Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1257280 original size:20 final size:19
Alignment explanation
Indices: 1257235--1257272 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1257225 AACGCGAATT
1257235 TAGTTTCGCGTTGCGATTA
1 TAGTTTCGCGTTGCGATTA
1257254 TAGTTTCGTCGTTGCGATT
1 TAGTTTCG-CGTTGCGATT
1257273 TTCATTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.13, C:0.16, G:0.26, T:0.45
Consensus pattern (19 bp):
TAGTTTCGCGTTGCGATTA
Found at i:1258850 original size:21 final size:21
Alignment explanation
Indices: 1258784--1258850 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1258774 ATGAATCGGG
1258784 CTCTTGAATGGTGGG-AGGGA
1 CTCTTGAATGGTGGGAAGGGA
* * * ** * *
1258804 CCTCTTCAACGATGACAATGGC
1 -CTCTTGAATGGTGGGAAGGGA
1258826 CTCTTGAATGGTGGGAAGGGA
1 CTCTTGAATGGTGGGAAGGGA
1258847 CTCT
1 CTCT
1258851 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 14, Indels: 2
0.66 0.30 0.04
Matches are distributed among these distances:
21 28 0.90
22 3 0.10
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAAGGGA
Found at i:1260763 original size:20 final size:20
Alignment explanation
Indices: 1260740--1260795 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1260730 TGAAATGAAA
1260740 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
1260760 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
*
1260780 ATCGCAACGAAAGAAT
1 ATCGCAACGAGAGAAT
1260796 CGTAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:1260876 original size:19 final size:19
Alignment explanation
Indices: 1260731--1260868 Score: 107
Period size: 19 Copynumber: 7.7 Consensus size: 19
1260721 TCTTTTGGTT
*
1260731 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
**
1260750 GAGAATGACTATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1260770 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1260788 GAAA-G--AATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
1260804 GAAATGAAAATCACAACGC
1 GAAATGAAAATCGCAACGC
*
1260823 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1260840 G--AT-AGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1260856 GAAATGAAAATCG
1 GAAATGAAAATCG
1260869 TAATGCGATT
Statistics
Matches: 96, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
14 15 0.16
15 2 0.02
16 8 0.08
17 7 0.07
18 3 0.03
19 31 0.32
20 28 0.29
21 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1260894 original size:19 final size:19
Alignment explanation
Indices: 1260872--1260993 Score: 74
Period size: 20 Copynumber: 6.5 Consensus size: 19
1260862 AAAATCGTAA
** *
1260872 TGCGATTTTGGTTTTGCGT
1 TGCGATTTTCATTTCGCGT
1260891 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
1260910 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
1260924 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** **
1260945 TGCGATAGTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
**
1260965 TGCGATTTTCATTTTCATGT
1 TGCGATTTTCA-TTTCGCGT
1260985 TGCGATTTT
1 TGCGATTTT
1260994 AAGTTTAGAA
Statistics
Matches: 86, Mismatches: 10, Indels: 13
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.12
16 3 0.03
17 3 0.03
19 21 0.24
20 31 0.36
21 18 0.21
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.50
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1260991 original size:20 final size:20
Alignment explanation
Indices: 1260922--1260993 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
1260912 CGATTCTCTC
1260922 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
**
1260942 CGTTGCGATAGTCATTTTCAT
1 -GTTGCGATTTTCATTTTCAT
1260963 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
1260983 GTTGCGATTTT
1 GTTGCGATTTT
1260994 AAGTTTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.14, C:0.17, G:0.18, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:1261572 original size:20 final size:20
Alignment explanation
Indices: 1261547--1261737 Score: 163
Period size: 20 Copynumber: 9.4 Consensus size: 20
1261537 TTAAAAATCA
1261547 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
1261567 CGTTGCGATTTTACGTAT-TG
1 CGTTGCGA-TTTACGGATACG
1261587 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTACGGATACG
* * * *
1261608 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
*
1261628 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACG
* * *
1261648 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACG
* *
1261668 TGTTACGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
1261688 CGTTGCAATTTTAC--ATATTG
1 CGTTGCGA-TTTACGGATA-CG
* *
1261708 TCGTTGCGATTTATGGATACT
1 -CGTTGCGATTTACGGATACG
*
1261729 AGTTGCGAT
1 CGTTGCGAT
1261738 AGTCAGAATC
Statistics
Matches: 132, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.02
20 97 0.73
21 29 0.22
22 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:1261631 original size:40 final size:41
Alignment explanation
Indices: 1261547--1261737 Score: 269
Period size: 40 Copynumber: 4.7 Consensus size: 41
1261537 TTAAAAATCA
*
1261547 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1261588 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
1261628 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * * *
1261668 TGTTACGATTTACGGATACGCGTTGCAATTTTACATATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* **
1261709 CGTTGCGATTTATGGATACTAGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
1261738 AGTCAGAATC
Statistics
Matches: 133, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 73 0.55
41 60 0.45
ACGTcount: A:0.20, C:0.17, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:1261772 original size:20 final size:20
Alignment explanation
Indices: 1261749--1261798 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1261739 GTCAGAATCG
*
1261749 CGTTGCGATTTAT-ATGTTCA
1 CGTTGCGATTT-TCATATTCA
*
1261769 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCA
1261789 CGTTGCGATT
1 CGTTGCGATT
1261799 ATGGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCA
Found at i:1261798 original size:121 final size:121
Alignment explanation
Indices: 1261547--1261798 Score: 305
Period size: 121 Copynumber: 2.1 Consensus size: 121
1261537 TTAAAAATCA
* *
1261547 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTTACATATTGTCGTTGCGATTTACGGATACGCATT
* * * * * *
1261612 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
66 GCGATTCACGTAATCGCGTTGCGATTTACAGATACACGTTGCGATTTACATATTCG
* * * *
1261668 TGTTACGATTTACGGATACGCGTTGCAATTTTACATATTGTCGTTGCGATTTATGGATAC-TAGT
1 CGTTGCGATTTACGGATACGCGTTGCAATTTTACATATTGTCGTTGCGATTTACGGATACGCA-T
* * *
1261732 TGCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCACGTTGCGATTTTCATATTCG
65 TGCGAT--TCACGTAATCGCGTTGCGATTTACA-GATACACGTTGCGATTTACATATTCG
1261789 CGTTGCGATT
1 CGTTGCGATT
1261799 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
120 1 0.01
121 105 0.95
122 2 0.02
123 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACGCGTTGCAATTTTACATATTGTCGTTGCGATTTACGGATACGCATT
GCGATTCACGTAATCGCGTTGCGATTTACAGATACACGTTGCGATTTACATATTCG
Found at i:1261851 original size:13 final size:13
Alignment explanation
Indices: 1261833--1261869 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1261823 TACTATCGCA
*
1261833 TTGCGATTCTGCG
1 TTGCGATTCTGAG
*
1261846 TTGCGATTCTGAT
1 TTGCGATTCTGAG
1261859 TTGCGATTCTG
1 TTGCGATTCTG
1261870 GAGATCGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.19, G:0.27, T:0.43
Consensus pattern (13 bp):
TTGCGATTCTGAG
Found at i:1266971 original size:65 final size:64
Alignment explanation
Indices: 1266839--1266994 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
1266829 ACACCCTAAT
* * *
1266839 TCGAATGCATTTTTTGTACCGATGCACAACCATGCATCGATGCACTCCTGATTTTATTAAAACA
1 TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTAAAACA
* * * * *
1266903 TCGAATGCATTTTATGTACCGATGCATAGAGCATGCATCGATACACTCCTGGCTCTT-TTGAAGC
1 TCGAATGCATTTTATGTACCGATGCACA-ACCATGCATCGATACACTCCT-GATCTTATTAAAAC
1266967 A
64 A
* *
1266968 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
1266995 TAGGTCTTAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 29 0.37
65 45 0.58
66 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATACACTCCTGATCTTATTAAAACA
Found at i:1272020 original size:24 final size:24
Alignment explanation
Indices: 1271976--1272025 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1271966 ATAAAGAACC
*
1271976 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1272000 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
1272024 AA
1 AA
1272026 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1274494 original size:21 final size:21
Alignment explanation
Indices: 1274426--1274494 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1274416 CACAATGCAT
1274426 CGATACACTATGACAG-TGTAC
1 CGATACACTATGA-AGATGTAC
* * * * *
1274447 CGATGCATCTTTTGAATATGCAT
1 CGATACA-C-TATGAAGATGTAC
1274470 CGATACACTATGAAGATGTAC
1 CGATACACTATGAAGATGTAC
1274491 CGAT
1 CGAT
1274495 GTATTCCTTC
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
21 19 0.54
22 3 0.09
23 13 0.37
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (21 bp):
CGATACACTATGAAGATGTAC
Found at i:1276366 original size:29 final size:28
Alignment explanation
Indices: 1276334--1276400 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
1276324 GTGTTTAAAC
*
1276334 ATTTTGAATATTTGACTTTG-TTTGTTTG
1 ATTTTGAATATTT-ACTTTGAATTGTTTG
*
1276362 AATTTTGAATATTTAGTTTGAATTGTTTG
1 -ATTTTGAATATTTACTTTGAATTGTTTG
1276391 -TTTTGAATAT
1 ATTTTGAATAT
1276401 AGTTTGGATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 10 0.29
28 5 0.14
29 20 0.57
ACGTcount: A:0.24, C:0.01, G:0.16, T:0.58
Consensus pattern (28 bp):
ATTTTGAATATTTACTTTGAATTGTTTG
Found at i:1277213 original size:65 final size:65
Alignment explanation
Indices: 1277060--1277215 Score: 167
Period size: 65 Copynumber: 2.4 Consensus size: 65
1277050 ACACCCTAAT
* * *
1277060 TCGAATGCAT-TTTGTGTACCGATGGACAGCCATGCATCGATGCACTCATGATTTTATTAAAACA
1 TCGAATGCATATTAGTGTACCGATGCACAGCCATGCATCGATGCACTCATGATCTTATTAAAACA
* ** * * * *
1277124 TCGAATGCATTTTA-TGTAATGATGCACAGAGCATGCATCGATGCACTCCTGGCTCTT-TTGAAA
1 TCGAATGCATATTAGTGTACCGATGCACAG-CCATGCATCGATGCACTCAT-GATCTTATTAAAA
1277187 CA
64 CA
*
1277189 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATATTAGTGTACCGATGCAC
1277216 CCCAAGTGTA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
64 25 0.33
65 46 0.61
66 4 0.05
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (65 bp):
TCGAATGCATATTAGTGTACCGATGCACAGCCATGCATCGATGCACTCATGATCTTATTAAAACA
Found at i:1278001 original size:40 final size:40
Alignment explanation
Indices: 1277910--1278076 Score: 219
Period size: 40 Copynumber: 4.2 Consensus size: 40
1277900 ACTCAACATG
*
1277910 ACCTTATGTGTAATGCACTTTGGTGCATATGG-GGGCACA
1 ACCTTATGTGTAATGCACTTCGGTGCATATGGTGGGCACA
*
1277949 ACCTTATGTGTAATGAACTTCGGTGCATATGGTGGGCACA
1 ACCTTATGTGTAATGCACTTCGGTGCATATGGTGGGCACA
* * * *
1277989 AGCTTATATGTAATGCACTTCGATGCATATGGTGGGCACG
1 ACCTTATGTGTAATGCACTTCGGTGCATATGGTGGGCACA
* * * * *
1278029 ACCTTATGTATAATGCTCTTTGGTGCATATTGTGGGCACG
1 ACCTTATGTGTAATGCACTTCGGTGCATATGGTGGGCACA
*
1278069 ACGTTATG
1 ACCTTATG
1278077 AGCAAGCACT
Statistics
Matches: 112, Mismatches: 15, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 30 0.27
40 82 0.73
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (40 bp):
ACCTTATGTGTAATGCACTTCGGTGCATATGGTGGGCACA
Found at i:1289465 original size:23 final size:23
Alignment explanation
Indices: 1289415--1289540 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 23
1289405 CACCGAAGTG
1289415 CCGCGTAGAATATG-CACTGAAGTG-
1 CCGCGTAGAA-ATGTC-CTGAAG-GA
*
1289439 CCACGTAGAAATGTCCTGAAGGA
1 CCGCGTAGAAATGTCCTGAAGGA
* * * * * *
1289462 CCACATAGAATTTTCCCGAAGGG
1 CCGCGTAGAAATGTCCTGAAGGA
*
1289485 CCGCGTAGAAATGT-CTCGAAGGG
1 CCGCGTAGAAATGTCCT-GAAGGA
**
1289508 CCGCGTAGAAATGTCCCAAAGGA
1 CCGCGTAGAAATGTCCTGAAGGA
1289531 CCGCGTAGAA
1 CCGCGTAGAA
1289541 CCCTCAATTC
Statistics
Matches: 84, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
22 2 0.02
23 71 0.85
24 11 0.13
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (23 bp):
CCGCGTAGAAATGTCCTGAAGGA
Found at i:1289494 original size:46 final size:46
Alignment explanation
Indices: 1289433--1289540 Score: 119
Period size: 46 Copynumber: 2.3 Consensus size: 46
1289423 AATATGCACT
* * * *
1289433 GAAGTGCCACGTAGAAATGTC-CTGAAGGACCACATAGAATTTTCCC
1 GAAGGGCCGCGTAGAAATGTCTC-GAAGGACCACATAGAAATGTCCC
* * *
1289479 GAAGGGCCGCGTAGAAATGTCTCGAAGGGCCGCGTAGAAATGTCCC
1 GAAGGGCCGCGTAGAAATGTCTCGAAGGACCACATAGAAATGTCCC
* *
1289525 AAAGGACCGCGTAGAA
1 GAAGGGCCGCGTAGAA
1289541 CCCTCAATTC
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 51 0.98
47 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.29, T:0.17
Consensus pattern (46 bp):
GAAGGGCCGCGTAGAAATGTCTCGAAGGACCACATAGAAATGTCCC
Found at i:1290288 original size:15 final size:15
Alignment explanation
Indices: 1290265--1290319 Score: 92
Period size: 15 Copynumber: 3.7 Consensus size: 15
1290255 TTGTCCATTA
1290265 GTATCGATGCCCTTG
1 GTATCGATGCCCTTG
*
1290280 GTATTGATGCCCTTG
1 GTATCGATGCCCTTG
*
1290295 GTATTGATGCCCTTG
1 GTATCGATGCCCTTG
1290310 GTATCGATGC
1 GTATCGATGC
1290320 TACTCCTTCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (15 bp):
GTATCGATGCCCTTG
Found at i:1293763 original size:25 final size:24
Alignment explanation
Indices: 1293735--1293781 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1293725 AACATGTTAT
*
1293735 ACTTATACATGGACGGGCCTGAAAC
1 ACTTATACATGAACGGG-CTGAAAC
*
1293760 ACTTGTACATGAACGGGCTGAA
1 ACTTATACATGAACGGGCTGAA
1293782 TTAGGGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (24 bp):
ACTTATACATGAACGGGCTGAAAC
Found at i:1293789 original size:92 final size:93
Alignment explanation
Indices: 1293604--1293790 Score: 245
Period size: 94 Copynumber: 2.0 Consensus size: 93
1293594 TATATGTGGA
* * * * *
1293604 TTCCTCAAATTTTGGGTCTTAAGACGTCACATACTATACTTATACATGGACGGACCTGAATATAT
1 TTCCTCAAATTTTGGATCCTAAGACGTAACATACTATACTTATACATGGACGGACCTGAATACAC
* *
1293669 TTGTACATGAACGGGTGTGAATTGGGGT
66 TTGTACATGAACGGGTCTGAATTAGGGT
** *
1293697 TTCCTC-AATTTTGGATCCTAAGACGAGTAACATGTTATACTTATACATGGACGGGCCTGAA-AC
1 TTCCTCAAATTTTGGATCCTAAGAC--GTAACATACTATACTTATACATGGACGGACCTGAATAC
1293760 ACTTGTACATGAACGGG-CTGAATTAGGGT
64 ACTTGTACATGAACGGGTCTGAATTAGGGT
1293789 TT
1 TT
1293791 GATTTGGTTG
Statistics
Matches: 82, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
92 28 0.34
93 23 0.28
94 31 0.38
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.32
Consensus pattern (93 bp):
TTCCTCAAATTTTGGATCCTAAGACGTAACATACTATACTTATACATGGACGGACCTGAATACAC
TTGTACATGAACGGGTCTGAATTAGGGT
Found at i:1295270 original size:16 final size:16
Alignment explanation
Indices: 1295251--1295284 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1295241 TAAATTGCAC
*
1295251 TGATATTTACTTAACT
1 TGATATTTACCTAACT
1295267 TGATATTTACCTAACT
1 TGATATTTACCTAACT
1295283 TG
1 TG
1295285 TAAGTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (16 bp):
TGATATTTACCTAACT
Found at i:1295534 original size:19 final size:19
Alignment explanation
Indices: 1295510--1295546 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1295500 CCATCATTAT
* *
1295510 ATTACTAGATTTACTTTAA
1 ATTACTAAATTAACTTTAA
1295529 ATTACTAAATTAACTTTA
1 ATTACTAAATTAACTTTA
1295547 TATATTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (19 bp):
ATTACTAAATTAACTTTAA
Found at i:1296399 original size:57 final size:57
Alignment explanation
Indices: 1296325--1296440 Score: 196
Period size: 57 Copynumber: 2.0 Consensus size: 57
1296315 ATTCATTTAT
* *
1296325 ATGCTTGCTGAAATTTATGAAAATTAATCAAAAAGCATTAAATGTAAAAGCAGTAGC
1 ATGCTTACTGAAATTTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
* *
1296382 ATGCTTACTGAAATTTATGAAAATTAATGAAAAAGCAGTAAATGTAAAAGCAGTGGC
1 ATGCTTACTGAAATTTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
1296439 AT
1 AT
1296441 CTACAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.46, C:0.09, G:0.17, T:0.28
Consensus pattern (57 bp):
ATGCTTACTGAAATTTATGAAAATTAATCAAAAAGCAGTAAATGTAAAAGCAGTAGC
Found at i:1298855 original size:64 final size:63
Alignment explanation
Indices: 1298787--1298929 Score: 166
Period size: 64 Copynumber: 2.3 Consensus size: 63
1298777 TAATAGACTT
*
1298787 ATAAGTGACCAAAATAT-AATCAAACAAAAACAACACATCATAATTAAAATAAAACT-AAATGTA
1 ATAAGTGACCAAAATATGAA-CAAACAAAAACAACACATCAAAATTAAAATAAAA-TAAAATGT-
1298850 A
63 A
** * * *
1298851 ATAAGTGACCAAGTTATGAACAAACAAAAATAGCATATCAAAATTAAAATAAAATAAAAATGTA
1 ATAAGTGACCAAAATATGAACAAACAAAAACAACACATCAAAATTAAAATAAAAT-AAAATGTA
*
1298915 A-AAGTGACTAAAATA
1 ATAAGTGACCAAAATA
1298930 AAATAAAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
63 12 0.18
64 47 0.70
65 8 0.12
ACGTcount: A:0.60, C:0.11, G:0.08, T:0.21
Consensus pattern (63 bp):
ATAAGTGACCAAAATATGAACAAACAAAAACAACACATCAAAATTAAAATAAAATAAAATGTA
Found at i:1299358 original size:2 final size:2
Alignment explanation
Indices: 1299343--1299415 Score: 60
Period size: 2 Copynumber: 36.0 Consensus size: 2
1299333 TGGAGAGTTC
* * * *
1299343 AT AT AT AGT TT AT AT AT A- AT AT AT AA AT AT AA ACT AT AC AGT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
*
1299385 TT AT AT -T 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
1299416 TAACATATTA
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
1 2 0.04
2 52 0.93
3 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1299398 original size:33 final size:33
Alignment explanation
Indices: 1299344--1299408 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1299334 GGAGAGTTCA
*
1299344 TATATAGTTTATATATAATATATAAATATAAAC
1 TATACAGTTTATATATAATATATAAATATAAAC
*
1299377 TATACAGTTTATATTATATATATATATATATA
1 TATACAGTTTATA-TATA-ATATATAAATATA
1299409 TATATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 12 0.43
34 4 0.14
35 12 0.43
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (33 bp):
TATACAGTTTATATATAATATATAAATATAAAC
Found at i:1304949 original size:19 final size:19
Alignment explanation
Indices: 1304920--1304962 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1304910 GTTCTTCTTC
*
1304920 TTTTGTTTTCAT-TTTTAT
1 TTTTATTTTCATGTTTTAT
1304938 TATTTATTTTCATGTTTTAT
1 T-TTTATTTTCATGTTTTAT
1304958 TTTTA
1 TTTTA
1304963 AATATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 14 0.64
20 7 0.32
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTATTTTCATGTTTTAT
Found at i:1307556 original size:2 final size:2
Alignment explanation
Indices: 1307551--1307627 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
1307541 ATGATACGAT
1307551 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
*
1307593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1307628 GGTTACGATC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1313104 original size:24 final size:21
Alignment explanation
Indices: 1313054--1313107 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 21
1313044 TGATTGGACA
1313054 AAAATATTATTTTTTTAATGT
1 AAAATATTATTTTTTTAATGT
*
1313075 ATAATATCTATTTTTTAATAAT-T
1 AAAATAT-TATTTTTT--TAATGT
1313098 CAAAATATTA
1 -AAAATATTA
1313108 AATATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.22
22 8 0.30
23 3 0.11
24 10 0.37
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (21 bp):
AAAATATTATTTTTTTAATGT
Found at i:1313118 original size:16 final size:15
Alignment explanation
Indices: 1313099--1313132 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1313089 TTAATAATTC
*
1313099 AAAATATTAAATATTA
1 AAAATATAAAATA-TA
1313115 AAAATATAAAATATA
1 AAAATATAAAATATA
1313130 AAA
1 AAA
1313133 TAATTTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATATAAAATATA
Found at i:1314564 original size:19 final size:20
Alignment explanation
Indices: 1314540--1314587 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1314530 GTAAAACATC
1314540 AAATAATAAC-AAATGATAG
1 AAATAATAACAAAATGATAG
1314559 AAATAATAACAAAATGATAG
1 AAATAATAACAAAATGATAG
1314579 AAATAATAA
1 AAATAATAA
1314588 TGTTTTCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.21
Consensus pattern (20 bp):
AAATAATAACAAAATGATAG
Found at i:1314920 original size:6 final size:6
Alignment explanation
Indices: 1314909--1314969 Score: 53
Period size: 6 Copynumber: 11.2 Consensus size: 6
1314899 ACGATCATAA
* *
1314909 ACGAAC ACGAAC A-TAA- ACGAAC ACGAAC A-TAA- ACGAAC ACGAAC
1 ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC
*
1314953 A-TAA- ACGAAC ACGAAC A
1 ACGAAC ACGAAC ACGAAC A
1314970 TAAATGAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
4 3 0.07
5 12 0.28
6 28 0.65
ACGTcount: A:0.56, C:0.26, G:0.13, T:0.05
Consensus pattern (6 bp):
ACGAAC
Found at i:1314923 original size:16 final size:16
Alignment explanation
Indices: 1314899--1314991 Score: 159
Period size: 16 Copynumber: 5.8 Consensus size: 16
1314889 TAATAAATAA
*
1314899 ACGATCATAAACGAAC
1 ACGAACATAAACGAAC
1314915 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1314931 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1314947 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1314963 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1314979 ATGAACATAAACG
1 ACGAACATAAACG
1314992 TTGGATATCC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 73 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1318444 original size:22 final size:22
Alignment explanation
Indices: 1318419--1318461 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1318409 TGAATTATGT
*
1318419 ACAGAAGCAATCTCTGTGTAGG
1 ACAGAAGCAATCTCAGTGTAGG
1318441 ACAGAAGCAATCTCAGTGTAG
1 ACAGAAGCAATCTCAGTGTAG
1318462 ATTGTTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
ACAGAAGCAATCTCAGTGTAGG
Found at i:1321127 original size:34 final size:34
Alignment explanation
Indices: 1321084--1321149 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
1321074 AAAGTTAGTG
*
1321084 CTAATTCCGTTATAGACAGCTGATCGACAGGTGC
1 CTAATTCCGTTATAGACAGCTGATCAACAGGTGC
1321118 CTAATTCCGTTATAGACAGCTGATCAACAGGT
1 CTAATTCCGTTATAGACAGCTGATCAACAGGT
1321150 ACCGGATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (34 bp):
CTAATTCCGTTATAGACAGCTGATCAACAGGTGC
Found at i:1325750 original size:31 final size:30
Alignment explanation
Indices: 1325712--1325792 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 30
1325702 AATTTATTTT
1325712 TTTTAAATACTAATTATTTAATCACT-AATTA
1 TTTTAAATACTAATTATTTAAT-A-TAAATTA
1325743 TTTTAAATA-TAAATTATTTAAATATAAATTA
1 TTTTAAATACT-AATTATTT-AATATAAATTA
* *
1325774 -TATAAAAACTAATTATTTA
1 TTTTAAATACTAATTATTTA
1325793 CATAAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
29 1 0.02
30 16 0.36
31 24 0.55
32 3 0.07
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TTTTAAATACTAATTATTTAATATAAATTA
Found at i:1325762 original size:15 final size:15
Alignment explanation
Indices: 1325713--1325792 Score: 85
Period size: 15 Copynumber: 5.3 Consensus size: 15
1325703 ATTTATTTTT
1325713 TTTAAATACTAATTA
1 TTTAAATACTAATTA
1325728 TTT-AATCACTAATTA
1 TTTAAAT-ACTAATTA
1325743 TTTTAAATA-TAAATTA
1 -TTTAAATACT-AATTA
1325759 TTTAAATA-TAAATTA
1 TTTAAATACT-AATTA
* *
1325774 TATAAAAACTAATTA
1 TTTAAATACTAATTA
1325789 TTTA
1 TTTA
1325793 CATAAACTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 3 0.05
15 41 0.72
16 10 0.18
17 3 0.05
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
TTTAAATACTAATTA
Found at i:1325810 original size:30 final size:30
Alignment explanation
Indices: 1325754--1325811 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1325744 TTTAAATATA
*
1325754 AATTATTTAAATATAAATTATATAAAAACT
1 AATTATTTAAATATAAATAATATAAAAACT
* *
1325784 AATTATTTACATA-AACTAATATTAAAAA
1 AATTATTTAAATATAAATAATA-TAAAAA
1325812 ATAAAAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTATTTAAATATAAATAATATAAAAACT
Found at i:1326144 original size:20 final size:20
Alignment explanation
Indices: 1326116--1326207 Score: 157
Period size: 20 Copynumber: 4.6 Consensus size: 20
1326106 TAGTTGAAAA
1326116 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* *
1326136 TCGCATTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
*
1326156 TCGCGTTGCGCTTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1326176 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
1326196 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1326208 AGTTGAAAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:1326248 original size:22 final size:22
Alignment explanation
Indices: 1326220--1326291 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
1326210 TTGAAAATTG
*
1326220 CGTTGCGATAGTCTACAGCTGT
1 CGTTGCGATAGTCTACAGATGT
* * *
1326242 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGATGT
*
1326261 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGATGT
1326283 CGTTGCGAT
1 CGTTGCGAT
1326292 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.36
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGATGT
Found at i:1326265 original size:19 final size:19
Alignment explanation
Indices: 1326241--1326306 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
1326231 TCTACAGCTG
1326241 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * **
1326260 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
1326281 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
1326301 TCGTTG
1 TCGTTG
1326307 TGATAGTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 6
0.72 0.16 0.12
Matches are distributed among these distances:
19 16 0.44
20 5 0.14
21 5 0.14
22 10 0.28
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:1326265 original size:41 final size:41
Alignment explanation
Indices: 1326214--1326313 Score: 173
Period size: 41 Copynumber: 2.4 Consensus size: 41
1326204 CGATAGTTGA
1326214 AAATTGCGTTGCGATAGTCTACAGCTGTCGTTGCGATTTTCC
1 AAATT-CGTTGCGATAGTCTACAGCTGTCGTTGCGATTTTCC
*
1326256 AAATTCGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCC
1 AAATTCGTTGCGATAGTCTACAGCTGTCGTTGCGATTTTCC
*
1326297 AAATTCGTTGTGATAGT
1 AAATTCGTTGCGATAGT
1326314 TAAAAAAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
41 51 0.91
42 5 0.09
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
AAATTCGTTGCGATAGTCTACAGCTGTCGTTGCGATTTTCC
Found at i:1326931 original size:6 final size:6
Alignment explanation
Indices: 1326920--1326973 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
1326910 GTCTCGTCTT
* *
1326920 GTGGTC GTGGTC GTGGTC GTGTTC GTGGTC GTGTTC GTGGTC GTGGTC
1 GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC GTGGTC
1326968 GTGGTC
1 GTGGTC
1326974 ATACGTGTCT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.00, C:0.17, G:0.46, T:0.37
Consensus pattern (6 bp):
GTGGTC
Found at i:1327903 original size:31 final size:31
Alignment explanation
Indices: 1327865--1328049 Score: 318
Period size: 31 Copynumber: 6.0 Consensus size: 31
1327855 CCCGAAGGAC
* * *
1327865 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1327896 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1327927 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1327958 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1327989 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1328020 CAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1328050 CCCTCGACCC
Statistics
Matches: 148, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1328320 original size:16 final size:17
Alignment explanation
Indices: 1328290--1328322 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1328280 TGTTGTATTT
1328290 TCATGTAAGCATATAAA
1 TCATGTAAGCATATAAA
1328307 TCATGTAA-CATATAAA
1 TCATGTAAGCATATAAA
1328323 CATACATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
TCATGTAAGCATATAAA
Found at i:1329227 original size:13 final size:15
Alignment explanation
Indices: 1329196--1329231 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1329186 TTCACACGTG
1329196 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
1329211 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
1329223 GAGAAGAGA
1 GAGAAGAGA
1329232 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:1332321 original size:31 final size:31
Alignment explanation
Indices: 1332283--1332467 Score: 309
Period size: 31 Copynumber: 6.0 Consensus size: 31
1332273 CCCGAAGGAC
* * *
1332283 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1332314 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1332345 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1332376 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1332407 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1332438 TAGTCCATATGTCCCGAAGAACATAGGTAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAA
1332468 CCCTCGACCC
Statistics
Matches: 147, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1332735 original size:16 final size:17
Alignment explanation
Indices: 1332705--1332737 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
1332695 TGTTGTATTT
1332705 TCATGTAAGCATATAAA
1 TCATGTAAGCATATAAA
1332722 TCATGTAA-CATATAAA
1 TCATGTAAGCATATAAA
1332738 CATACATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (17 bp):
TCATGTAAGCATATAAA
Found at i:1333642 original size:13 final size:15
Alignment explanation
Indices: 1333611--1333646 Score: 51
Period size: 13 Copynumber: 2.6 Consensus size: 15
1333601 TTCACACGTG
1333611 GAGAAGAGAAAATGA
1 GAGAAGAGAAAATGA
1333626 -AGAAG-GAAAA-GA
1 GAGAAGAGAAAATGA
1333638 GAGAAGAGA
1 GAGAAGAGA
1333647 TTTTTCTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
12 2 0.11
13 10 0.53
14 7 0.37
ACGTcount: A:0.61, C:0.00, G:0.36, T:0.03
Consensus pattern (15 bp):
GAGAAGAGAAAATGA
Found at i:1333956 original size:19 final size:19
Alignment explanation
Indices: 1333930--1334055 Score: 171
Period size: 19 Copynumber: 6.5 Consensus size: 19
1333920 CAACGAATTT
1333930 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
* * * **
1333949 TTGCAACGACAACTGTAGACTA
1 TCGCAACG--AA-TTTGGAAAA
1333971 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
*
1333990 TCGTAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1334009 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1334028 TCGCAACGAATTTGGAAAA
1 TCGCAACGAATTTGGAAAA
1334047 TCGCAACGA
1 TCGCAACGA
1334056 CAACTGTAGA
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
19 76 0.83
20 2 0.02
21 2 0.02
22 12 0.13
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
TCGCAACGAATTTGGAAAA
Found at i:1334108 original size:21 final size:21
Alignment explanation
Indices: 1334065--1334108 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1334055 ACAACTGTAG
** *
1334065 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
1334086 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
1334107 AC
1 AC
1334109 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:1334498 original size:26 final size:27
Alignment explanation
Indices: 1334438--1334501 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
1334428 GGGATAAGAT
*
1334438 GTTGTTACACAATGTTAAACTCTTTTA
1 GTTGTTACACAATGTAAAACTCTTTTA
1334465 GTTGTTACACAATGTAAAACTCTTTTA
1 GTTGTTACACAATGTAAAACTCTTTTA
1334492 GTT-TTACACA
1 GTTGTTACACA
1334502 GGTTTAGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 7 0.19
27 29 0.81
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (27 bp):
GTTGTTACACAATGTAAAACTCTTTTA
Found at i:1336126 original size:35 final size:35
Alignment explanation
Indices: 1336087--1336154 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
1336077 AAAATACTTT
*
1336087 AATTTAGGGTTTAGAATGTAATTAAAGTATTTTGG
1 AATTTAGGGTTTAGAAGGTAATTAAAGTATTTTGG
* * * *
1336122 AATTTGGGGTTTATAAGGTAATTGAAGTGTTTT
1 AATTTAGGGTTTAGAAGGTAATTAAAGTATTTT
1336155 TTGAATTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAAGGTAATTAAAGTATTTTGG
Found at i:1338563 original size:138 final size:138
Alignment explanation
Indices: 1338312--1338679 Score: 533
Period size: 138 Copynumber: 2.7 Consensus size: 138
1338302 CTTTACCCTT
* * *
1338312 AATTTT-ACTCAATTATGTGATTTGAATAATTAAAATGGAACCTCGAGCAAAAGTGAGGATCAAA
1 AATTTTAAC-CAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAA
* * *
1338376 TTAAAAAAT-CCTTAATTTTAAGGATTAAGTTTGAAATTAAGCCTAAAATGGAGGCTATAATTAT
65 TTAAAAATTCCCCTAA-TTTAAGGACTAAGTTTGAAATTAAGCCTAAAATGGAGGCTATAATTAT
1338440 TAAACTAGTC
129 TAAACTAGTC
* * * *
1338450 AATTTTAACCAATTATTTGATTTGAACAATTAAAAAGGAACCTCGAGGAAAAGCGAGGACCAAAT
1 AATTTTAACCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
* * * *
1338515 TAAAAATTCCCCTAATTTAATGACTACGTTTGAAATTAAGCCTCAAATGGAGGCTCTAATTATTA
66 TAAAAATTCCCCTAATTTAAGGACTAAGTTTGAAATTAAGCCTAAAATGGAGGCTATAATTATTA
*
1338580 ACCTAGTC
131 AACTAGTC
* * **
1338588 AATTTTAACTATTTATTTGATTCAAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
1 AATTTTAACCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
1338653 TAAAAATTCCCCTAATTTAAGGACTAA
66 TAAAAATTCCCCTAATTTAAGGACTAA
1338680 TTTAAAAAGG
Statistics
Matches: 204, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
138 197 0.97
139 7 0.03
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (138 bp):
AATTTTAACCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAAGCGAGGAACAAAT
TAAAAATTCCCCTAATTTAAGGACTAAGTTTGAAATTAAGCCTAAAATGGAGGCTATAATTATTA
AACTAGTC
Found at i:1341884 original size:22 final size:21
Alignment explanation
Indices: 1341859--1341955 Score: 67
Period size: 22 Copynumber: 4.5 Consensus size: 21
1341849 TGAGGATTTG
1341859 TTTTCATTTATTATTTTCTTTT
1 TTTTCATTTATT-TTTTCTTTT
*
1341881 TTTTCATTT-TCATTTTCCTTTT
1 TTTTCATTTAT--TTTTTCTTTT
* *
1341903 TCTT-ATTT-CTTTTTCTTCTT
1 TTTTCATTTATTTTTTCTT-TT
1341923 TTTTCCTATTCTATTTTTTCTTTT
1 TTTT-C-ATT-TATTTTTTCTTTT
*
1341947 TCTT-ATTTA
1 TTTTCATTTA
1341956 AATAAAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
19 7 0.12
20 7 0.12
21 8 0.13
22 20 0.33
23 4 0.07
24 6 0.10
25 8 0.13
ACGTcount: A:0.10, C:0.15, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCATTTATTTTTTCTTTT
Found at i:1341946 original size:44 final size:41
Alignment explanation
Indices: 1341872--1341954 Score: 112
Period size: 44 Copynumber: 2.0 Consensus size: 41
1341862 TCATTTATTA
*
1341872 TTTTCTTTTTTTTCATTTTCATTTTCCTTTTTCTTATTTCT
1 TTTTCTTTTTTTTCATATTCATTTTCCTTTTTCTTATTTCT
* *
1341913 TTTTCTTCTTTTTTCCTATTCTATTTTTTCTTTTTCTTATTT
1 TTTTCTT-TTTTTTCATATTC-A-TTTTCCTTTTTCTTATTT
1341955 AAATAAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 7 0.19
42 11 0.31
43 1 0.03
44 17 0.47
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (41 bp):
TTTTCTTTTTTTTCATATTCATTTTCCTTTTTCTTATTTCT
Found at i:1342340 original size:39 final size:39
Alignment explanation
Indices: 1342297--1342390 Score: 170
Period size: 39 Copynumber: 2.4 Consensus size: 39
1342287 AGGTCAAACA
*
1342297 AGTTCTTCTCATTATGGACTTCTTCTCCCTCTTCGGACG
1 AGTTCTTCTCATTATGGAATTCTTCTCCCTCTTCGGACG
1342336 AGTTCTTCTCATTATGGAATTCTTCTCCCTCTTCGGACG
1 AGTTCTTCTCATTATGGAATTCTTCTCCCTCTTCGGACG
*
1342375 AGCTCTTCTCATTATG
1 AGTTCTTCTCATTATG
1342391 AACCCTTCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.15, C:0.29, G:0.15, T:0.41
Consensus pattern (39 bp):
AGTTCTTCTCATTATGGAATTCTTCTCCCTCTTCGGACG
Found at i:1342344 original size:22 final size:22
Alignment explanation
Indices: 1342316--1342384 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
1342306 CATTATGGAC
1342316 TTCTTCTCCCTCTTCGGACGAG
1 TTCTTCTCCCTCTTCGGACGAG
*
1342338 TTCTTCT-CAT-TAT-GGA--A-
1 TTCTTCTCCCTCT-TCGGACGAG
1342355 TTCTTCTCCCTCTTCGGACGAG
1 TTCTTCTCCCTCTTCGGACGAG
*
1342377 CTCTTCTC
1 TTCTTCTC
1342385 ATTATGAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 14
0.69 0.06 0.26
Matches are distributed among these distances:
17 7 0.19
18 4 0.11
19 4 0.11
20 4 0.11
21 4 0.11
22 14 0.38
ACGTcount: A:0.12, C:0.33, G:0.14, T:0.41
Consensus pattern (22 bp):
TTCTTCTCCCTCTTCGGACGAG
Found at i:1342493 original size:157 final size:160
Alignment explanation
Indices: 1342177--1342508 Score: 501
Period size: 157 Copynumber: 2.1 Consensus size: 160
1342167 AGGTTGAACA
* *
1342177 AGTTCTTCTCATTAT-GAACTTATCTCCCCCTCTTCGGAAGAGTTCTTCTCATTATGAACTCTTC
1 AGTTCTTCTCATTATGGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTC
* * * * *
1342241 CATTGGAAATGATTACCCACCTCCTTCTGTGTTGGATTTGAGTAAAAGGTCAAACAAGTTCTTCT
66 CATTGGAAATGATGACCCACATCCTTCAGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCT
* *
1342306 CATTATGGACTTCTTCTCCCTCTTCGGACG
131 CATTATGAACTTCTTCTCCCTCTTCAGACG
* * *
1342336 AGTTCTTCTCATTATGGAA-TTCT-TCTCCCTCTTCGGACGAGCTCTTCTCATTATGAACCCTTC
1 AGTTCTTCTCATTATGGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTC
* *
1342399 CATTGGAAATGATGATCCACATCCTTCAGTGAT-GATTTGAGCAAAAGGTCGAACAAGTTCTTCT
66 CATTGGAAATGATGACCCACATCCTTCAGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCT
*
1342463 TATTATGAACTTCTTCTCCCTCTTCAGACG
131 CATTATGAACTTCTTCTCCCTCTTCAGACG
1342493 AGTTCTTCTCATTATG
1 AGTTCTTCTCATTATG
1342509 AACCATTCTT
Statistics
Matches: 157, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
157 72 0.46
158 64 0.41
159 18 0.11
160 3 0.02
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.37
Consensus pattern (160 bp):
AGTTCTTCTCATTATGGAACTTATCTCCCCCTCTTCGGAAGAGCTCTTCTCATTATGAACCCTTC
CATTGGAAATGATGACCCACATCCTTCAGTGATGGATTTGAGCAAAAGGTCAAACAAGTTCTTCT
CATTATGAACTTCTTCTCCCTCTTCAGACG
Found at i:1342517 original size:19 final size:19
Alignment explanation
Indices: 1342495--1342535 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1342485 TTCAGACGAG
1342495 TTCTTCTCATTATGAACCA
1 TTCTTCTCATTATGAACCA
1342514 TTCTTCTCATTATGAACCA
1 TTCTTCTCATTATGAACCA
1342533 TTC
1 TTC
1342536 CATTGGGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.27, G:0.05, T:0.44
Consensus pattern (19 bp):
TTCTTCTCATTATGAACCA
Found at i:1342568 original size:137 final size:138
Alignment explanation
Indices: 1342378--1342650 Score: 422
Period size: 138 Copynumber: 2.0 Consensus size: 138
1342368 TCGGACGAGC
* *
1342378 TCTTCTCATTATGAACCCTTCCATTGGAAATGATGATCCACATCCTTCAGTGAT-GATTTGAGCA
1 TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCAGTGATGGATTTGAGCA
* * *
1342442 AAAGGTCGAACAAGTTCTTCTTATTATGAACTTCTTCTCCCTCTTCAGACGAGTTCTTCTCATTA
66 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
1342507 TGAACCAT
131 TGAACCAT
* * *
1342515 TCTTCTCATTATGAACCATTCCATTGGGAATGATGATCCACCTCATTCTGTGATGGATTTGAGCA
1 TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCAGTGATGGATTTGAGCA
* * * * *
1342580 AAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTCCTTATTCGGACGAGTTCTTCTCATTA
66 AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
1342645 TGAACC
131 TGAACC
1342651 CTTTCATTAG
Statistics
Matches: 122, Mismatches: 13, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
137 49 0.40
138 73 0.60
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.37
Consensus pattern (138 bp):
TCTTCTCATTATGAACCATTCCATTGGAAATGATGATCCACATCATTCAGTGATGGATTTGAGCA
AAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTATTCAGACGAGTTCTTCTCATTA
TGAACCAT
Found at i:1343209 original size:36 final size:36
Alignment explanation
Indices: 1343169--1343261 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 36
1343159 AAATGATTTC
* * * *
1343169 GTTTTAAGAGAGACTATCTCAAGCGAGATGAAATTG
1 GTTTTAAGAAAAACAATCTCAAGCGAGATAAAATTG
*
1343205 GTTTTAAGAAAAACAATCTCAAGTGAGATAAAATT-
1 GTTTTAAGAAAAACAATCTCAAGCGAGATAAAATTG
* *
1343240 -TTTTCAAGTAAAACAATTTCAA
1 GTTTT-AAGAAAAACAATCTCAA
1343262 AATTTGTGTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 4 0.08
35 15 0.31
36 30 0.61
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (36 bp):
GTTTTAAGAAAAACAATCTCAAGCGAGATAAAATTG
Found at i:1343357 original size:22 final size:22
Alignment explanation
Indices: 1343323--1343376 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1343313 AAAAACAATC
*
1343323 TCAAGTGAAATAAATTTTTGTT
1 TCAAGGGAAATAAATTTTTGTT
*
1343345 TCAAGGGAGATAAATTTTTGTT
1 TCAAGGGAAATAAATTTTTGTT
*
1343367 TCAAGTGAAA
1 TCAAGGGAAA
1343377 CAATTTCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.39
Consensus pattern (22 bp):
TCAAGGGAAATAAATTTTTGTT
Found at i:1343442 original size:125 final size:122
Alignment explanation
Indices: 1343223--1343461 Score: 334
Period size: 125 Copynumber: 1.9 Consensus size: 122
1343213 AAAAACAATC
* * **
1343223 TCAAGTGAGATAAAATTTTTTCAAGTAAAACAATTTCAAAATTTGTGTTTCAAGGGGAACTGTCT
1 TCAAGGGAGATAAAATTTTTTCAAGTAAAACAATTTCAAAATTTGTATTTCAAGGAAAACTGTCT
1343288 CAAGTGAGATGAAATTAGTTTTAAGAAAAACAATCTCAAGTGAAATAAATTTTTGTT
66 CAAGTGAGATGAAATTAGTTTTAAGAAAAACAATCTCAAGTGAAATAAATTTTTGTT
* * * * *
1343345 TCAAGGGAGATAAATTTTTGTTTCAAGTGAAACAATTTCAAGATTTTTATTTCAATGGAAAATTG
1 TCAAGGGAGATAAA-ATTT-TTTCAAGTAAAACAATTTCAAAATTTGTATTTCAA-GGAAAACTG
* * * *
1343410 TCTCACGTGAGATGGAATTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAA
63 TCTCAAGTGAGATGAAATTAGTTTTAAGAAAAACAATCTCAAGTGAAATAAA
1343462 AATTTTGCTT
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
122 13 0.13
123 3 0.03
124 31 0.31
125 54 0.53
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.34
Consensus pattern (122 bp):
TCAAGGGAGATAAAATTTTTTCAAGTAAAACAATTTCAAAATTTGTATTTCAAGGAAAACTGTCT
CAAGTGAGATGAAATTAGTTTTAAGAAAAACAATCTCAAGTGAAATAAATTTTTGTT
Found at i:1346390 original size:14 final size:14
Alignment explanation
Indices: 1346356--1346390 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1346346 ATACAAGTGC
1346356 ACAAATACAAAGAT
1 ACAAATACAAAGAT
*
1346370 ACGAATACAAAGAT
1 ACAAATACAAAGAT
*
1346384 GCAAATA
1 ACAAATA
1346391 TTTGAATGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.60, C:0.14, G:0.11, T:0.14
Consensus pattern (14 bp):
ACAAATACAAAGAT
Found at i:1346408 original size:28 final size:28
Alignment explanation
Indices: 1346373--1346448 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
1346363 CAAAGATACG
*
1346373 AATACAAAGATGCAAATATTTGAATGTA
1 AATACAAAGATGCAAATATATGAATGTA
* *
1346401 AATGCAAAGATGCAAAGATATGAATGTA
1 AATACAAAGATGCAAATATATGAATGTA
*
1346429 AATACAAAGATGTAAATATA
1 AATACAAAGATGCAAATATA
1346449 AATACAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.25
Consensus pattern (28 bp):
AATACAAAGATGCAAATATATGAATGTA
Found at i:1346466 original size:20 final size:20
Alignment explanation
Indices: 1346413--1346456 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1346403 TGCAAAGATG
* * *
1346413 CAAAGATATGAATGTAAATA
1 CAAAGATGTAAATATAAATA
1346433 CAAAGATGTAAATATAAATA
1 CAAAGATGTAAATATAAATA
1346453 CAAA
1 CAAA
1346457 CTGTAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.23
Consensus pattern (20 bp):
CAAAGATGTAAATATAAATA
Found at i:1349102 original size:138 final size:138
Alignment explanation
Indices: 1348629--1349293 Score: 673
Period size: 139 Copynumber: 4.8 Consensus size: 138
1348619 AAGAATATGA
* * * * * * *
1348629 TATTAATCCAAATCATTTTTAATAAATTA-TTGAGTCGAATAATCAAAATGGAACCTCGAGCATA
1 TATTAA-CCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* * ** * * * * * * * * *
1348693 GGCGAGGACCAAATT-AAGTTTTCTCTTAAATTAAAGGACTAAATATCACATTAAACCTAAGATA
65 AGAGAGGACCAAATTAAAAATTTC-CCT-AATTTAAGGACTAAGTTTAAAATTAAGCCTAAAATG
1348757 GAGGCTCT-AT
128 GAGGCTCTAAT
*
1348767 TAATTAACCTAATTAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
1 T-ATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
* * ** * *
1348832 AGCGAGGACCAAATTAAAAATTTGCCTAAATTTAAATACCAAG--TGAAATTAAGCCTAAAATGG
65 AGAGAGGACCAAATTAAAAATTTCCCT-AATTTAAGGACTAAGTTTAAAATTAAGCCTAAAATGG
* *
1348895 AGGATATAA-
129 AGGCTCTAAT
* * *
1348904 TATTAATCCTAATTAATTTTAGTCAATTATGTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
1 TATTAA-CCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAA
*
1348969 AGAGAGAACCAAATTAAAAA-TTCCCTAATTTTAAGGACTAAGTTTAAAATTAAGCCTAAAATGG
65 AGAGAGGACCAAATTAAAAATTTCCCTAA-TTTAAGGACTAAGTTTAAAATTAAGCCTAAAATGG
*
1349033 AGGCTGTAAT
129 AGGCTCTAAT
* * * * * *
1349043 TATTAACCTAGTCAATTTTAATCAATTATTTGATTGGAACAATTAAAAGGGGACATCGAGCAAAA
1 TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
* ** * * *
1349108 GCGATTACCAAATTAAAAAATTTCCTTAATTTAATGACTAAGTTTGAAATTAAGCCTAAAATGGA
66 GAGAGGACCAAATT-AAAAATTTCCCTAATTTAAGGACTAAGTTTAAAATTAAGCCTAAAATGGA
*
1349173 GACTCTAAT
130 GGCTCTAAT
* * * ** * *
1349182 TATTAACCTAGTCAATTCTAATTAATTATTTGATTCAAATAATTAAAATGTAACCTCAAGC-AAA
1 TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
* * *
1349246 GACGAGGACCAAATTAAAAATTCCCCTAATTTATGGTCTAA-TTTAAAA
66 GA-GAGGACCAAATTAAAAATTTCCCTAATTTAAGGACTAAGTTTAAAA
1349294 AGGATCTAAA
Statistics
Matches: 443, Mismatches: 72, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
135 2 0.00
136 20 0.05
137 101 0.23
138 132 0.30
139 176 0.40
140 12 0.03
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (138 bp):
TATTAACCTAATCAATTTTAATCAATTATTTGATTTGAATAATTAAAATGGAACCTCGAGCAAAA
GAGAGGACCAAATTAAAAATTTCCCTAATTTAAGGACTAAGTTTAAAATTAAGCCTAAAATGGAG
GCTCTAAT
Found at i:1349120 original size:275 final size:272
Alignment explanation
Indices: 1348623--1349293 Score: 751
Period size: 275 Copynumber: 2.4 Consensus size: 272
1348613 AATTTAAAGA
* * * * *
1348623 ATATGATATTAATCCAAATCATTTTTAATAAATTATTGAGTCGAATAATCAAAATGGAACCTCGA
1 ATATAATATTAATCCTAATCAATTTTAATAAATTATTGATTCGAATAATTAAAATGGAACCTCGA
* * * *** * * * * *
1348688 GCATAGGCGAGGACCAAATTAAGTTTTCTCTTAAATTAAAGGACTAAATATCACATTAAACCTAA
66 GCAAAAGAGAGGACCAAATTAAAAATTC-CCT-AATTTAAGGACT-AATTTAAAATTAAACCTAA
* * * * *
1348753 GATAGAGGCTCTATTAATTAACCTAATTAATTTTAATCAATTATTTGATTTGAATAATTAAAATG
128 AATAGAGGCTCTATTAATTAACCTAATCAATTTTAATCAATTATTTGATTGGAACAATTAAAAGG
*
1348818 GAACCTCGAGCAAAAGCGAGGACCAAATT-AAAAATTTGCCTAAATTTAAAT-ACCAAG-TGAAA
193 GAACATCGAGCAAAAGCGAGGACCAAATTAAAAAATTT-CCTAAATTT-AATGACCAAGTTGAAA
1348880 TTAAGCCTAAAATGGAGG
256 TTAAGCCTAAAATGGA-G
* * * *
1348898 ATATAATATTAATCCTAATTAATTTTAGTCAATTATGTGATTTGAATAATTAAAATGGAACCTCG
1 ATATAATATTAATCCTAATCAATTTTAATAAATTAT-TGATTCGAATAATTAAAATGGAACCTCG
* *
1348963 AGCAAAAGAGAGAACCAAATTAAAAATTCCCTAATTTTAAGGACTAAGTTTAAAATTAAGCCTAA
65 AGCAAAAGAGAGGACCAAATTAAAAATTCCCTAA-TTTAAGGACTAA-TTTAAAATTAAACCTAA
* * *
1349028 AATGGAGGCTGTAATT-ATTAACCTAGTCAATTTTAATCAATTATTTGATTGGAACAATTAAAAG
128 AATAGAGGCTCT-ATTAATTAACCTAATCAATTTTAATCAATTATTTGATTGGAACAATTAAAAG
* ** * *
1349092 GGGACATCGAGCAAAAGCGATTACCAAATTAAAAAATTTCCTTAATTTAATGACTAAGTTTGAAA
192 GGAACATCGAGCAAAAGCGAGGACCAAATTAAAAAATTTCCTAAATTTAATGACCAAG-TTGAAA
1349157 TTAAGCCTAAAATGGAG
256 TTAAGCCTAAAATGGAG
* * * * * *
1349174 ACTCTAATTATTAA-CCTAGTCAATTCTAATTAATTATTTGATTCAAATAATTAAAATGTAACCT
1 A-TATAA-TATTAATCCTAATCAATTTTAATAAATTA-TTGATTCGAATAATTAAAATGGAACCT
* * *
1349238 CAAGC-AAAGACGAGGACCAAATTAAAAATTCCCCTAATTTATGGTCTAATTTAAAA
63 CGAGCAAAAGA-GAGGACCAAATTAAAAATT-CCCTAATTTAAGGACTAATTTAAAA
1349294 AGGATCTAAA
Statistics
Matches: 334, Mismatches: 49, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
274 7 0.02
275 145 0.43
276 72 0.22
277 97 0.29
278 13 0.04
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (272 bp):
ATATAATATTAATCCTAATCAATTTTAATAAATTATTGATTCGAATAATTAAAATGGAACCTCGA
GCAAAAGAGAGGACCAAATTAAAAATTCCCTAATTTAAGGACTAATTTAAAATTAAACCTAAAAT
AGAGGCTCTATTAATTAACCTAATCAATTTTAATCAATTATTTGATTGGAACAATTAAAAGGGAA
CATCGAGCAAAAGCGAGGACCAAATTAAAAAATTTCCTAAATTTAATGACCAAGTTGAAATTAAG
CCTAAAATGGAG
Found at i:1349599 original size:13 final size:13
Alignment explanation
Indices: 1349581--1349617 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 13
1349571 TTTAAAGGAC
*
1349581 TGAAATTAAATGT
1 TGAAATTAAAGGT
1349594 TGAAATATAAAGGT
1 TGAAAT-TAAAGGT
1349608 TGAAATTAAA
1 TGAAATTAAA
1349618 ATAACAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.51, C:0.00, G:0.16, T:0.32
Consensus pattern (13 bp):
TGAAATTAAAGGT
Found at i:1351357 original size:18 final size:20
Alignment explanation
Indices: 1351328--1351364 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1351318 TAAAACTATT
1351328 TTTTATTATATTA-TATTTA
1 TTTTATTATATTATTATTTA
1351347 TTTTA-TATATTATTATTT
1 TTTTATTATATTATTATTT
1351365 GAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTATTATATTATTATTTA
Found at i:1352354 original size:60 final size:60
Alignment explanation
Indices: 1352256--1352369 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 60
1352246 TTGACACGAC
* * * *** *
1352256 GCCTTCAAGTTCCAGGGGGAGGCATTCAACTGTGAGCTTCTTCGACCTCAATGTCGAGAT
1 GCCTTCAAGTTCAAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAGAT
*
1352316 GCCTTCAAGTTCAAGGGGAAGGCATGCAACTACCAGCTTGTTCGACCTAAATGT
1 GCCTTCAAGTTCAAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGT
1352370 TGATATCATG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (60 bp):
GCCTTCAAGTTCAAGGGGAAGGCATGCAACTACCAGCTTCTTCGACCTAAATGTCGAGAT
Found at i:1361014 original size:21 final size:22
Alignment explanation
Indices: 1360972--1361023 Score: 72
Period size: 21 Copynumber: 2.4 Consensus size: 22
1360962 AAATATGAAA
1360972 TATAATAAA-TAATATTATTTAT
1 TATAA-AAATTAATATTATTTAT
1360994 TATAAAAATTAATATTA-TTAT
1 TATAAAAATTAATATTATTTAT
*
1361015 TTTAAAAAT
1 TATAAAAAT
1361024 ATTAGAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 15 0.54
22 13 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATAAAAATTAATATTATTTAT
Found at i:1361212 original size:23 final size:23
Alignment explanation
Indices: 1361184--1361231 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1361174 TATATTGTAT
1361184 TTTTAAA-ATTATTAATAAATATA
1 TTTTAAATATTATTAATAAA-ATA
* *
1361207 TTTTAAATATTTTTATTAAAATA
1 TTTTAAATATTATTAATAAAATA
1361230 TT
1 TT
1361232 ATTAGACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAAATATTATTAATAAAATA
Found at i:1361233 original size:11 final size:13
Alignment explanation
Indices: 1361181--1361235 Score: 53
Period size: 12 Copynumber: 4.4 Consensus size: 13
1361171 GAGTATATTG
*
1361181 TATTTTTAAA-AT
1 TATTATTAAATAT
*
1361193 TATTAATAAATA-
1 TATTATTAAATAT
1361205 TATT-TTAAATAT
1 TATTATTAAATAT
*
1361217 TTTTATTAAAATAT
1 TATTATT-AAATAT
1361231 TATTA
1 TATTA
1361236 GACTATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.18
12 15 0.44
13 3 0.09
14 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTATTAAATAT
Found at i:1361675 original size:26 final size:26
Alignment explanation
Indices: 1361620--1361684 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
1361610 AAAAATCGAG
*
1361620 AAAAT-AAAAATAAAAATGTTAAGAAA
1 AAAATAAAAAAT-AAAATGTGAAGAAA
1361646 AAAATAAAAAATAAAA-GTGAAGAAA
1 AAAATAAAAAATAAAATGTGAAGAAA
1361671 TAAAA-AAAAGAATA
1 -AAAATAAAA-AATA
1361685 TATGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 12 0.34
26 17 0.49
27 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.15
Consensus pattern (26 bp):
AAAATAAAAAATAAAATGTGAAGAAA
Found at i:1364273 original size:34 final size:34
Alignment explanation
Indices: 1364230--1364297 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
1364220 TCCACACGTT
* *
1364230 TTAGTGGAGCAGTAAGTGGAGATGAATTATCTAC
1 TTAGTGGAGCAATAAGTGGAAATGAATTATCTAC
* *
1364264 TTAGTGGAGCAATAAGTGGAAATGAGTTGTCTAC
1 TTAGTGGAGCAATAAGTGGAAATGAATTATCTAC
1364298 AGTTGCCCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.09, G:0.29, T:0.29
Consensus pattern (34 bp):
TTAGTGGAGCAATAAGTGGAAATGAATTATCTAC
Found at i:1364593 original size:48 final size:48
Alignment explanation
Indices: 1364508--1364710 Score: 223
Period size: 48 Copynumber: 4.2 Consensus size: 48
1364498 GCTGTCACTC
* * ** *
1364508 AGGGAATATCAAATCTTGAATG-AGAGGGATATATTCTG-TTTTTGTTGA
1 AGGGAATATCAAATCTTGAA-GAAGAGAGATATGTTCTGCTTACT-CTGA
* *
1364556 AGGGAATATCAAATCTTGAAGAAGAAAGACT-TGTTCTGCTTACTCCGA
1 AGGGAATATCAAATCTTGAAGAAGAGAGA-TATGTTCTGCTTACTCTGA
* * *
1364604 AGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTCCGCTTACTCTGA
1 AGGGAATATCAAATCTTGAAGAAGAGAGATATGTTCTGCTTACTCTGA
** ** *
1364652 AGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGA
1 AGGGAATATCAAATCTTGAAGAAGAGAGATATGTTCTGCTTACTCTGA
1364700 AGGGAATATCA
1 AGGGAATATCA
1364711 GATATGGGGG
Statistics
Matches: 136, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
47 2 0.01
48 130 0.96
49 4 0.03
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (48 bp):
AGGGAATATCAAATCTTGAAGAAGAGAGATATGTTCTGCTTACTCTGA
Found at i:1364614 original size:96 final size:96
Alignment explanation
Indices: 1364508--1364710 Score: 266
Period size: 96 Copynumber: 2.1 Consensus size: 96
1364498 GCTGTCACTC
* * ** *
1364508 AGGGAATATCAAATCTTGAATG-AGAGGGATATATTCTG-TTTTTGTTGAAGGGAATATCAAATC
1 AGGGAATATCAAATCTTGAA-GAAGAGAGATATATTCCGCTTACT-CTGAAGGGAATATCAAATC
* **
1364571 TTGAAGAAGAAAGACTTGTTCTGCTTACTCCGA
64 TTGAAGAAGAAAGACCTGTTCCACTTACTCCGA
* * *
1364604 AGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTCCGCTTACTCTGAAGGGAATATCAAATCTT
1 AGGGAATATCAAATCTTGAAGAAGAGAGATATATTCCGCTTACTCTGAAGGGAATATCAAATCTT
*
1364669 GAAGAAGAGAGACCTGTTCCACTTACTCCGA
66 GAAGAAGAAAGACCTGTTCCACTTACTCCGA
1364700 AGGGAATATCA
1 AGGGAATATCA
1364711 GATATGGGGG
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
95 1 0.01
96 89 0.96
97 3 0.03
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (96 bp):
AGGGAATATCAAATCTTGAAGAAGAGAGATATATTCCGCTTACTCTGAAGGGAATATCAAATCTT
GAAGAAGAAAGACCTGTTCCACTTACTCCGA
Found at i:1364805 original size:46 final size:46
Alignment explanation
Indices: 1364738--1364874 Score: 193
Period size: 46 Copynumber: 2.9 Consensus size: 46
1364728 CCATTGAATC
*
1364738 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
* *
1364785 GAAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATTTTGAA
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
* * *
1364831 GAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATATCAGATCT
1 G-A-AGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
1364875 GGGGGAGTTG
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
46 40 0.50
47 5 0.06
48 35 0.44
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (46 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
Found at i:1364869 original size:48 final size:48
Alignment explanation
Indices: 1364553--1364710 Score: 228
Period size: 48 Copynumber: 3.3 Consensus size: 48
1364543 CTGTTTTTGT
* **
1364553 TGAAGGGAATATCAAATCTTGAAGAAGAAAGACTTGTTCTGCTTACTC
1 TGAAGGGAATATCAAATCTTGAAGAAGAGAGACTTGTTCCACTTACTC
* * *
1364601 CGAAGGGAATATCAAATCTTGGAGAAGAGAGA-TCTGTTCCGCTTACTC
1 TGAAGGGAATATCAAATCTTGAAGAAGAGAGACT-TGTTCCACTTACTC
*
1364649 TGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTC
1 TGAAGGGAATATCAAATCTTGAAGAAGAGAGACTTGTTCCACTTACTC
*
1364697 CGAAGGGAATATCA
1 TGAAGGGAATATCA
1364711 GATATGGGGG
Statistics
Matches: 99, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
47 1 0.01
48 98 0.99
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (48 bp):
TGAAGGGAATATCAAATCTTGAAGAAGAGAGACTTGTTCCACTTACTC
Found at i:1364872 original size:159 final size:159
Alignment explanation
Indices: 1364576--1365146 Score: 953
Period size: 159 Copynumber: 3.6 Consensus size: 159
1364566 AAATCTTGAA
** * *
1364576 GAAGAAAGACTTGTTCTGCTTACTCCGAAGGGAATATCAAATCTTGGAGAAGAGAGATCTGTTCC
1 GAAG-AAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGA-CT-TGTTCC
1364641 GCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAA
63 GCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAA
*
1364706 TATCAGATATGGGGGAGTTAATCCATTGAATC
128 TATCAGATATGGGGGAGTTGATCCATTGAATC
1364738 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
1 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
*
1364803 TACTCTGAAGGGAATATCAAATTTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
66 TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
*
1364868 CAGATCTGGGGGAGTTGATCCATTGAATC
131 CAGATATGGGGGAGTTGATCCATTGAATC
*
1364897 GTAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
1 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
* *
1364962 TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGATACATGTTCCACTTACTCCGAAGGGAATAT
66 TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
*
1365027 CAGATATGGGGGAATTGATCCATTGAATC
131 CAGATATGGGGGAGTTGATCCATTGAATC
* * * *
1365056 GAAGAAGACTTGTTCTACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCA
1 GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAG-A-AGAGACTTGTTCCG
*
1365121 CTTACTCTGAAGGGAATATCAGATCT
64 CTTACTCTGAAGGGAATATCAAATCT
1365147 GGGGGAGTTG
Statistics
Matches: 388, Mismatches: 19, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
159 298 0.77
160 2 0.01
161 84 0.22
162 4 0.01
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (159 bp):
GAAGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAGAGACTTGTTCCGCT
TACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCACTTACTCCGAAGGGAATAT
CAGATATGGGGGAGTTGATCCATTGAATC
Found at i:1364964 original size:46 final size:46
Alignment explanation
Indices: 1364902--1365028 Score: 200
Period size: 46 Copynumber: 2.7 Consensus size: 46
1364892 GAATCGTAGA
*
1364902 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAGAAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAG
*
1364948 AGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAAG
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAG
* *
1364994 AGATACATGTTCCACTTACTCCGAAGGGAATATCA
1 AG--ACTTGTTCCACTTACTCTGAAGGGAATATCA
1365029 GATATGGGGG
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
46 46 0.62
48 28 0.38
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (46 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAG
Found at i:1365081 original size:113 final size:112
Alignment explanation
Indices: 1364944--1365167 Score: 376
Period size: 113 Copynumber: 2.0 Consensus size: 112
1364934 AAATCTTGGA
* *
1364944 GAAGAGACTTGTTCCGCTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGATACATGTTCCAC
1 GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATGTTCCAC
1365009 TTACTCCGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC
66 TTACTCCGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC
* *
1365056 GAAGAAGACTTGTTCTACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACCTGTTCCA
1 GAAG-AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATGTTCCA
* * *
1365121 CTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAAT
65 CTTACTCCGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAAT
1365168 TGGGATCAAA
Statistics
Matches: 104, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
112 4 0.04
113 100 0.96
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.27
Consensus pattern (112 bp):
GAAGAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAAGAAGAGAGACATGTTCCAC
TTACTCCGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC
Found at i:1365118 original size:48 final size:47
Alignment explanation
Indices: 1365056--1365146 Score: 146
Period size: 48 Copynumber: 1.9 Consensus size: 47
1365046 CCATTGAATC
* *
1365056 GAAGAAGACTTGTTCTACTTACTCTGAAGGGAATATCAAATCTTGAA
1 GAAGAAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
*
1365103 GAAGAGAGACCTGTTCCACTTACTCTGAAGGGAATATCAGATCT
1 GAAGA-AGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCT
1365147 GGGGGAGTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 5 0.12
48 35 0.88
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (47 bp):
GAAGAAGACCTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGAA
Found at i:1373508 original size:11 final size:11
Alignment explanation
Indices: 1373494--1373523 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1373484 TGCAATGTAG
1373494 ATGCAATATGA
1 ATGCAATATGA
*
1373505 ATGCAAAATGA
1 ATGCAATATGA
1373516 ATGCAATA
1 ATGCAATA
1373524 CAAGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (11 bp):
ATGCAATATGA
Found at i:1378756 original size:34 final size:34
Alignment explanation
Indices: 1378718--1378785 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
1378708 TCCACACGTT
* * *
1378718 TTAGTGGAGCAGTAAGTGGAGATGAATTATCTAC
1 TTAGTGGAGCAATAACTGGAAATGAATTATCTAC
* *
1378752 TTAGTGGAGCAATAACTGGAAATGAGTTGTCTAC
1 TTAGTGGAGCAATAACTGGAAATGAATTATCTAC
1378786 ACCCCGAGCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.29
Consensus pattern (34 bp):
TTAGTGGAGCAATAACTGGAAATGAATTATCTAC
Found at i:1379003 original size:20 final size:20
Alignment explanation
Indices: 1378978--1379040 Score: 81
Period size: 20 Copynumber: 3.1 Consensus size: 20
1378968 ATGGTGGCGC
1378978 GCGGCGGCAAGTCGCGGTGT
1 GCGGCGGCAAGTCGCGGTGT
* * * *
1378998 GCGGCGGTAAGTGGCGGCGC
1 GCGGCGGCAAGTCGCGGTGT
*
1379018 GCGGTGGCAAGTCGCGGTGT
1 GCGGCGGCAAGTCGCGGTGT
1379038 GCG
1 GCG
1379041 ATGGTAAGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.10, C:0.24, G:0.52, T:0.14
Consensus pattern (20 bp):
GCGGCGGCAAGTCGCGGTGT
Found at i:1379027 original size:40 final size:40
Alignment explanation
Indices: 1378973--1379056 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
1378963 GAACCATGGT
*
1378973 GGCGCGCGGCGGCAAGTCGCGGTGTGCGGCGGTAAGTGGC
1 GGCGCGCGGCGGCAAGTCGCGGTGTGCGACGGTAAGTGGC
* *
1379013 GGCGCGCGGTGGCAAGTCGCGGTGTGCGATGGTAAGTGGC
1 GGCGCGCGGCGGCAAGTCGCGGTGTGCGACGGTAAGTGGC
1379053 GGCG
1 GGCG
1379057 TCAGCGACCG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.11, C:0.23, G:0.52, T:0.14
Consensus pattern (40 bp):
GGCGCGCGGCGGCAAGTCGCGGTGTGCGACGGTAAGTGGC
Found at i:1379049 original size:20 final size:20
Alignment explanation
Indices: 1378986--1379054 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
1378976 GCGCGGCGGC
*
1378986 AAGTCGCGGTGTGCGGCGGT
1 AAGTCGCGGTGTGCGGTGGT
* * * *
1379006 AAGTGGCGGCGCGCGGTGGC
1 AAGTCGCGGTGTGCGGTGGT
*
1379026 AAGTCGCGGTGTGCGATGGT
1 AAGTCGCGGTGTGCGGTGGT
*
1379046 AAGTGGCGG
1 AAGTCGCGG
1379055 CGTCAGCGAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.13, C:0.19, G:0.51, T:0.17
Consensus pattern (20 bp):
AAGTCGCGGTGTGCGGTGGT
Found at i:1380748 original size:124 final size:124
Alignment explanation
Indices: 1380528--1380870 Score: 560
Period size: 124 Copynumber: 2.8 Consensus size: 124
1380518 ATTGGACATG
1380528 ATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
*
1380593 GATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGACGGATGCTGCTTGTGGGCACA
66 GATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGACGGATGCTGCATGTGGGCACA
* * * * * *
1380652 ATATCATTCGTCGTGAAGTTTAAATCGTGGATGACTCATTCATTGTGAAGCTAAGCTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
* * * *
1380717 GATATCCTTTGTTGTGAAGTTGAAATCCAATCTAGAGATGGATGTTGCATGTGGGCACG
66 GATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGACGGATGCTGCATGTGGGCACA
* *
1380776 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCTTTCGTTGTGAAGTTGAGCTTTGAATTG
1 ATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
*
1380841 GATATCCTTCGTTGTGAAGTTAAAATCCAA
66 GATATCCTTCGTTGTGAAGTTGAAATCCAA
1380871 GGGTTGTTTC
Statistics
Matches: 199, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
124 199 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (124 bp):
ATATCCTTCGTCGTGAAGTTAAAATCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTTGAATTG
GATATCCTTCGTTGTGAAGTTGAAATCCAATCTAGAGACGGATGCTGCATGTGGGCACA
Found at i:1381029 original size:64 final size:64
Alignment explanation
Indices: 1380952--1381247 Score: 459
Period size: 64 Copynumber: 4.6 Consensus size: 64
1380942 TTACATTGTT
*
1380952 TTGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* * * *
1381016 TTGAGTCCAATATCATTTGTTGTGAAGTTGAAATTGATTTTGAATGAAACTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* * *
1381080 TTGAGTCCAATATCCTTCGTTGTGAAGTTTAAATTGACTCTGAATGAAATTGG-AAGTTATTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* * * *
1381143 TTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAATCTGGAAAGTTGTTTG
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
* *
1381207 TTGAGTCTAATATCCTTCGTTGTGAAGTTAAAATTGACTCT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCT
1381248 AAAAGCTGCA
Statistics
Matches: 209, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
63 56 0.27
64 153 0.73
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.39
Consensus pattern (64 bp):
TTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTG
Found at i:1381189 original size:127 final size:128
Alignment explanation
Indices: 1380952--1381247 Score: 495
Period size: 127 Copynumber: 2.3 Consensus size: 128
1380942 TTACATTGTT
* * *
1380952 TTGAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTATTTGT
* * *
1381017 TGAGTCCAATATCATTTGTTGTGAAGTTGAAATTGATTTTGAATGAAACTGGAAAGTTGTTTG
66 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTG
* *
1381080 TTGAGTCCAATATCCTTCGTTGTGAAGTTTAAATTGACTCTGAATGAAATTGG-AAGTTATTTGT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTATTTGT
*
1381144 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAATCTGGAAAGTTGTTTG
66 TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTG
*
1381207 TTGAGTCTAATATCCTTCGTTGTGAAGTTAAAATTGACTCT
1 TTGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCT
1381248 AAAAGCTGCA
Statistics
Matches: 158, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
127 108 0.68
128 50 0.32
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.39
Consensus pattern (128 bp):
TTGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTCTGAATGAAACTGGAAAGTTATTTGT
TGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTGGAAAGTTGTTTG
Found at i:1382370 original size:99 final size:99
Alignment explanation
Indices: 1382194--1382391 Score: 279
Period size: 99 Copynumber: 2.0 Consensus size: 99
1382184 CAACTCAATA
* * * * ** *
1382194 TATAAACATCTTTATCAGGTTAGTTGAATCTTATCCATAAAGCTAGGGTGTTTAACCAATTGCTT
1 TATAAACACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTGCTC
**
1382259 TAGAGGGGCAACTCAAGCTTTATTGTATAGATAT
66 TAGAGGAACAACTCAAGCTTTATTGTATAGATAT
* *
1382293 TATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTC
1 TATAAACACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTGCTC
* *
1382358 TAGATGAACAACTCAAGCTTTATTGTATATATAT
66 TAGAGGAACAACTCAAGCTTTATTGTATAGATAT
1382392 AATATTATAA
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
99 86 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (99 bp):
TATAAACACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCAGGGCATTTAACCAATTGCTC
TAGAGGAACAACTCAAGCTTTATTGTATAGATAT
Found at i:1387524 original size:20 final size:20
Alignment explanation
Indices: 1387495--1387535 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1387485 GTTGTGGTTG
*
1387495 TTGCCGAGGAAACCGACGGT
1 TTGCCAAGGAAACCGACGGT
1387515 TTGCCAAGGAAACCGACGGT
1 TTGCCAAGGAAACCGACGGT
1387535 T
1 T
1387536 GACCGAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.17
Consensus pattern (20 bp):
TTGCCAAGGAAACCGACGGT
Found at i:1387726 original size:2 final size:2
Alignment explanation
Indices: 1387721--1387751 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1387711 GATGTGTAAA
1387721 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
1387752 AATAAGGACG
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:1391678 original size:29 final size:30
Alignment explanation
Indices: 1391645--1391719 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
1391635 GTTTAATCTG
**
1391645 AATTTTTAAAATTTTGAGGGATC-AAATTA-
1 AATTTTTAAAATTTT-AAAGATCTAAATTAT
*
1391674 AATTTTTAAAATTGTAAAGATCTAAATTAT
1 AATTTTTAAAATTTTAAAGATCTAAATTAT
*
1391704 AATTTTTTAAATTTTA
1 AATTTTTAAAATTTTA
1391720 GAAGGACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.13
29 20 0.51
30 14 0.36
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (30 bp):
AATTTTTAAAATTTTAAAGATCTAAATTAT
Found at i:1395044 original size:12 final size:13
Alignment explanation
Indices: 1394994--1395046 Score: 51
Period size: 12 Copynumber: 4.3 Consensus size: 13
1394984 GCCTGCAAAC
*
1394994 ATATGTAATAA-A
1 ATATATAATAATA
1395006 AT-TATTAATAAT-
1 ATATA-TAATAATA
1395018 ATATATAATAATA
1 ATATATAATAATA
*
1395031 ATA-ATATTAATA
1 ATATATAATAATA
1395043 ATAT
1 ATAT
1395047 TTTTTAAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
11 1 0.03
12 28 0.82
13 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (13 bp):
ATATATAATAATA
Found at i:1395047 original size:9 final size:9
Alignment explanation
Indices: 1395008--1395047 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
1394998 GTAATAAAAT
1395008 TATTAATAA
1 TATTAATAA
1395017 TA-TATATAA
1 TATTA-ATAA
*
1395026 TAATAATAA
1 TATTAATAA
1395035 TATTAATAA
1 TATTAATAA
1395044 TATT
1 TATT
1395048 TTTTAAGCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 2 0.07
9 24 0.86
10 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATTAATAA
Found at i:1395443 original size:134 final size:131
Alignment explanation
Indices: 1395201--1395943 Score: 351
Period size: 136 Copynumber: 5.7 Consensus size: 131
1395191 CATTGGATTG
* *
1395201 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTCATTATGAACTCT
* * * *
1395266 CTATTAAAATGTCAATCCCTCAAGCGAGACGTTACTGATTCGAAACGTCGTGAATCAAGTGATAG
66 CCATTAAAATATCAATCCCTCAAGCGAGAC--TA-GGAATCGAAACGTCGTGAATCAAGTGATAG
1395331 GTCA
128 GTCA
*
1395335 AACAAGCTCTTCTCATTATGAATTTCTTCTTCCTCTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCT-TCGGATGAGTTCTTCTCATTATGAACTC
** *** * **
1395400 TCCATTAAAAATATTGATCCACCTCTTTCTATGA-T-GGAATCGAAA----G-GAA-CAAGTTCT
65 TCCATT-AAAATATCAAT-C-CCTCAAGCGA-GACTAGGAATCGAAACGTCGTGAATCAAGTGAT
**
1395457 -TCTCA
126 AGGTCA
** * * *** * *
1395462 TTATGAA-CT-TTCTCCTT-TAGGACGAGTTCTT-CTCATT---ATGA-AT-TTCT--TCT-GGA
1 --AACAAGCTCTTCTCATTAT-GAACTTCTTCTTCCTC-TTCGGATGAGTTCTTCTCAT-TATGA
* * **** * * * * ** * * *
1395515 AATGT-C---AATCCCTC-AT-GC-GAGGTGTCACT--GATTCGAAATGTCGTGAATCGAGTGAT
61 ACTCTCCATTAAAATATCAATCCCTCAAGCGAGACTAGGAATCGAAACGTCGTGAATCAAGTGAT
*
1395571 AGGTCG
126 AGGTCA
* * *
1395577 AATAAGCTCTTCTCATTATGAACTTCTTCTCCCACTGTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCT-TCGGATGAGTTCTTCTCATTATGAACTC
* * * ** * * *** *
1395642 TCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGAT
65 TCCATT-AAAATATCAATCCCTCAAGCGA-GACT-A-GGAATCGAAACGTCGTGAATCAAGTGAT
*
1395707 AGGTCG
126 AGGTCA
* * *
1395713 AACAAGATCTTCTCATTATGAACTTCTTC-TCTATCTTTTGGATGAGTTCTTCTCATTATGAACT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTC-CTC-TTCGGATGAGTTCTTCTCATTATGAACT
* * * * * * * *
1395777 CTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGCCACTGATTCGAAATGTCGTGAATCGAGTGA
64 CTCCATT-AAAATATCAATCCCTCAAGCGA-G-ACTA-GGAATCGAAACGTCGTGAATCAAGTGA
*
1395842 TAGGTCG
125 TAGGTCA
* *
1395849 AACAAGCTTTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTC-TTCGGATGAGTTCTTCTCATTATGAACTC
* ** * *
1395914 TCAATTAGAAATGCCAACCCCTCAAACGAG
65 TCCATTA-AAATATCAATCCCTCAAGCGAG
1395944 GTATCACTGA
Statistics
Matches: 459, Mismatches: 101, Indels: 97
0.70 0.15 0.15
Matches are distributed among these distances:
108 9 0.02
109 1 0.00
110 1 0.00
112 1 0.00
113 8 0.02
114 10 0.02
115 17 0.04
116 4 0.01
118 1 0.00
119 10 0.02
120 2 0.00
121 8 0.02
122 2 0.00
123 10 0.02
126 5 0.01
127 18 0.04
128 11 0.02
129 8 0.02
130 2 0.00
131 3 0.01
132 1 0.00
134 42 0.09
135 34 0.07
136 240 0.52
137 3 0.01
138 6 0.01
139 2 0.00
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (131 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCTCATTATGAACTCT
CCATTAAAATATCAATCCCTCAAGCGAGACTAGGAATCGAAACGTCGTGAATCAAGTGATAGGTC
A
Found at i:1395508 original size:17 final size:17
Alignment explanation
Indices: 1395453--1395511 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1395443 AAGGAACAAG
1395453 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAA-T
* * *
1395471 TTC-TC-CTTTAGGACGAG
1 TTCTTCTCATTATGA--AT
1395488 TTCTTCTCATTATGAAT
1 TTCTTCTCATTATGAAT
1395505 TTCTTCT
1 TTCTTCT
1395512 GGAAATGTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
16 6 0.19
17 13 0.42
18 6 0.19
19 6 0.19
ACGTcount: A:0.19, C:0.22, G:0.10, T:0.49
Consensus pattern (17 bp):
TTCTTCTCATTATGAAT
Found at i:1395629 original size:242 final size:258
Alignment explanation
Indices: 1395200--1395925 Score: 880
Period size: 242 Copynumber: 2.8 Consensus size: 258
1395190 TCATTGGATT
1395200 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTTGGATGAGTTCTTCTCATTATGAACTC
1 GAACAAGTTCTTCTCATTATGAACTTCTTC-TCCT-TTTGGATGAGTTCTTCTCATTATGAA-TC
* ** * * *
1395265 TCTAT-T-AAAATGTCAATCCCTCAAGCGAGACGTTACTGATTCGAAACGTCGTGAATCAAGTGA
63 TCT-TCTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGA
* * *
1395328 TAGGTCAAACAAGCTCTTCTCATTATGAATTTCTTCTTCCTCTGTCGGATGAGTTCTTCTCATTA
127 TAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTA
* * ** * *
1395393 TGAACTCTCCATTAAAAATATTGATCCAC-C-TC-T-T-TCT-A-T-G-AT-G-GAATCGA-A-A
192 TGAACTCTCAATTAGAAATATCAATCC-CTCAGCGTGTCACTGATTCGAATCGTGAATCGAGATA
1395445 -G-
256 GGC
* * *
1395446 GAACAAGTTCTTCTCATTATGAAC-T-TTCTCCTTTAGGACGAGTTCTTCTCATTATGAATTTCT
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTTGGATGAGTTCTTCTCATTATGAATCTCT
*
1395509 TCTGGAAATGTCAATCCCTCATGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGG
66 TCTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGG
* *
1395574 TCGAATAAGCTCTTCTCATTATGAACTTCTTCTCCCACTGTCGGATGAGTTCTTCTCATTATGAA
131 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAA
* *
1395639 CTCTCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCGAGT
196 CTCTCAATTAGAAATATCAATCCCTC-AGC---GTGTCACTGATTCG-AAT--CGTGAATCGA--
1395704 GATAGGTC
252 GATAGG-C
*
1395712 GAACAAGATCTTCTCATTATGAACTTCTTCTCTATCTTTTGGATGAGTTCTTCTCATTATGAA-C
1 GAACAAGTTCTTCTCATTATGAACTTCTTCTC---CTTTTGGATGAGTTCTTCTCATTATGAATC
* *
1395776 TCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGCCACTGATTCGAAATGTCGTGAATCGAGTG
63 TCTTC--TGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTG
* *
1395841 ATAGGTCGAACAAGCTTTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATT
126 ATAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATT
1395906 ATGAACTCTCAATTAGAAAT
191 ATGAACTCTCAATTAGAAAT
1395926 GCCAACCCCT
Statistics
Matches: 411, Mismatches: 35, Indels: 42
0.84 0.07 0.09
Matches are distributed among these distances:
240 1 0.00
241 6 0.01
242 156 0.38
243 4 0.01
244 4 0.01
245 1 0.00
246 24 0.06
248 1 0.00
249 1 0.00
250 2 0.00
251 1 0.00
252 1 0.00
253 1 0.00
255 2 0.00
258 1 0.00
259 7 0.02
262 1 0.00
263 1 0.00
264 1 0.00
266 23 0.06
267 1 0.00
268 5 0.01
270 4 0.01
271 26 0.06
272 136 0.33
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (258 bp):
GAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTTTGGATGAGTTCTTCTCATTATGAATCTCT
TCTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGATAGG
TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTATGAA
CTCTCAATTAGAAATATCAATCCCTCAGCGTGTCACTGATTCGAATCGTGAATCGAGATAGGC
Found at i:1395682 original size:136 final size:136
Alignment explanation
Indices: 1395446--1396065 Score: 790
Period size: 136 Copynumber: 4.5 Consensus size: 136
1395436 GAATCGAAAG
* * *
1395446 GAACAAGTTCTTCTCATTATGAAC-T-TTCT--C-CTTTAGGACGAGTTCTTCTCATTATGAA-T
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCACTTTCGGATGAGTTCTTCTCATTATGAACT
* * *
1395505 TTC-TTCTGGAAATGTCAATCCCTCATGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTG
66 CTCAAT-TGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTG
1395569 ATAGGTC
130 ATAGGTC
* *
1395576 GAATAAGCTCTTCTCATTATGAACTTCTTCTCCCACTGTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCACTTTCGGATGAGTTCTTCTCATTATGAACT
**
1395641 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATACCGTGAATCGAGTGA
66 CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGA
1395706 TAGGTC
131 TAGGTC
* * *
1395712 GAACAAGATCTTCTCATTATGAACTTCTTCT-CTATCTTTTGGATGAGTTCTTCTCATTATGAAC
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCA-CTTTCGGATGAGTTCTTCTCATTATGAAC
* *
1395776 TCTCCATTGGAAATGTCAATCCCTCAAGCGAGGTGCCACTGATTCGAAATGTCGTGAATCGAGTG
65 TCTCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTG
1395841 ATAGGTC
130 ATAGGTC
* *
1395848 GAACAAGCTTTTCTCATTATGAACTTCTTCTCCCTCTTTCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCACTTTCGGATGAGTTCTTCTCATTATGAACT
* * * * *
1395913 CTCAATTAGAAATGCCAACCCCTCAAACGAGGTATCACTGATTCAAAATACCCTGATTTGAAATG
66 CTCAATTGGAAATGTCAATCCCTCAAGCGAGG------TG--TC-----A--CTGATTCGAAATG
*
1395978 ACGTGAATCGAGTGATA-GTGC
116 TCGTGAATCGAGTGATAGGT-C
* *
1395999 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCGGATGAGTTCTTCTCATTATGAACT
1 GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCACTTTCGGATGAGTTCTTCTCATTATGAACT
1396064 CT
66 CT
1396066 GTACTGGAAA
Statistics
Matches: 431, Mismatches: 34, Indels: 29
0.87 0.07 0.06
Matches are distributed among these distances:
130 22 0.05
131 1 0.00
132 4 0.01
134 1 0.00
135 27 0.06
136 274 0.64
137 2 0.00
142 2 0.00
144 1 0.00
149 1 0.00
150 2 0.00
151 94 0.22
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (136 bp):
GAACAAGCTCTTCTCATTATGAACTTCTTCTCCCACTTTCGGATGAGTTCTTCTCATTATGAACT
CTCAATTGGAAATGTCAATCCCTCAAGCGAGGTGTCACTGATTCGAAATGTCGTGAATCGAGTGA
TAGGTC
Found at i:1396287 original size:91 final size:89
Alignment explanation
Indices: 1396130--1396345 Score: 335
Period size: 91 Copynumber: 2.4 Consensus size: 89
1396120 CCCGATGGAT
* * * * *
1396130 TTAAAAATCAAGAAACCCCCAAAAGCTCAGTTTCTTAAATCTTATTTGAAAACATCCTGCACTGA
1 TTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTC-TAAATATCATTTGAAAACATCCTGCACTGA
*
1396195 AGGTCTTATGGATGG-CTCGAAGGAC
65 AGGTCTTATGGATGGCCT-GAAGAAC
1396220 TTAAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAGATATCATTTGAAAACATCCTGCACTG
1 TT-AAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAA-ATATCATTTGAAAACATCCTGCACTG
1396285 AAGGTCTTATGGATGGCCTGAAGAAC
64 AAGGTCTTATGGATGGCCTGAAGAAC
1396311 TTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCT
1 TTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCT
1396346 TAATTGTCAC
Statistics
Matches: 117, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
90 38 0.32
91 77 0.66
92 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (89 bp):
TTAAAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAATATCATTTGAAAACATCCTGCACTGAA
GGTCTTATGGATGGCCTGAAGAAC
Found at i:1396458 original size:43 final size:43
Alignment explanation
Indices: 1396397--1396736 Score: 422
Period size: 43 Copynumber: 7.9 Consensus size: 43
1396387 TAAGTGTTCA
* **
1396397 TCAAGTTTGTCATCAAGAAACCTTTACATATCACGATGGT-CT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
*
1396439 CTCAAGCATGTCATCAAGAAACCCCTACATATCACGATGGT-CT
1 -TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
* * *
1396482 CTCAAGCATATCATCAA-AGAACCCCTACATATCACGATGCTCCT
1 -TCAAGCTTGTCATCAAGA-AACCCCTACATATCACGATGGTCCT
* * * *
1396526 TTAAGCTTGTTATCAAGGAACCCCTACATAACACGATGGTCCT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
* * *
1396569 TCAAGCTTATCATCAAGAAACCCCTACATATCACGAT-GACTT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
1396611 CTCAAGCTTGTCATCAA-AGAACCCCTA-ATATCACGATGGTCCT
1 -TCAAGCTTGTCATCAAGA-AACCCCTACATATCACGATGGTCCT
* * *
1396654 TTAAGCTTGTCATCAAGGAACCTCTACATATCACGATGGTCCT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
* *
1396697 TCAAGCTTTTCATCAAGAAACCCCTGCATATCACGATGGT
1 TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGT
1396737 TTCTCAAAAC
Statistics
Matches: 258, Mismatches: 31, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
42 37 0.14
43 219 0.85
44 2 0.01
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.27
Consensus pattern (43 bp):
TCAAGCTTGTCATCAAGAAACCCCTACATATCACGATGGTCCT
Found at i:1396701 original size:128 final size:128
Alignment explanation
Indices: 1396403--1396743 Score: 506
Period size: 128 Copynumber: 2.6 Consensus size: 128
1396393 TTCATCAAGT
* * * *
1396403 TTGTCATCAAGAAACCTTTACATATCACGATGGT-CTCTCAAGCATGTCATCAAGAAACCCCTAC
1 TTGTCATCAAGGAACCTCTACATATCACGATGGTCCT-TCAAGCTTATCATCAAGAAACCCCTAC
*
1396467 ATATCACGATGGTCTCTCAAGCATATCATCAAAGAACCCCTACATATCACGATGCTCCTTTAAGC
65 ATATCACGATGCT-TCTCAAGCATATCATCAAAGAACCCCTACATATCACGATGCTCCTTTAAGC
* * *
1396532 TTGTTATCAAGGAACCCCTACATAACACGATGGTCCTTCAAGCTTATCATCAAGAAACCCCTACA
1 TTGTCATCAAGGAACCTCTACATATCACGATGGTCCTTCAAGCTTATCATCAAGAAACCCCTACA
* * *
1396597 TATCACGATGACTTCTCAAGCTTGTCATCAAAGAACCCCTA-ATATCACGATGGTCCTTTAAGC
66 TATCACGATG-CTTCTCAAGCATATCATCAAAGAACCCCTACATATCACGATGCTCCTTTAAGC
* *
1396660 TTGTCATCAAGGAACCTCTACATATCACGATGGTCCTTCAAGCTTTTCATCAAGAAACCCCTGCA
1 TTGTCATCAAGGAACCTCTACATATCACGATGGTCCTTCAAGCTTATCATCAAGAAACCCCTACA
*
1396725 TATCACGATGGTTTCTCAA
66 TATCACGAT-GCTTCTCAA
1396744 AACATTGTGT
Statistics
Matches: 192, Mismatches: 17, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
128 97 0.51
129 92 0.48
130 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (128 bp):
TTGTCATCAAGGAACCTCTACATATCACGATGGTCCTTCAAGCTTATCATCAAGAAACCCCTACA
TATCACGATGCTTCTCAAGCATATCATCAAAGAACCCCTACATATCACGATGCTCCTTTAAGC
Found at i:1396867 original size:36 final size:36
Alignment explanation
Indices: 1396815--1397051 Score: 243
Period size: 36 Copynumber: 6.6 Consensus size: 36
1396805 TATCTCAAAA
* *
1396815 GAGATAAAATTTGTTTCAAGGGAAACTGTGTCAAGG
1 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
1396851 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
1 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
* *
1396887 GAGACAAAATTTGTTTCAAGTGAAATTGTCTCAAGG
1 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
* *
1396923 GAGAC------TGTCTCAAGGGAAACTGTCTCAAGA
1 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
* * * * *
1396953 GAGACAAAACTCGTTTCTAGGGAAATTGTCTCAAGC
1 GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
* * *
1396989 GAGATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGC
1 GAGACAAAA---TTTGTTTCAAGGGAAACTGTCTCAAGG
*
1397028 GAGATAAAATCTTTTGTTTCAAGG
1 GAGACAAAA---TTTGTTTCAAGG
1397052 AAAAACAATC
Statistics
Matches: 173, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
30 26 0.15
36 101 0.58
39 46 0.27
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (36 bp):
GAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGG
Found at i:1396871 original size:21 final size:21
Alignment explanation
Indices: 1396845--1396906 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1396835 GGAAACTGTG
1396845 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
1396866 TCAA-GG-G---AAA-CTGTC
1 TCAAGGGAGACAAAATTTGTT
1396881 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
1396902 TCAAG
1 TCAAG
1396907 TGAAATTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 1 0.03
19 1 0.03
20 5 0.16
21 12 0.39
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:1396920 original size:15 final size:15
Alignment explanation
Indices: 1396902--1396951 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
1396892 AAAATTTGTT
* *
1396902 TCAAGTGAAATTGTC
1 TCAAGGGAAACTGTC
*
1396917 TCAAGGGAGACTGTC
1 TCAAGGGAAACTGTC
1396932 TCAAGGGAAACTGTC
1 TCAAGGGAAACTGTC
1396947 TCAAG
1 TCAAG
1396952 AGAGACAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (15 bp):
TCAAGGGAAACTGTC
Found at i:1396978 original size:66 final size:66
Alignment explanation
Indices: 1396866--1396992 Score: 200
Period size: 66 Copynumber: 1.9 Consensus size: 66
1396856 AAAATTTGTT
* * * * *
1396866 TCAAGGGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGTGAAATTGTCTCAAGGGAGACTGT
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGGGAAATTGTCTCAAGCGAGACTGT
1396931 C
66 C
*
1396932 TCAAGGGAAACTGTCTCAAGAGAGACAAAACTCGTTTCTAGGGAAATTGTCTCAAGCGAGA
1 TCAAGGGAAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGGGAAATTGTCTCAAGCGAGA
1396993 TAAAATCTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (66 bp):
TCAAGGGAAACTGTCTCAAGAGAGACAAAACTCGTTTCAAGGGAAATTGTCTCAAGCGAGACTGT
C
Found at i:1397014 original size:39 final size:39
Alignment explanation
Indices: 1396932--1397090 Score: 180
Period size: 39 Copynumber: 4.1 Consensus size: 39
1396922 GGAGACTGTC
* * * *
1396932 TCAAGGGAAACTGTCTCAAGAGAGACAAAA-C--TCGTT
1 TCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTT
* * *
1396968 TCTAGGGAAATTGTCTCAAGCGAGATAAAATCTTTTGTT
1 TCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTT
1397007 TCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTT
1 TCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTT
* * ** *
1397046 TCAAGGAAAAACAATCTTGAGCGAGATAAAATCTTCTGTT
1 TCAAGG-GAAACTATCTCAAGCGAGATAAAATCTTTTGTT
1397086 TCAAG
1 TCAAG
1397091 AAAAAACAAT
Statistics
Matches: 106, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
36 26 0.25
37 1 0.01
39 46 0.43
40 33 0.31
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.28
Consensus pattern (39 bp):
TCAAGGGAAACTATCTCAAGCGAGATAAAATCTTTTGTT
Found at i:1397080 original size:40 final size:40
Alignment explanation
Indices: 1396986--1397118 Score: 187
Period size: 40 Copynumber: 3.4 Consensus size: 40
1396976 AATTGTCTCA
* * **
1396986 AGCGAGATAAAATCTTTTGTTTCAAGG-GAAACTATCTCA
1 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
1397025 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
1 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
* *
1397065 AGCGAGATAAAATCTTCTGTTTCAAGAAAAAACAATCTTG
1 AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
**
1397105 AATGAGATAAAATC
1 AGCGAGATAAAATC
1397119 CAAGTGAGAC
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 27 0.32
40 58 0.68
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.29
Consensus pattern (40 bp):
AGCGAGATAAAATCTTTTGTTTCAAGGAAAAACAATCTTG
Found at i:1406325 original size:18 final size:18
Alignment explanation
Indices: 1406302--1406337 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1406292 TCACTTTAGG
1406302 TGAAATATCATAAATGAA
1 TGAAATATCATAAATGAA
1406320 TGAAATATCATAAATGAA
1 TGAAATATCATAAATGAA
1406338 ATGCTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.11, T:0.28
Consensus pattern (18 bp):
TGAAATATCATAAATGAA
Found at i:1407328 original size:5 final size:5
Alignment explanation
Indices: 1407318--1407355 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
1407308 GGGGAGAAAT
1407318 GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAA
1 GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAA
1407356 AATGATGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (5 bp):
GAAGG
Found at i:1409934 original size:59 final size:59
Alignment explanation
Indices: 1409859--1409994 Score: 173
Period size: 59 Copynumber: 2.3 Consensus size: 59
1409849 AATTTTTTTA
* * * *
1409859 AGAAATAAACACATACTTGAACTGGTGTAAGTATGCACATTTCTCAATATCTTAATACCT
1 AGAAA-AAACATATACTTGAACTGGTGTAAGTATACACATCTCCCAATATCTTAATACCT
* * * * *
1409919 AGAAAAAACATATACTTGCACTGGTTTAAGTATATATATCTCCCAATATCTTAATACTT
1 AGAAAAAACATATACTTGAACTGGTGTAAGTATACACATCTCCCAATATCTTAATACCT
*
1409978 ACAAAAAACATATACTT
1 AGAAAAAACATATACTT
1409995 ACACTAGTAT
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 61 0.92
60 5 0.08
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (59 bp):
AGAAAAAACATATACTTGAACTGGTGTAAGTATACACATCTCCCAATATCTTAATACCT
Found at i:1411257 original size:17 final size:17
Alignment explanation
Indices: 1411235--1411282 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
1411225 TTTCTATTTG
*
1411235 AACAAAAATATTGTTAT
1 AACAAAAATGTTGTTAT
1411252 AACAAAAATGTTGTTAT
1 AACAAAAATGTTGTTAT
*
1411269 AACACAAATGTTGT
1 AACAAAAATGTTGT
1411283 ACATGAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.33
Consensus pattern (17 bp):
AACAAAAATGTTGTTAT
Found at i:1420168 original size:23 final size:23
Alignment explanation
Indices: 1420142--1420211 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
1420132 TATATGTGAC
*
1420142 CCTTTGGGATATTTCTACGTGGT
1 CCTTTGGGATAATTCTACGTGGT
** * *
1420165 CCTTCAGGATAAATGCTACGCGGT
1 CCTTTGGGAT-AATTCTACGTGGT
*
1420189 CCTTTGGGACAAATTCTACGTGG
1 CCTTTGGGA-TAATTCTACGTGG
1420212 CACTTCGGTG
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
23 8 0.23
24 27 0.77
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (23 bp):
CCTTTGGGATAATTCTACGTGGT
Found at i:1422144 original size:185 final size:186
Alignment explanation
Indices: 1421857--1422239 Score: 583
Period size: 185 Copynumber: 2.1 Consensus size: 186
1421847 CATAACATGC
* *
1421857 GTAAAAATAAAAATACAATTAATATATACATAAAATATTATTTATTAAATTATATTATACATAGA
1 GTAAAAATAATAATACAATTAATATATACATAAAATATTATTTATTAAATTATATCATACATAGA
* *
1421922 AAGAAAAGATTAATAATATAGCGCATATGTATGAATTTAAAATTCCTAAGAA-GTTATACATCAA
66 AAGAAAAGATTAATAATATAGCACATATGTATGAATTTAAAATTCCTAA-AATGTTATACATAAA
* * * * *
1421986 AAAAATAAAATTTCTAAGATTT-AATATCTATTTACATATATATAT-TTTTAACTTAG
130 AAAAATAAAATTTCAAAGATTTCAA-ATCTATTTACACACACATATATATTAACTTAG
* * *
1422042 GTAAAAATAATAATACAATTAATATATGCATAAAATATTATTTATTAATTTATATCATACTTAGA
1 GTAAAAATAATAATACAATTAATATATACATAAAATATTATTTATTAAATTATATCATACATAGA
*
1422107 AAGCAAAGATTAATAATATAGCACATATGTATGAATTTAAAATTCCTAAAATGTTATACATAAAA
66 AAGAAAAGATTAATAATATAGCACATATGTATGAATTTAAAATTCCTAAAATGTTATACATAAAA
*
1422172 AAAATAAAATTTCAAAGTTTTCAAATCTATTTACACACACATATATATTAACTTAG
131 AAAATAAAATTTCAAAGATTTCAAATCTATTTACACACACATATATATTAACTTAG
*
1422228 GATAGAAATAAT
1 G-TAAAAATAAT
1422240 TATATTATAT
Statistics
Matches: 179, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
184 2 0.01
185 155 0.87
186 13 0.07
187 9 0.05
ACGTcount: A:0.50, C:0.08, G:0.07, T:0.36
Consensus pattern (186 bp):
GTAAAAATAATAATACAATTAATATATACATAAAATATTATTTATTAAATTATATCATACATAGA
AAGAAAAGATTAATAATATAGCACATATGTATGAATTTAAAATTCCTAAAATGTTATACATAAAA
AAAATAAAATTTCAAAGATTTCAAATCTATTTACACACACATATATATTAACTTAG
Done.