-GTATATAAAC
1 TATAGTTTATATGTAAACTATAGTTCATATGTATATAAAC
*
1132435 -ATAGTTTATATGTAAACTATAGTTCATATATATA
1 TATAGTTTATATGTAAACTATAGTTCATATGTATA
1132469 GTATATAAAT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
35 22 0.35
36 8 0.13
38 4 0.06
39 6 0.10
41 1 0.02
42 22 0.35
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (40 bp):
TATAGTTTATATGTAAACTATAGTTCATATGTATATAAAC
Found at i:1132440 original size:17 final size:17
Alignment explanation
Indices: 1132336--1132499 Score: 101
Period size: 18 Copynumber: 9.4 Consensus size: 17
1132326 TAGTATATAA
*
1132336 ATATCAACTATAGTT-T
1 ATATAAACTATAGTTAT
1132352 ATAT--A-TATAGTTCAT
1 ATATAAACTATAGTT-AT
*
1132367 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTT-AT
1132385 ATGTAAATATTAACTATAGTTTAT
1 A--T--ATA--AACTATAG-TTAT
*
1132409 ATGTAAACTATAGTTAGT
1 ATATAAACTATAGTTA-T
1132427 ATATAAAC-ATAGTTTAT
1 ATATAAACTATAG-TTAT
*
1132444 ATGTAAACTATAGTTCAT
1 ATATAAACTATAGTT-AT
* * *
1132462 ATATATAGTATA--TAA
1 ATATAAACTATAGTTAT
1132477 ATATAAACTATAGTT-T
1 ATATAAACTATAGTTAT
1132493 ATATAAA
1 ATATAAA
1132500 TAGTATAAAA
Statistics
Matches: 118, Mismatches: 12, Indels: 36
0.71 0.07 0.22
Matches are distributed among these distances:
13 7 0.06
14 1 0.01
15 15 0.13
16 12 0.10
17 19 0.16
18 45 0.38
20 3 0.03
22 3 0.03
24 11 0.09
25 2 0.02
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (17 bp):
ATATAAACTATAGTTAT
Found at i:1132484 original size:33 final size:32
Alignment explanation
Indices: 1132447--1132513 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
1132437 AGTTTATATG
*
1132447 TAAACTATAGTTCATATATATAGTATATAAATA
1 TAAACTATAGTTCATATAAATAGTATA-AAATA
*
1132480 TAAACTATAGTTTATATAAATAGTATAAAATA
1 TAAACTATAGTTCATATAAATAGTATAAAATA
1132512 TA
1 TA
1132514 GTATATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (32 bp):
TAAACTATAGTTCATATAAATAGTATAAAATA
Found at i:1132488 original size:20 final size:20
Alignment explanation
Indices: 1132464--1132537 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
1132454 TAGTTCATAT
1132464 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1132484 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
1132509 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
1132529 TTATAGTAT
1 ATATAGTAT
1132538 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:1132513 original size:25 final size:23
Alignment explanation
Indices: 1132464--1132524 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
1132454 TAGTTCATAT
1132464 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
1132484 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
1132509 ATATAGTATATAAATA
1 ATATAGTATATAAATA
1132525 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:1132516 original size:12 final size:13
Alignment explanation
Indices: 1132477--1132526 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
1132467 TAGTATATAA
1132477 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
1132491 TTATATAA-ATAGT
1 ATATA-AATATAGT
1132504 ATA-AAATATAGT
1 ATATAAATATAGT
1132516 ATATAAATATA
1 ATATAAATATA
1132527 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:1132525 original size:29 final size:29
Alignment explanation
Indices: 1132493--1132561 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1132483 ACTATAGTTT
1132493 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGTTATATAA
** *
1132522 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAG-TTATATAA
1132551 ATATAAATATA
1 ATATAAATATA
1132562 AACTCTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGTTATATAA
Found at i:1132604 original size:27 final size:28
Alignment explanation
Indices: 1132560--1132619 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
1132550 AATATAAATA
* *
1132560 TAAACTCTACATCATAAACCCTA-ACCC
1 TAAACTCTACACCATAAACACTAGACCC
* *
1132587 TAAACTCTACACCCTAAACATTAGACCC
1 TAAACTCTACACCATAAACACTAGACCC
1132615 TAAAC
1 TAAAC
1132620 CCTAAGCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 19 0.68
28 9 0.32
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.22
Consensus pattern (28 bp):
TAAACTCTACACCATAAACACTAGACCC
Found at i:1132614 original size:14 final size:14
Alignment explanation
Indices: 1132560--1132619 Score: 61
Period size: 14 Copynumber: 4.4 Consensus size: 14
1132550 AATATAAATA
* *
1132560 TAAACTCTACATCA
1 TAAACTCTACACCC
*
1132574 TAAACCCTA-ACCC
1 TAAACTCTACACCC
1132587 TAAACTCTACACCC
1 TAAACTCTACACCC
*
1132601 TAAACAT-TAGACCC
1 TAAAC-TCTACACCC
1132615 TAAAC
1 TAAAC
1132620 CCTAAGCCAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
13 10 0.26
14 28 0.72
15 1 0.03
ACGTcount: A:0.42, C:0.35, G:0.02, T:0.22
Consensus pattern (14 bp):
TAAACTCTACACCC
Found at i:1132623 original size:7 final size:7
Alignment explanation
Indices: 1132574--1132624 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
1132564 CTCTACATCA
1132574 TAAACCC
1 TAAACCC
1132581 T-AACCC
1 TAAACCC
*
1132587 TAAACTC
1 TAAACCC
*
1132594 TACACCC
1 TAAACCC
**
1132601 TAAACAT
1 TAAACCC
*
1132608 TAGACCC
1 TAAACCC
1132615 TAAACCC
1 TAAACCC
1132622 TAA
1 TAA
1132625 GCCATATATA
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
6 6 0.18
7 27 0.82
ACGTcount: A:0.41, C:0.37, G:0.02, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:1132641 original size:2 final size:2
Alignment explanation
Indices: 1132628--1132774 Score: 66
Period size: 2 Copynumber: 77.5 Consensus size: 2
1132618 ACCCTAAGCC
* * *
1132628 AT AT AT ACT AT AT AT AT AT AA ACT AT AT A- AT TT TT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * *
1132671 AT AT AT AT A- AT AT A- AT TT AT AC A- AT AT AT AT -T AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
1132709 A- AT -T AT AC AT A- AT AT AT AA AT AT AA AT -T GT AT AGT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
*
1132748 AT AT A- AT -T CAT AT AT A- AT TT AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT A
1132775 AACTATGTAG
Statistics
Matches: 109, Mismatches: 20, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
1 12 0.11
2 92 0.84
3 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1132675 original size:28 final size:28
Alignment explanation
Indices: 1132631--1132774 Score: 101
Period size: 28 Copynumber: 5.3 Consensus size: 28
1132621 CTAAGCCATA
1132631 TATACTATATATATATAAACT-ATATAATT
1 TATA-TATATATATATAAA-TAATATAATT
* *
1132660 TTTATATATATATATATATAATATAATT
1 TATATATATATATATAAATAATATAATT
* * *
1132688 TATACA-ATATATAT-TAT-TTATAA-T
1 TATATATATATATATAAATAATATAATT
*
1132712 TATACATA-ATATATAAAT-ATA-AATT
1 TATATATATATATATAAATAATATAATT
*
1132737 GTATAGT-T-TATATATAATTCATATATAATT
1 -TATA-TATATATATATAAAT-A-ATATAATT
1132767 TATATATA
1 TATATATA
1132775 AACTATGTAG
Statistics
Matches: 93, Mismatches: 9, Indels: 25
0.73 0.07 0.20
Matches are distributed among these distances:
24 15 0.16
25 11 0.12
26 17 0.18
27 9 0.10
28 26 0.28
29 11 0.12
30 4 0.04
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (28 bp):
TATATATATATATATAAATAATATAATT
Found at i:1132697 original size:23 final size:21
Alignment explanation
Indices: 1132666--1132733 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 21
1132656 AATTTTTATA
*
1132666 TATATATATATATAATATAATT
1 TATACATATATATAATATAA-T
*
1132688 TATACAATATATATTATTTATAAT
1 TATAC-ATATATA-TA-ATATAAT
1132712 TATACATAATATATAAATATAA
1 TATACAT-ATATAT-AATATAA
1132734 ATTGTATAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 4 0.11
23 15 0.39
24 14 0.37
25 5 0.13
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TATACATATATATAATATAAT
Found at i:1132773 original size:13 final size:11
Alignment explanation
Indices: 1132664--1132775 Score: 59
Period size: 11 Copynumber: 9.8 Consensus size: 11
1132654 ATAATTTTTA
*
1132664 TATATATATATA
1 TATATATA-ATT
1132676 TATAATATAATT
1 TAT-ATATAATT
*
1132688 TATACAATATATAT
1 TATA-TATA-AT-T
*
1132702 TATTTATAA-T
1 TATATATAATT
*
1132712 TATACATAATAT
1 TATATATAAT-T
* *
1132724 ATAAATATAA-A
1 -TATATATAATT
* *
1132735 T-TGTATAGTT
1 TATATATAATT
1132745 TATATATAATT
1 TATATATAATT
*
1132756 CATATATAATT
1 TATATATAATT
1132767 TATATATAA
1 TATATATAA
1132776 ACTATGTAGT
Statistics
Matches: 74, Mismatches: 17, Indels: 19
0.67 0.15 0.17
Matches are distributed among these distances:
9 4 0.05
10 10 0.14
11 26 0.35
12 13 0.18
13 17 0.23
14 4 0.05
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (11 bp):
TATATATAATT
Found at i:1132786 original size:42 final size:42
Alignment explanation
Indices: 1132628--1132793 Score: 142
Period size: 42 Copynumber: 3.9 Consensus size: 42
1132618 ACCCTAAGCC
* * *
1132628 ATATATACTATATATATATAAACTATATAATTTTTATATATATAT
1 ATATATAATAT-TATATATAAACTATATAGTTTATATATA-AT-T
* * *
1132673 ATATATAATATAATTTATACAA-TATATA--TTATTTATAATT
1 ATATATAATATTATATATA-AACTATATAGTTTATATATAATT
* * * *
1132713 ATACATAATATATAAATATAAATTGTATAGTTTATATATAATT
1 ATATATAATAT-TATATATAAACTATATAGTTTATATATAATT
* *
1132756 CATATATAAT-TTATATATAAACTATGTAGTTTCTATAT
1 -ATATATAATATTATATATAAACTATATAGTTTATATAT
1132794 GGTTCAATAG
Statistics
Matches: 98, Mismatches: 17, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
40 13 0.13
41 12 0.12
42 29 0.30
43 12 0.12
44 20 0.20
45 12 0.12
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (42 bp):
ATATATAATATTATATATAAACTATATAGTTTATATATAATT
Found at i:1132863 original size:27 final size:28
Alignment explanation
Indices: 1132817--1132955 Score: 89
Period size: 27 Copynumber: 5.2 Consensus size: 28
1132807 ATATATAAAC
* **
1132817 TATATAGTATTATAGTTTATACATGGTA
1 TATATAGTATTATACTTTATACATAATA
1132845 TATATAGT-TTATACTTTATACATAATA
1 TATATAGTATTATACTTTATACATAATA
* ** *
1132872 TATATA-TA--A-ACTATATAGTTTATA
1 TATATAGTATTATACTTTATACATAATA
* * *
1132896 TATATAATACATATACTTTATATATAA-A
1 TATATAGTA-TTATACTTTATACATAATA
*
1132924 CTATATAGT-TTATA--TTATATATATATA
1 -TATATAGTATTATACTTTATACATA-ATA
1132951 TATAT
1 TATAT
1132956 CTAAGTTGTT
Statistics
Matches: 89, Mismatches: 13, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
24 17 0.19
25 12 0.13
26 7 0.08
27 27 0.30
28 10 0.11
29 16 0.18
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (28 bp):
TATATAGTATTATACTTTATACATAATA
Found at i:1132876 original size:2 final size:2
Alignment explanation
Indices: 1132869--1132955 Score: 61
Period size: 2 Copynumber: 42.0 Consensus size: 2
1132859 TTTATACATA
* * *
1132869 AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT ACT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * *
1132913 TT AT AT AT AA ACT AT AT AGT TT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1132956 CTAAGTTGTT
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
1 2 0.03
2 59 0.89
3 5 0.08
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1132895 original size:20 final size:20
Alignment explanation
Indices: 1132872--1132938 Score: 91
Period size: 20 Copynumber: 3.2 Consensus size: 20
1132862 ATACATAATA
1132872 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
*
1132892 TATATATATAA-TACATATACTT
1 TATATATA-AACT--ATATAGTT
1132914 TATATATAAACTATATAGTT
1 TATATATAAACTATATAGTT
1132934 TATAT
1 TATAT
1132939 TATATATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
20 21 0.51
21 4 0.10
22 16 0.39
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATAAACTATATAGTT
Found at i:1132928 original size:42 final size:42
Alignment explanation
Indices: 1132845--1132955 Score: 144
Period size: 42 Copynumber: 2.8 Consensus size: 42
1132835 ATACATGGTA
1132845 TATATAGTTTATACT-T-T-ATACATA-ATATATATATAAAC
1 TATATAGTTTATACTATATAATACATATATATATATATAAAC
*
1132883 TATATAGTTTATA-TATATAATACATATACTTTATATATAAAC
1 TATATAGTTTATACTATATAATACATATA-TATATATATAAAC
* *
1132925 TATATAGTTTATATTATAT-ATATATATATAT
1 TATATAGTTTATACTATATAATACATATATAT
1132956 CTAAGTTGTT
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
37 1 0.02
38 14 0.22
39 1 0.02
40 7 0.11
41 3 0.05
42 33 0.52
43 5 0.08
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (42 bp):
TATATAGTTTATACTATATAATACATATATATATATATAAAC
Found at i:1132948 original size:20 final size:20
Alignment explanation
Indices: 1132843--1132950 Score: 82
Period size: 20 Copynumber: 5.4 Consensus size: 20
1132833 TTATACATGG
1132843 TATATATAGTTTATACTT-TA
1 TATATATAGTTTATA-TTATA
* *
1132863 TACATA-A-TATATA-TATA
1 TATATATAGTTTATATTATA
*
1132880 AACTATATAGTTTATATATATAA
1 TA-TATATAGTTTATAT-TAT-A
* *
1132903 TACATATACTTTATA-TATA
1 TATATATAGTTTATATTATA
*
1132922 AACTATATAGTTTATATTATA
1 TA-TATATAGTTTATATTATA
1132943 TATATATA
1 TATATATA
1132951 TATATCTAAG
Statistics
Matches: 67, Mismatches: 12, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
16 1 0.01
17 3 0.04
18 8 0.12
19 4 0.06
20 30 0.45
21 5 0.07
22 14 0.21
23 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (20 bp):
TATATATAGTTTATATTATA
Found at i:1133342 original size:210 final size:212
Alignment explanation
Indices: 1132981--1133795 Score: 1187
Period size: 210 Copynumber: 3.8 Consensus size: 212
1132971 TTTTTTCTCA
* * * *
1132981 ACTTATTACTTATTTATATTTAGT-AATTGGCTCATAACTTTTTAAATGAGTATAATTTAGTAC-
1 ACTTATTACTTATTTCTATTT-TTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACT
* * *
1133044 ATTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGAT--TATTTTTGTGTTGTT
65 TTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCTATATGTGTGTTGTT
1133107 TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
130 TAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTG
1133172 CACATGAAATTGACCCAT
195 CACATGAAATTGACCCAT
1133190 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * *
1133255 TTTTGTATTAATTTTAACCTCAAAATTTAAAATTATTTCGATTTGATCCT-T-TTTGTGTAGTTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCTATATGTGTGTTGTTT
1133318 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
131 AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
*
1133383 ATC-TGAAATTGACTCAT
196 A-CATGAAATTGACCCAT
*
1133400 ACTTATTACTTATTTCTATTTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTTAGTACTT
1 ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
* * **
1133465 TTTTGTATTAATTTCAACATCACAATTTAAAATTATTTTAATTTGATCCCTCATCAATGTGTGTT
66 TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGAT-CCT-AT--ATGTGTGTT
* * *
1133530 GTTTAATTTATTTAAAATTTTATTTGTAATTTCATATTTGTTCAATTTAGTCATCCAAATTTTAT
127 GTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTAT
* * * *
1133595 TTGTATATGAAATTGATCTAT
192 TTGCACATGAAATTGACCCAT
* * * *
1133616 ACTTATTACTTAATTCTTGTTTTTTTAATTGGCCCATAACTTTTTAAATGGATATAATTTAGTA-
1 ACTTATTACTTATTTC-T-ATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTAC
** *
1133680 TTTTTTGTATTAATTTCAACCTCGCAATTTAAAATTATTTCGATTTGACCCCTCATCAATGTGTG
64 TTTTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGA-TCCT-AT--ATGTGTG
*
1133745 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
125 TTGTTTAATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
1133796 ATTATTAAAT
Statistics
Matches: 556, Mismatches: 35, Indels: 22
0.91 0.06 0.04
Matches are distributed among these distances:
208 1 0.00
209 57 0.10
210 242 0.44
211 5 0.01
212 1 0.00
213 1 0.00
216 98 0.18
217 110 0.20
218 41 0.07
ACGTcount: A:0.30, C:0.11, G:0.08, T:0.51
Consensus pattern (212 bp):
ACTTATTACTTATTTCTATTTTTAAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTT
TTTTGTATTAATTTCAACCTCAAAATTTAAAATTATTTCGATTTGATCCTATATGTGTGTTGTTT
AATATATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTTGC
ACATGAAATTGACCCAT
Found at i:1137135 original size:3 final size:3
Alignment explanation
Indices: 1137127--1137182 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
1137117 ATATAATTCG
* * *
1137127 AAT AAT AAT AAT AAT AAT AAT AAT ATT TAT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1137175 AAT AAT AA
1 AAT AAT AA
1137183 AGGTACAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:1138500 original size:147 final size:147
Alignment explanation
Indices: 1138217--1138559 Score: 487
Period size: 147 Copynumber: 2.3 Consensus size: 147
1138207 AAGTTTTTAG
*
1138217 AGAGTATTAATGG-TATGTTTTGACATTTTTCGGGCATGGTGCATTATTAGAGATGACATTTCAC
1 AGAGTATTAATGGCT-CGTTTTGACA-TTTTCGGGCATGGTGCATTATTAGAGATGACATTTCAC
* * * * * *
1138281 TGAAAAGTTACTGAAGATGATTATGAGGCACTAAAAAGTTGTTGACCTTTTCTGGTATCCTATAT
64 TAAAAAGTTACTGAAGATGATTATGAGGCACTAAAAAGTTGCTGACATTTTCTGGCATCATACAT
*
1138346 TAATAATGGCCCGTTCTGA
129 TAATAATGGCCCATTCTGA
1138365 AGAGTATTAATGGCTCGTTTTGACATTTTCGGGCATGGTGCATTATTAGAGATGACA-TTCACTA
1 AGAGTATTAATGGCTCGTTTTGACATTTTCGGGCATGGTGCATTATTAGAGATGACATTTCACTA
* *
1138429 AAAAGTTACTGAAGATGATTGATG-GGACACTGAAAAA-TTGCTGGCATTTTCTGGCATCATGCA
66 AAAAGTTACTGAAGATGATT-ATGAGG-CACT-AAAAAGTTGCTGACATTTTCTGGCATCATACA
* *
1138492 TTATTAATGGTCCATTCTGA
128 TTAATAATGGCCCATTCTGA
* *
1138512 AGAGTATTAATGGCTCGTTTTGACATTTTCGGGCATGATACATTATTA
1 AGAGTATTAATGGCTCGTTTTGACATTTTCGGGCATGGTGCATTATTA
1138560 AATTGGCTTA
Statistics
Matches: 177, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
146 28 0.16
147 121 0.68
148 27 0.15
149 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (147 bp):
AGAGTATTAATGGCTCGTTTTGACATTTTCGGGCATGGTGCATTATTAGAGATGACATTTCACTA
AAAAGTTACTGAAGATGATTATGAGGCACTAAAAAGTTGCTGACATTTTCTGGCATCATACATTA
ATAATGGCCCATTCTGA
Found at i:1141360 original size:28 final size:28
Alignment explanation
Indices: 1141328--1141387 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
1141318 AACCATATAC
*
1141328 TTAACTAAACTCAAAATCATGCACATAT
1 TTAACTAAACTCAAAATCATACACATAT
* * *
1141356 TTAACTAAACTCATATTCATACATATAT
1 TTAACTAAACTCAAAATCATACACATAT
1141384 TTAA
1 TTAA
1141388 AATATTTTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (28 bp):
TTAACTAAACTCAAAATCATACACATAT
Found at i:1146066 original size:2 final size:2
Alignment explanation
Indices: 1146061--1146091 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1146051 TTTAACTACA
1146061 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1146092 ATTTTAAAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1148919 original size:2 final size:2
Alignment explanation
Indices: 1148907--1148936 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1148897 GGCCTCATGC
1148907 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1148937 AAAGGGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1160312 original size:31 final size:30
Alignment explanation
Indices: 1160270--1160337 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
1160260 ATTACAATTC
*
1160270 AAACACCTAAAA-ATATAATATTGAAAATATT
1 AAACACCTAAAAGATATAAGA--GAAAATATT
* *
1160301 AAACACTTAAAAGTGTATAAGAGAAAATATT
1 AAACACCTAAAAG-ATATAAGAGAAAATATT
1160332 AAACAC
1 AAACAC
1160338 ATTTTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 26 0.81
33 6 0.19
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.25
Consensus pattern (30 bp):
AAACACCTAAAAGATATAAGAGAAAATATT
Found at i:1160836 original size:15 final size:15
Alignment explanation
Indices: 1160818--1160848 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1160808 AAATTCTAAA
1160818 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1160833 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1160848 T
1 T
1160849 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1171752 original size:32 final size:31
Alignment explanation
Indices: 1171716--1171788 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
1171706 AAGATATAAA
*
1171716 TTTTATTTTTTTAAATATATTTAT-TGAATATT
1 TTTTATTTTATT-AAT-TATTTATATGAATATT
* * *
1171748 TTTTATATTATTAATTATTTATAATTACTATT
1 TTTTATTTTATTAATTATTTAT-ATGAATATT
1171780 TTTTATTTT
1 TTTTATTTT
1171789 CTGTACTTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
30 7 0.21
31 3 0.09
32 24 0.71
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (31 bp):
TTTTATTTTATTAATTATTTATATGAATATT
Found at i:1172876 original size:14 final size:14
Alignment explanation
Indices: 1172849--1172878 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1172839 TAAATTTTAA
*
1172849 TATTTTTATTTAAT
1 TATTTTTATATAAT
1172863 TATTTTTATATAAT
1 TATTTTTATATAAT
1172877 TA
1 TA
1172879 GAATCTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATATAAT
Found at i:1174016 original size:31 final size:31
Alignment explanation
Indices: 1173973--1174032 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
1173963 GCATATTAAT
1173973 TGTAATGTTTTTAATATTTCTTTATGTTTTA
1 TGTAATGTTTTTAATATTTCTTTATGTTTTA
* *
1174004 TGTATTGTTTTTAATATTTGTTTATGTTT
1 TGTAATGTTTTTAATATTTCTTTATGTTT
1174033 AACGGAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.67
Consensus pattern (31 bp):
TGTAATGTTTTTAATATTTCTTTATGTTTTA
Found at i:1176095 original size:31 final size:31
Alignment explanation
Indices: 1176056--1176127 Score: 117
Period size: 31 Copynumber: 2.3 Consensus size: 31
1176046 TTTAAAAAAT
*
1176056 ATAAGATATGATCACTTTCGTTTTTATTTAA
1 ATAAGATATGATCACGTTCGTTTTTATTTAA
* *
1176087 TTAAGATATGATCACGTTCTTTTTTATTTAA
1 ATAAGATATGATCACGTTCGTTTTTATTTAA
1176118 ATAAGATATG
1 ATAAGATATG
1176128 GTAATAACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (31 bp):
ATAAGATATGATCACGTTCGTTTTTATTTAA
Found at i:1176315 original size:27 final size:27
Alignment explanation
Indices: 1176264--1176351 Score: 90
Period size: 27 Copynumber: 3.3 Consensus size: 27
1176254 ACCTAAAAAT
* ** *
1176264 ATATTTTTAAATGAAAATAAAAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
1176291 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAGTTAATAATAAA
* * *
1176318 ACATATTT-AA-TAAGTTAATATAAAAA
1 ATATTTTTAAATTAAGTTAATA-ATAAA
1176344 ATATTTTT
1 ATATTTTT
1176352 TAAGTTAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
25 10 0.20
26 12 0.24
27 29 0.57
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (27 bp):
ATATTTTTAAATTAAGTTAATAATAAA
Found at i:1176347 original size:24 final size:24
Alignment explanation
Indices: 1176303--1176363 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1176293 ATTTTTAAAT
*
1176303 TAAGTTAATAATAAAACATATTTAA
1 TAAGTTAAT-ATAAAAAATATTTAA
**
1176328 TAAGTTAATATAAAAAATATTTTT
1 TAAGTTAATATAAAAAATATTTAA
1176352 TAAGTTAATATA
1 TAAGTTAATATA
1176364 TATATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
24 24 0.73
25 9 0.27
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
TAAGTTAATATAAAAAATATTTAA
Found at i:1176353 original size:27 final size:29
Alignment explanation
Indices: 1176279--1176359 Score: 82
Period size: 24 Copynumber: 2.9 Consensus size: 29
1176269 TTTAAATGAA
* *
1176279 AATAAAAATAAAATATTTTTAAATTAAGTT
1 AATAATAA-AAAATATTTTTTAATTAAGTT
*
1176309 AATAATAAAACATA---TTTAA-TAAGTT
1 AATAATAAAAAATATTTTTTAATTAAGTT
1176334 AAT-ATAAAAAATATTTTTTAAGTTAA
1 AATAATAAAAAATATTTTTTAA-TTAA
1176360 TATATATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
24 9 0.21
25 9 0.21
26 4 0.10
27 5 0.12
29 8 0.19
30 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.40
Consensus pattern (29 bp):
AATAATAAAAAATATTTTTTAATTAAGTT
Found at i:1176364 original size:2 final size:2
Alignment explanation
Indices: 1176359--1176395 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1176349 TTTTAAGTTA
1176359 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1176396 AATTTAAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1176434 original size:21 final size:21
Alignment explanation
Indices: 1176408--1176458 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
1176398 TTTAAGTATT
1176408 TATACACTAAGAAATAAAATA
1 TATACACTAAGAAATAAAATA
1176429 TATACACTAAGAAATAAAATA
1 TATACACTAAGAAATAAAATA
1176450 TATACACTA
1 TATACACTA
1176459 TGTTGTTTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.59, C:0.12, G:0.04, T:0.25
Consensus pattern (21 bp):
TATACACTAAGAAATAAAATA
Found at i:1178137 original size:174 final size:178
Alignment explanation
Indices: 1177845--1178195 Score: 640
Period size: 175 Copynumber: 2.0 Consensus size: 178
1177835 TAAATTTTAT
1177845 TTTAAAGCGAAGATGTCAACTTGTAACAAATTAATATTCTATAAGCCCAGCATTTCCTGTAAAGC
1 TTTAAAGCGAAGATGTCAACTTGTAACAAATTAATATTCTATAAGCCCAGCATTTCCTGTAAAGC
1177910 TATGCATTCAAGTATCTATAATTCATATCGATTTCTCAAATAAAATCTTCATGTTGAG-AAAAAA
66 TATGCATTCAAGTATCTATAATTCATATCGATTTCTCAAATAAAATCTTCATGTTGAGAAAAAAA
1177974 AAAAAAACATAATTCACCTCATGGTAGCCGAGAAAG-AAAAAAGATTC
131 AAAAAAACATAATTCACCTCATGGTAGCCGAGAAAGAAAAAAAGATTC
1178021 TTTAAAGCGAAGATGTCAACTTGTAAACAAATT-A-ATTCTATAAGCCCAGCATTTCCTGT-AAG
1 TTTAAAGCGAAGATGTCAACTTGT-AACAAATTAATATTCTATAAGCCCAGCATTTCCTGTAAAG
1178083 CTATGCATTCAAGTATCTATAATTCATATCGATTTCTCAAATAAAATCTTCATGTTGAGAAAAAA
65 CTATGCATTCAAGTATCTATAATTCATATCGATTTCTCAAATAAAATCTTCATGTTGAGAAAAAA
* *
1178148 AAAAAAAACATCATTCACTTCATGGTAGCCGAGAAAGAAAAAAAGATT
130 AAAAAAAACATAATTCACCTCATGGTAGCCGAGAAAGAAAAAAAGATT
1178196 ACATCTTTAA
Statistics
Matches: 170, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
174 62 0.36
175 65 0.38
176 35 0.21
177 8 0.05
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (178 bp):
TTTAAAGCGAAGATGTCAACTTGTAACAAATTAATATTCTATAAGCCCAGCATTTCCTGTAAAGC
TATGCATTCAAGTATCTATAATTCATATCGATTTCTCAAATAAAATCTTCATGTTGAGAAAAAAA
AAAAAAACATAATTCACCTCATGGTAGCCGAGAAAGAAAAAAAGATTC
Found at i:1185929 original size:2 final size:2
Alignment explanation
Indices: 1185922--1186000 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
1185912 AACATTCTTA
1185922 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
1185964 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1186001 ATTTTAAGTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1189296 original size:20 final size:19
Alignment explanation
Indices: 1189243--1189297 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
1189233 GAGGACTAAC
*
1189243 TTTATTTTAATTTAATATA
1 TTTATTTTAACTTAATATA
* *
1189262 TTTAATTTAAGTTAATATA
1 TTTATTTTAACTTAATATA
1189281 TTTATTATTAACTTAAT
1 TTTATT-TTAACTTAAT
1189298 TTAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 22 0.71
20 9 0.29
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATTTTAACTTAATATA
Found at i:1190131 original size:26 final size:26
Alignment explanation
Indices: 1190095--1190150 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1190085 AAATAGATAA
1190095 TTTACTTTTTTTAATTATACGTTAAC
1 TTTACTTTTTTTAATTATACGTTAAC
1190121 TTTACTTTTTTTAATTATACGTTAAC
1 TTTACTTTTTTTAATTATACGTTAAC
1190147 TTTA
1 TTTA
1190151 TAATTTTGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTACTTTTTTTAATTATACGTTAAC
Found at i:1192163 original size:34 final size:33
Alignment explanation
Indices: 1192120--1192347 Score: 136
Period size: 34 Copynumber: 6.8 Consensus size: 33
1192110 CTCCAAACAG
1192120 ATATCTTTTAATATTAAAATTTAAATAGATAATA
1 ATATCTTTTAATATTAAAATTTAAATAGAT-ATA
*
1192154 ATATCTTTTAAT-TTGAAATATTCAAA-AGATATA
1 ATATCTTTTAATATT-AAA-ATTTAAATAGATATA
* * * *
1192187 A-ACTCATTTTACTATTCATACTTAAATAGATAT-
1 ATA-TC-TTTTAATATTAAAATTTAAATAGATATA
* *
1192220 -TA--TTTTAATATAAAATATTTAAAAAAGATATA
1 ATATCTTTTAATATTAAA-ATTT-AAATAGATATA
1192252 ATTATCTTTTAATATTCAAAA-TTAAATAGATAATAA
1 A-TATCTTTTAATATT-AAAATTTAAATAGAT-AT-A
* * * *
1192288 ATATCTTTTTGATTTTAATATTCAAA-AGA-ATAA
1 ATATC-TTTTAATATTAAAATTTAAATAGATAT-A
**
1192321 ATATCCTACTAATATTAAAA-TTAAATA
1 ATAT-CTTTTAATATTAAAATTTAAATA
1192348 ATGTTTTTTA
Statistics
Matches: 149, Mismatches: 24, Indels: 43
0.69 0.11 0.20
Matches are distributed among these distances:
29 9 0.06
30 3 0.02
31 9 0.06
32 5 0.03
33 32 0.21
34 42 0.28
35 22 0.15
36 24 0.16
37 3 0.02
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.42
Consensus pattern (33 bp):
ATATCTTTTAATATTAAAATTTAAATAGATATA
Found at i:1193940 original size:20 final size:20
Alignment explanation
Indices: 1193915--1193964 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1193905 TCTATGGGGA
1193915 GTATCGATACCTTACCCATG
1 GTATCGATACCTTACCCATG
1193935 GTATCGATACCTTACCCATG
1 GTATCGATACCTTACCCATG
1193955 GTATCGATAC
1 GTATCGATAC
1193965 TCTATGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTTACCCATG
Found at i:1194484 original size:65 final size:65
Alignment explanation
Indices: 1194379--1194538 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
1194369 GAATAAACTG
* * * *
1194379 AACATCGAATACATTTCATGCATCGATGCA-CATACTATGCATCGATTCACTCAGAGT-TTTATG
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGACTATTT-TG
1194442 AA
65 -A
* * *
1194444 AACATCGAATGCATTTGATACATCGATGCACCA-GCCATGCATCGATGCACTCAGACTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGACTATTTTGA
*
1194508 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
1194539 TCTTCGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
64 30 0.36
65 49 0.58
66 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACCATACCATGCATCGATGCACTCAGACTATTTTGA
Found at i:1204865 original size:14 final size:14
Alignment explanation
Indices: 1204848--1204880 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1204838 ATTTCTATGT
*
1204848 AGGGAATTATTTGC
1 AGGGAATTATTTAC
1204862 AGGGAATTATTTAC
1 AGGGAATTATTTAC
1204876 AGGGA
1 AGGGA
1204881 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:1207566 original size:11 final size:11
Alignment explanation
Indices: 1207550--1207595 Score: 62
Period size: 11 Copynumber: 4.5 Consensus size: 11
1207540 TGATGCATCG
1207550 ATGCACCAGCC
1 ATGCACCAGCC
1207561 ATGCACCAGCC
1 ATGCACCAGCC
*
1207572 ATGCATC-G--
1 ATGCACCAGCC
1207580 ATGCACCAGCC
1 ATGCACCAGCC
1207591 ATGCA
1 ATGCA
1207596 TCGATGCACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 6 0.20
9 1 0.03
10 1 0.03
11 22 0.73
ACGTcount: A:0.28, C:0.39, G:0.20, T:0.13
Consensus pattern (11 bp):
ATGCACCAGCC
Found at i:1207583 original size:19 final size:19
Alignment explanation
Indices: 1207561--1207604 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
1207551 TGCACCAGCC
1207561 ATGCACCAGCCATGCATCG
1 ATGCACCAGCCATGCATCG
1207580 ATGCACCAGCCATGCATCG
1 ATGCACCAGCCATGCATCG
1207599 ATGCAC
1 ATGCAC
1207605 TCAGGCTATT
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:0.27, C:0.36, G:0.20, T:0.16
Consensus pattern (19 bp):
ATGCACCAGCCATGCATCG
Found at i:1214912 original size:22 final size:23
Alignment explanation
Indices: 1214859--1214914 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
1214849 GAAAAATGGT
*
1214859 TGATATCGATACTCTGGGTATAG
1 TGATATCGATACTTTGGGTATAG
*
1214882 T-AT-T-GATACTTTTGGTAT-G
1 TGATATCGATACTTTGGGTATAG
1214901 TGATATCGATACTT
1 TGATATCGATACTT
1214915 AGTTGAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 2 0.07
20 14 0.50
21 2 0.07
22 9 0.32
23 1 0.04
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (23 bp):
TGATATCGATACTTTGGGTATAG
Found at i:1219232 original size:35 final size:35
Alignment explanation
Indices: 1219186--1219258 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
1219176 TAAACCATGT
1219186 ATTCAAAAAACAAAATTATAATTTTAAGTTAGATA
1 ATTCAAAAAACAAAATTATAATTTTAAGTTAGATA
1219221 ATTCAAAAAACAAAATTATAATTTTAAGTTAGATA
1 ATTCAAAAAACAAAATTATAATTTTAAGTTAGATA
1219256 ATT
1 ATT
1219259 TAGAAAATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (35 bp):
ATTCAAAAAACAAAATTATAATTTTAAGTTAGATA
Found at i:1220199 original size:75 final size:76
Alignment explanation
Indices: 1220030--1220237 Score: 294
Period size: 75 Copynumber: 2.8 Consensus size: 76
1220020 CAAAGCCAAA
* * * **
1220030 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
1220095 TTTGGCCCCGAG
65 TTTGGCCCCGAG
*
1220107 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
1220172 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
1220182 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCT
1220238 TTGTACAACG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
74 18 0.15
75 40 0.34
76 36 0.30
77 25 0.21
ACGTcount: A:0.25, C:0.32, G:0.24, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:1228785 original size:54 final size:55
Alignment explanation
Indices: 1228697--1228820 Score: 180
Period size: 54 Copynumber: 2.3 Consensus size: 55
1228687 CCCTATAGGA
** *
1228697 GGAACCGATT-CCCCCTAAATGGTTTTGGCCCCGAGATTTCCAGAATGCTCGGAG
1 GGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAG
* *
1228751 GGAACCGATTCCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAGTATGCTCGGAG
1 GGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAG
*
1228805 GGAACCGATCCCCCCC
1 GGAACCGATTCCCCCC
1228821 AAGGGGGTAC
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 49 0.78
55 14 0.22
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (55 bp):
GGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAGAATGCTCGGAG
Found at i:1232085 original size:23 final size:23
Alignment explanation
Indices: 1232055--1232100 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1232045 AAAATGGCTG
1232055 AAGTGAAAACGACTACTAGACCT
1 AAGTGAAAACGACTACTAGACCT
*
1232078 AAGTGAAAACGACTACTATACCT
1 AAGTGAAAACGACTACTAGACCT
1232101 TACTTCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.22, G:0.15, T:0.20
Consensus pattern (23 bp):
AAGTGAAAACGACTACTAGACCT
Found at i:1234743 original size:20 final size:20
Alignment explanation
Indices: 1234720--1234811 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
1234710 AAAATCAAAT
* *
1234720 AACAATGAACCCATTCAAGA
1 AACAAAGAACCCATTCGAGA
** *
1234740 AACAACTAACCCATTCGAGC
1 AACAAAGAACCCATTCGAGA
* * *
1234760 AATAAAGAACTCGTTCGAGA
1 AACAAAGAACCCATTCGAGA
*
1234780 AACAAAGAACTCATTCGAGA
1 AACAAAGAACCCATTCGAGA
*
1234800 AATAAAGAACCC
1 AACAAAGAACCC
1234812 TTTTTTAAAA
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.15
Consensus pattern (20 bp):
AACAAAGAACCCATTCGAGA
Found at i:1236243 original size:25 final size:25
Alignment explanation
Indices: 1236209--1236265 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
1236199 AAATGAAATA
1236209 AAAGAAATTAAATTTCTTTAAAAAC
1 AAAGAAATTAAATTTCTTTAAAAAC
1236234 AAAGAAATTAAATTTCTTTAAAAAC
1 AAAGAAATTAAATTTCTTTAAAAAC
1236259 AAAGAAA
1 AAAGAAA
1236266 AATACTCTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (25 bp):
AAAGAAATTAAATTTCTTTAAAAAC
Found at i:1237574 original size:2 final size:2
Alignment explanation
Indices: 1237567--1237633 Score: 125
Period size: 2 Copynumber: 33.0 Consensus size: 2
1237557 TTTTATTTAG
1237567 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1237609 TA TA TA TA TA TA TA GTA TA TA TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA
1237634 GTTTTTATAA
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 62 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1237719 original size:82 final size:80
Alignment explanation
Indices: 1237612--1237932 Score: 256
Period size: 83 Copynumber: 4.2 Consensus size: 80
1237602 ATATATATAT
* *
1237612 ATATATATATAGTATATATATAGTTTTTATAAA-ATTTTGAAAACATATATAATATATAGTTCTA
1 ATATATATATA-TATA-ATATAGTTTTTAAAAATATTTTGAAAACATATACAATATATAGTT-T-
*
1237676 TAAAATAACG-TTTTGAAAAC
62 TAAAA-AA-GATTTTAAAAAC
* **
1237696 ATATATATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATACAATATATAGTTTTTGA
1 ATATATATATATATAATATAGTTTTTAAAAATATTTTGAAAACATATACAATATATAGTTTTAAA
1237761 AAAGATTTTAAAAAC
66 AAAGATTTTAAAAAC
* *
1237776 ATATATATATATAT-ATATAGTTTTTGAAAATA---T------ATAT--AATATATAGTTTT-TA
1 ATATATATATATATAATATAGTTTTTAAAAATATTTTGAAAACATATACAATATATAGTTTTAAA
* *
1237828 AAATATTTT-GAAA-
66 AAAGATTTTAAAAAC
* * * *
1237841 ATATATATA-ATAT-ATA-A-TTTTTGAAAATATTTTGAAAACATATATATAATATATAATTTTT
1 ATATATATATATATAATATAGTTTTTAAAAATATTTTGAAAAC--ATATACAATATATAGTTTTA
* *
1237902 GAAAATATTTTGAAAAA-
64 AAAAAGATTTT-AAAAAC
1237919 ATATATAT-TATATA
1 ATATATATATATATA
1237933 GTTTTTTAAA
Statistics
Matches: 204, Mismatches: 13, Indels: 45
0.78 0.05 0.17
Matches are distributed among these distances:
62 12 0.06
63 1 0.00
64 7 0.03
65 10 0.05
66 3 0.01
67 9 0.04
68 13 0.06
70 4 0.02
73 4 0.02
75 12 0.06
76 11 0.05
78 15 0.07
79 18 0.09
80 25 0.12
81 3 0.01
82 16 0.08
83 30 0.15
84 11 0.05
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (80 bp):
ATATATATATATATAATATAGTTTTTAAAAATATTTTGAAAACATATACAATATATAGTTTTAAA
AAAGATTTTAAAAAC
Found at i:1237741 original size:39 final size:38
Alignment explanation
Indices: 1237616--1237944 Score: 285
Period size: 37 Copynumber: 8.7 Consensus size: 38
1237606 ATATATATAT
*
1237616 ATATATAGTATATATATAGTTTTTATAAA-ATTTTGAAA
1 ATATATA-TATATATATAGTTTTTAAAAATATTTTGAAA
* *
1237654 ACATATATA-ATATATAG-TTCTATAAAATAACGTTTTGAAAACA
1 ATATATATATATATATAGTTTTTA-AAAAT-A--TTTTG--AA-A
1237697 TATATATATATATAATATAGTTTTTAAAAATATTTTGAAA
1 -ATATATATATAT-ATATAGTTTTTAAAAATATTTTGAAA
* * *
1237737 ATATATACA-ATATATAGTTTTTGAAAAGATTTT-AAA
1 ATATATATATATATATAGTTTTTAAAAATATTTTGAAA
* * * *
1237773 A-ACATATATATATATA---TAT-ATAGT-TTTTGAAA
1 ATATATATATATATATAGTTTTTAAAAATATTTTGAAA
1237805 ATATATATAATATAT--AGTTTTT-AAAATATTTTGAAA
1 ATATATAT-ATATATATAGTTTTTAAAAATATTTTGAAA
* *
1237841 ATATATATA-ATATATAATTTTTGAAAATATTTTGAAA
1 ATATATATATATATATAGTTTTTAAAAATATTTTGAAA
* * *
1237878 ACATATATATAATATATAATTTTTGAAAATATTTTGAAA
1 ATATATATAT-ATATATAGTTTTTAAAAATATTTTGAAA
*
1237917 AAATATATAT-TATATAGTTTTTTAAAAA
1 ATATATATATATATATAG-TTTTTAAAAA
1237945 AAAACTATAT
Statistics
Matches: 242, Mismatches: 23, Indels: 52
0.76 0.07 0.16
Matches are distributed among these distances:
31 4 0.02
32 7 0.03
33 7 0.03
34 10 0.04
35 15 0.06
36 44 0.18
37 50 0.21
38 18 0.07
39 45 0.19
40 6 0.02
41 2 0.01
42 2 0.01
43 6 0.02
44 8 0.03
45 3 0.01
46 11 0.05
47 4 0.02
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (38 bp):
ATATATATATATATATAGTTTTTAAAAATATTTTGAAA
Found at i:1237818 original size:36 final size:36
Alignment explanation
Indices: 1237698--1237856 Score: 108
Period size: 36 Copynumber: 4.2 Consensus size: 36
1237688 TTGAAAACAT
* *
1237698 ATATATATATATAATATAGTTTTTAAAAATAT-TTTGA
1 ATATATATATAT-ATATAGTTTTTGAAAATATATAT-A
* * * * *
1237735 AAATATATACAATATATAGTTTTTGAAAAGATTTTAAAAACA
1 ATATATATA-TATATATAGTTTTTG-AAA-A---TATATATA
1237777 TATATATATATATATATAGTTTTTGAAAATATATATA
1 -ATATATATATATATATAGTTTTTGAAAATATATATA
* * *
1237814 ATATATAGT-T-TTTAAAATATTTTGAAAATATATATA
1 ATATATA-TATATATATAGT-TTTTGAAAATATATATA
1237850 ATATATA
1 ATATATA
1237857 ATTTTTGAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
35 5 0.05
36 32 0.33
37 25 0.26
38 5 0.05
39 1 0.01
40 1 0.01
41 3 0.03
42 17 0.18
43 8 0.08
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (36 bp):
ATATATATATATATATAGTTTTTGAAAATATATATA
Found at i:1237825 original size:25 final size:27
Alignment explanation
Indices: 1237778--1237833 Score: 98
Period size: 26 Copynumber: 2.1 Consensus size: 27
1237768 TTAAAAACAT
1237778 ATATATATATATATATAGTTTTTGAAA
1 ATATATATATATATATAGTTTTTGAAA
1237805 ATATATATA-ATATATAGTTTTT-AAA
1 ATATATATATATATATAGTTTTTGAAA
1237830 ATAT
1 ATAT
1237834 TTTGAAAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 7 0.24
26 13 0.45
27 9 0.31
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
ATATATATATATATATAGTTTTTGAAA
Found at i:1237853 original size:104 final size:104
Alignment explanation
Indices: 1237698--1237909 Score: 340
Period size: 104 Copynumber: 2.0 Consensus size: 104
1237688 TTGAAAACAT
*
1237698 ATATATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATACAATATATAGTTTTTGAAA
1 ATATATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATACAATATATAATTTTTGAAA
1237763 AGATTTTAAAAACATATATATATATATATATAGTTTTTGAAA
66 AGATTTTAAAAACATATATATA-ATATATA-A-TTTTTGAAA
*
1237805 ATATATATA-AT-ATATAGTTTTT-AAAATATTTTGAAAATATATATAATATATAATTTTTGAAA
1 ATATATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATACAATATATAATTTTTGAAA
* *
1237867 ATATTTTGAAAACATATATATAATATATAATTTTTGAAA
66 AGATTTTAAAAACATATATATAATATATAATTTTTGAAA
1237906 ATAT
1 ATAT
1237910 TTTGAAAAAA
Statistics
Matches: 101, Mismatches: 4, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
101 13 0.13
102 1 0.01
103 7 0.07
104 58 0.57
105 11 0.11
106 2 0.02
107 9 0.09
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (104 bp):
ATATATATATATAATATAGTTTTTAAAAATATTTTGAAAATATATACAATATATAATTTTTGAAA
AGATTTTAAAAACATATATATAATATATAATTTTTGAAA
Done.