Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167915.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_18, 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: 20765110
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 90000 characters in sequence are not A, C, G, or T
File 5 of 117
Found at i:1219582 original size:2 final size:2
Alignment explanation
Indices: 1219577--1219605 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1219567 ACACACACAG
1219577 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 A
1219606 CTTATGCTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1222930 original size:2 final size:2
Alignment explanation
Indices: 1222885--1222915 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1222875 TCTTCAGAAA
1222885 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
1222916 AACTACTACT
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:1227705 original size:60 final size:59
Alignment explanation
Indices: 1227546--1227704 Score: 227
Period size: 60 Copynumber: 2.7 Consensus size: 59
1227536 TTTTGTGCAG
*
1227546 GAAAAATTGATACTTTTAACTTTTCCTC-AAAATA-TTTTTTAAAAAGCTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAAGCTTATTTTTAA
* * *
1227603 GAAAAATTGATACTTTCAACTTTT-TTCCAAGAATATATTTTTTAGAAAGCTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCT-CAAAAATAT-TTTTTTAAAAAGCTTATTTTTAA
1227663 -AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1 GA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
1227705 TGAATTTTAT
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
56 1 0.01
57 24 0.27
58 5 0.06
59 7 0.08
60 52 0.58
61 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAAAGCTTATTTTTAA
Found at i:1227729 original size:5 final size:5
Alignment explanation
Indices: 1227721--1227779 Score: 59
Period size: 5 Copynumber: 11.8 Consensus size: 5
1227711 TTATTTAAAG
* **
1227721 AAAAT AAAAT AAAAT AATA- AAAAT AAAGG AAAAT -AAAT AAAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT
1227771 AAAAT AAAA
1 AAAAT AAAA
1227780 AATATTAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 7 0.16
5 28 0.62
6 10 0.22
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1227747 original size:6 final size:6
Alignment explanation
Indices: 1227721--1227780 Score: 54
Period size: 6 Copynumber: 9.7 Consensus size: 6
1227711 TTATTTAAAG
1227721 AAAAT- AAAATAA AATAATA AAAATA AAGGAA-A ATAAATA AAAATA AAAAT-
1 AAAATA AAAAT-A AA-AATA AAAATA AA--AATA A-AAATA AAAATA AAAATA
1227771 AAAATA AAAA
1 AAAATA AAAA
1227781 ATATTAAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
5 10 0.21
6 22 0.47
7 9 0.19
8 6 0.13
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:1228725 original size:19 final size:18
Alignment explanation
Indices: 1228688--1228854 Score: 71
Period size: 19 Copynumber: 9.0 Consensus size: 18
1228678 TAATAATAAG
* *
1228688 GATAACATATTAATTAATA
1 GATAA-ATAATAATAAATA
1228707 GATAAATAATATATAAATA
1 GATAAATAATA-ATAAATA
1228726 GATAAATAATAATAATAATA
1 GATAAATAATAAT-A-AATA
* *
1228746 TAGAAATAGATAA-ATAATA
1 GATAAATA-ATAATA-AATA
* * **
1228765 -ATACATATATATATCAGCA
1 GATAAATA-ATA-ATAAATA
1228784 GATAAATAATAA-AAATA
1 GATAAATAATAATAAATA
1228801 -ATAAAATAA-AATAACTATA
1 GAT-AAATAATAATAA--ATA
* *
1228820 GATTAATAAATAGT-AATA
1 GATAAAT-AATAATAAATA
1228838 -ATAAATACATAA-AAATA
1 GATAAATA-ATAATAAATA
1228855 CAAAATAAAG
Statistics
Matches: 114, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
16 5 0.04
17 22 0.19
18 19 0.17
19 41 0.36
20 21 0.18
21 6 0.05
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (18 bp):
GATAAATAATAATAAATA
Found at i:1228745 original size:28 final size:28
Alignment explanation
Indices: 1228702--1228803 Score: 123
Period size: 28 Copynumber: 3.5 Consensus size: 28
1228692 ACATATTAAT
1228702 TAATAGATAAATAATATATAAATAGATAAA
1 TAATA-AT-AATAATATATAAATAGATAAA
*
1228732 TAATAATAATAATATAGAAATAGATAAA
1 TAATAATAATAATATATAAATAGATAAA
* **
1228760 TAATAATACATATATATATCAGCAGATAAA
1 TAATAATA-ATA-ATATATAAATAGATAAA
*
1228790 TAATAAAAATAATA
1 TAATAATAATAATA
1228804 AAATAAAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
28 31 0.48
29 8 0.12
30 25 0.39
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (28 bp):
TAATAATAATAATATATAAATAGATAAA
Found at i:1228767 original size:14 final size:14
Alignment explanation
Indices: 1228722--1228795 Score: 62
Period size: 14 Copynumber: 5.1 Consensus size: 14
1228712 ATAATATATA
1228722 AATAGATAAATAAT
1 AATAGATAAATAAT
1228736 AATA-ATAATATAGA-
1 AATAGATAA-ATA-AT
1228750 AATAGATAAATAAT
1 AATAGATAAATAAT
* *
1228764 AATACATATATATAT
1 AATAGATAAATA-AT
**
1228779 CAGCAGATAAATAAT
1 -AATAGATAAATAAT
1228794 AA
1 AA
1228796 AAATAATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
13 5 0.11
14 25 0.53
15 9 0.19
16 8 0.17
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (14 bp):
AATAGATAAATAAT
Found at i:1228872 original size:23 final size:23
Alignment explanation
Indices: 1228846--1228912 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 23
1228836 TAATAAATAC
1228846 ATAAAAATACAAAATAAAGTAAA-
1 ATAAAAATA-AAAATAAAGTAAAT
1228869 ATAAAATATAAAAATATAAG-AAAT
1 ATAAAA-ATAAAAATA-AAGTAAAT
* *
1228893 ACAAAAATATAAAATGAAGT
1 ATAAAAATA-AAAATAAAGT
1228913 GGGCCTACCC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.21
Consensus pattern (23 bp):
ATAAAAATAAAAATAAAGTAAAT
Found at i:1228892 original size:17 final size:17
Alignment explanation
Indices: 1228872--1228904 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1228862 AAGTAAAATA
*
1228872 AAATATAAAAATATAAG
1 AAATACAAAAATATAAG
1228889 AAATACAAAAATATAA
1 AAATACAAAAATATAA
1228905 AATGAAGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (17 bp):
AAATACAAAAATATAAG
Found at i:1228893 original size:32 final size:32
Alignment explanation
Indices: 1228831--1228893 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
1228821 ATTAATAAAT
*
1228831 AGTAATAATAAATACATAAAAATACAAAATAA
1 AGTAATAATAAATACATAAAAATAAAAAATAA
*
1228863 AGTAA-AATAAA-ATATAAAAATATAAGAAATA
1 AGTAATAATAAATACATAAAAATA-AA-AAATA
1228894 CAAAAATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 10 0.37
31 7 0.26
32 10 0.37
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (32 bp):
AGTAATAATAAATACATAAAAATAAAAAATAA
Found at i:1229249 original size:83 final size:82
Alignment explanation
Indices: 1229092--1229382 Score: 352
Period size: 83 Copynumber: 3.5 Consensus size: 82
1229082 TTGATCAAAA
* * *
1229092 CTCCTCTAAGCAAAGGCTCAACGACTTTGAAAAACATAAACAATGCTCCTCTAATCAGAGGCTCA
1 CTCCTCTAATCAGAGGCTCAACGACTTTG-AAAA-ATAAACGAT--TCCTCTAATCAGAGGCTCA
1229157 ACGACTTTGAAAATGAATAAA-G
62 ACGACTTTGAAAA--AATAAAGG
*
1229179 CTCCTCTAATCAGAGGCTCAACGACTTCGAAAAATAAACGATTCCTCTAATCAGAGGCTCAACGA
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACGATTCCTCTAATCAGAGGCTCAACGA
1229244 CTTTG-AAAAATAAATGG
66 CTTTGAAAAAATAAA-GG
* * * ** *
1229261 CTTCTCTAATCAGAGGCTCAACAACTTTTGAAAAATAAAAGGCTCCTTTAATCAGAGGCTCAACG
1 CTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAACGATTCCTCTAATCAGAGGCTCAACG
*
1229326 ACTTTTGAAAAAAAAAAGG
65 AC-TTTGAAAAAATAAAGG
* ** *
1229345 CCCCTCTAATCAGAGGCTCAATAACTTTGAAAAGTAAA
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
1229383 TTGCTCCTCT
Statistics
Matches: 183, Mismatches: 16, Indels: 14
0.86 0.08 0.07
Matches are distributed among these distances:
80 6 0.03
82 27 0.15
83 76 0.42
84 28 0.15
85 16 0.09
86 4 0.02
87 26 0.14
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (82 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACGATTCCTCTAATCAGAGGCTCAACGA
CTTTGAAAAAATAAAGG
Found at i:1229392 original size:41 final size:41
Alignment explanation
Indices: 1229092--1229474 Score: 346
Period size: 42 Copynumber: 9.1 Consensus size: 41
1229082 TTGATCAAAA
* * *
1229092 CTCCTCTAAGCAAAGGCTCAACGACTTTGAAAAACATAAACAATG
1 CTCCTCTAATCAGAGGCTCAACGACTTTG-AAAA-AT-AA-ATTG
1229137 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAATGAATAAA--G
1 CTCCTCTAATCAGAGGCTCAACGACTTTG-AAA--AATAAATTG
* *
1229179 CTCCTCTAATCAGAGGCTCAACGACTTCGAAAAATAAA-CG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATTG
* *
1229219 ATTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGG
1 -CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATTG
* * **
1229261 CTTCTCTAATCAGAGGCTCAACAACTTTTGAAAAATAAAAGG
1 CTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAATTG
* * **
1229303 CTCCTTTAATCAGAGGCTCAACGACTTTTGAAAAAAAAAAGG
1 CTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAATTG
* ** *
1229345 CCCCTCTAATCAGAGGCTCAATAACTTTGAAAAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATTG
* * * *
1229386 CTCCTCTAAAT-AGAGGCAACCATGACTTTGAAAAGTAAATTG
1 CTCCTCT-AATCAGAGGC-TCAACGACTTTGAAAAATAAATTG
* * *
1229428 CTCTTCTAAACAGAGG--CAATGAAACTTTGAAAAAATAAATTG
1 CTCCTCTAATCAGAGGCTCAACG--ACTTTG-AAAAATAAATTG
*
1229470 TTCCT
1 CTCCT
1229475 TGACAATCAT
Statistics
Matches: 294, Mismatches: 32, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
39 10 0.03
40 1 0.00
41 93 0.32
42 153 0.52
44 1 0.00
45 33 0.11
46 2 0.01
47 1 0.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (41 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATTG
Found at i:1229436 original size:83 final size:82
Alignment explanation
Indices: 1229135--1229475 Score: 277
Period size: 83 Copynumber: 4.1 Consensus size: 82
1229125 ACATAAACAA
* *
1229135 TGCTCCTCT-AATCAGAGGCTCAACGACTTTGAAAATGAATAAA--GCTCCTCTAATCAGAGGCT
1 TGCTCCT-TAAATCAGAGGCACAACGACTTTG-AAA--AATAAATGGCTCTTCTAATCAGAGGCT
** *
1229197 CAACGACTTCGAAAAATAAA-
62 CAATAACTTTGAAAAATAAAT
* * *
1229217 CGATTCCTCT-AATCAGAGGCTCAACGACTTTGAAAAATAAATGGCT-TCTCTAATCAGAGGCTC
1 TG-CTCCT-TAAATCAGAGGCACAACGACTTTGAAAAATAAATGGCTCT-TCTAATCAGAGGCTC
* *
1229280 AACAACTTTTGAAAAATAAAA
63 AATAAC-TTTGAAAAATAAAT
* * * * * * *
1229301 GGCTCCTTTAATCAGAGGCTCAACGACTTTTGAAAAAAAAAAGGCCCCTCTAATCAGAGGCTCAA
1 TGCTCCTTAAATCAGAGGCACAACGAC-TTTGAAAAATAAATGGCTCTTCTAATCAGAGGCTCAA
*
1229366 TAACTTTGAAAAGTAAAT
65 TAACTTTGAAAAATAAAT
* * * * *
1229384 TGCTCCTCTAAAT-AGAGGCAACCATGACTTTGAAAAGTAAATTGCTCTTCTAAACAGAGG--CA
1 TGCTCCT-TAAATCAGAGGC-ACAACGACTTTGAAAAATAAATGGCTCTTCTAATCAGAGGCTCA
1229446 ATGAAACTTTGAAAAAATAAAT
64 AT--AACTTTG-AAAAATAAAT
*
1229468 TGTTCCTT
1 TGCTCCTT
1229476 GACAATCATG
Statistics
Matches: 217, Mismatches: 28, Indels: 27
0.80 0.10 0.10
Matches are distributed among these distances:
80 6 0.03
81 4 0.02
82 28 0.13
83 119 0.55
84 60 0.28
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (82 bp):
TGCTCCTTAAATCAGAGGCACAACGACTTTGAAAAATAAATGGCTCTTCTAATCAGAGGCTCAAT
AACTTTGAAAAATAAAT
Found at i:1229455 original size:125 final size:122
Alignment explanation
Indices: 1229094--1229462 Score: 304
Period size: 125 Copynumber: 2.9 Consensus size: 122
1229084 GATCAAAACT
* * *
1229094 CCTCTAAGCAAAGGCTCAACGACTTTGAAAAACATAAACAAT-GCTCCTCTAATCAGAGGCTCAA
1 CCTCTAATCAGAGGCTCAACAACTTTG-AAAA-AT--A-AATGGCTCCTCTAATCAGAGGC-CAA
* * * * * * * **
1229158 CGAC-TTTG-AAAATGAATAAAGCTCCTCTAATCAGAGGCTCAACGACTTCGAAAAATAAACGAT
60 CAACTTTTGAAAAAT-AA-AAGGCTCCTTTAAACAGAGGCTCAAC-ACTTTGAAAAAAAAAAGGC
*
1229221 T
122 C
* *
1229222 CCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAATGGCTTCTCTAATCAGAGGCTCAACAACT
1 CCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGC-CAACAACT
*
1229287 TTTGAAAAATAAAAGGCTCCTTTAATCAGAGGCTCAACGACTTTTGAAAAAAAAAAGGCC
65 TTTGAAAAATAAAAGGCTCCTTTAAACAGAGGCTCAAC-AC-TTTGAAAAAAAAAAGGCC
* * *
1229347 CCTCTAATCAGAGGCTCAATAACTTTGAAAAGTAAATTGCTCCTCTAAAT-AGAGG-CAACCATG
1 CCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATGGCTCCTCT-AATCAGAGGCCAA-CA--
* ** *
1229410 AC-TTTGAAAAGTAAATTGCT-CTTCTAAACAGAGGCAATGAA-ACTTTGAAAAAA
62 ACTTTTGAAAAATAAAAGGCTCCTT-TAAACAGAGGC--TCAACACTTTGAAAAAA
1229463 TAAATTGTTC
Statistics
Matches: 208, Mismatches: 22, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
123 6 0.03
124 67 0.32
125 91 0.44
126 12 0.06
127 7 0.03
128 25 0.12
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (122 bp):
CCTCTAATCAGAGGCTCAACAACTTTGAAAAATAAATGGCTCCTCTAATCAGAGGCCAACAACTT
TTGAAAAATAAAAGGCTCCTTTAAACAGAGGCTCAACACTTTGAAAAAAAAAAGGCC
Found at i:1230089 original size:22 final size:21
Alignment explanation
Indices: 1230042--1230093 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
1230032 TCACTCAAAG
* *
1230042 ATTCTCATTTTGAAACTCAAAG
1 ATTCTCA-TTTGAAACTAAAAA
*
1230064 ATTCTCATTTGAATTCTAAAAA
1 ATTCTCATTTGAA-ACTAAAAA
1230086 ATTCTCAT
1 ATTCTCAT
1230094 CAAATATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (21 bp):
ATTCTCATTTGAAACTAAAAA
Found at i:1231266 original size:8 final size:8
Alignment explanation
Indices: 1231240--1231302 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
1231230 TTTGAATCTT
1231240 TTTTTTTA
1 TTTTTTTA
* *
1231248 TTTTCTCA
1 TTTTTTTA
1231256 TTTTTTTA
1 TTTTTTTA
1231264 TTTTTTT-
1 TTTTTTTA
1231271 TTCTTTCTT-
1 TT-TTT-TTA
*
1231280 TTTTTTCA
1 TTTTTTTA
*
1231288 TTTTTTCA
1 TTTTTTTA
1231296 TTTTTTT
1 TTTTTTT
1231303 CATCATCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 3 0.07
8 39 0.85
9 4 0.09
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1231267 original size:25 final size:24
Alignment explanation
Indices: 1231238--1231293 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
1231228 AATTTGAATC
* * *
1231238 TTTTTTTTTATTTTCTCATTTTTTTA
1 TTTTTTTTT-CTTTCT-TTTTTTTCA
1231264 TTTTTTTTTCTTTCTTTTTTTTCA
1 TTTTTTTTTCTTTCTTTTTTTTCA
1231288 TTTTTT
1 TTTTTT
1231294 CATTTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 13 0.48
25 5 0.19
26 9 0.33
ACGTcount: A:0.07, C:0.09, G:0.00, T:0.84
Consensus pattern (24 bp):
TTTTTTTTTCTTTCTTTTTTTTCA
Found at i:1231299 original size:32 final size:35
Alignment explanation
Indices: 1231248--1231320 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 35
1231238 TTTTTTTTTA
* * *
1231248 TTTTCTCATTTTTTTATTTTTTT-TTC-T-TTCTT
1 TTTTTTCATTTTTTCATTTTTTTCATCATCTTCTT
1231280 TTTTTTCATTTTTTCATTTTTTTCATCATCTTCTT
1 TTTTTTCATTTTTTCATTTTTTTCATCATCTTCTT
1231315 TTTTTT
1 TTTTTT
1231321 TTCTCATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 21 0.60
33 2 0.06
34 1 0.03
35 11 0.31
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (35 bp):
TTTTTTCATTTTTTCATTTTTTTCATCATCTTCTT
Found at i:1231303 original size:9 final size:9
Alignment explanation
Indices: 1231239--1231305 Score: 56
Period size: 9 Copynumber: 8.1 Consensus size: 9
1231229 ATTTGAATCT
*
1231239 TTTTTTTTA
1 TTTTTTTCA
*
1231248 -TTTTCTCA
1 TTTTTTTCA
1231256 TTTTTTT-A
1 TTTTTTTCA
1231264 -TTTTTT--
1 TTTTTTTCA
* *
1231270 TTTCTTTCT
1 TTTTTTTCA
1231279 TTTTTTTCA
1 TTTTTTTCA
1231288 -TTTTTTCA
1 TTTTTTTCA
1231296 TTTTTTTCA
1 TTTTTTTCA
1231305 T
1 T
1231306 CATCTTCTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
7 11 0.23
8 15 0.32
9 21 0.45
ACGTcount: A:0.09, C:0.10, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:1234989 original size:60 final size:59
Alignment explanation
Indices: 1234859--1235021 Score: 209
Period size: 60 Copynumber: 2.7 Consensus size: 59
1234849 TTGTGCAGGA
* * * * * *
1234859 AAAATTGATACTTTCAACTTTTCTCAAAAAATTTTTTTTTTTTGAAAACCTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTC-CCAAAAA--TATATTTTTTAAAAACCTTATTTTCAAAG
* *
1234921 AAAATTGATACTTTCAACTTTTTCCCAAGAATATATTTTTTAAAAAGCTTATTTTCAAAG
1 AAAATTGATACTTTCAAC-TTTTCCCAAAAATATATTTTTTAAAAACCTTATTTTCAAAG
1234981 AAAATTGATACTTTCAACTTTTCCTCAAAAATATATTTTTT
1 AAAATTGATACTTTCAACTTTTCC-CAAAAATATATTTTTT
1235022 TGAATTTTAT
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
59 6 0.07
60 56 0.62
62 23 0.26
63 5 0.06
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCCAAAAATATATTTTTTAAAAACCTTATTTTCAAAG
Found at i:1235962 original size:5 final size:5
Alignment explanation
Indices: 1235954--1235999 Score: 56
Period size: 5 Copynumber: 8.4 Consensus size: 5
1235944 AGGAAAGAAG
1235954 AAAAT AAAAT AAAAT AAAAT AAAAAAT AAAAT AAAAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT --AAAAT AAAAT -AAAAT AA-AAT AA
1236000 TAAGGATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
5 22 0.59
6 10 0.27
7 5 0.14
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1235981 original size:12 final size:11
Alignment explanation
Indices: 1235954--1235999 Score: 67
Period size: 12 Copynumber: 4.1 Consensus size: 11
1235944 AGGAAAGAAG
1235954 AAAATAAAAT-
1 AAAATAAAATA
1235964 AAAATAAAATAA
1 AAAATAAAAT-A
1235976 AAAATAAAATA
1 AAAATAAAATA
1235987 AAAATAATAATA
1 AAAATAA-AATA
1235999 A
1 A
1236000 TAAGGATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.30
11 8 0.24
12 15 0.45
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:1236031 original size:4 final size:4
Alignment explanation
Indices: 1236019--1236211 Score: 66
Period size: 4 Copynumber: 48.0 Consensus size: 4
1236009 CATATTAATT
* * *
1236019 AATA GATA AAT- AATA TATA AATA GATA AAT- AAT- AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
* * * * * * * *
1236064 GATA AAT- AAT- AATA CATATA TATA TATA TATA TATC AACA GATA AAT-
1 AATA AATA AATA AATA -A-ATA AATA AATA AATA AATA AATA AATA AATA
*
1236111 AATAA AATAA AATA AATA TAGATT AATA AATA GTAAT- AATA AATA AATA
1 AAT-A AAT-A AATA AATA -A-ATA AATA AATA --AATA AATA AATA AATA
* * *
1236160 AA-A TAATA AATA CATAA AATA GA-A AATA AAGTAA AATA AA-A TATA
1 AATA -AATA AATA AAT-A AATA AATA AATA AA-T-A AATA AATA AATA
1236205 AA-A AATA
1 AATA AATA
1236212 CAAAAATACA
Statistics
Matches: 145, Mismatches: 24, Indels: 40
0.69 0.11 0.19
Matches are distributed among these distances:
3 29 0.20
4 88 0.61
5 17 0.12
6 11 0.08
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (4 bp):
AATA
Found at i:1236055 original size:22 final size:22
Alignment explanation
Indices: 1236027--1236177 Score: 102
Period size: 22 Copynumber: 7.0 Consensus size: 22
1236017 TTAATAGATA
1236027 AATAATATATAAATAGATAAAT
1 AATAATATATAAATAGATAAAT
*
1236049 AATAATAAATAAATAGATAAAT
1 AATAATATATAAATAGATAAAT
* * *
1236071 AATAATACAT--ATATATATAT
1 AATAATATATAAATAGATAAAT
* *
1236091 -AT-ATATATCAACAGATAAAT
1 AATAATATATAAATAGATAAAT
* *
1236111 AATAAAATA-AAATAAATATAGATT
1 AATAATATATAAATAGATA-A-A-T
1236135 AATAA-ATAGT-AATA-ATAAAT
1 AATAATATA-TAAATAGATAAAT
* *
1236155 AAATAAAATAATAAATACATAAA
1 -AATAATAT-ATAAATAGATAAA
1236178 ATAGAAAATA
Statistics
Matches: 103, Mismatches: 12, Indels: 26
0.73 0.09 0.18
Matches are distributed among these distances:
18 5 0.05
19 2 0.02
20 16 0.16
21 14 0.14
22 39 0.38
23 12 0.12
24 15 0.15
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (22 bp):
AATAATATATAAATAGATAAAT
Found at i:1236149 original size:37 final size:38
Alignment explanation
Indices: 1236108--1236206 Score: 111
Period size: 37 Copynumber: 2.7 Consensus size: 38
1236098 TCAACAGATA
*
1236108 AATAATAAAATAAAAT-AAATATAGATTA-AT-AAATAG
1 AATAATAAAATAAAATAAAATATA-AATACATAAAATAG
1236144 TAATAAT-AAAT-AAATAAAATAATAAATACATAAAATAG
1 -AATAATAAAATAAAATAAAAT-ATAAATACATAAAATAG
*
1236182 AA-AATAAAGTAAAATAAAATATAAA
1 AATAATAAAATAAAATAAAATATAAA
1236207 AAATACAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
35 4 0.07
36 14 0.26
37 21 0.39
38 15 0.28
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (38 bp):
AATAATAAAATAAAATAAAATATAAATACATAAAATAG
Found at i:1241474 original size:17 final size:17
Alignment explanation
Indices: 1241452--1241486 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1241442 AAAGATATAG
1241452 ACTTTGAAGCTTTAAAA
1 ACTTTGAAGCTTTAAAA
**
1241469 ACTTTGATTCTTTAAAA
1 ACTTTGAAGCTTTAAAA
1241486 A
1 A
1241487 AATGAAAATG
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:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
ACTTTGAAGCTTTAAAA
Found at i:1244645 original size:15 final size:16
Alignment explanation
Indices: 1244614--1244646 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1244604 TATAATTTCA
1244614 TTTAA-TTTTAATTTT
1 TTTAATTTTTAATTTT
1244629 TTTAATTTTTTAATTTT
1 TTTAA-TTTTTAATTTT
1244646 T
1 T
1244647 GATTCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
17 11 0.69
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTAATTTTTAATTTT
Found at i:1251892 original size:28 final size:26
Alignment explanation
Indices: 1251841--1251901 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
1251831 AATAGAAATG
1251841 ATTAAATTAATTTTTTTATCAAATATAA
1 ATTAAATTAATTTTTTTA-CAAAT-TAA
1251869 ATTAAATTAATTTAATTTTA-AAATTAA
1 ATTAAATTAATTT--TTTTACAAATTAA
1251896 A-TAAAT
1 ATTAAAT
1251902 AAATCATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.16
27 4 0.13
28 17 0.55
30 5 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
ATTAAATTAATTTTTTTACAAATTAA
Found at i:1265675 original size:26 final size:26
Alignment explanation
Indices: 1265619--1265675 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
1265609 TGAACACTTT
* * **
1265619 TTTATATTAATTTAATTATTTTTTTA
1 TTTATATGAATCTAATTATTTTTAAA
*
1265645 GTTATATGAATCTAATTATTTTTAAA
1 TTTATATGAATCTAATTATTTTTAAA
1265671 TTTAT
1 TTTAT
1265676 GATATTTATG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (26 bp):
TTTATATGAATCTAATTATTTTTAAA
Found at i:1266777 original size:30 final size:30
Alignment explanation
Indices: 1266736--1266792 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1266726 TTTTTTATTT
* * *
1266736 ATATATATATTTATATAATGATATTTTTAA
1 ATATATATATTTAAAAAATAATATTTTTAA
*
1266766 ATATTTATATTTAAAAAATAATATTTT
1 ATATATATATTTAAAAAATAATATTTT
1266793 ATTAATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (30 bp):
ATATATATATTTAAAAAATAATATTTTTAA
Found at i:1267837 original size:14 final size:13
Alignment explanation
Indices: 1267803--1267849 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 13
1267793 TATAATTGTG
*
1267803 ATTAAAAAAATTT
1 ATTAAATAAATTT
*
1267816 AATAAATAAATTAT
1 ATTAAATAAATT-T
1267830 ATTAAATAAATTTT
1 ATTAAATAAA-TTT
1267844 ATTAAA
1 ATTAAA
1267850 ATTAACATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 10 0.34
14 17 0.59
15 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATTAAATAAATTT
Found at i:1299973 original size:62 final size:62
Alignment explanation
Indices: 1299894--1300012 Score: 202
Period size: 62 Copynumber: 1.9 Consensus size: 62
1299884 GTGGGGCCCG
*
1299894 TCTCCGTGTTAAGCGGGGTGATTGGAAAAGGTAAAGAAGCGAACGACGTCGTTCGCTGGCCA
1 TCTCCGTGTTAAACGGGGTGATTGGAAAAGGTAAAGAAGCGAACGACGTCGTTCGCTGGCCA
* * *
1299956 TCTCCGTGTTAAACGGGGTGATTGGAATAGGTAAAGAATCGAAGGACGTCGTTCGCT
1 TCTCCGTGTTAAACGGGGTGATTGGAAAAGGTAAAGAAGCGAACGACGTCGTTCGCT
1300013 TGAGTAGATA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.24
Consensus pattern (62 bp):
TCTCCGTGTTAAACGGGGTGATTGGAAAAGGTAAAGAAGCGAACGACGTCGTTCGCTGGCCA
Found at i:1307738 original size:18 final size:20
Alignment explanation
Indices: 1307704--1307744 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
1307694 AGTATAATAA
1307704 TTATTATAAATTTATAAAAT
1 TTATTATAAATTTATAAAAT
*
1307724 TTATT-TAAA-TTATAAATT
1 TTATTATAAATTTATAAAAT
1307742 TTA
1 TTA
1307745 CAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 11 0.55
19 4 0.20
20 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTATAAATTTATAAAAT
Found at i:1310629 original size:2 final size:2
Alignment explanation
Indices: 1310622--1310647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1310612 AAAACACGGT
1310622 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
1310648 AATTTTGTAT
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):
TA
Found at i:1311792 original size:23 final size:22
Alignment explanation
Indices: 1311766--1311827 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
1311756 ACGTCTATGT
1311766 AGATAATTTTTTTAAATGACACA
1 AGATAATTTTTTTAAATGA-ACA
* * *
1311789 AGATAATTTTTTAAAAAGAATA
1 AGATAATTTTTTTAAATGAACA
1311811 AGAT-ATTTTATTTAAAT
1 AGATAATTTT-TTTAAAT
1311828 TACAAATTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 5 0.15
22 11 0.33
23 17 0.52
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (22 bp):
AGATAATTTTTTTAAATGAACA
Found at i:1311856 original size:13 final size:13
Alignment explanation
Indices: 1311838--1311864 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1311828 TACAAATTAG
1311838 ATAATTGAAAATT
1 ATAATTGAAAATT
1311851 ATAATTGAAAATT
1 ATAATTGAAAATT
1311864 A
1 A
1311865 AATCAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
ATAATTGAAAATT
Found at i:1311936 original size:21 final size:21
Alignment explanation
Indices: 1311912--1311954 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1311902 TGGAATATGG
* *
1311912 ATTTTATTTTTTTAATAAATA
1 ATTTTAGTTGTTTAATAAATA
*
1311933 ATTTTAGTTGTTTACTAAATA
1 ATTTTAGTTGTTTAATAAATA
1311954 A
1 A
1311955 CCTTATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTTTAGTTGTTTAATAAATA
Found at i:1312142 original size:30 final size:30
Alignment explanation
Indices: 1312082--1312143 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
1312072 TTTAAAAAAG
* * **
1312082 TTATGTAAGATATTAAAAATTTAAGCAATT
1 TTATGTAAAATATTAAAAATTCAAAAAATT
*
1312112 TTATGTAAAATTTTAAAAATTCAAAAAATT
1 TTATGTAAAATATTAAAAATTCAAAAAATT
1312142 TT
1 TT
1312144 CATCTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (30 bp):
TTATGTAAAATATTAAAAATTCAAAAAATT
Found at i:1312372 original size:2 final size:2
Alignment explanation
Indices: 1312365--1312410 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
1312355 ATGTAATCTA
* *
1312365 AT AT AT AT AT AT AT AA AA AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1312406 AT AT A
1 AT AT A
1312411 ACAACATACG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1312997 original size:697 final size:677
Alignment explanation
Indices: 1311710--1313738 Score: 2666
Period size: 697 Copynumber: 3.0 Consensus size: 677
1311700 TGTTTTGTAC
* *** *
1311710 ATATATATATATTATAACAATATACGTAAATAAATTTG-TCACATAAACGTCTATGTAGATAATT
1 ATATATATATATTATAACAACATACGTAAATAAATTTGCT-AC-TAGGTGCCTATGTAGATAATT
* *
1311774 TTTTTAAATGACAC--AAGATAATTTTTTAAAAAGAATAAGATATTTTATTTAAATTACAAATTA
64 TTTTTAAATGACACATAAGATAATTTTTT-AAAAGAATAAGATATTTTCTTTTAATTACAAATTA
* *
1311837 GATAA---T---TGA---AAATTATAATTGAAAATTAAATCAATTTAGAGATATATTTTTTAAAA
128 GATAATTTTAAATTATTCAAATTATAATTGAAAATCAAATCAATTTAGAGATATATTTTTTAAAA
* * * *
1311893 TTAAAAATATGGAATATGGATTTTATTTTTTTAATAAATAATTTTAGTTGTTTA-CTAAATAACC
193 TTAAAAATATGAAATATGAATTAT-TTTTTTTAATAAATAA-TTTAGTTGTTTATCCAAATAACC
* ** *
1311957 TTATTTAAAATTTTATTTAATTTTCAAAATCTTTCAAACATGTTTAAAATTTATAAAGATTAAGT
256 TAATTTAAAAAATTATTTAATTATCAAAATCTTTCAAACATGTTTAAAA-TTATAAAGATTAAGT
* * * * *
1312022 TTATCCAAATCTTTCAATAAT-TTTTTTATCTTGATTTAAAAAATTATCTTTTTAAAAAAGTTAT
320 TTATACAAATATTTTAATAATCATTTTTATCTTGATTTAAAAAATTATCTTTTTAAAAAAATTA-
*
1312086 GTAAGATATTAAAAATTTAAGCAATTTTATGTAAAATTTTAAAAATTCAAAAAATTTTCATCTTA
384 ATAAGATATTAAAAATTTAAGCAATTTTATGT-AAATTTTAAAAATTCAAAAAATTTTCATCTTA
* * * *
1312151 AATCTTTAAATAATAAGATTATCAAAATGATTATATCCATTTGAACTTTAATTATCAAATTCATA
448 AATCTTTAAATAATAAGATTATCAAAATAATTATATTCATTTGAACTATAATTATC-AATTTATA
* * *
1312216 TTTCAAATACATGCAAAAAAATTTAATATTATCTTTATGATTTATTATATCCATTTTAAATTTTA
512 TTTCAAATAAATGCAAAAAAATTTAATATTATCTTTATCACTTATTATATCCATTTTAAATTTT-
* *
1312281 AAAAATTAATTTAAAAATTATTTATTTAATCTTAATTGCCATTAAAGAAATTTTTTACAATTTTA
576 AAAAATTAATTTAAAAATTATTTATTTAATCCTAATTGCCATTAAAGAAATTTTTTACAAATTTA
1312346 TGACTACAAATGTAATCTAATATATATATATATAAAAATATATATAT
641 TGACTACAAATGTAATC-----TA-ATATATAT----ATATATATAT
* * *
1312393 ATATATATATATTATATAACAACATACGTAAATAGATTTGCTACGTAGGTGCCTATGTAAACAAT
1 ATATATATATA-T-TATAACAACATACGTAAATAAATTTGCTAC-TAGGTGCCTATGTAGATAAT
* * *
1312458 TTTTTTAAATGACACATAAGATAATTATTTAAAAGAATAAAATATTTTCTTTTAATTACAAACTA
63 TTTTTTAAATGACACATAAGATAATTTTTTAAAAGAATAAGATATTTTCTTTTAATTACAAATTA
* * *
1312523 GATAATTTTAAATATATTCAAATTATAATTGAAAATCAAATCAATTTAGAGATAAAATTTCTAAA
128 GATAATTTTAAAT-TATTCAAATTATAATTGAAAATCAAATCAATTTAGAGATATATTTTTTAAA
1312588 ATTAAAAATATGAAATATGAAATATATTTTTTTTAATAAATAATTTAAGTTGTTTATCCAAA-AA
192 ATTAAAAATATGAAATATG-AAT-TATTTTTTTTAATAAATAATTT-AGTTGTTTATCCAAATAA
* *
1312652 CCTCATTTAAAAAATTATTTAATTATCAAAATCTTTTAAACATGTTTAAATATTATAAAGATTAA
254 CCTAATTTAAAAAATTATTTAATTATCAAAATCTTTCAAACATGTTTAAA-ATTATAAAGATTAA
* * ***
1312717 GTTTATTCAAATATTTTAATAATCATTTTTATCTGGATTTAAAAAATTAT-TTAAAAAAAAAATT
318 GTTTATACAAATATTTTAATAATCATTTTTATCTTGATTTAAAAAATTATCTTTTTAAAAAAATT
* *
1312781 ACATAAGATATTAAAATTTTAAGCAATTATTTTATGTAGAATTTTGAAAATTCAAAAAATTTTCA
383 A-ATAAGATATTAAAAATTTAAGC-A--ATTTTATGTA-AATTTTAAAAATTCAAAAAATTTTCA
*
1312846 TCCTAAATCTTTAAATAATAAGATTATCAAAATAATTATATTCATTTGAACTATAATTATCAATT
443 TCTTAAATCTTTAAATAATAAGATTATCAAAATAATTATATTCATTTGAACTATAATTATCAATT
** * *
1312911 TATATTTCAAATAAATGCAAAAAAAAATAATATTATCTATATCACTTATTATATCCATTTTTAAT
508 TATATTTCAAATAAATGCAAAAAAATTTAATATTATCTTTATCACTTATTATATCCATTTTAAAT
* ** * *
1312976 TTTTAATTTTAATTT-AAAATTATCTATTTAATCCTAATTACCATTAAAGAAATTTTTTACAAAT
573 TTTAAAAATTAATTTAAAAATTATTTATTTAATCCTAATTGCCATTAAAGAAATTTTTTACAAAT
*
1313040 TTATAACTACAAATGTAATCTAATATATATATATATATAT
638 TTATGACTACAAATGTAATCTAATATATATATATATATAT
** * * *
1313080 ATATATATATATTATAACAACATATATAAATAAATTTGCTA-TTGGATGCCTATGTGGATAACTT
1 ATATATATATATTATAACAACATACGTAAATAAATTTGCTACTAGG-TGCCTATGTAGATAATTT
* * * *
1313144 TCTTAAATGACATATAGGATAATTTTTTAAAAGAATAAGATATTTTCTTTTAATTGCAAATTAGA
65 TTTTAAATGACACATAAGATAATTTTTTAAAAGAATAAGATATTTTCTTTTAATTACAAATTAGA
*
1313209 TAATTTTAAATTTATTCAAATTATAATTAAAAATCAAATCAATTTAGAGATATATTTTTTAAAAT
130 TAATTTTAAA-TTATTCAAATTATAATTGAAAATCAAATCAATTTAGAGATATATTTTTTAAAAT
*
1313274 TAAAAATATGAAATATGAATT-TTATTTTTAATAAATAACTTTAGTTGTTTAT-CAAATAACCTA
194 TAAAAATATGAAATATGAATTATTTTTTTTAATAAATAA-TTTAGTTGTTTATCCAAATAACCTA
* * *
1313337 ATTTAAAAAATTAATTAATTATCAAAATCTGTCAAACATATTTAAAAATTATAAAGATTAAGTTT
258 ATTTAAAAAATTATTTAATTATCAAAATCTTTCAAACATGTTT-AAAATTATAAAGATTAAGTTT
* ** * *
1313402 ATACAAATATTTTAACAGCCATTTTTATCTTGATTTAAAAAATTATCTTTTTAAAAAATTTATTA
322 ATACAAATATTTTAATAATCATTTTTATCTTGATTTAAAAAATTATCTTTTTAAAAAAATTAATA
* * * *
1313467 AGATATTAAAAATTCAAGCAATTTTATGTAAGATTTTAAAAATT-TAAAATTTTTTATCTTAAAT
387 AGATATTAAAAATTTAAGCAATTTTATGTAA-ATTTTAAAAATTCAAAAAATTTTCATCTTAAAT
* * *
1313531 CTTTAAATAATAAGATTATCAAAATTATTATA-TCTATTCGAACTCA-AATTATTAAATTTATAT
451 CTTTAAATAATAAGATTATCAAAATAATTATATTC-ATTTGAACT-ATAATTA-TCAATTTATAT
* *
1313594 TTCAAATAAATGTAAAAAAATTTAATACTATCTTTATCACTTATTATATCCATTTTAAAATTTTA
513 TTCAAATAAATGCAAAAAAATTTAATATTATCTTTATCACTTATTATATCCATTTT-AAATTTTA
* *
1313659 AAAATTAATTTAAAAATTATTTATTTAATCCTAATTGCTATTAAAG-AATTCTTCTACAAATTTA
577 AAAATTAATTTAAAAATTATTTATTTAATCCTAATTGCCATTAAAGAAATT-TTTTACAAATTTA
* *
1313723 AGATTACAAATGTAAT
641 TGACTACAAATGTAAT
1313739 ATGTTATACA
Statistics
Matches: 1186, Mismatches: 122, Indels: 79
0.86 0.09 0.06
Matches are distributed among these distances:
676 2 0.00
677 61 0.05
678 83 0.07
679 19 0.02
680 61 0.05
681 148 0.12
682 18 0.02
683 17 0.01
684 149 0.13
685 82 0.07
686 38 0.03
687 33 0.03
689 1 0.00
691 8 0.01
692 3 0.00
693 1 0.00
696 63 0.05
697 202 0.17
698 41 0.03
699 65 0.05
700 91 0.08
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (677 bp):
ATATATATATATTATAACAACATACGTAAATAAATTTGCTACTAGGTGCCTATGTAGATAATTTT
TTTAAATGACACATAAGATAATTTTTTAAAAGAATAAGATATTTTCTTTTAATTACAAATTAGAT
AATTTTAAATTATTCAAATTATAATTGAAAATCAAATCAATTTAGAGATATATTTTTTAAAATTA
AAAATATGAAATATGAATTATTTTTTTTAATAAATAATTTAGTTGTTTATCCAAATAACCTAATT
TAAAAAATTATTTAATTATCAAAATCTTTCAAACATGTTTAAAATTATAAAGATTAAGTTTATAC
AAATATTTTAATAATCATTTTTATCTTGATTTAAAAAATTATCTTTTTAAAAAAATTAATAAGAT
ATTAAAAATTTAAGCAATTTTATGTAAATTTTAAAAATTCAAAAAATTTTCATCTTAAATCTTTA
AATAATAAGATTATCAAAATAATTATATTCATTTGAACTATAATTATCAATTTATATTTCAAATA
AATGCAAAAAAATTTAATATTATCTTTATCACTTATTATATCCATTTTAAATTTTAAAAATTAAT
TTAAAAATTATTTATTTAATCCTAATTGCCATTAAAGAAATTTTTTACAAATTTATGACTACAAA
TGTAATCTAATATATATATATATATAT
Found at i:1313107 original size:2 final size:2
Alignment explanation
Indices: 1313062--1313095 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1313052 ATGTAATCTA
1313062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1313096 ACAACATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1313899 original size:14 final size:14
Alignment explanation
Indices: 1313880--1313921 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1313870 TTCTTATGAA
1313880 AAAAATATTTTTTT
1 AAAAATATTTTTTT
1313894 AAAAATATTTTTTT
1 AAAAATATTTTTTT
* *
1313908 -TACATATTTTTTT
1 AAAAATATTTTTTT
1313921 A
1 A
1313922 CATTTTTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (14 bp):
AAAAATATTTTTTT
Found at i:1340811 original size:2 final size:2
Alignment explanation
Indices: 1340804--1340846 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1340794 TAATGAAAGT
1340804 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1340846 T
1 T
1340847 TATACATGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1354508 original size:25 final size:25
Alignment explanation
Indices: 1354474--1354523 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1354464 AAATGGTTAG
1354474 TCAGTCTTGAGTAGCTTACCAATAC
1 TCAGTCTTGAGTAGCTTACCAATAC
*
1354499 TCAGTCTTGAGTAGCTTACTAATAC
1 TCAGTCTTGAGTAGCTTACCAATAC
1354524 AGAATAGCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (25 bp):
TCAGTCTTGAGTAGCTTACCAATAC
Found at i:1359959 original size:2 final size:2
Alignment explanation
Indices: 1359954--1359984 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1359944 ACTATATAAG
1359954 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1359985 CGATTTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1379009 original size:21 final size:21
Alignment explanation
Indices: 1378985--1379035 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1378975 ATCATTAATT
1378985 TTAATTTTATCA-TAATAATAA
1 TTAATTTTATCATTAA-AATAA
*
1379006 TTAATTTTATTATTAAAATAA
1 TTAATTTTATCATTAAAATAA
1379027 TT-ATTTTAT
1 TTAATTTTAT
1379036 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATTTTATCATTAAAATAA
Found at i:1379383 original size:11 final size:11
Alignment explanation
Indices: 1379367--1379391 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1379357 TCGAGCAGAC
1379367 ATTAAATAAAA
1 ATTAAATAAAA
1379378 ATTAAATAAAA
1 ATTAAATAAAA
1379389 ATT
1 ATT
1379392 TATTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTAAATAAAA
Found at i:1380013 original size:23 final size:21
Alignment explanation
Indices: 1379983--1380030 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
1379973 AATATATTTT
* *
1379983 TTATTTTTGTTAAACTTATAAA
1 TTATTTTT-CTAAAATTATAAA
*
1380005 TTATCTTTTCTAAAATTTTAAA
1 TTAT-TTTTCTAAAATTATAAA
1380027 TTAT
1 TTAT
1380031 ATTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.56
Consensus pattern (21 bp):
TTATTTTTCTAAAATTATAAA
Found at i:1382774 original size:15 final size:15
Alignment explanation
Indices: 1382725--1382786 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 15
1382715 TTAACAAAAA
1382725 TAAAATAA-TTAATT
1 TAAAATAATTTAATT
**
1382739 TAATTTAATTTAATT
1 TAAAATAATTTAATT
*
1382754 TTAAATAATTTAATT
1 TAAAATAATTTAATT
* * *
1382769 CAAAATAAATTAAAT
1 TAAAATAATTTAATT
1382784 TAA
1 TAA
1382787 CCGAATTAAC
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
14 6 0.16
15 31 0.84
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATAATTTAATT
Found at i:1385807 original size:24 final size:24
Alignment explanation
Indices: 1385766--1385813 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1385756 TAACATTACG
1385766 AATTATTATATATGTAAT-TAAAA
1 AATTATTATATATGTAATATAAAA
1385789 AATTAATTATATA-GTTAATATAAAA
1 AATT-ATTATATATG-TAATATAAAA
1385814 CTATTACTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 5 0.23
24 12 0.55
25 5 0.23
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (24 bp):
AATTATTATATATGTAATATAAAA
Found at i:1391814 original size:123 final size:120
Alignment explanation
Indices: 1391531--1391807 Score: 363
Period size: 119 Copynumber: 2.3 Consensus size: 120
1391521 TTGTGTAGGA
1391531 AAAATTGATACTTTCAACTTTTCCCCAAAAATAC----TTTTTTGAAAATTTATTTTTAAGGAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-CTTTTTTTTTTGAAAATTTATTTTTAAGGAAA
* *
1391592 ATTGATACTTCCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGG
65 ATTGATACTTCCAACTTTTCCCCAAAAATA--TTTTTTTGAAAATTTGATTTCCAAGG
* *
1391650 AAAATTGATACTTTCAATTTTTCCTCAAAAATCTTTTTTTTTTGGAAAATTTATTTTTAAGGAAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTTT-GAAAATTTATTTTTAAGGAAA
** **
1391715 ATTGATACTTTTAACTTTTCCCCAAAAATA-TTTTTTGAAAATTT-ATTTTTAAGG
65 ATTGATACTTCCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTGATTTCCAAGG
*
1391769 AAAATTGATA-TTTACAACTTTTCCGCC-AAAATATTTTTT
1 AAAATTGATACTTT-CAACTTTTCC-CCAAAAATCTTTTTT
1391808 GATTTTTATT
Statistics
Matches: 140, Mismatches: 11, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
118 4 0.03
119 68 0.49
120 14 0.10
122 6 0.04
123 48 0.34
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (120 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTTTGAAAATTTATTTTTAAGGAAAA
TTGATACTTCCAACTTTTCCCCAAAAATATTTTTTTGAAAATTTGATTTCCAAGG
Found at i:1391847 original size:22 final size:22
Alignment explanation
Indices: 1391822--1391863 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1391812 TTTATTTAAA
1391822 GAAAATAGAACAAA-ATAAAAGT
1 GAAAATA-AACAAAGATAAAAGT
*
1391844 GAAAATAAATAAAGATAAAA
1 GAAAATAAACAAAGATAAAA
1391864 AAATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (22 bp):
GAAAATAAACAAAGATAAAAGT
Found at i:1391868 original size:18 final size:17
Alignment explanation
Indices: 1391845--1391914 Score: 54
Period size: 18 Copynumber: 3.9 Consensus size: 17
1391835 AATAAAAGTG
1391845 AAAATAAATAAAGATAAA
1 AAAATAAATAAA-ATAAA
*
1391863 AAAATAAAGAAAAGTAAA
1 AAAATAAATAAAA-TAAA
*
1391881 ACAA-AAATAAAAATAAGA
1 AAAATAAAT-AAAATAA-A
1391899 TAAAGATAAA-AAAATA
1 -AAA-ATAAATAAAATA
1391915 TTAAATAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
17 7 0.17
18 23 0.55
19 8 0.19
20 1 0.02
21 3 0.07
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.14
Consensus pattern (17 bp):
AAAATAAATAAAATAAA
Found at i:1391907 original size:17 final size:16
Alignment explanation
Indices: 1391845--1391910 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
1391835 AATAAAAGTG
1391845 AAAATAAATAAAGAT-
1 AAAATAAATAAAGATA
1391860 AAAA-AAATAAAG--A
1 AAAATAAATAAAGATA
* * *
1391873 AAAGTAAAACAAAAATA
1 AAAAT-AAATAAAGATA
1391890 AAAATAAGATAAAGATA
1 AAAATAA-ATAAAGATA
1391907 AAAA
1 AAAA
1391911 AATATTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 3 0.08
14 8 0.21
15 10 0.26
16 2 0.05
17 16 0.41
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAATAAATAAAGATA
Found at i:1391909 original size:22 final size:21
Alignment explanation
Indices: 1391823--1391923 Score: 55
Period size: 22 Copynumber: 4.6 Consensus size: 21
1391813 TTATTTAAAG
* *
1391823 AAAATAGAACAAA-ATAAAAGTG
1 AAAATA-AATAAAGATAAAA-TA
*
1391845 AAAATAAATAAAGATAAAAAA
1 AAAATAAATAAAGATAAAATA
* *
1391866 ATAAAGAAAAGTAAA-ACAAAAATA
1 A-AAA-TAAA-TAAAGA-TAAAATA
1391890 AAAATAAGATAAAGATAAAA-A
1 AAAATAA-ATAAAGATAAAATA
*
1391911 AATATTAAATAAA
1 AA-AATAAATAAA
1391924 TCTAATCTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
21 14 0.23
22 29 0.47
23 9 0.15
24 10 0.16
ACGTcount: A:0.74, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAAATAAATAAAGATAAAATA
Found at i:1391964 original size:26 final size:25
Alignment explanation
Indices: 1391877--1391966 Score: 72
Period size: 26 Copynumber: 3.4 Consensus size: 25
1391867 TAAAGAAAAG
* * *
1391877 TAAAACAAAAATAAAAATAAGATAAAGA
1 TAAAA-AAAATTAAAAA-AATAT-AATA
* * *
1391905 TAAAAAAATATTAAATAAATCTAATC
1 TAAAAAAA-ATTAAAAAAATATAATA
1391931 TAATAAAAAATTAAAAAAATATATATA
1 TAA-AAAAAATTAAAAAAATATA-ATA
1391958 TAAAAAAAA
1 TAAAAAAAA
1391967 AAACCTGGAG
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 23 0.46
27 16 0.32
28 11 0.22
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.23
Consensus pattern (25 bp):
TAAAAAAAATTAAAAAAATATAATA
Found at i:1392937 original size:20 final size:20
Alignment explanation
Indices: 1392912--1392962 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1392902 AAGAAAGAAA
* *
1392912 AAAAATATAATAATAATAAT
1 AAAAATAAAATAAAAATAAT
*
1392932 AAAAATAAAATAAAAATAAA
1 AAAAATAAAATAAAAATAAT
1392952 ATAAAATAAAA
1 A-AAAATAAAA
1392963 AACATATACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (20 bp):
AAAAATAAAATAAAAATAAT
Found at i:1392941 original size:5 final size:5
Alignment explanation
Indices: 1392888--1392962 Score: 59
Period size: 5 Copynumber: 15.0 Consensus size: 5
1392878 AGTAAATAGC
* * *
1392888 TAAAA TAAAA -AAAGA -AGAAA GAAAA -AAAA TATAA TAATAA TAATA
1 TAAAA TAAAA TAAA-A TA-AAA TAAAA TAAAA TAAAA TAA-AA TAAAA
1392933 -AAAA TAAAA TAAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA T-AAAA TAAAA TAAAA TAAAA
1392963 AACATATACC
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
4 10 0.17
5 36 0.61
6 13 0.22
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:1392963 original size:6 final size:6
Alignment explanation
Indices: 1392889--1392963 Score: 59
Period size: 6 Copynumber: 12.7 Consensus size: 6
1392879 GTAAATAGCT
* * * *
1392889 AAAATA AAAA-A AGAAGA AAGAAAA AAAATA TAATAATA ATAATA AAAAT-
1 AAAATA AAAATA AAAATA AA-AATA AAAATA -AA-AATA AAAATA AAAATA
1392938 AAAATA AAAAT- AAAAT- AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
1392964 ACATATACCT
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
5 19 0.33
6 26 0.46
7 8 0.14
8 4 0.07
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:1392963 original size:11 final size:11
Alignment explanation
Indices: 1392909--1392962 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
1392899 AAGAAGAAAG
1392909 AAAAA-AAATAT
1 AAAAATAAA-AT
*
1392920 AATAATAATAAT
1 AAAAATAA-AAT
1392932 AAAAATAAAAT
1 AAAAATAAAAT
1392943 AAAAATAAAAT
1 AAAAATAAAAT
1392954 -AAAATAAAA
1 AAAAATAAAA
1392963 AACATATACC
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
10 9 0.23
11 18 0.46
12 11 0.28
13 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:1393125 original size:17 final size:18
Alignment explanation
Indices: 1393103--1393148 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
1393093 ATTTAACTCA
1393103 ATATTTTTATTTT-TTTT
1 ATATTTTTATTTTGTTTT
1393120 ATATTTTT-TGTTTGTTTT
1 ATATTTTTAT-TTTGTTTT
*
1393138 -TGTTTTTATTT
1 ATATTTTTATTT
1393149 ATTTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 19 0.76
18 5 0.20
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (18 bp):
ATATTTTTATTTTGTTTT
Found at i:1393159 original size:10 final size:9
Alignment explanation
Indices: 1393106--1393159 Score: 54
Period size: 10 Copynumber: 5.7 Consensus size: 9
1393096 TAACTCAATA
1393106 TTTTTATTT
1 TTTTTATTT
*
1393115 TTTTTATAT
1 TTTTTATTT
*
1393124 TTTTTGTTT
1 TTTTTATTT
*
1393133 GTTTTTGTTT
1 -TTTTTATTT
1393143 TTATTTATTT
1 TT-TTTATTT
1393153 ATTTTTA
1 -TTTTTA
1393160 CCAAAGCTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 17 0.45
10 19 0.50
11 2 0.05
ACGTcount: A:0.13, C:0.00, G:0.06, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:1393234 original size:41 final size:41
Alignment explanation
Indices: 1393165--1393375 Score: 314
Period size: 41 Copynumber: 5.1 Consensus size: 41
1393155 TTTTACCAAA
* * * *
1393165 GCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* * *
1393206 GCTCTTCTAAATAGAGCCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1393247 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
1393288 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1393329 ACTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
1393370 ACTCCT
1 GCTCCT
1393376 TGACAATCAT
Statistics
Matches: 155, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 155 1.00
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:1398722 original size:57 final size:57
Alignment explanation
Indices: 1398594--1398933 Score: 428
Period size: 57 Copynumber: 5.8 Consensus size: 57
1398584 TCTTGTGTAG
*
1398594 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTGGAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAATTTATTTTTAA
* * *
1398652 GAAAAATTGATACTTCCAACTTTTCCTCAAAAATATTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAA
* * * * **
1398709 GAAAAATTAATACTTCCAACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATA---TTTTTTGAAAATTT-ATTTTTAA
* * *
1398770 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAA-------TATTTTTTGAAAATTTATTTTTAA
*
1398834 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAA
* *
1398891 GAAAAATTGATACTTACAACTTTTCCCCCAAAATATTTTTTGA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGA
1398934 TTTTTATTTA
Statistics
Matches: 248, Mismatches: 23, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
57 116 0.47
58 33 0.13
60 12 0.05
61 36 0.15
64 37 0.15
65 13 0.05
68 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (57 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGAAAATTTATTTTTAA
Found at i:1398897 original size:182 final size:176
Alignment explanation
Indices: 1398596--1398931 Score: 537
Period size: 182 Copynumber: 1.9 Consensus size: 176
1398586 TTGTGTAGGA
*
1398596 AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTGGAAATTTATTTTTAAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTGAAAATTTATTTTTAAGAAAAATTG
* *
1398661 ATACTTCCAACTTTTCCTCAAAAATATTTTTTAAAAATTTATTTTTAAGAAAAATTAATACTTCC
66 ATACTTCCAACTTTTCCCCAAAAATATTTTTTAAAAATTTATTTTTAAGAAAAATTAATACTTAC
*
1398726 AACTTTTCCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGG
131 AACTTTTCCCCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGG
* *
1398772 AAAATTGATACTTTCAACTTTTCCTCAAAAATCCTTTTTTTTTTTTGAAAATTTATTTTTAAGAA
1 AAAATTGATACTTTCAACTTTTCCCCAAAAATAC------TTTTTTGAAAATTTATTTTTAAGAA
* *
1398837 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAAAAATTTATTTTTAAGAAAAATTGAT
60 AAATTGATACTTCCAACTTTTCCCCAAAAATATTTTTTAAAAATTTATTTTTAAGAAAAATTAAT
*
1398902 ACTTACAACTTTTCCCCCAAAATATTTTTT
125 ACTTACAACTTTTCCCCAAAAATATTTTTT
1398932 GATTTTTATT
Statistics
Matches: 145, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
176 32 0.22
182 113 0.78
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (176 bp):
AAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTTGAAAATTTATTTTTAAGAAAAATTG
ATACTTCCAACTTTTCCCCAAAAATATTTTTTAAAAATTTATTTTTAAGAAAAATTAATACTTAC
AACTTTTCCCCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGG
Found at i:1398971 original size:22 final size:22
Alignment explanation
Indices: 1398946--1398987 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1398936 TTTATTTAAA
1398946 GAAAATAGAACAAA-ATAAAAGT
1 GAAAATA-AACAAAGATAAAAGT
*
1398968 GAAAATAAATAAAGATAAAA
1 GAAAATAAACAAAGATAAAA
1398988 AAATAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.14
Consensus pattern (22 bp):
GAAAATAAACAAAGATAAAAGT
Found at i:1398992 original size:18 final size:17
Alignment explanation
Indices: 1398969--1399016 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
1398959 AATAAAAGTG
1398969 AAAATAAATAAAGATAAA
1 AAAATAAATAAA-ATAAA
*
1398987 AAAATAAAGAAAAGTAAA
1 AAAATAAATAAAA-TAAA
*
1399005 ACAA-AAATAAAA
1 AAAATAAATAAAA
1399017 ATAAGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.12
Consensus pattern (17 bp):
AAAATAAATAAAATAAA
Found at i:1399031 original size:17 final size:16
Alignment explanation
Indices: 1398969--1399034 Score: 59
Period size: 17 Copynumber: 4.2 Consensus size: 16
1398959 AATAAAAGTG
1398969 AAAATAAATAAAGAT-
1 AAAATAAATAAAGATA
1398984 AAAA-AAATAAAG--A
1 AAAATAAATAAAGATA
* * *
1398997 AAAGTAAAACAAAAATA
1 AAAAT-AAATAAAGATA
1399014 AAAATAAGATAAAGATA
1 AAAATAA-ATAAAGATA
1399031 AAAA
1 AAAA
1399035 ATATTAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
13 3 0.08
14 8 0.21
15 10 0.26
16 2 0.05
17 16 0.41
ACGTcount: A:0.77, C:0.02, G:0.08, T:0.14
Consensus pattern (16 bp):
AAAATAAATAAAGATA
Found at i:1399033 original size:22 final size:21
Alignment explanation
Indices: 1398947--1399033 Score: 52
Period size: 22 Copynumber: 3.9 Consensus size: 21
1398937 TTATTTAAAG
* *
1398947 AAAATAGAACAAA-ATAAAAGTG
1 AAAATA-AATAAAGATAAAA-TA
*
1398969 AAAATAAATAAAGATAAAAAA
1 AAAATAAATAAAGATAAAATA
* *
1398990 ATAAAGAAAAGTAAA-ACAAAAATA
1 A-AAA-TAAA-TAAAGA-TAAAATA
1399014 AAAATAAGATAAAGATAAAA
1 AAAATAA-ATAAAGATAAAA
1399034 AATATTAAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
21 6 0.12
22 25 0.50
23 9 0.18
24 10 0.20
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.14
Consensus pattern (21 bp):
AAAATAAATAAAGATAAAATA
Found at i:1399068 original size:8 final size:8
Alignment explanation
Indices: 1399055--1399088 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
1399045 ATTTTAATCT
1399055 AATAAAAA
1 AATAAAAA
1399063 AATAAAAA
1 AATAAAAA
**
1399071 AATCTAAA
1 AATAAAAA
1399079 AATAAAAA
1 AATAAAAA
1399087 AA
1 AA
1399089 ACCTGGAGTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (8 bp):
AATAAAAA
Found at i:1399074 original size:21 final size:19
Alignment explanation
Indices: 1399050--1399089 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
1399040 AAATAATTTT
1399050 AATCTAATAAAAAAATAAAAA
1 AATCTAA-AAAAAAA-AAAAA
1399071 AATCTAAAAATAAAAAAAA
1 AATCTAAAAA-AAAAAAAA
1399090 CCTGGAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AATCTAAAAAAAAAAAAAA
Found at i:1399444 original size:20 final size:20
Alignment explanation
Indices: 1399416--1399456 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1399406 TGAATTTCGT
*
1399416 CGGATTCTGAAAAATGTCAC
1 CGGAATCTGAAAAATGTCAC
* *
1399436 CGGAATCTGGAAAATTTCAC
1 CGGAATCTGAAAAATGTCAC
1399456 C
1 C
1399457 AAAAGTTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
CGGAATCTGAAAAATGTCAC
Found at i:1399897 original size:17 final size:16
Alignment explanation
Indices: 1399875--1399912 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1399865 CAAGTCAGAT
1399875 AAATCAAAAAAGAAAAA
1 AAATC-AAAAAGAAAAA
*
1399892 AAATC-AAAAGAAAAT
1 AAATCAAAAAGAAAAA
1399907 AAATCA
1 AAATCA
1399913 GATAAACCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 14 0.74
17 5 0.26
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (16 bp):
AAATCAAAAAGAAAAA
Found at i:1399902 original size:15 final size:15
Alignment explanation
Indices: 1399882--1399912 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1399872 GATAAATCAA
1399882 AAAAGAAAAAAAATC
1 AAAAGAAAAAAAATC
*
1399897 AAAAGAAAATAAATC
1 AAAAGAAAAAAAATC
1399912 A
1 A
1399913 GATAAACCAG
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:0.77, C:0.06, G:0.06, T:0.10
Consensus pattern (15 bp):
AAAAGAAAAAAAATC
Found at i:1400046 original size:5 final size:5
Alignment explanation
Indices: 1400031--1400083 Score: 70
Period size: 5 Copynumber: 10.0 Consensus size: 5
1400021 AGTAAATAGC
*
1400031 TAAAA TAAAAA TAAAA TAAAA TAAAA TAAAAA CAAAAA TAAAA TAAAA
1 TAAAA T-AAAA TAAAA TAAAA TAAAA T-AAAA -TAAAA TAAAA TAAAA
1400079 TAAAA
1 TAAAA
1400084 AACATATACC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
5 30 0.70
6 13 0.30
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:1400068 original size:22 final size:21
Alignment explanation
Indices: 1400031--1400085 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 21
1400021 AGTAAATAGC
*
1400031 TAAAATAAAAATAAAATAAAA
1 TAAAATAAAAAAAAAATAAAA
1400052 TAAAATAAAAACAAAAATAAAA
1 TAAAATAAAAA-AAAAATAAAA
1400074 TAAAATAAAAAA
1 TAAAATAAAAAA
1400086 CATATACCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 12 0.38
22 20 0.62
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (21 bp):
TAAAATAAAAAAAAAATAAAA
Found at i:1400068 original size:27 final size:27
Alignment explanation
Indices: 1400032--1400083 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1400022 GTAAATAGCT
*
1400032 AAAATAAAAATAAAATAAAATAAAATA
1 AAAACAAAAATAAAATAAAATAAAATA
1400059 AAAACAAAAATAAAATAAAATAAAA
1 AAAACAAAAATAAAATAAAATAAAA
1400084 AACATATACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.83, C:0.02, G:0.00, T:0.15
Consensus pattern (27 bp):
AAAACAAAAATAAAATAAAATAAAATA
Found at i:1403366 original size:25 final size:25
Alignment explanation
Indices: 1403329--1403382 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
1403319 TCCCCACAAT
* *
1403329 ATTCATAAGGGTATTTAATTTAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
1403354 ATTCATAAAGGTATTTAATTAAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
1403379 ATTC
1 ATTC
1403383 TTATTTAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.09, G:0.17, T:0.39
Consensus pattern (25 bp):
ATTCATAAAGGTATTTAATTAAGGC
Found at i:1403665 original size:81 final size:80
Alignment explanation
Indices: 1403558--1403916 Score: 378
Period size: 81 Copynumber: 4.3 Consensus size: 80
1403548 GAGAGGAAAA
* * *
1403558 AGGGCTACGTTGAGGGATCGGATTCTGTTCAAGATCAGGTTCTGTTCAAGCTACTGCAAATGTCG
1 AGGGCTTCGTTGAGGGATCGG-TTCTGTTCAAGATCGGGTTCTGTTCAAGCTACTGCAAACGTCG
*
1403623 AATAGGTGGAACGAGC
65 AATGGGTGGAACGAGC
*
1403639 AGGGCTTCGTTGAGGGATCAGGTTCTGTTCAAGATCGGGTTCTGTTCAAGCTACTGCAAACGTTG
1 AGGGCTTCGTTGAGGGATC-GGTTCTGTTCAAGATCGGGTTCTGTTCAAGCTACTGCAAACGTCG
1403704 AATGGGTGGAACGAGC
65 AATGGGTGGAACGAGC
* * * * * ** * *
1403720 AGGGCTTCGTTGAGGGATCGAGTTTTGTTGAAGCT-GCTGTAAACGTCGAATGGATGCTACTACA
1 AGGGCTTCGTTGAGGGATCG-GTTCTGTTCAAGATCG-GGT--TC-T-G--TTCAAGCTACTGCA
* *
1403784 AACGTCAAATGGGTGAAACGAGC
58 AACGTCGAATGGGTGGAACGAGC
* * ** *
1403807 AGGGCTTCATTGAGGGATCGGGTTCTGTTCAAGATCGGGTTCTGTTGAAGCCGCTGTAAACGTCG
1 AGGGCTTCGTTGAGGGATC-GGTTCTGTTCAAGATCGGGTTCTGTTCAAGCTACTGCAAACGTCG
*
1403872 AATGGGTGGAACGAAC
65 AATGGGTGGAACGAGC
* * *
1403888 AGGGTTTCATTGAAGGATCGGGTTCTGTT
1 AGGGCTTCGTTGAGGGATC-GGTTCTGTT
1403917 GAAGCTGCTG
Statistics
Matches: 233, Mismatches: 34, Indels: 22
0.81 0.12 0.08
Matches are distributed among these distances:
80 2 0.01
81 160 0.69
82 2 0.01
83 2 0.01
84 2 0.01
85 2 0.01
87 61 0.26
88 2 0.01
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (80 bp):
AGGGCTTCGTTGAGGGATCGGTTCTGTTCAAGATCGGGTTCTGTTCAAGCTACTGCAAACGTCGA
ATGGGTGGAACGAGC
Found at i:1403679 original size:17 final size:17
Alignment explanation
Indices: 1403654--1403688 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1403644 TTCGTTGAGG
1403654 GATCAGGTTCTGTTCAA
1 GATCAGGTTCTGTTCAA
*
1403671 GATCGGGTTCTGTTCAA
1 GATCAGGTTCTGTTCAA
1403688 G
1 G
1403689 CTACTGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (17 bp):
GATCAGGTTCTGTTCAA
Found at i:1403824 original size:168 final size:168
Alignment explanation
Indices: 1403607--1403940 Score: 488
Period size: 168 Copynumber: 2.0 Consensus size: 168
1403597 TTCTGTTCAA
* * * * *
1403607 GCTACTGCAAATGTCGAATAGGTGGAACGAGCAGGGCTTCGTTGAGGGATCAGGTTCTGTTCAAG
1 GCTACTACAAACGTCAAATAGGTGAAACGAGCAGGGCTTCATTGAGGGATCAGGTTCTGTTCAAG
* * * * *
1403672 ATCGGGTTCTGTTCAAGCTACTGCAAACGTTGAATGGGTGGAACGAGCAGGGCTTCGTTGAGGGA
66 ATCGGGTTCTGTTCAAGCCACTGCAAACGTCGAATGGGTGGAACGAACAGGGCTTCATTGAAGGA
* *
1403737 TCGAGTTTTGTTGAAGCTGCTGTAAACGTCGAATGGAT
131 TCGAGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGAT
* *
1403775 GCTACTACAAACGTCAAATGGGTGAAACGAGCAGGGCTTCATTGAGGGATCGGGTTCTGTTCAAG
1 GCTACTACAAACGTCAAATAGGTGAAACGAGCAGGGCTTCATTGAGGGATCAGGTTCTGTTCAAG
* * * *
1403840 ATCGGGTTCTGTTGAAGCCGCTGTAAACGTCGAATGGGTGGAACGAACAGGGTTTCATTGAAGGA
66 ATCGGGTTCTGTTCAAGCCACTGCAAACGTCGAATGGGTGGAACGAACAGGGCTTCATTGAAGGA
* *
1403905 TCGGGTTCTGTTGAAGCTGCTGCAAATGTCGAATGG
131 TCGAGTTCTGTTGAAGCTGCTGCAAACGTCGAATGG
1403941 GTGGAACGAG
Statistics
Matches: 146, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
168 146 1.00
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (168 bp):
GCTACTACAAACGTCAAATAGGTGAAACGAGCAGGGCTTCATTGAGGGATCAGGTTCTGTTCAAG
ATCGGGTTCTGTTCAAGCCACTGCAAACGTCGAATGGGTGGAACGAACAGGGCTTCATTGAAGGA
TCGAGTTCTGTTGAAGCTGCTGCAAACGTCGAATGGAT
Found at i:1403913 original size:64 final size:64
Alignment explanation
Indices: 1403839--1403980 Score: 212
Period size: 64 Copynumber: 2.2 Consensus size: 64
1403829 TTCTGTTCAA
* *
1403839 GATCGGGTTCTGTTGAAGCCGCTGTAAACGTCGAATGGGTGGAACGAACAGGGTTTCATTGAAG
1 GATCGGGTTCTGTTGAAGCCGCTGCAAACGTCGAATGGGTGGAACGAACAGGGCTTCATTGAAG
* * * * *
1403903 GATCGGGTTCTGTTGAAGCTGCTGCAAATGTCGAATGGGTGGAACGAGCAGGGCTTCGTTGAGG
1 GATCGGGTTCTGTTGAAGCCGCTGCAAACGTCGAATGGGTGGAACGAACAGGGCTTCATTGAAG
*
1403967 GATCGGGTTTTGTT
1 GATCGGGTTCTGTT
1403981 CAAGATCAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.21, C:0.15, G:0.37, T:0.27
Consensus pattern (64 bp):
GATCGGGTTCTGTTGAAGCCGCTGCAAACGTCGAATGGGTGGAACGAACAGGGCTTCATTGAAG
Found at i:1404026 original size:32 final size:32
Alignment explanation
Indices: 1403990--1404061 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
1403980 TCAAGATCAA
1403990 GTTCTGTTGAAGCTACTGCAAACATCGAATGG
1 GTTCTGTTGAAGCTACTGCAAACATCGAATGG
* *
1404022 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGG
1 GTTCTGTTGAAGCTACTGCAAACATCGAATGG
1404054 GTTCTGTT
1 GTTCTGTT
1404062 CAAGATCCGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (32 bp):
GTTCTGTTGAAGCTACTGCAAACATCGAATGG
Found at i:1408212 original size:28 final size:29
Alignment explanation
Indices: 1408181--1408237 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1408171 AGATGGTAAA
*
1408181 ATAATG-TATTAGTATTGTAAAAAAATAT
1 ATAATGATATTAGTATTATAAAAAAATAT
* * *
1408209 ATAATGATTTTATTTTTATAAAAAAATAT
1 ATAATGATATTAGTATTATAAAAAAATAT
1408238 TATTAATGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (29 bp):
ATAATGATATTAGTATTATAAAAAAATAT
Found at i:1408335 original size:18 final size:19
Alignment explanation
Indices: 1408291--1408340 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
1408281 TATATCCATG
*
1408291 TTATTATATATATATATAT
1 TTATTATATATATAAATAT
1408310 TTATT-TATAATTATAAAT-T
1 TTATTATAT-A-TATAAATAT
1408329 TTATTAT-TATAT
1 TTATTATATATAT
1408341 GTTTACATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 3 0.11
18 4 0.15
19 13 0.48
20 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTATTATATATATAAATAT
Found at i:1408380 original size:27 final size:27
Alignment explanation
Indices: 1408327--1408383 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1408317 TAATTATAAA
** *
1408327 TTTTATTATTATATGTTTACATTTATT
1 TTTTATTATTATAAATTTACATATATT
1408354 TTTTATTATTAATAAATTTA-ATATATT
1 TTTTATTATT-ATAAATTTACATATATT
1408381 TTT
1 TTT
1408384 AAAAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTATTATTATAAATTTACATATATT
Found at i:1408750 original size:49 final size:49
Alignment explanation
Indices: 1408693--1408789 Score: 176
Period size: 49 Copynumber: 2.0 Consensus size: 49
1408683 AGAAAGAGGT
*
1408693 AGGGATGGAAAGTGGAGAGAGAAGAGGAAATGATGAGGGTAGATTGGTA
1 AGGGATGGAAAGTGGAGAGAGAAGAGGAAATAATGAGGGTAGATTGGTA
*
1408742 AGGGATGGAAAGTGGAGAGAGAAGAGGGAATAATGAGGGTAGATTGGT
1 AGGGATGGAAAGTGGAGAGAGAAGAGGAAATAATGAGGGTAGATTGGT
1408790 GGAAAGGCGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.45, T:0.16
Consensus pattern (49 bp):
AGGGATGGAAAGTGGAGAGAGAAGAGGAAATAATGAGGGTAGATTGGTA
Found at i:1416506 original size:11 final size:10
Alignment explanation
Indices: 1416492--1416533 Score: 52
Period size: 9 Copynumber: 4.2 Consensus size: 10
1416482 ATTTTAATTC
1416492 ATATCATTTTT
1 ATAT-ATTTTT
1416503 ATAT-TTTTT
1 ATATATTTTT
1416512 ATATTATTTTT
1 ATA-TATTTTT
1416523 ATAT-TTTTT
1 ATATATTTTT
1416532 AT
1 AT
1416534 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
9 15 0.52
10 2 0.07
11 12 0.41
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (10 bp):
ATATATTTTT
Found at i:1416512 original size:9 final size:9
Alignment explanation
Indices: 1416498--1416533 Score: 54
Period size: 9 Copynumber: 3.8 Consensus size: 9
1416488 ATTCATATCA
1416498 TTTTTATAT
1 TTTTTATAT
1416507 TTTTTATATT
1 TTTTTATA-T
1416517 ATTTTTATAT
1 -TTTTTATAT
1416527 TTTTTAT
1 TTTTTAT
1416534 TAAAATTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 15 0.60
10 2 0.08
11 8 0.32
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTATAT
Found at i:1416520 original size:20 final size:20
Alignment explanation
Indices: 1416492--1416533 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1416482 ATTTTAATTC
1416492 ATATCATTTTTATATTTTTT
1 ATATCATTTTTATATTTTTT
*
1416512 ATATTATTTTTATATTTTTT
1 ATATCATTTTTATATTTTTT
1416532 AT
1 AT
1416534 TAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (20 bp):
ATATCATTTTTATATTTTTT
Found at i:1421889 original size:80 final size:82
Alignment explanation
Indices: 1421737--1421905 Score: 263
Period size: 80 Copynumber: 2.1 Consensus size: 82
1421727 TAAAATTTTA
*
1421737 TATTTGATTAACTTATCATAAAAAAGTAATTTTTTTAAAAAAAAGTAAGACAAAAATTATATGTC
1 TATTTGATTAACTTATCATAAAAAAGTAATTTTTTT-AAAAAAAGTAAGAAAAAAATTATATGTC
1421802 TTCACTTTACAGC-ATATT
65 TTCACTTTACA-CTATATT
* *
1421820 TATTTGATTAATTTATCATAAAAAA-TAATTTTTTT-TAAAAAGTAAGAAAAAAATTATATGTCT
1 TATTTGATTAACTTATCATAAAAAAGTAATTTTTTTAAAAAAAGTAAGAAAAAAATTATATGTCT
*
1421883 TTACTTTACACTATATT
66 TCACTTTACACTATATT
1421900 TATTTG
1 TATTTG
1421906 CAATAATATT
Statistics
Matches: 81, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
79 1 0.01
80 46 0.57
82 10 0.12
83 24 0.30
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.43
Consensus pattern (82 bp):
TATTTGATTAACTTATCATAAAAAAGTAATTTTTTTAAAAAAAGTAAGAAAAAAATTATATGTCT
TCACTTTACACTATATT
Found at i:1424720 original size:474 final size:474
Alignment explanation
Indices: 1423833--1424779 Score: 1786
Period size: 474 Copynumber: 2.0 Consensus size: 474
1423823 ATTTTCTTCA
1423833 AATATCAAAACACTCTTTTAATTGCTTGCCAATGTAAGTTACTTGGATTACTTGTGTACTTACTC
1 AATATCAAAACACTCTTTTAATTGCTTGCCAATGTAAGTTACTTGGATTACTTGTGTACTTACTC
1423898 AACTTTCTAATAGCAAATGCTATGTCTGATCTTGTACAAGTCATTGCATACATCAGACAACCAAT
66 AACTTTCTAATAGCAAATGCTATGTCTGATCTTGTACAAGTCATTGCATACATCAGACAACCAAT
* *
1423963 TACTCTTACATATTACAATTGATCAATTATTTTACCAGTATTAAATACTAATTTTAGTTGATAAT
131 TACTCTTACATATTACAATTGATCAATTATTCTACCAGTATTAAATACTAATTTTAGTTGAGAAT
1424028 CCATGGTTATAAATATTGAAATACAACAAAAAGGATCAAACTTTTTAAGAACTTTTTCGATTGTG
196 CCATGGTTATAAATATTGAAATACAACAAAAAGGATCAAACTTTTTAAGAACTTTTTCGATTGTG
*
1424093 ACAATGTTATGCCACTATCATTCCAAATTATTCTAATTCCAAGAATAATATCCGCTACACCAATA
261 ACAATATTATGCCACTATCATTCCAAATTATTCTAATTCCAAGAATAATATCCGCTACACCAATA
1424158 TCTTTTATTGAAAAGTTATTTAATAAAAATTTCTTTGTTTCCTTAACTTATTCTAAATCAGTGTC
326 TCTTTTATTGAAAAGTTATTTAATAAAAATTTCTTTGTTTCCTTAACTTATTCTAAATCAGTGTC
* *
1424223 AAATATTAGCATATCATCCACATATAAACAAAATTTGACTCCTTTACCATTTTTAAATTTGCTAT
391 AAATATTAGCATATCATCCACATATAAACAAAATTTGACTCATTTACCATTTTCAAATTTGCTAT
1424288 ACATACACTTATCTGACTC
456 ACATACACTTATCTGACTC
* *
1424307 AATATCAAAACACTCTTTTAATTGCTTGTCAATGTAAGTTACTTGGATTATTTGTGTACTTACTC
1 AATATCAAAACACTCTTTTAATTGCTTGCCAATGTAAGTTACTTGGATTACTTGTGTACTTACTC
*
1424372 AACTTTCTAATAGCAAATGCTATGTCTGATTTTGTACAAGTCATTGCATACATCAGACAACCAAT
66 AACTTTCTAATAGCAAATGCTATGTCTGATCTTGTACAAGTCATTGCATACATCAGACAACCAAT
1424437 TACTCTTACATATTACAATTGATCAATTATTCTACCAGTATTAAATACTAATTTTAGTTGAGAAT
131 TACTCTTACATATTACAATTGATCAATTATTCTACCAGTATTAAATACTAATTTTAGTTGAGAAT
1424502 CCATGGTTATAAATATTGAAATACAACAAAAAGGATCAAACTTTTTAAGAACTTTTTCGATTGTG
196 CCATGGTTATAAATATTGAAATACAACAAAAAGGATCAAACTTTTTAAGAACTTTTTCGATTGTG
*
1424567 ACAATATTATGCCACTATCATTCCAAATTATTCTAATTCCAAGAATAATATTCGCTACACCAATA
261 ACAATATTATGCCACTATCATTCCAAATTATTCTAATTCCAAGAATAATATCCGCTACACCAATA
* *
1424632 TCTTTTATTGAAAAGTTATTTAATAAAAATTTCTTTGTTTCCTTAACTTATTTTGAATCAGTGTC
326 TCTTTTATTGAAAAGTTATTTAATAAAAATTTCTTTGTTTCCTTAACTTATTCTAAATCAGTGTC
*
1424697 AAATATTAGCATATCATCCACATATAAACAAATTTTGACTCATTTACCATTTTCAAATTTGCTAT
391 AAATATTAGCATATCATCCACATATAAACAAAATTTGACTCATTTACCATTTTCAAATTTGCTAT
1424762 ACATACACTTATCTGACT
456 ACATACACTTATCTGACT
1424780 TATTAATTCT
Statistics
Matches: 461, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
474 461 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.38
Consensus pattern (474 bp):
AATATCAAAACACTCTTTTAATTGCTTGCCAATGTAAGTTACTTGGATTACTTGTGTACTTACTC
AACTTTCTAATAGCAAATGCTATGTCTGATCTTGTACAAGTCATTGCATACATCAGACAACCAAT
TACTCTTACATATTACAATTGATCAATTATTCTACCAGTATTAAATACTAATTTTAGTTGAGAAT
CCATGGTTATAAATATTGAAATACAACAAAAAGGATCAAACTTTTTAAGAACTTTTTCGATTGTG
ACAATATTATGCCACTATCATTCCAAATTATTCTAATTCCAAGAATAATATCCGCTACACCAATA
TCTTTTATTGAAAAGTTATTTAATAAAAATTTCTTTGTTTCCTTAACTTATTCTAAATCAGTGTC
AAATATTAGCATATCATCCACATATAAACAAAATTTGACTCATTTACCATTTTCAAATTTGCTAT
ACATACACTTATCTGACTC
Found at i:1428637 original size:22 final size:22
Alignment explanation
Indices: 1428612--1428658 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1428602 TTTTAATATA
* * *
1428612 AAATATATTTTTATTTTTTATC
1 AAATATATATCTAATTTTTATC
*
1428634 AAATTTATATCTAATTTTTATC
1 AAATATATATCTAATTTTTATC
1428656 AAA
1 AAA
1428659 ATTTTAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
AAATATATATCTAATTTTTATC
Found at i:1428781 original size:23 final size:22
Alignment explanation
Indices: 1428754--1428813 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 22
1428744 TAAAATTACG
*
1428754 AATTATTATATGTTTAATTATAA
1 AATTATTATATATTTAA-TATAA
1428777 AATTATTTAATATATTTAATATAA
1 AATTA-TT-ATATATTTAATATAA
*
1428801 ATTTATTACTATA
1 AATTATTA-TATA
1428814 AATAATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 1 0.03
23 11 0.34
24 11 0.34
25 9 0.28
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
AATTATTATATATTTAATATAA
Found at i:1428806 original size:24 final size:25
Alignment explanation
Indices: 1428754--1428807 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
1428744 TAAAATTACG
*
1428754 AATTA-TT-ATATGTTTAATTATAA
1 AATTATTTAATATATTTAATTATAA
1428777 AATTATTTAATATATTTAA-TATAA
1 AATTATTTAATATATTTAATTATAA
*
1428801 ATTTATT
1 AATTATT
1428808 ACTATAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 5 0.19
24 13 0.48
25 9 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
AATTATTTAATATATTTAATTATAA
Found at i:1432032 original size:14 final size:14
Alignment explanation
Indices: 1432013--1432042 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1432003 ATAAATATCT
1432013 ATGTAATAGTATAA
1 ATGTAATAGTATAA
1432027 ATGTAATAGTATAA
1 ATGTAATAGTATAA
1432041 AT
1 AT
1432043 ATCTATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (14 bp):
ATGTAATAGTATAA
Found at i:1432393 original size:23 final size:25
Alignment explanation
Indices: 1432340--1432395 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 25
1432330 AATATTTTTA
*
1432340 ATTTA-ATTTAATTAATTTTAAGAT
1 ATTTATATTTAATTAAATTTAAGAT
*
1432364 A-TAATATTTAA-TAAATTTAA-AT
1 ATTTATATTTAATTAAATTTAAGAT
1432386 ATTTATATTT
1 ATTTATATTT
1432396 TTTATTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 3 0.11
23 17 0.63
24 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (25 bp):
ATTTATATTTAATTAAATTTAAGAT
Found at i:1437529 original size:13 final size:13
Alignment explanation
Indices: 1437489--1437529 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1437479 TTTTTAAATT
1437489 AACAAAAAAAAAA
1 AACAAAAAAAAAA
* * *
1437502 TACAAACAATAAA
1 AACAAAAAAAAAA
1437515 AACAAAAAAAAAA
1 AACAAAAAAAAAA
1437528 AA
1 AA
1437530 GAAATTATGA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.85, C:0.10, G:0.00, T:0.05
Consensus pattern (13 bp):
AACAAAAAAAAAA
Found at i:1438049 original size:3 final size:3
Alignment explanation
Indices: 1438043--1438079 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
1438033 TTGTTGTTGT
1438043 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1438080 AAGAGTGAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
TGG
Found at i:1439472 original size:2 final size:2
Alignment explanation
Indices: 1439465--1439489 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1439455 GTTTGTTGCT
1439465 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 T
1439490 TAATTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1443548 original size:25 final size:25
Alignment explanation
Indices: 1443515--1443564 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1443505 AACCAACCAC
1443515 CACACTTGTGCAAGAAGGCATGGTA
1 CACACTTGTGCAAGAAGGCATGGTA
*
1443540 CACACTTGTGTAAGAAGGCATGGTA
1 CACACTTGTGCAAGAAGGCATGGTA
1443565 GTTAGACTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (25 bp):
CACACTTGTGCAAGAAGGCATGGTA
Found at i:1445456 original size:5 final size:5
Alignment explanation
Indices: 1445438--1445477 Score: 71
Period size: 5 Copynumber: 7.8 Consensus size: 5
1445428 AATTCCTCGC
1445438 CCAGA CCAAGA CCAGA CCAGA CCAGA CCAGA CCAGA CCAG
1 CCAGA CC-AGA CCAGA CCAGA CCAGA CCAGA CCAGA CCAG
1445478 TGTCTTACCG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.40, C:0.40, G:0.20, T:0.00
Consensus pattern (5 bp):
CCAGA
Found at i:1449061 original size:190 final size:190
Alignment explanation
Indices: 1448738--1449110 Score: 719
Period size: 190 Copynumber: 2.0 Consensus size: 190
1448728 ATATCGAAAA
1448738 TTGAATACAGTAGTCGGTTTGTTAAAATGGTGGTTATGTAACAAGTTATGAATGTATGGCTGGGT
1 TTGAATACAGTAGTCGGTTTGTTAAAATGGTGGTTATGTAACAAGTTATGAATGTATGGCTGGGT
1448803 CTAGGAGTTGTTTATACATCAGGTTTATGCTGACTTATTGTTTGGATATCTTTATGTTTATGCTA
66 CTAGGAGTTGTTTATACATCAGGTTTATGCTGACTTATTGTTTGGATATCTTTATGTTTATGCTA
1448868 TTTTCAGTTAGTTGGGTGTGAGGGTTTAGTTTTGAATGCTCCTGTACTATTAAAATGGTT
131 TTTTCAGTTAGTTGGGTGTGAGGGTTTAGTTTTGAATGCTCCTGTACTATTAAAATGGTT
1448928 TTGAATACAGTAGTCGGTTTGTTAAAATGGTGGTTATGTAACAAGTTATGAATGTATGGCTGGGT
1 TTGAATACAGTAGTCGGTTTGTTAAAATGGTGGTTATGTAACAAGTTATGAATGTATGGCTGGGT
1448993 CTAGGAGTTGTTTATACATCAGGTTTATGCTGACTTATTGTTTGGATATCTTTATGTTTATGCTA
66 CTAGGAGTTGTTTATACATCAGGTTTATGCTGACTTATTGTTTGGATATCTTTATGTTTATGCTA
* * *
1449058 TTTTCTGTTGGTTGGGTGTGAGGGTTTGGTTTTGAATGCTCCTGTACTATTAA
131 TTTTCAGTTAGTTGGGTGTGAGGGTTTAGTTTTGAATGCTCCTGTACTATTAA
1449111 CCACAATAAT
Statistics
Matches: 180, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
190 180 1.00
ACGTcount: A:0.22, C:0.09, G:0.26, T:0.43
Consensus pattern (190 bp):
TTGAATACAGTAGTCGGTTTGTTAAAATGGTGGTTATGTAACAAGTTATGAATGTATGGCTGGGT
CTAGGAGTTGTTTATACATCAGGTTTATGCTGACTTATTGTTTGGATATCTTTATGTTTATGCTA
TTTTCAGTTAGTTGGGTGTGAGGGTTTAGTTTTGAATGCTCCTGTACTATTAAAATGGTT
Found at i:1449338 original size:15 final size:15
Alignment explanation
Indices: 1449318--1449350 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1449308 TGGAGGTGGG
*
1449318 GATGGAGGTGATGAT
1 GATGGAGATGATGAT
1449333 GATGGAGATGATGAT
1 GATGGAGATGATGAT
1449348 GAT
1 GAT
1449351 TATTTCGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.42, T:0.27
Consensus pattern (15 bp):
GATGGAGATGATGAT
Found at i:1454987 original size:24 final size:25
Alignment explanation
Indices: 1454959--1455019 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
1454949 TAATTATGAC
1454959 TTTTAAT-TATTAATTGAAAAAAT-
1 TTTTAATATATTAATTGAAAAAATA
* * *
1454982 TATTTAGTATAATAATTTAAAAAATA
1 T-TTTAATATATTAATTGAAAAAATA
1455008 TTTTAATATATT
1 TTTTAATATATT
1455020 CGTTAACAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.03
24 5 0.17
25 23 0.77
26 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (25 bp):
TTTTAATATATTAATTGAAAAAATA
Found at i:1455585 original size:12 final size:12
Alignment explanation
Indices: 1455570--1455596 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1455560 TATAAATATA
1455570 TATATATGTATT
1 TATATATGTATT
1455582 TATATATGTATT
1 TATATATGTATT
1455594 TAT
1 TAT
1455597 GAAATGCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TATATATGTATT
Found at i:1459012 original size:12 final size:12
Alignment explanation
Indices: 1458995--1459039 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1458985 TTGTGTTAAT
1458995 TGAAAAAGAAAA
1 TGAAAAAGAAAA
1459007 TG-AAAAG-AAA
1 TGAAAAAGAAAA
*
1459017 -GAGAAAGAAAA
1 TGAAAAAGAAAA
*
1459028 AGAAAAAGAAAA
1 TGAAAAAGAAAA
1459040 GGGGACAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
9 1 0.04
10 7 0.25
11 8 0.29
12 12 0.43
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.04
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:1464110 original size:20 final size:20
Alignment explanation
Indices: 1464078--1464115 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1464068 GCTATTAGGT
*
1464078 AAAAAAACATCTTCAATCAC
1 AAAAAAACATCTTAAATCAC
1464098 AAAAAAA-AGTCTTAAATC
1 AAAAAAACA-TCTTAAATC
1464116 TTCCATTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.06
20 15 0.94
ACGTcount: A:0.58, C:0.18, G:0.03, T:0.21
Consensus pattern (20 bp):
AAAAAAACATCTTAAATCAC
Found at i:1470319 original size:2 final size:2
Alignment explanation
Indices: 1470308--1470338 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1470298 CAATTCATTT
1470308 TA TA -A 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
1470339 AAGGATCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1472189 original size:2 final size:2
Alignment explanation
Indices: 1472182--1472208 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1472172 AATAAAGTTA
1472182 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 A
1472209 CACACACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1473535 original size:16 final size:16
Alignment explanation
Indices: 1473514--1473552 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1473504 TTAAAAAACT
* *
1473514 AAGAAAAGATTAAATA
1 AAGAAAAGATCAAAAA
1473530 AAGAAAAGATCAAAAA
1 AAGAAAAGATCAAAAA
1473546 AAGAAAA
1 AAGAAAA
1473553 AAAAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.74, C:0.03, G:0.13, T:0.10
Consensus pattern (16 bp):
AAGAAAAGATCAAAAA
Found at i:1474025 original size:20 final size:21
Alignment explanation
Indices: 1473982--1474032 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1473972 AAAATAAAAA
1473982 AATTTTAAAATATATATTTAT
1 AATTTTAAAATATATATTTAT
1474003 AATTTTAAAATA-A-ATTATAT
1 AATTTTAAAATATATATT-TAT
*
1474023 AATATTAAAA
1 AATTTTAAAA
1474033 AAAAATGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 12 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
AATTTTAAAATATATATTTAT
Found at i:1474033 original size:21 final size:19
Alignment explanation
Indices: 1473985--1474038 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1473975 ATAAAAAAAT
*
1473985 TTTAAAATATATATTTATAA
1 TTTAAAA-ATAAATTTATAA
*
1474005 TTTTAAAATAAATTATATAA
1 TTTAAAAATAAATT-TATAA
*
1474025 TATTAAAAAAAAAT
1 T-TTAAAAATAAAT
1474039 GGGCTGACGC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 6 0.21
20 12 0.43
21 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTAAAAATAAATTTATAA
Found at i:1489305 original size:6 final size:6
Alignment explanation
Indices: 1489296--1489346 Score: 52
Period size: 6 Copynumber: 8.7 Consensus size: 6
1489286 TTTATTTAAT
* * *
1489296 TTTATA TTTATA TATATT TGTTATA -TT-TA TTTAAA TTTATA TTTATA
1 TTTATA TTTATA TTTATA T-TTATA TTTATA TTTATA TTTATA TTTATA
1489343 TTTA
1 TTTA
1489347 AAAAATAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
4 2 0.06
5 4 0.11
6 27 0.75
7 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (6 bp):
TTTATA
Found at i:1489535 original size:20 final size:20
Alignment explanation
Indices: 1489510--1489549 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1489500 AAAAACCCAC
1489510 CCCACCCCACTTTGATCCGT
1 CCCACCCCACTTTGATCCGT
1489530 CCCACCCCACTTTGATCCGT
1 CCCACCCCACTTTGATCCGT
1489550 TGCTATCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.10, T:0.25
Consensus pattern (20 bp):
CCCACCCCACTTTGATCCGT
Found at i:1498394 original size:9 final size:9
Alignment explanation
Indices: 1498355--1498390 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
1498345 TTAATTGTGT
1498355 TTAATCATA
1 TTAATCATA
1498364 TTAATCATA
1 TTAATCATA
*
1498373 TATAATCATG
1 T-TAATCATA
1498383 TTAATCAT
1 TTAATCAT
1498391 GTTATGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.42, C:0.11, G:0.03, T:0.44
Consensus pattern (9 bp):
TTAATCATA
Found at i:1503038 original size:2 final size:2
Alignment explanation
Indices: 1503031--1503059 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1503021 TGTAAATCAC
1503031 CT CT 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 C
1503060 ATGCATGTTT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1506686 original size:23 final size:22
Alignment explanation
Indices: 1506620--1506686 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 22
1506610 AAAAACTAGC
* * *
1506620 AAAA-CAAAATAAACACTAAAA
1 AAAATCAAAATAAAAAATAAAT
*
1506641 AAAACTCAAAATATAAAATAAAT
1 AAAA-TCAAAATAAAAAATAAAT
1506664 AAAATCAAAATCAAAAAATAAAT
1 AAAATCAAAAT-AAAAAATAAAT
1506687 TTAAAATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 4 0.11
22 7 0.18
23 27 0.71
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.16
Consensus pattern (22 bp):
AAAATCAAAATAAAAAATAAAT
Found at i:1507498 original size:8 final size:8
Alignment explanation
Indices: 1507487--1507536 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
1507477 AGAAAGAAAG
*
1507487 AAAATTAT
1 AAAATAAT
1507495 AAAATAAT
1 AAAATAAT
*
1507503 AATATAAT
1 AAAATAAT
*
1507511 AATATAAT
1 AAAATAAT
1507519 AATAATAAT
1 AA-AATAAT
*
1507528 AATATAAT
1 AAAATAAT
1507536 A
1 A
1507537 CTATAATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
8 30 0.81
9 7 0.19
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAAATAAT
Done.