Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, 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: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 5 of 20
Found at i:1593249 original size:118 final size:118
Alignment explanation
Indices: 1593036--1593284 Score: 435
Period size: 118 Copynumber: 2.1 Consensus size: 118
1593026 ACACAAGGTA
* *
1593036 AAAAGTCGATCTTGTTATGATTTTCCTTTAGGATCTACTACATTAAGGGGGGTAGTCGATCTTGG
1 AAAAGTCGATCTTGCTATGATTTTCCTTTAGGATCTACTACACTAAGGGGGGTAGTCGATCTTGG
1593101 TGCAAAAAGTTGCCCCTTGTTGGGAAAAATTCCTAGGATCGACTTCTTAAGGC
66 TGCAAAAAGTTGCCCCTTGTTGGGAAAAATTCCTAGGATCGACTTCTTAAGGC
* * *
1593154 AAAATTCGATCTTGCTATGATTTTCCTTTAGGATCTACTACACTGATGGGGGTAGTCGATCTTGG
1 AAAAGTCGATCTTGCTATGATTTTCCTTTAGGATCTACTACACTAAGGGGGGTAGTCGATCTTGG
* *
1593219 TGCAAAAAGTTTCCCCTTGTTTGGAAAAATTCCTAGGATCGACTTCTTAAGGC
66 TGCAAAAAGTTGCCCCTTGTTGGGAAAAATTCCTAGGATCGACTTCTTAAGGC
1593272 AAAAGTCGATCTT
1 AAAAGTCGATCTT
1593285 TCCACCTCCA
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 123 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (118 bp):
AAAAGTCGATCTTGCTATGATTTTCCTTTAGGATCTACTACACTAAGGGGGGTAGTCGATCTTGG
TGCAAAAAGTTGCCCCTTGTTGGGAAAAATTCCTAGGATCGACTTCTTAAGGC
Found at i:1599264 original size:80 final size:80
Alignment explanation
Indices: 1599111--1599353 Score: 242
Period size: 80 Copynumber: 3.0 Consensus size: 80
1599101 CAGTTCCAAT
* * * * * *
1599111 AATCA-TCATCATGATTAGCCCATAATGTATATGACTATCTCAATACATACATTTGATGGCGTAT
1 AATCACTCA-CATGCTTAACCCATAGTGTATATGACTAACTCAACACATACATTTGATAGCGTAT
* *
1599175 ATTTTATAACCTCCTA
65 ATTTCATAACCTCATA
***
1599191 AATCACTCACATGCTTAGGTCATAGTGTATATGACTAACTCAACACATACATCTT-ATAGCGT-T
1 AATCACTCACATGCTTAACCCATAGTGTATATGACTAACTCAACACATACAT-TTGATAGCGTAT
1599254 CATTTCATAACCTCATA
65 -ATTTCATAACCTCATA
* * * ** * * *
1599271 AATCACTTACATGCTTAACCCATAGTGTATATGACTATC-CGAACAAATACATACGATGGCATTT
1 AATCACTCACATGCTTAACCCATAGTGTATATGACTAACTC-AACACATACATTTGATAGCGTAT
*
1599335 ACTTCATAACCTCATA
65 ATTTCATAACCTCATA
1599351 AAT
1 AAT
1599354 GGAGCTCATA
Statistics
Matches: 137, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
79 2 0.01
80 129 0.94
81 6 0.04
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (80 bp):
AATCACTCACATGCTTAACCCATAGTGTATATGACTAACTCAACACATACATTTGATAGCGTATA
TTTCATAACCTCATA
Found at i:1600391 original size:21 final size:20
Alignment explanation
Indices: 1600365--1600444 Score: 58
Period size: 21 Copynumber: 3.9 Consensus size: 20
1600355 CTAAAAAAAT
1600365 TGTATCGATACATTATGAACA
1 TGTATC-ATACATTATGAACA
* *
1600386 TGTATCA-ATA-TATGACCATA
1 TGTATCATACATTATGA--ACA
**
1600406 TGTATCGATACACCATGAACA
1 TGTATC-ATACATTATGAACA
1600427 TGTATCAGTACATT-TGAA
1 TGTATCA-TACATTATGAA
1600445 ATAGAATGCA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
18 5 0.11
19 2 0.04
20 14 0.30
21 19 0.41
22 2 0.04
23 4 0.09
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.33
Consensus pattern (20 bp):
TGTATCATACATTATGAACA
Found at i:1616524 original size:9 final size:9
Alignment explanation
Indices: 1616505--1616543 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
1616495 ATATTTTTAT
*
1616505 TTAATCATG
1 TTAAACATG
*
1616514 TTAAACTTG
1 TTAAACATG
1616523 TTAAACATG
1 TTAAACATG
*
1616532 TTAATCATG
1 TTAAACATG
1616541 TTA
1 TTA
1616544 TTGGTCGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (9 bp):
TTAAACATG
Found at i:1616775 original size:21 final size:21
Alignment explanation
Indices: 1616751--1616805 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1616741 AAGTCTAGCT
*
1616751 TAAAGTAAATTAAAGCAAAAA
1 TAAAGTAAATTAAAACAAAAA
* *
1616772 TAAAGTAAAATAAAACTAAAA
1 TAAAGTAAATTAAAACAAAAA
**
1616793 TAACTTAAATTAA
1 TAAAGTAAATTAA
1616806 CTACTTAACA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.24
Consensus pattern (21 bp):
TAAAGTAAATTAAAACAAAAA
Found at i:1624520 original size:32 final size:32
Alignment explanation
Indices: 1624428--1624537 Score: 112
Period size: 32 Copynumber: 3.3 Consensus size: 32
1624418 TTTTTAAAGC
* * *
1624428 TCAAGCATAACATTTACAATGCCTTTCAAGGA
1 TCAAGCACAACCTTCACAATGCCTTTCAAGGA
* * *
1624460 TCAAGTACAACCTTTCCATCAATGCCTTTTATGGA
1 TCAAGCACAACC-TT-CA-CAATGCCTTTCAAGGA
* *
1624495 TCAAGCACAACCTTCACAATGCCTTTAAAGGC
1 TCAAGCACAACCTTCACAATGCCTTTCAAGGA
*
1624527 TAAAGCACAAC
1 TCAAGCACAAC
1624538 GTTTTCTCTC
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
32 32 0.50
33 4 0.06
34 3 0.05
35 25 0.39
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (32 bp):
TCAAGCACAACCTTCACAATGCCTTTCAAGGA
Found at i:1625167 original size:21 final size:20
Alignment explanation
Indices: 1625142--1625222 Score: 56
Period size: 21 Copynumber: 3.8 Consensus size: 20
1625132 TGTAAAGGAG
* *
1625142 GTTTAAAACTAATTTAAAGAA
1 GTTTAAAACT-ATTCAAACAA
*
1625163 GTTTAGAAGCTATTCAAACAA
1 GTTTA-AAACTATTCAAACAA
*
1625184 GTTTAAAAATCATT-AAAGCAA
1 GTTTAAAACT-ATTCAAA-CAA
*
1625205 TTTTCAAAACTTATTCAA
1 GTTT-AAAAC-TATTCAA
1625223 GTAATTTTGA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.13
21 27 0.57
22 11 0.23
23 3 0.06
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.33
Consensus pattern (20 bp):
GTTTAAAACTATTCAAACAA
Found at i:1625310 original size:22 final size:21
Alignment explanation
Indices: 1625279--1625347 Score: 102
Period size: 21 Copynumber: 3.2 Consensus size: 21
1625269 TCATTTAAAA
*
1625279 AAGTTTAAAAATTAGTCAAAC
1 AAGTTTAAAAATTATTCAAAC
*
1625300 AAGTTTAAAAACTCATTCAAAC
1 AAGTTTAAAAA-TTATTCAAAC
*
1625322 AACTTTAAAAATTATTCAAAC
1 AAGTTTAAAAATTATTCAAAC
1625343 AAGTT
1 AAGTT
1625348 CAAAGATCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 24 0.57
22 18 0.43
ACGTcount: A:0.51, C:0.13, G:0.06, T:0.30
Consensus pattern (21 bp):
AAGTTTAAAAATTATTCAAAC
Found at i:1625329 original size:43 final size:43
Alignment explanation
Indices: 1625264--1625347 Score: 132
Period size: 43 Copynumber: 2.0 Consensus size: 43
1625254 TAGGCACTTC
* *
1625264 AAAACTCATTTAAAAAAGTTTAAAAATTAGTCAAACAAGTTTA
1 AAAACTCATTCAAAAAACTTTAAAAATTAGTCAAACAAGTTTA
* *
1625307 AAAACTCATTCAAACAACTTTAAAAATTATTCAAACAAGTT
1 AAAACTCATTCAAAAAACTTTAAAAATTAGTCAAACAAGTT
1625348 CAAAGATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.30
Consensus pattern (43 bp):
AAAACTCATTCAAAAAACTTTAAAAATTAGTCAAACAAGTTTA
Found at i:1625498 original size:21 final size:20
Alignment explanation
Indices: 1625457--1625521 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
1625447 TAAAAACATT
**
1625457 TTCAAACAACTTCAAAAATCA
1 TTCAAACAA-TTCAAGGATCA
1625478 TTCAAACAAGTTCAAGGATCA
1 TTCAAACAA-TTCAAGGATCA
* * *
1625499 CTCAAAGACATTCACGGATCA
1 TTCAAACA-ATTCAAGGATCA
1625520 TT
1 TT
1625522 GAACCAATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
21 35 0.97
22 1 0.03
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (20 bp):
TTCAAACAATTCAAGGATCA
Found at i:1628790 original size:40 final size:40
Alignment explanation
Indices: 1628730--1628822 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 40
1628720 ATTTGTACTT
* * *
1628730 TCGAGTTCTCTTTCTCACCATCCCACTTTCTCAAATTTTA
1 TCGATTTCTCTCTCTCACCATCCCACTCTCTCAAATTTTA
*
1628770 TCGATTTCTCTCTCTCACCATCCCACTCTCTCTAATTTTA
1 TCGATTTCTCTCTCTCACCATCCCACTCTCTCAAATTTTA
*
1628810 TCGATTTATCTCT
1 TCGATTTCTCTCT
1628823 TTAGCATTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.18, C:0.33, G:0.04, T:0.44
Consensus pattern (40 bp):
TCGATTTCTCTCTCTCACCATCCCACTCTCTCAAATTTTA
Found at i:1628890 original size:23 final size:23
Alignment explanation
Indices: 1628848--1628892 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1628838 TATGCTCTTG
**
1628848 ATTTCTCTTTCCTGTGTTTTCAT
1 ATTTCTCTTTCCTGCATTTTCAT
1628871 ATTTCTCTTTCCTGCATTTTCA
1 ATTTCTCTTTCCTGCATTTTCA
1628893 AGACACCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.24, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTTCTCTTTCCTGCATTTTCAT
Found at i:1629337 original size:24 final size:25
Alignment explanation
Indices: 1629301--1629351 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
1629291 AAATATGACG
1629301 TGTAACAACAATA-TTTTTTCAACA
1 TGTAACAACAATATTTTTTTCAACA
* *
1629325 TGTACCAATAATATTTTTTTCAACA
1 TGTAACAACAATATTTTTTTCAACA
1629350 TG
1 TG
1629352 GCATGTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (25 bp):
TGTAACAACAATATTTTTTTCAACA
Found at i:1629393 original size:25 final size:26
Alignment explanation
Indices: 1629307--1629387 Score: 78
Period size: 26 Copynumber: 3.2 Consensus size: 26
1629297 GACGTGTAAC
* **
1629307 AACAATATTTTTTCAACAT-GTA-CC
1 AACAATATTTTTTCAACATAGCATGT
* *
1629331 AATAATATTTTTTTCAACATGGCATGT
1 AACAATA-TTTTTTCAACATAGCATGT
1629358 AACAATATTTTTT-AACCATAGCATGT
1 AACAATATTTTTTCAA-CATAGCATGT
1629384 AACA
1 AACA
1629388 TGTTTTTGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 6 0.13
25 14 0.30
26 21 0.45
27 6 0.13
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.38
Consensus pattern (26 bp):
AACAATATTTTTTCAACATAGCATGT
Found at i:1629523 original size:121 final size:122
Alignment explanation
Indices: 1629391--1629699 Score: 336
Period size: 122 Copynumber: 2.5 Consensus size: 122
1629381 TGTAACATGT
* * * *
1629391 TTTTGTACATGACGTGTAACAACCTAACCATGGGATGTAATATGTTTTTATACATGGCATGTAAT
1 TTTTGTACATGACGTGTAACAATCTAATCATGAGATGTAATATGTTTTTATACATGGTATGTAAT
* ** * * * *
1629456 AACAGTA-TTCTTTTTCAACATGGTGTGTAACAATCTAACTATGACATGT-TACATAC
66 AACAGTATTTCTTTTTCAACATAGCATGTAACAACCTAACCATAACATATCT-CATAC
* * * *
1629512 TTTTGTACATGACGTGTAACAATTTAATCATGATG-TGTAATATATTTTTGTACAAGGTATGTAA
1 TTTTGTACATGACGTGTAACAATCTAATCATGA-GATGTAATATGTTTTTATACATGGTATGTAA
* * * *
1629576 CAACAGTATTTTTTTTTCAAGATAGCATGTAACAACCTAACCATAACATATCTCATAT
65 TAACAGTATTTCTTTTTCAACATAGCATGTAACAACCTAACCATAACATATCTCATAC
* * * * * * * *
1629634 TTTTGTACATAACATGTAATAGTCTAATCACGACATATAATATGTTTCTATACATGGTATGTAAT
1 TTTTGTACATGACGTGTAACAATCTAATCATGAGATGTAATATGTTTTTATACATGGTATGTAAT
1629699 A
66 A
1629700 TCATGGTATG
Statistics
Matches: 152, Mismatches: 32, Indels: 7
0.80 0.17 0.04
Matches are distributed among these distances:
121 61 0.40
122 90 0.59
123 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (122 bp):
TTTTGTACATGACGTGTAACAATCTAATCATGAGATGTAATATGTTTTTATACATGGTATGTAAT
AACAGTATTTCTTTTTCAACATAGCATGTAACAACCTAACCATAACATATCTCATAC
Found at i:1630817 original size:2 final size:2
Alignment explanation
Indices: 1630810--1630846 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1630800 ATCACAAAGT
1630810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1630847 CAAAATTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1631980 original size:15 final size:15
Alignment explanation
Indices: 1631957--1632011 Score: 64
Period size: 13 Copynumber: 3.9 Consensus size: 15
1631947 GTTAAATCTT
*
1631957 TAATTT-TTAATTT-
1 TAATTTGTTTATTTA
1631970 TAATTTGTTTATTTA
1 TAATTTGTTTATTTA
1631985 TAATTT-TTT-TTTA
1 TAATTTGTTTATTTA
*
1631998 TAATTAGTTTATTT
1 TAATTTGTTTATTT
1632012 TTAAGTGAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
13 15 0.42
14 12 0.33
15 9 0.25
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (15 bp):
TAATTTGTTTATTTA
Found at i:1631992 original size:28 final size:28
Alignment explanation
Indices: 1631957--1632011 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1631947 GTTAAATCTT
*
1631957 TAATTTTTAATTT-TAATTTGTTTATTTA
1 TAATTTTT-ATTTATAATTAGTTTATTTA
*
1631985 TAATTTTTTTTTATAATTAGTTTATTT
1 TAATTTTTATTTATAATTAGTTTATTT
1632012 TTAAGTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (28 bp):
TAATTTTTATTTATAATTAGTTTATTTA
Found at i:1633656 original size:19 final size:19
Alignment explanation
Indices: 1633632--1633668 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1633622 ACATATTGAC
1633632 TATAAAACCATTTCATGGA
1 TATAAAACCATTTCATGGA
*
1633651 TATAAAGCCATTTCATGG
1 TATAAAACCATTTCATGG
1633669 CTACATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (19 bp):
TATAAAACCATTTCATGGA
Found at i:1635991 original size:21 final size:21
Alignment explanation
Indices: 1635949--1636007 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
1635939 TGAAAAATTA
* *
1635949 TATCAATACATGATG-AATATG
1 TATCAATACATTA-GAAACATG
*
1635970 TATCGATACATTAGAAACATG
1 TATCAATACATTAGAAACATG
* *
1635991 TATTAATACATTTGAAA
1 TATCAATACATTAGAAA
1636008 TAGAATATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
20 1 0.03
21 30 0.97
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (21 bp):
TATCAATACATTAGAAACATG
Found at i:1637973 original size:36 final size:36
Alignment explanation
Indices: 1637832--1638052 Score: 211
Period size: 35 Copynumber: 6.3 Consensus size: 36
1637822 TCTCAAGCAC
* * *
1637832 TTGATTAAAATTGTTTAATTAAGTTA-T--GCTTAA
1 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
* * * * *
1637865 TTCATTAAA-TTGTTTAATTAAGTCATTGAGCGTAA
1 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
* **** * * *
1637900 TTAATTAAA-TTAAACAATTACGTTATTGGACCTAA
1 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
*
1637935 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCGAA
1 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
* *
1637971 TTGATTAAA-TTGTTTAATTAAGTTATTGAGCCTAA
1 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
* *
1638006 TTGATTAAATTTTTTTAATCAAGTTATTGGGACTAA
1 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
1638042 TTGATTAAATT
1 TTGATTAAATT
1638053 AAACAATTAA
Statistics
Matches: 154, Mismatches: 29, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
32 15 0.10
33 9 0.06
35 70 0.45
36 60 0.39
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (36 bp):
TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
Found at i:1637978 original size:71 final size:71
Alignment explanation
Indices: 1637862--1638071 Score: 255
Period size: 71 Copynumber: 2.9 Consensus size: 71
1637852 AAGTTATGCT
* * * * * *
1637862 TAATTCATTAAA-TTGTTTAATTAAGTCATTGAGCGTAATTAATTAAATTAAACAATTACGTTAT
1 TAATTGATTAAATTTGTTTAATCAAGTTATTGGGCG-AATTGATTAAATTAAACAATTAAGTTAT
1637926 TGGA-CC
65 TGGAGCC
****
1637932 TAATTGATTAAATTTGTTTAATCAAGTTATTGGGCCGAATTGATTAAATTGTTTAATTAAGTTAT
1 TAATTGATTAAATTTGTTTAATCAAGTTATTGGG-CGAATTGATTAAATTAAACAATTAAGTTAT
1637997 T-GAGCC
65 TGGAGCC
* *
1638003 TAATTGATTAAATTTTTTTAATCAAGTTATTGGGACTAATTGATTAAATTAAACAATTAAGTTAA
1 TAATTGATTAAATTTGTTTAATCAAGTTATTGGG-CGAATTGATTAAATTAAACAATTAAGTT-A
1638068 TTGG
64 TTGG
1638072 GCTTCTTAAG
Statistics
Matches: 118, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
70 13 0.11
71 99 0.84
72 5 0.04
73 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (71 bp):
TAATTGATTAAATTTGTTTAATCAAGTTATTGGGCGAATTGATTAAATTAAACAATTAAGTTATT
GGAGCC
Found at i:1647547 original size:30 final size:31
Alignment explanation
Indices: 1647485--1647573 Score: 90
Period size: 31 Copynumber: 2.8 Consensus size: 31
1647475 ATACTATAGG
* * *
1647485 ATTGGAACTAGATGTTTGTTTTGAATTTTGGAC
1 ATTGGAA-TTGATATTTGTTTTG-ACTTTGGAC
*
1647518 TTTGGAATTGATA-TTGTTTTGACTTTGGAC
1 ATTGGAATTGATATTTGTTTTGACTTTGGAC
* * *
1647548 ATTGGATTTGGTATTTGTTTAGACTT
1 ATTGGAATTGATATTTGTTTTGACTT
1647574 CCATCTTTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
30 18 0.38
31 19 0.40
32 4 0.09
33 6 0.13
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.49
Consensus pattern (31 bp):
ATTGGAATTGATATTTGTTTTGACTTTGGAC
Found at i:1654438 original size:21 final size:21
Alignment explanation
Indices: 1654414--1654476 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
1654404 CTTATTCCTT
1654414 CTTTCTCCCTTTCTCTCTTTC
1 CTTTCTCCCTTTCTCTCTTTC
**
1654435 CTTTCTTTCTTTCTCTTCTTT-
1 CTTTCTCCCTTTCTC-TCTTTC
1654456 CTTTCTCTCCTTTCTCT-TTTC
1 CTTTCTC-CCTTTCTCTCTTTC
1654477 TTCTTGGTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
20 3 0.09
21 20 0.57
22 12 0.34
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (21 bp):
CTTTCTCCCTTTCTCTCTTTC
Found at i:1654444 original size:4 final size:4
Alignment explanation
Indices: 1654412--1654461 Score: 55
Period size: 4 Copynumber: 12.0 Consensus size: 4
1654402 TTCTTATTCC
** *
1654412 TTCT TTCT CCCT TTCT CTCT TTCCT TTCT TTCT TTCT CTTCT TTCT TTCT
1 TTCT TTCT TTCT TTCT TTCT TT-CT TTCT TTCT TTCT -TTCT TTCT TTCT
1654462 CTCCTTTCTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
4 30 0.79
5 8 0.21
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
TTCT
Found at i:1654444 original size:17 final size:17
Alignment explanation
Indices: 1654422--1654474 Score: 63
Period size: 17 Copynumber: 3.0 Consensus size: 17
1654412 TTCTTTCTCC
1654422 CTTTCTCTCTTTCCTTT
1 CTTTCTCTCTTTCCTTT
*
1654439 CTTTCTTTCTCTT-CTTT
1 CTTTCTCTCT-TTCCTTT
1654456 CTTTCTCTCCTTTCTCTTT
1 CTTTCTCT-CTTTC-CTTT
1654475 TCTTCTTGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 22 0.73
18 4 0.13
19 4 0.13
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTCTCTCTTTCCTTT
Found at i:1654461 original size:13 final size:13
Alignment explanation
Indices: 1654411--1654481 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
1654401 TTTCTTATTC
**
1654411 CTTCTTTCTCCCT
1 CTTCTTTCTTTCT
*
1654424 -TTCTCTCTTTC-
1 CTTCTTTCTTTCT
1654435 CTTTCTTTCTTTCT
1 C-TTCTTTCTTTCT
1654449 CTTCTTTCTTTCT
1 CTTCTTTCTTTCT
* *
1654462 CTCCTTTCTCTTTT
1 CTTCTTTCT-TTCT
1654476 CTTCTT
1 CTTCTT
1654482 GGTAGTGGAC
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
12 8 0.17
13 30 0.64
14 9 0.19
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTCTTTCTTTCT
Found at i:1656208 original size:38 final size:38
Alignment explanation
Indices: 1656144--1656240 Score: 151
Period size: 38 Copynumber: 2.6 Consensus size: 38
1656134 TGTATGCTCT
**
1656144 TGAGTGGTTATAC-TTAACTGATTAAAAAGGTAGTATC
1 TGAGTGGTTATACTTTAACCAATTAAAAAGGTAGTATC
* *
1656181 TGAGTGGTTATACTTTAACCAATTAAAATGGTAGTATT
1 TGAGTGGTTATACTTTAACCAATTAAAAAGGTAGTATC
1656219 TGAGTGGTTATACTTTAACCAA
1 TGAGTGGTTATACTTTAACCAA
1656241 AGTAAAAGGT
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
37 13 0.24
38 42 0.76
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (38 bp):
TGAGTGGTTATACTTTAACCAATTAAAAAGGTAGTATC
Found at i:1670875 original size:38 final size:38
Alignment explanation
Indices: 1670831--1670911 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
1670821 TAGAAAGTTT
** *
1670831 AATCACGCACGGCATCAAAGTGATTAGTGAAAAGTTCA
1 AATCACGCACAACACCAAAGTGATTAGTGAAAAGTTCA
* * * *
1670869 AATCACGCACAACACCGAAGTGATTGGTGGAGAGTTCA
1 AATCACGCACAACACCAAAGTGATTAGTGAAAAGTTCA
1670907 AATCA
1 AATCA
1670912 TGCTCATCGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (38 bp):
AATCACGCACAACACCAAAGTGATTAGTGAAAAGTTCA
Found at i:1672414 original size:20 final size:20
Alignment explanation
Indices: 1672367--1672463 Score: 151
Period size: 20 Copynumber: 4.8 Consensus size: 20
1672357 TTCTTACCAT
*
1672367 AAATGTATCGATACATTTCATG
1 AAATGTATCGATACA--TGATG
1672389 -AATGTATCGATACATGATG
1 AAATGTATCGATACATGATG
1672408 AAATGTATCGATACATGATG
1 AAATGTATCGATACATGATG
1672428 AAATGTATCGATACATGATG
1 AAATGTATCGATACATGATG
*
1672448 AAATGTATCAATACAT
1 AAATGTATCGATACAT
1672464 TTCCTCCAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
19 4 0.06
20 54 0.75
21 14 0.19
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.32
Consensus pattern (20 bp):
AAATGTATCGATACATGATG
Found at i:1672813 original size:2 final size:2
Alignment explanation
Indices: 1672808--1672856 Score: 73
Period size: 2 Copynumber: 24.5 Consensus size: 2
1672798 CATATATGTA
*
1672808 TG TG TG TC TG TG TG TG -G ATG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG -TG TG TG TG TG TG TG TG TG TG TG TG
1672850 TG TG TG T
1 TG TG TG T
1672857 ATTATTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 1 0.02
2 41 0.95
3 1 0.02
ACGTcount: A:0.02, C:0.02, G:0.47, T:0.49
Consensus pattern (2 bp):
TG
Found at i:1675560 original size:28 final size:28
Alignment explanation
Indices: 1675493--1675560 Score: 66
Period size: 32 Copynumber: 2.3 Consensus size: 28
1675483 TATGGCACTG
*
1675493 TCAC-TTTAGCAAGCAATGTTAACGTCA
1 TCACATTTAGCAAGCAACGTTAACGTCA
* *
1675520 TCGTATTACTTTAGCATGCAACGTTAACGTCA
1 TC--A-CA-TTTAGCAAGCAACGTTAACGTCA
1675552 TCACATTTA
1 TCACATTTA
1675561 ATGGTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
27 2 0.06
28 4 0.12
29 2 0.06
30 1 0.03
32 23 0.72
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (28 bp):
TCACATTTAGCAAGCAACGTTAACGTCA
Found at i:1676291 original size:28 final size:28
Alignment explanation
Indices: 1676248--1676304 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
1676238 ATCGAATTAA
*
1676248 TTCAATTATTTGTAAAATTTGA-TTCGAT
1 TTCAATTATTTGT-AAATATGATTTCGAT
* *
1676276 TTCAGTTATTTTTAAATATGATTTCGAT
1 TTCAATTATTTGTAAATATGATTTCGAT
1676304 T
1 T
1676305 ATTAGATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.53
Consensus pattern (28 bp):
TTCAATTATTTGTAAATATGATTTCGAT
Found at i:1677160 original size:12 final size:12
Alignment explanation
Indices: 1677143--1677168 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1677133 TGATTAGAAT
1677143 GAAGGCTACAAA
1 GAAGGCTACAAA
1677155 GAAGGCTACAAA
1 GAAGGCTACAAA
1677167 GA
1 GA
1677169 GCAGCGAGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.27, T:0.08
Consensus pattern (12 bp):
GAAGGCTACAAA
Found at i:1679255 original size:18 final size:20
Alignment explanation
Indices: 1679228--1679266 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
1679218 TCTCAAAGAA
1679228 CTTGTAAGCAA-AG-TCCAC
1 CTTGTAAGCAACAGTTCCAC
*
1679246 CTTGTCAGCAACAGTTCCAC
1 CTTGTAAGCAACAGTTCCAC
1679266 C
1 C
1679267 ATTGACTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 2 0.11
20 6 0.33
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.23
Consensus pattern (20 bp):
CTTGTAAGCAACAGTTCCAC
Found at i:1689412 original size:53 final size:54
Alignment explanation
Indices: 1689274--1689412 Score: 163
Period size: 53 Copynumber: 2.5 Consensus size: 54
1689264 ACCATAATGA
* * * * *
1689274 TGTCGCATTCACTTCAAGGAATGCACGGATTTATAATTTTTTTATTAGTATCTCGTT
1 TGTCGCATTCACTTCAAGGAATGAAC--ATTCATAA-TCTTTTATTAGTAACTCATT
** *
1689331 TGTCATATTCACTTCAAGGAATAAACATTCATAA-CTTTTATTAGTAACTCATT
1 TGTCGCATTCACTTCAAGGAATGAACATTCATAATCTTTTATTAGTAACTCATT
*
1689384 TGTCGCATTCACTTCAAGGAATGGACATT
1 TGTCGCATTCACTTCAAGGAATGAACATT
1689413 TATGGTTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 41 0.59
55 7 0.10
57 22 0.31
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (54 bp):
TGTCGCATTCACTTCAAGGAATGAACATTCATAATCTTTTATTAGTAACTCATT
Found at i:1718369 original size:30 final size:30
Alignment explanation
Indices: 1718335--1718440 Score: 108
Period size: 30 Copynumber: 3.6 Consensus size: 30
1718325 AATAATTAGT
* *
1718335 TATAAGAGTTTATTTGATTTAAAATAAAAA
1 TATAAGAATTTATTTAATTTAAAATAAAAA
*
1718365 TATAATAATTTATTTAATTTAAAATAAAAA
1 TATAAGAATTTATTTAATTTAAAATAAAAA
* * **
1718395 TATAAAAATTTGATTGAACGT--AATAAAAA
1 TATAAGAATTT-ATTTAATTTAAAATAAAAA
* *
1718424 TATAAAAACTTATTTAA
1 TATAAGAATTTATTTAA
1718441 ATTTTTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
28 5 0.08
29 18 0.27
30 37 0.56
31 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.39
Consensus pattern (30 bp):
TATAAGAATTTATTTAATTTAAAATAAAAA
Found at i:1719979 original size:14 final size:13
Alignment explanation
Indices: 1719907--1720007 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 13
1719897 ATATAATGTT
*
1719907 TATAAAATAATTA
1 TATAAAAAAATTA
**
1719920 TATTAAAAATTTTA
1 TA-TAAAAAAATTA
1719934 TATTTAATAAAAA-TA
1 TA--TAA-AAAAATTA
*
1719949 TA-AAACAAATTA
1 TATAAAAAAATTA
*
1719961 GATAAAAAAATTCA
1 TATAAAAAAATT-A
1719975 TAT--AAAAATTA
1 TATAAAAAAATTA
*
1719986 TATAAATAAATT-
1 TATAAAAAAATTA
1719998 T-TAAAAAAAT
1 TATAAAAAAAT
1720008 CTTTATTATT
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
11 16 0.23
12 13 0.19
13 16 0.23
14 13 0.19
15 8 0.12
16 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (13 bp):
TATAAAAAAATTA
Found at i:1719981 original size:13 final size:12
Alignment explanation
Indices: 1719885--1720007 Score: 56
Period size: 12 Copynumber: 9.8 Consensus size: 12
1719875 ATATTTAAAA
*
1719885 ATAAAAAATTAA
1 ATAAAAAATTAT
* **
1719897 ATATAATGTT-T
1 ATAAAAAATTAT
1719908 ATAAAATAATTAT
1 ATAAAA-AATTAT
*
1719921 ATTAAAAATTTTAT
1 A-TAAAAA-ATTAT
*
1719935 ATTTAATAAAAATAT
1 A--TAA-AAAATTAT
*
1719950 A-AAACAAATTAG
1 ATAAA-AAATTAT
1719962 ATAAAAAAATTCAT
1 AT-AAAAAATT-AT
1719976 AT-AAAAATTAT
1 ATAAAAAATTAT
*
1719987 ATAAATAAATTTT
1 ATAAA-AAATTAT
1720000 A-AAAAAAT
1 ATAAAAAAT
1720008 CTTTATTATT
Statistics
Matches: 85, Mismatches: 14, Indels: 25
0.69 0.11 0.20
Matches are distributed among these distances:
11 14 0.16
12 29 0.34
13 15 0.18
14 16 0.19
15 8 0.09
16 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (12 bp):
ATAAAAAATTAT
Found at i:1720497 original size:14 final size:15
Alignment explanation
Indices: 1720463--1720495 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1720453 TATTAAATAA
*
1720463 AAAAAT-TTAAAATT
1 AAAAATATTAAAAGT
1720477 AAAAATATTAAAAGT
1 AAAAATATTAAAAGT
1720492 AAAA
1 AAAA
1720496 TAAAGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AAAAATATTAAAAGT
Found at i:1726546 original size:2 final size:2
Alignment explanation
Indices: 1726539--1726576 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1726529 TTTGAGCCAT
1726539 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1726577 GTAACACCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1727463 original size:21 final size:19
Alignment explanation
Indices: 1727439--1727478 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
1727429 AAAGTTATAA
1727439 TATTTGAAAAAACTTCTAAAT
1 TATTT-AAAAAACTT-TAAAT
*
1727460 TATTTAAAAAAGTTTAAAT
1 TATTTAAAAAACTTTAAAT
1727479 AGGTTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 8 0.44
21 5 0.28
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (19 bp):
TATTTAAAAAACTTTAAAT
Found at i:1727477 original size:19 final size:19
Alignment explanation
Indices: 1727415--1727478 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
1727405 GAGGTGAATG
*
1727415 TAAATATATGTAAAAAAG-T
1 TAAAT-TATTTAAAAAAGTT
*
1727434 TATAA-TATTTGAAAAAACTT
1 TA-AATTATTT-AAAAAAGTT
1727454 CTAAATTATTTAAAAAAGTT
1 -TAAATTATTTAAAAAAGTT
1727474 TAAAT
1 TAAAT
1727479 AGGTTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 4 0.11
19 13 0.35
20 13 0.35
21 7 0.19
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.38
Consensus pattern (19 bp):
TAAATTATTTAAAAAAGTT
Found at i:1732695 original size:21 final size:21
Alignment explanation
Indices: 1732669--1732712 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1732659 TTTTTCTCGA
*
1732669 AATGTATCGATATATTATTTC
1 AATGTATCGATACATTATTTC
*
1732690 AATGTATCGATACATTTTTTC
1 AATGTATCGATACATTATTTC
1732711 AA
1 AA
1732713 AATTAGGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (21 bp):
AATGTATCGATACATTATTTC
Found at i:1732780 original size:47 final size:46
Alignment explanation
Indices: 1732711--1732807 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 46
1732701 ACATTTTTTC
1732711 AAAATTAGGATAGATGTATCAATACATCAAGAGGAAAGGCAAAAAAT
1 AAAATTAGGATAGATGTATCAATACATCAAGAGGAAAGGC-AAAAAT
1732758 AAAATTAGGATAGATGTATCAATACATCAAGAGGAAAGGCAAAAAT
1 AAAATTAGGATAGATGTATCAATACATCAAGAGGAAAGGCAAAAAT
1732804 AAAA
1 AAAA
1732808 AAAAGTTCAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 10 0.20
47 40 0.80
ACGTcount: A:0.55, C:0.08, G:0.19, T:0.19
Consensus pattern (46 bp):
AAAATTAGGATAGATGTATCAATACATCAAGAGGAAAGGCAAAAAT
Found at i:1736131 original size:14 final size:14
Alignment explanation
Indices: 1736112--1736145 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1736102 ATTTTAAACT
1736112 AAATTATTATATCC
1 AAATTATTATATCC
*
1736126 AAATTATTATATCT
1 AAATTATTATATCC
1736140 AAATTA
1 AAATTA
1736146 AACTAACTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTATTATATCC
Found at i:1740603 original size:23 final size:21
Alignment explanation
Indices: 1740569--1740612 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
1740559 AATGATTATT
*
1740569 TATTTTATTTTAAAATATAAAA
1 TATTTTAATTTAAAAT-TAAAA
*
1740591 TATTTATAATTTATAATTAAAA
1 TATTT-TAATTTAAAATTAAAA
1740613 CTTTAGCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTTTAATTTAAAATTAAAA
Found at i:1744890 original size:6 final size:6
Alignment explanation
Indices: 1744879--1744903 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1744869 GCTTTGCTCT
1744879 CATTTC CATTTC CATTTC CATTTC C
1 CATTTC CATTTC CATTTC CATTTC C
1744904 TCTTGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.36, G:0.00, T:0.48
Consensus pattern (6 bp):
CATTTC
Found at i:1748109 original size:18 final size:18
Alignment explanation
Indices: 1748073--1748120 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 18
1748063 AAATTTATCA
*
1748073 TATAGTATATTAATAAG-
1 TATACTATATTAATAAGT
1748090 T-TACTATATTAATGTAAGT
1 TATACTATATTAA--TAAGT
1748109 TATACTATATTA
1 TATACTATATTA
1748121 CCATAGCATA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 4 0.15
19 1 0.04
20 10 0.38
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (18 bp):
TATACTATATTAATAAGT
Found at i:1754600 original size:4 final size:4
Alignment explanation
Indices: 1754591--1754616 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1754581 CTCTTCCTTA
1754591 CTGT CTGT CTGT CTGT CTGT CTGT CT
1 CTGT CTGT CTGT CTGT CTGT CTGT CT
1754617 CTCTTCTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.27, G:0.23, T:0.50
Consensus pattern (4 bp):
CTGT
Found at i:1771101 original size:28 final size:28
Alignment explanation
Indices: 1771068--1771170 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 28
1771058 TGTTTGAATT
* *
1771068 ATTATTATATGCCATATTAGAAAAAAAA
1 ATTATTACATGCTATATTAGAAAAAAAA
* * *
1771096 ATTATTACATACTATGTTTG-AAAAAAA
1 ATTATTACATGCTATATTAGAAAAAAAA
* *
1771123 ATTGTTACATG---T-TGA-AAAAAAAA
1 ATTATTACATGCTATATTAGAAAAAAAA
*
1771146 ATTATTATATGCTATATT-GAAAAAA
1 ATTATTACATGCTATATTAGAAAAAA
1771171 TATTACAGTC
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
23 17 0.30
24 1 0.02
26 1 0.02
27 23 0.40
28 15 0.26
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (28 bp):
ATTATTACATGCTATATTAGAAAAAAAA
Found at i:1772020 original size:9 final size:9
Alignment explanation
Indices: 1772002--1772034 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1771992 TTTTTTTGAA
*
1772002 ATATTTTAT
1 ATATTATAT
1772011 ATATTATAT
1 ATATTATAT
1772020 ATA-TATAT
1 ATATTATAT
1772028 ATATTAT
1 ATATTAT
1772035 TGAAGTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATATTATAT
Found at i:1775854 original size:15 final size:15
Alignment explanation
Indices: 1775836--1775875 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1775826 AATGATAATT
1775836 AATTAAATAAAATAA
1 AATTAAATAAAATAA
*
1775851 AATTAAATATAATAA
1 AATTAAATAAAATAA
1775866 AA--AAATAAAA
1 AATTAAATAAAA
1775876 AATTATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 7 0.30
15 16 0.70
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AATTAAATAAAATAA
Found at i:1787521 original size:45 final size:45
Alignment explanation
Indices: 1787459--1787644 Score: 246
Period size: 45 Copynumber: 4.1 Consensus size: 45
1787449 GAAAGAAGTT
** * *
1787459 GAAGAAGTATTAAAGGAAGAGATGGTTCAAAGGAAGGAAGCTGAA
1 GAAGAAGTATGGAAGGAAGAGATGGTTGAAAGGAAAGAAGCTGAA
* *
1787504 GAAGAAGTATGGAAGGAAGAGATGTTTGAAAGGAAAGAAGCTGAG
1 GAAGAAGTATGGAAGGAAGAGATGGTTGAAAGGAAAGAAGCTGAA
* * * *
1787549 GAAGAAGTACGGAAGAAAGAGATGGTTGTAAGGAAAGAAGTTGAA
1 GAAGAAGTATGGAAGGAAGAGATGGTTGAAAGGAAAGAAGCTGAA
* * * *
1787594 GAAGAAGTATGGAGGGAAGAGGTGGTTGAAGGGAAAGAAGTTGAA
1 GAAGAAGTATGGAAGGAAGAGATGGTTGAAAGGAAAGAAGCTGAA
1787639 GAAGAA
1 GAAGAA
1787645 CCAAAGGAAG
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 123 1.00
ACGTcount: A:0.45, C:0.02, G:0.38, T:0.15
Consensus pattern (45 bp):
GAAGAAGTATGGAAGGAAGAGATGGTTGAAAGGAAAGAAGCTGAA
Found at i:1787666 original size:42 final size:42
Alignment explanation
Indices: 1787213--1787665 Score: 370
Period size: 42 Copynumber: 10.6 Consensus size: 42
1787203 TAAAGAGGAG
* * *
1787213 GTACCAAGGGAAGAGGTGGTTGAAAGGAAGGAAGCTGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTTGAAGAA
* * * * ** *
1787255 GTACTAATGGAACAGGCGACTGAAAGGAAGGAAGTTGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTTGAAGAA
* * *
1787297 GTACCAACGGAAGAGGTGGTTCAAAGG-AAGAAAGTTGAAGAC
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAG-AAGTTGAAGAA
* * *
1787339 GTACCAATGAAAGAGGTGGCTGAAAGGAAAGAAGTTGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTTGAAGAA
*
1787381 GTACCAATGGAAGAGGTGGTT-AAAGGGAAAGAAGTTGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAA-GGAAAGAAGTTGAAGAA
* * ** **
1787423 GTACTAATGGAAGAGGTACTCCAAAGGAAAGAAGTTGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTTGAAGAA
** * * * *
1787465 GTATTAAAGGAAGAGATGGTTCAAAGGAAGGAAGCTGAAGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAG-T--TGAAGAA
*** * * *
1787510 GTATGGAAGGAAGAGATGTTTGAAAGGAAAGAAGCTGAGGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAG-T--TGAAGAA
** * * *
1787555 GTACGGAAGAAAGAGATGGTTGTAAGGAAAGAAGTTGAAGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTT---GAAGAA
*** * *
1787600 GTATGGAGGGAAGAGGTGGTTGAAGGGAAAGAAGTTGAAGAA
1 GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTTGAAGAA
* *
1787642 GAACCAAAGGAAGATGTGGTTGAA
1 GTACCAAAGGAAGAGGTGGTTGAA
1787666 GTACAAGAGG
Statistics
Matches: 343, Mismatches: 58, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.01
42 219 0.64
43 7 0.02
44 1 0.00
45 111 0.32
ACGTcount: A:0.43, C:0.06, G:0.36, T:0.15
Consensus pattern (42 bp):
GTACCAAAGGAAGAGGTGGTTGAAAGGAAAGAAGTTGAAGAA
Found at i:1788254 original size:165 final size:165
Alignment explanation
Indices: 1787943--1788255 Score: 384
Period size: 165 Copynumber: 1.9 Consensus size: 165
1787933 GAAGAGGTAA
* *
1787943 CAAATGTAGAATTGGTTGAAAAGAAGGAACCTGAAAAGGTACCAAGGCCAGAGCTTGTCGAAAAG
1 CAAAGGTAGAATTGGTTGAAAAGAAGGAACCTGAAAAGATACCAAGGCCAGAGCTTGTCGAAAAG
* * * * * * *
1788008 AAGAAACCTCAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAGAAGAAACCTCAAGAAGTACCCAA
66 AAGAAACCTCAAGAGCTACCAAAGGTAAAGCTTGTTGAAAAGAAAAAACCTAAAGAAGAACCAAA
*
1788073 GATAGAGCTTGTTGAAAATAAACTTGGACAGATAC
131 GATAGAGATTGTTGAAAATAAACTTGGACAGATAC
* * * * * *
1788108 CAAAGGTAGAATTGGTTGAAGAGGAGGAACTTGATAAGATACCAAAGG-TAGAGCTTGTTGAAAA
1 CAAAGGTAGAATTGGTTGAAAAGAAGGAACCTGAAAAGATACC-AAGGCCAGAGCTTGTCGAAAA
* *
1788172 G-AGAAAACCTCGAGAGCTACCAAAGGTAAAGCTTGTTGAAAA-AAAACAACCTAAAGAGGAACC
65 GAAG-AAACCTCAAGAGCTACCAAAGGTAAAGCTTGTTGAAAAGAAAA-AACCTAAAGAAGAACC
1788235 AAA-AGTAGA-ATTGGTTGAAAA
128 AAAGA-TAGAGATT-GTTGAAAA
1788256 GAAGGGACTT
Statistics
Matches: 125, Mismatches: 18, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
164 8 0.06
165 113 0.90
166 4 0.03
ACGTcount: A:0.44, C:0.13, G:0.25, T:0.18
Consensus pattern (165 bp):
CAAAGGTAGAATTGGTTGAAAAGAAGGAACCTGAAAAGATACCAAGGCCAGAGCTTGTCGAAAAG
AAGAAACCTCAAGAGCTACCAAAGGTAAAGCTTGTTGAAAAGAAAAAACCTAAAGAAGAACCAAA
GATAGAGATTGTTGAAAATAAACTTGGACAGATAC
Found at i:1788405 original size:42 final size:42
Alignment explanation
Indices: 1787705--1788412 Score: 487
Period size: 42 Copynumber: 16.9 Consensus size: 42
1787695 AGTAGAAGTG
* *
1787705 GTTGAAGAAAAAGAAGC-TGAAGTGGTACC-AAGTGTAGAGCTT
1 GTTGAA-AAAAAGAAACTTGAAGAGGTACCAAAG-GTAGAGCTT
* * *
1787747 GTTGAAAAAAAGAAACCTCAAGAGGTACCAAGGGTAGAGCTT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * ** * *
1787789 GTTGAAAAAAATAAAATTGAAGAGGTAATAAAGGCAGA-ATT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * *
1787830 GGTT-AAAAAAAAAGAACTTGAAAACGTACCAAGGGCAGAGCTT
1 -GTTGAAAAAAAGA-AACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * * *
1787873 GTTGAAAAGAAGAAACCTAAAGAGGTACTAAGGGTAGCGCTT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * * *
1787915 ATTGAAAAGAAGAAACATGAAGAGGTAACAAATGTAGA-ATT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * *
1787956 GGTTGAAAAGAAGGAACCTGAAAAGGTACC-AAGGCCAGAGCTT
1 -GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGG-TAGAGCTT
* * * * *
1787999 GTCGAAAAGAAGAAACCTCAAGAGGTACCAAGGGTAGAGCTT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * * *
1788041 GTTGAAAAGAAGAAACCTCAAGAAGTACCCAAGATAGAGCTT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * *
1788083 GTTG---AAAATAAACTTGGACAGATACCAAAGGTAGA-ATT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* ** * *
1788121 GGTTGAAGAGGAGGAACTTGATA-AGATACCAAAGGTAGAGCTT
1 -GTTGAAAAAAAGAAACTTGA-AGAGGTACCAAAGGTAGAGCTT
* * * *
1788164 GTTGAAAAGAGAA-AACCTCG-AGAGCTACCAAAGGTAAAGCTT
1 GTTGAAAA-A-AAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * *
1788206 GTTGAAAAAAA-ACAACCTAAAGAGGAACCAAAAGTAGA-ATT
1 GTTGAAAAAAAGA-AACTTGAAGAGGTACCAAAGGTAGAGCTT
* ** * *
1788247 GGTTGAAAAGAAGGGACTTGAAAAGGTACCAACGGTAGAGCTT
1 -GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* * * * *
1788290 GTTGAAAAAAAGAAACCTAAAGAGGTACCAAGGGAAGA-ATT
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
*
1788331 GGTTGAAAAGAAAG-AACTTGAAAAGGTACCAAAGGTAGAGCTT
1 -GTTGAAAA-AAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
* *
1788374 ATTGAAAAAAAGAAACTTGAAGTGGTACCAAAGGTAGAG
1 GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAG
1788413 TTAGATGAAA
Statistics
Matches: 518, Mismatches: 120, Indels: 56
0.75 0.17 0.08
Matches are distributed among these distances:
38 2 0.00
39 25 0.05
40 3 0.01
41 36 0.07
42 420 0.81
43 31 0.06
44 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.18
Consensus pattern (42 bp):
GTTGAAAAAAAGAAACTTGAAGAGGTACCAAAGGTAGAGCTT
Found at i:1788422 original size:126 final size:125
Alignment explanation
Indices: 1787689--1788439 Score: 553
Period size: 126 Copynumber: 6.0 Consensus size: 125
1787679 TTGAAAAAGG
* * * **
1787689 ACCAAGAGTAGAAGTGGTTGAAGAAAAAGAAGC-TGAAGTGGTACC-AAGTGTAGAGCTTGTTGA
1 ACCAAGGGAAGAATTGGTTGAA-AAAAAGAA-CTTGAAAAGGTACCAAAG-GTAGAGCTTGTTGA
* * * ** *
1787752 AAAAAAGAAACCTCAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAATAAAATTGAAGAGGT
63 AAAGAAGAAACCTGAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAAGAAACCTAAAGAGGT
** * * * * * *
1787815 AATAAAGGCAGAATTGGTTAAAAAAAAAGAACTTGAAAACGTACCAAGGGCAGAGCTTGTTGAAA
1 ACCAAGGGAAGAATTGGTT-GAAAAAAAGAACTTGAAAAGGTACCAAAGGTAGAGCTTGTTGAAA
* * * * * * *
1787880 AGAAGAAACCTAAAGAGGTACTAAGGGTAGCGCTTATTGAAAAGAAGAAACATGAAGAGGT
65 AGAAGAAACCTGAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAAGAAACCTAAAGAGGT
* ** * * * * *
1787941 AACAAATGTAGAATTGGTTGAAAAGAAGGAACCTGAAAAGGTACC-AAGGCCAGAGCTTGTCGAA
1 ACCAAGGGAAGAATTGGTTGAAAA-AAAGAACTTGAAAAGGTACCAAAGG-TAGAGCTTGTTGAA
* * * *
1788005 AAGAAGAAACCTCAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAGAAGAAACCTCAAGAAGT
64 AAGAAGAAACCTGAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAAGAAACCTAAAGAGGT
* * * * * *
1788067 ACCCAA--GATAGAGCTT-GTTG-AAAATA-AACTTGGACAGATACCAAAGGTAGA-ATTGGTTG
1 A-CCAAGGGA-AGA-ATTGGTTGAAAAAAAGAACTTGAAAAGGTACCAAAGGTAGAGCTT-GTTG
* * * * * * * ** *
1788126 AAGAGGAGGAACTTGATA-AGATACCAAAGGTAGAGCTTGTTG-AAAAGAGAAAACCTCGAGAGC
62 AAAAGAAGAAACCTGA-AGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAAG-AAACCTAAAGAGG
1788189 T
125 T
* * * * * * *
1788190 ACCAAAGGTAA-AGCTT-GTTGAAAAAAAACAACCT-AAAGAGGAACCAAAAGTAGA-ATTGGTT
1 ACC-AAGGGAAGA-ATTGGTTG-AAAAAAAGAACTTGAAA-AGGTACCAAAGGTAGAGCTT-GTT
** * * *
1788251 GAAAAGAAGGGACTTGAAAAGGTACCAACGGTAGAGCTTGTTGAAAAAAAGAAACCTAAAGAGGT
61 GAAAAGAAGAAACCTGAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAAGAAACCTAAAGAGGT
*
1788316 ACCAAGGGAAGAATTGGTTGAAAAGAAAGAACTTGAAAAGGTACCAAAGGTAGAGCTTATTGAAA
1 ACCAAGGGAAGAATTGGTTGAAAA-AAAGAACTTGAAAAGGTACCAAAGGTAGAGCTTGTTGAAA
* * * * * * *
1788381 AAAAGAAACTTGAAGTGGTACCAAAGGTAGAG-TTAGATGAAAACAAGGAACCTAAAGAG
65 AGAAGAAACCTGAAGAGGTACCAAGGGTAGAGCTT-GTTGAAAAAAAGAAACCTAAAGAG
1788440 ATAGCAAAAG
Statistics
Matches: 503, Mismatches: 95, Indels: 54
0.77 0.15 0.08
Matches are distributed among these distances:
122 9 0.02
123 74 0.15
124 7 0.01
125 34 0.07
126 359 0.71
127 20 0.04
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.18
Consensus pattern (125 bp):
ACCAAGGGAAGAATTGGTTGAAAAAAAGAACTTGAAAAGGTACCAAAGGTAGAGCTTGTTGAAAA
GAAGAAACCTGAAGAGGTACCAAGGGTAGAGCTTGTTGAAAAAAAGAAACCTAAAGAGGT
Found at i:1796374 original size:2 final size:2
Alignment explanation
Indices: 1796367--1796398 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1796357 CAGCTTATTA
1796367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1796399 TCATATTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1800444 original size:24 final size:24
Alignment explanation
Indices: 1800394--1800441 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1800384 GCCTGGCAGC
* *
1800394 AGACCAAGACCTTGAAACGCTCCA
1 AGACAAAGACCTTGAAACGCCCCA
*
1800418 AGACAAAGACC-TGAAATGCCCCA
1 AGACAAAGACCTTGAAACGCCCCA
1800441 A
1 A
1800442 AGAACGATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.42, C:0.31, G:0.17, T:0.10
Consensus pattern (24 bp):
AGACAAAGACCTTGAAACGCCCCA
Found at i:1811103 original size:6 final size:6
Alignment explanation
Indices: 1811094--1811128 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
1811084 AAATGAAACA
* *
1811094 AGTATT AGTATT AGAATT AGTATT AATATT AGTAT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTAT
1811129 AGGGATCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (6 bp):
AGTATT
Found at i:1812326 original size:22 final size:21
Alignment explanation
Indices: 1812301--1812348 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
1812291 ATTCATTCCT
*
1812301 TTAAA-TATTTCATATTTAAATA
1 TTAAATTATTT-AT-TTTAAAAA
1812323 TTAAAATTATTTATTTTAAAAA
1 TT-AAATTATTTATTTTAAAAA
1812345 TTAA
1 TTAA
1812349 TAAACCCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 2 0.09
22 11 0.48
23 5 0.22
24 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TTAAATTATTTATTTTAAAAA
Found at i:1825758 original size:24 final size:23
Alignment explanation
Indices: 1825727--1825773 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
1825717 TTAGATGATT
1825727 TTATTTTGTAAATGTT-AATTTTA
1 TTATTTTGT-AATGTTAAATTTTA
*
1825750 TTATCTTTGTTATGTTAAATTTTA
1 TTAT-TTTGTAATGTTAAATTTTA
1825774 AATGTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.28, C:0.02, G:0.09, T:0.62
Consensus pattern (23 bp):
TTATTTTGTAATGTTAAATTTTA
Found at i:1829157 original size:3 final size:3
Alignment explanation
Indices: 1829149--1829174 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1829139 CACGGACACG
1829149 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
1829175 CGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1829749 original size:19 final size:19
Alignment explanation
Indices: 1829725--1829775 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1829715 ATACTCTCCC
1829725 TCAGAATGCTCATGAATAT
1 TCAGAATGCTCATGAATAT
1829744 TCAGAATGCTCATGAATAT
1 TCAGAATGCTCATGAATAT
*
1829763 TCAAAATGCTCAT
1 TCAGAATGCTCAT
1829776 CTTGCTTAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (19 bp):
TCAGAATGCTCATGAATAT
Found at i:1832037 original size:2 final size:2
Alignment explanation
Indices: 1832030--1832087 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1832020 ATGTGTACAC
1832030 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1832072 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1832088 ATGAAGAGGT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1837341 original size:27 final size:27
Alignment explanation
Indices: 1837311--1837374 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
1837301 AGCGCCTAAT
* *
1837311 GGTGTTTCAAATACAGAAATACCTAGG
1 GGTGTTCCAAATACAGAAACACCTAGG
* * *
1837338 GGTGTTCCAAGTGCAGAAGCACCTAGG
1 GGTGTTCCAAATACAGAAACACCTAGG
*
1837365 GGCGTTCCAA
1 GGTGTTCCAA
1837375 GCGTAGAAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (27 bp):
GGTGTTCCAAATACAGAAACACCTAGG
Found at i:1837375 original size:27 final size:27
Alignment explanation
Indices: 1837331--1837387 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1837321 ATACAGAAAT
* *
1837331 ACCTAGGGGTGTTCCAAGTGCAGAAGC
1 ACCTAGGGGCGTTCCAAGCGCAGAAGC
*
1837358 ACCTAGGGGCGTTCCAAGCGTAGAAGC
1 ACCTAGGGGCGTTCCAAGCGCAGAAGC
1837385 ACC
1 ACC
1837388 CAAAGCACGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.32, T:0.16
Consensus pattern (27 bp):
ACCTAGGGGCGTTCCAAGCGCAGAAGC
Found at i:1838543 original size:52 final size:52
Alignment explanation
Indices: 1838483--1838731 Score: 284
Period size: 52 Copynumber: 4.8 Consensus size: 52
1838473 CGCTATTAGT
* *
1838483 CGCAAGCTTTATCGTTCATTTCTTGGCCATAGTTTGCTATTCACATATTAGC
1 CGCAAGCTTTATCGTTCACTTCTTGGCCATAGTTTGCTATTCACATATTGGC
* * * *
1838535 CGCAAGCTTTATCGCTCACTTTTTAGCCATAGTTTGCTATTCACATATCGGC
1 CGCAAGCTTTATCGTTCACTTCTTGGCCATAGTTTGCTATTCACATATTGGC
* * * * * * *
1838587 TGCAAGCTTTATCACTT-ACTTCTTAGTCATAGTTTGCTATTCATAAATTGGT
1 CGCAAGCTTTATC-GTTCACTTCTTGGCCATAGTTTGCTATTCACATATTGGC
** ** * *
1838639 CATAAGCTTTATCGTTCACTTCTTGGTTATAGCTTGCTATTCACAAATTGGC
1 CGCAAGCTTTATCGTTCACTTCTTGGCCATAGTTTGCTATTCACATATTGGC
* * *
1838691 CGCAAGCTTTATTGCTCACTTCTTGGCCATAGTTTGTTATT
1 CGCAAGCTTTATCGTTCACTTCTTGGCCATAGTTTGCTATT
1838732 TACAGAAAGG
Statistics
Matches: 163, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
51 2 0.01
52 160 0.98
53 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (52 bp):
CGCAAGCTTTATCGTTCACTTCTTGGCCATAGTTTGCTATTCACATATTGGC
Found at i:1839853 original size:33 final size:33
Alignment explanation
Indices: 1839750--1839854 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 33
1839740 AATGGCATTA
* * * *
1839750 ACATCATCACCACCAACTCCACTAGTAGCACCC
1 ACATCATCACCACCAACTCTAGTAGCAGCATCC
* * * * **
1839783 ATATCGTCATCACCAACTCTAGTAGCAACATTG
1 ACATCATCACCACCAACTCTAGTAGCAGCATCC
*
1839816 ACATCATCACCACCAACTCTAGTAGCAGCGTCC
1 ACATCATCACCACCAACTCTAGTAGCAGCATCC
1839849 ACATCA
1 ACATCA
1839855 CCATCATTAA
Statistics
Matches: 55, Mismatches: 17, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.33, C:0.37, G:0.10, T:0.20
Consensus pattern (33 bp):
ACATCATCACCACCAACTCTAGTAGCAGCATCC
Found at i:1843151 original size:2 final size:2
Alignment explanation
Indices: 1843144--1843174 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1843134 AGAGATAGAA
1843144 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
1843175 AACGTATTAT
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:1848039 original size:2 final size:2
Alignment explanation
Indices: 1848034--1848064 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1848024 ATATATATAT
*
1848034 AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1848065 TTGAATGACG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1853027 original size:29 final size:28
Alignment explanation
Indices: 1852980--1853122 Score: 171
Period size: 29 Copynumber: 5.0 Consensus size: 28
1852970 TGGCAACTTT
1852980 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAA
1853008 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
1853037 AATATGTTTGTCTTAATTTAAAACAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
1853067 AATATTTTTTATCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
*
1853096 AACATATTTGT-TTCAATTTAGACAAGA
1 AACATGTTTGTCTT-AATTTAGACAAGA
1853123 TAAAATATTT
Statistics
Matches: 100, Mismatches: 10, Indels: 10
0.83 0.08 0.08
Matches are distributed among these distances:
27 2 0.02
28 36 0.36
29 38 0.38
30 12 0.12
31 12 0.12
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:1853095 original size:59 final size:58
Alignment explanation
Indices: 1852980--1853142 Score: 206
Period size: 59 Copynumber: 2.8 Consensus size: 58
1852970 TGGCAACTTT
* * ** *
1852980 AACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
* *
1853037 AATATGTTTGTCTTAATTTAAAACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
1 AACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
*
1853096 AACATATTTGT-TTCAATTTAGACAAGATAAAATA-TTTTTATCTTAAT
1 AACATGTTTGTCTT-AATTTAGACAAGA-AAAATATTTTTTATCTTAAT
1853143 TAAAGATAAG
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
57 18 0.20
58 28 0.30
59 46 0.50
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTATCTTAATCTAGACAAGAA
Found at i:1853122 original size:28 final size:28
Alignment explanation
Indices: 1852980--1853132 Score: 159
Period size: 28 Copynumber: 5.3 Consensus size: 28
1852970 TGGCAACTTT
*
1852980 AACATGTTTGTCTTAATTTAGACAAGAA
1 AACATATTTGTCTTAATTTAGACAAGAA
*
1853008 AACATGTTTGGTCTTAATTTAGACAAGAA
1 AACATATTT-GTCTTAATTTAGACAAGAA
* * *
1853037 AATATGTTTGTCTTAATTTAAAACAAGAA
1 AACATATTTGTCTTAATTT-AGACAAGAA
* *
1853066 AA-ATATTTTTTATCTTAATCTAGACAAGAA
1 AACATA---TTTGTCTTAATTTAGACAAGAA
1853096 AACATATTTGT-TTCAATTTAGACAAGATA
1 AACATATTTGTCTT-AATTTAGACAAGA-A
1853125 AA-ATATTT
1 AACATATTT
1853133 TTATCTTAAT
Statistics
Matches: 109, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.02
28 43 0.39
29 40 0.37
30 10 0.09
31 14 0.13
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (28 bp):
AACATATTTGTCTTAATTTAGACAAGAA
Found at i:1854312 original size:4 final size:4
Alignment explanation
Indices: 1854295--1854341 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
1854285 GCTAATGAGA
*
1854295 AGAT AGAG AGAT AGAT AGAT AGAT AGAT -GAAT AGAT AGAT AGAT AGA
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AG-AT AGAT AGAT AGAT AGA
1854342 GAGAGAAGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 1 0.03
4 37 0.95
5 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (4 bp):
AGAT
Found at i:1857707 original size:21 final size:22
Alignment explanation
Indices: 1857678--1857721 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1857668 AAGTGATTAA
1857678 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
1857699 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
1857721 T
1 T
1857722 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:1858386 original size:12 final size:11
Alignment explanation
Indices: 1858371--1858414 Score: 63
Period size: 12 Copynumber: 3.9 Consensus size: 11
1858361 GAGATTTTTT
1858371 GAGGCAGCAAGA
1 GAGGCAGCAA-A
1858383 GAGGCAG-AAA
1 GAGGCAGCAAA
1858393 GAGGCAGCAAA
1 GAGGCAGCAAA
1858404 GGAGGCAGCAA
1 -GAGGCAGCAA
1858415 GAAACTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.27
11 5 0.17
12 17 0.57
ACGTcount: A:0.43, C:0.16, G:0.41, T:0.00
Consensus pattern (11 bp):
GAGGCAGCAAA
Found at i:1858396 original size:22 final size:22
Alignment explanation
Indices: 1858371--1858416 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1858361 GAGATTTTTT
1858371 GAGGCAGC-AAGAGAGGCAGAAA
1 GAGGCAGCAAAG-GAGGCAGAAA
*
1858393 GAGGCAGCAAAGGAGGCAGCAA
1 GAGGCAGCAAAGGAGGCAGAAA
1858415 GA
1 GA
1858417 AACTATTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.43, C:0.15, G:0.41, T:0.00
Consensus pattern (22 bp):
GAGGCAGCAAAGGAGGCAGAAA
Found at i:1861952 original size:107 final size:107
Alignment explanation
Indices: 1861823--1862031 Score: 303
Period size: 107 Copynumber: 2.0 Consensus size: 107
1861813 GTCGATTGGG
* * * * *
1861823 AAAAAAAACTATAAATCTACTAAGAAAGACAAATGAAATCAAAT-ATAAAAACCTAAAGCAATAT
1 AAAAAAAACTAAAAACCCACTAAGAAAAACAAAAGAAATCAAATGAT-AAAACCTAAAGCAATAT
* * * *
1861887 ATAAAAGAGCAGAACTTGTAAAGAAATATAGTAAAATTATGGA
65 ACAAAAGAGCACAACATGTAAAAAAATATAGTAAAATTATGGA
*
1861930 AAAAAAAACTAAAAACCCACTAAGAAAAACAAAAGAAATCAAATGCTAAAACCTAAAGCAATATA
1 AAAAAAAACTAAAAACCCACTAAGAAAAACAAAAGAAATCAAATGATAAAACCTAAAGCAATATA
*
1861995 CAAAAGAGCACAACATGTAAAAAAATATAGTGAAATT
66 CAAAAGAGCACAACATGTAAAAAAATATAGTAAAATT
1862032 CATCAGAAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
107 89 0.99
108 1 0.01
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.18
Consensus pattern (107 bp):
AAAAAAAACTAAAAACCCACTAAGAAAAACAAAAGAAATCAAATGATAAAACCTAAAGCAATATA
CAAAAGAGCACAACATGTAAAAAAATATAGTAAAATTATGGA
Found at i:1867366 original size:21 final size:22
Alignment explanation
Indices: 1867331--1867374 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
1867321 CTCTTAAAGT
1867331 AATTTAAAATAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
*
1867353 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACTTAA
1867374 A
1 A
1867375 TTAATCACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (22 bp):
AATTTAAAATAAAATAACTTAA
Found at i:1870941 original size:30 final size:29
Alignment explanation
Indices: 1870903--1870959 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1870893 TATTATATAG
1870903 AGTTATTTTGCCATA-TTTTTATGTTTTCA
1 AGTTATTTTG-CATAGTTTTTATGTTTTCA
*
1870932 AGTTGATTTTGTATAGTTTTTATGTTTT
1 AGTT-ATTTTGCATAGTTTTTATGTTTT
1870960 TCGTCATTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.61
Consensus pattern (29 bp):
AGTTATTTTGCATAGTTTTTATGTTTTCA
Found at i:1884064 original size:77 final size:77
Alignment explanation
Indices: 1883941--1884097 Score: 314
Period size: 77 Copynumber: 2.0 Consensus size: 77
1883931 TCAATCAATA
1883941 ATTTTGATTTTTTGCCTATTGCTTTGGTAGGTACGTGATTTGTTCTTTGCTAGTAGTTTTGCCCT
1 ATTTTGATTTTTTGCCTATTGCTTTGGTAGGTACGTGATTTGTTCTTTGCTAGTAGTTTTGCCCT
1884006 AAGCATGATTTG
66 AAGCATGATTTG
1884018 ATTTTGATTTTTTGCCTATTGCTTTGGTAGGTACGTGATTTGTTCTTTGCTAGTAGTTTTGCCCT
1 ATTTTGATTTTTTGCCTATTGCTTTGGTAGGTACGTGATTTGTTCTTTGCTAGTAGTTTTGCCCT
1884083 AAGCATGATTTG
66 AAGCATGATTTG
1884095 ATT
1 ATT
1884098 CTCTATTGAT
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 80 1.00
ACGTcount: A:0.16, C:0.13, G:0.22, T:0.50
Consensus pattern (77 bp):
ATTTTGATTTTTTGCCTATTGCTTTGGTAGGTACGTGATTTGTTCTTTGCTAGTAGTTTTGCCCT
AAGCATGATTTG
Found at i:1887600 original size:20 final size:20
Alignment explanation
Indices: 1887575--1887612 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1887565 ATCTGATGTT
1887575 GTTACATAACAATTGACACA
1 GTTACATAACAATTGACACA
*
1887595 GTTACATAGCAATTGACA
1 GTTACATAACAATTGACA
1887613 TGATCACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (20 bp):
GTTACATAACAATTGACACA
Found at i:1896904 original size:28 final size:28
Alignment explanation
Indices: 1896864--1896919 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1896854 GCTACAATCC
*
1896864 ACTTATTAGATTTCCTTGTATCAAGCAA
1 ACTTATTAGATTTCCTCGTATCAAGCAA
1896892 ACTTATTAGATTTCCTCGTATCAAGCAA
1 ACTTATTAGATTTCCTCGTATCAAGCAA
1896920 GGGATCTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (28 bp):
ACTTATTAGATTTCCTCGTATCAAGCAA
Found at i:1899996 original size:2 final size:2
Alignment explanation
Indices: 1899989--1900015 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1899979 AGCTTAAAGC
1899989 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1900016 GTATCTAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1902513 original size:16 final size:16
Alignment explanation
Indices: 1902492--1902525 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1902482 AGACAGAGAC
1902492 GATCAGGGGGTGTCCG
1 GATCAGGGGGTGTCCG
1902508 GATCAGGGGGTGTCCG
1 GATCAGGGGGTGTCCG
1902524 GA
1 GA
1902526 GTTCTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.18, G:0.50, T:0.18
Consensus pattern (16 bp):
GATCAGGGGGTGTCCG
Found at i:1912749 original size:2 final size:2
Alignment explanation
Indices: 1912742--1912777 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1912732 ATCTCAGTAC
1912742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1912778 CTTGCCTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1915040 original size:28 final size:28
Alignment explanation
Indices: 1915009--1915063 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
1914999 ATATTACAAA
1915009 CAAATAAATTACACCAAACATAAATAAG
1 CAAATAAATTACACCAAACATAAATAAG
* * *
1915037 CAAATACATTACATCAAATATAAATAA
1 CAAATAAATTACACCAAACATAAATAA
1915064 AATTTCAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.60, C:0.16, G:0.02, T:0.22
Consensus pattern (28 bp):
CAAATAAATTACACCAAACATAAATAAG
Found at i:1918124 original size:30 final size:30
Alignment explanation
Indices: 1918090--1918149 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1918080 GATCTGCGGT
* * *
1918090 AAAACAGAACGGAGAAGGTGCGGGTGCGAC
1 AAAACAAAACGGAGAAGGTACGAGTGCGAC
*
1918120 AAAACAAAATGGAGAAGGTACGAGTGCGAC
1 AAAACAAAACGGAGAAGGTACGAGTGCGAC
1918150 GGTGCGATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.35, T:0.08
Consensus pattern (30 bp):
AAAACAAAACGGAGAAGGTACGAGTGCGAC
Found at i:1918170 original size:45 final size:43
Alignment explanation
Indices: 1918120--1918242 Score: 120
Period size: 35 Copynumber: 3.0 Consensus size: 43
1918110 CGGGTGCGAC
1918120 AAAACAAAATGGAGAAGGTACGAGTGCGACGGTGCGATCTGCGGT
1 AAAACAAAATGGAGAAGGT-CG-GTGCGACGGTGCGATCTGCGGT
*
1918165 AAAACAGAAA-GGAGAA--T--GTGC-A-GGTGCGA-CGGC-GT
1 AAAACA-AAATGGAGAAGGTCGGTGCGACGGTGCGATCTGCGGT
*
1918200 AAAACAGAATGGAGAAGGTGCTGGTGCGACGGTGCGATCTGCG
1 AAAACAAAATGGAGAAGGT-C-GGTGCGACGGTGCGATCTGCG
1918243 ACAAACAGAA
Statistics
Matches: 63, Mismatches: 3, Indels: 24
0.70 0.03 0.27
Matches are distributed among these distances:
34 2 0.03
35 14 0.22
36 3 0.05
37 8 0.13
38 1 0.02
39 4 0.06
41 4 0.06
42 1 0.02
43 8 0.13
44 3 0.05
45 12 0.19
46 3 0.05
ACGTcount: A:0.33, C:0.15, G:0.37, T:0.15
Consensus pattern (43 bp):
AAAACAAAATGGAGAAGGTCGGTGCGACGGTGCGATCTGCGGT
Found at i:1918241 original size:80 final size:75
Alignment explanation
Indices: 1918044--1918242 Score: 256
Period size: 75 Copynumber: 2.6 Consensus size: 75
1918034 CGATCAGCTG
* * * * *
1918044 CAAAACAAAACGGAGAAGGTACGAGTGTGGCAGTGCGATCTGCGGTAAAACAGAACGGAGAAGGT
1 CAAAACAAAATGGAGAAGGTACGAGTGCGACGGTGCGATCTGCGGTAAAACAGAAAGGAGAAGGT
*
1918109 GCGGGTGCGA
66 GCAGGTGCGA
*
1918119 CAAAACAAAATGGAGAAGGTACGAGTGCGACGGTGCGATCTGCGGTAAAACAGAAAGGAGAATGT
1 CAAAACAAAATGGAGAAGGTACGAGTGCGACGGTGCGATCTGCGGTAAAACAGAAAGGAGAAGGT
1918184 GCAGGTGCGA
66 GCAGGTGCGA
* *
1918194 CGGCGTAAAACAGAATGGAGAAGGTGCTG-GTGCGACGGTGCGATCTGCG
1 ---C--AAAACAAAATGGAGAAGGTAC-GAGTGCGACGGTGCGATCTGCG
1918243 ACAAACAGAA
Statistics
Matches: 109, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
75 68 0.62
78 1 0.01
80 39 0.36
81 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.37, T:0.14
Consensus pattern (75 bp):
CAAAACAAAATGGAGAAGGTACGAGTGCGACGGTGCGATCTGCGGTAAAACAGAAAGGAGAAGGT
GCAGGTGCGA
Found at i:1919786 original size:33 final size:32
Alignment explanation
Indices: 1919744--1919818 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1919734 TTGATGATAG
*
1919744 AAAATATTTTCAACGAGGTGATCTAAATAATAA
1 AAAATATTTTCAA-GAAGTGATCTAAATAATAA
* * * * *
1919777 AAAATATTTTTAATAATTTATTTAAATAATAA
1 AAAATATTTTCAAGAAGTGATCTAAATAATAA
1919809 AAAATATTTT
1 AAAATATTTT
1919819 ATGCAAAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 24 0.67
33 12 0.33
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.40
Consensus pattern (32 bp):
AAAATATTTTCAAGAAGTGATCTAAATAATAA
Found at i:1920828 original size:28 final size:30
Alignment explanation
Indices: 1920769--1920838 Score: 99
Period size: 28 Copynumber: 2.4 Consensus size: 30
1920759 TACATTTAAT
*
1920769 TAAACCCTTATACTTTTATTTTGAGTCAAA
1 TAAACCTTTATACTTTTATTTTGAGTCAAA
* *
1920799 TAAACTTTTATA-TTTT-TTTTGAGTCTAA
1 TAAACCTTTATACTTTTATTTTGAGTCAAA
1920827 TAAACCTTTATA
1 TAAACCTTTATA
1920839 ATTAATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 22 0.61
29 4 0.11
30 10 0.28
ACGTcount: A:0.33, C:0.13, G:0.06, T:0.49
Consensus pattern (30 bp):
TAAACCTTTATACTTTTATTTTGAGTCAAA
Found at i:1920954 original size:19 final size:19
Alignment explanation
Indices: 1920930--1920966 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1920920 TTAAAAATAA
* *
1920930 ATGAAAAATATTTTTAAAT
1 ATGAAAAAAATTCTTAAAT
1920949 ATGAAAAAAATTCTTAAA
1 ATGAAAAAAATTCTTAAA
1920967 GAAGTGTTAA
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:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (19 bp):
ATGAAAAAAATTCTTAAAT
Found at i:1927292 original size:24 final size:24
Alignment explanation
Indices: 1927265--1927314 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1927255 AAGTGGCACG
1927265 TTGGCCAAGCTTAACCTTGTGGTA
1 TTGGCCAAGCTTAACCTTGTGGTA
1927289 TTGGCCAAGCTTAACCTTGTGGTA
1 TTGGCCAAGCTTAACCTTGTGGTA
1927313 TT
1 TT
1927315 CTTACCCCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (24 bp):
TTGGCCAAGCTTAACCTTGTGGTA
Found at i:1931415 original size:2 final size:2
Alignment explanation
Indices: 1931402--1931514 Score: 172
Period size: 2 Copynumber: 56.5 Consensus size: 2
1931392 ACAGTCAAAG
* * *
1931402 AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1931444 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1931486 AT AT AT AT AC AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1931515 GGGGCGGAGC
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1931604 original size:13 final size:14
Alignment explanation
Indices: 1931588--1931620 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1931578 ATTTTTTTGT
1931588 TAATTTTTTA-AAA
1 TAATTTTTTATAAA
1931601 TAATTTTTTATTAAA
1 TAATTTTTTA-TAAA
1931616 TAATT
1 TAATT
1931621 AATATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
15 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATTTTTTATAAA
Found at i:1933406 original size:20 final size:19
Alignment explanation
Indices: 1933379--1933425 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1933369 ACTTGAATAA
*
1933379 AAAT-CTTTTTACTCCCTTT
1 AAATACTTTTT-CTCCCTCT
*
1933398 AAATACTTTTTTTCCCTCT
1 AAATACTTTTTCTCCCTCT
1933417 AAATACTTT
1 AAATACTTT
1933426 CTTTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.26, C:0.23, G:0.00, T:0.51
Consensus pattern (19 bp):
AAATACTTTTTCTCCCTCT
Found at i:1934121 original size:18 final size:18
Alignment explanation
Indices: 1934068--1934123 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
1934058 ATGGATGCTT
* *
1934068 ATAATCCACCAGAAGTGG
1 ATAACCCACCAAAAGTGG
* * *
1934086 ATAACCCATCATATGTGG
1 ATAACCCACCAAAAGTGG
*
1934104 ATCACCCACCAAAAGTGG
1 ATAACCCACCAAAAGTGG
1934122 AT
1 AT
1934124 GTGTACTTGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (18 bp):
ATAACCCACCAAAAGTGG
Found at i:1937992 original size:20 final size:19
Alignment explanation
Indices: 1937967--1938004 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
1937957 ATCTTCTTAC
1937967 TCCCTCTAAATACTTTTTTT
1 TCCCTCTAAATA-TTTTTTT
1937987 TCCCTCTAAATATTTTTT
1 TCCCTCTAAATATTTTTT
1938005 CTTATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (19 bp):
TCCCTCTAAATATTTTTTT
Found at i:1938839 original size:14 final size:15
Alignment explanation
Indices: 1938810--1938853 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
1938800 TTTTAATTGT
*
1938810 AAATTATAAAAATTA
1 AAATTTTAAAAATTA
* *
1938825 ATA-TTTAAAATTTA
1 AAATTTTAAAAATTA
1938839 AAATTTTAAAAATTA
1 AAATTTTAAAAATTA
1938854 TTAAGATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTTAAAAATTA
Found at i:1939413 original size:30 final size:30
Alignment explanation
Indices: 1939344--1939416 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
1939334 ACCTTTTAAC
*
1939344 ACACTACCTTTTCTTGAGGAAGTATAACCTT
1 ACACTACCTTTTCTT-AGGAAGTATAACCTA
* ** *
1939375 TCTTTACCTTTTC-TATGGAGGTATAACCTA
1 ACACTACCTTTTCTTA-GGAAGTATAACCTA
1939405 ACACTACCTTTT
1 ACACTACCTTTT
1939417 ACAATGGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
29 1 0.03
30 22 0.67
31 10 0.30
ACGTcount: A:0.26, C:0.23, G:0.11, T:0.40
Consensus pattern (30 bp):
ACACTACCTTTTCTTAGGAAGTATAACCTA
Found at i:1940026 original size:73 final size:73
Alignment explanation
Indices: 1939898--1940096 Score: 218
Period size: 73 Copynumber: 2.7 Consensus size: 73
1939888 TATCTTGAGA
* * * *
1939898 CTTTCTATTTTCTGAGAATCTATCTTTCCATTCTTGAGATATCAATTCTTCTTGTCTCACTTGAA
1 CTTTTTATTTTTTGAGAATCGATCTTTCCATTCTTGAGATATCAATTCTTCTTGTCTCACTTCAA
1939963 GGTTGAAG
66 GGTTGAAG
* * * ** *
1939971 CTTTTTATTTTTTGATAATCGATTTTTTCATTCTTGAGATATTGATTCTTTTTGTCTCACTTCAA
1 CTTTTTATTTTTTGAGAATCGATCTTTCCATTCTTGAGATATCAATTCTTCTTGTCTCACTTCAA
* *
1940036 GTTTGGAG
66 GGTTGAAG
* ** * * ** *
1940044 CCTTTTGGTTTTTGAGAATCGATCTTTGCAATCTTGAGGCATCGATTCTTCTT
1 CTTTTTATTTTTTGAGAATCGATCTTTCCATTCTTGAGATATCAATTCTTCTT
1940097 ATCTTGCTTT
Statistics
Matches: 103, Mismatches: 23, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
73 103 1.00
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.49
Consensus pattern (73 bp):
CTTTTTATTTTTTGAGAATCGATCTTTCCATTCTTGAGATATCAATTCTTCTTGTCTCACTTCAA
GGTTGAAG
Found at i:1950713 original size:25 final size:25
Alignment explanation
Indices: 1950664--1950719 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
1950654 CGGTCTGTGA
* * *
1950664 TTATATGTGGCAAGGACATGGGTTG
1 TTATACGTGGCAAGGACACGAGTTG
*
1950689 TTATACGTGGCAAGGCCACGAGTTG
1 TTATACGTGGCAAGGACACGAGTTG
*
1950714 ATATAC
1 TTATAC
1950720 ATGGTTACGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (25 bp):
TTATACGTGGCAAGGACACGAGTTG
Found at i:1958486 original size:17 final size:17
Alignment explanation
Indices: 1958466--1958502 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1958456 TTTTTGTAGG
*
1958466 GCACATATTTAGGGGGA
1 GCACATATTTAGGAGGA
*
1958483 GCACATGTTTAGGAGGA
1 GCACATATTTAGGAGGA
1958500 GCA
1 GCA
1958503 ATCCCTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.22
Consensus pattern (17 bp):
GCACATATTTAGGAGGA
Found at i:1969283 original size:21 final size:21
Alignment explanation
Indices: 1969248--1969297 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1969238 AGAATGGGGT
* *
1969248 TTTAATTAGTTATAATCATGG
1 TTTAATTGGCTATAATCATGG
*
1969269 TTTCATTGGCTATAATCATGG
1 TTTAATTGGCTATAATCATGG
1969290 TTTAATTG
1 TTTAATTG
1969298 ATTAAAGTGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTAATTGGCTATAATCATGG
Found at i:1976943 original size:14 final size:14
Alignment explanation
Indices: 1976924--1976963 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
1976914 TTGTACAACC
1976924 TTGGTGAAAGCTGT
1 TTGGTGAAAGCTGT
1976938 TTGGTGAAAGCTGT
1 TTGGTGAAAGCTGT
* *
1976952 TTAGTGGAAGCT
1 TTGGTGAAAGCT
1976964 CACCCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.07, G:0.35, T:0.35
Consensus pattern (14 bp):
TTGGTGAAAGCTGT
Found at i:1979256 original size:27 final size:26
Alignment explanation
Indices: 1979206--1979262 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1979196 TCTCTTTTGA
1979206 ATTTCATTTTTCTTATATTACTTGTCT
1 ATTTCATTTTTCTTATATTACTTGT-T
* *
1979233 ATTTCATTTTTCATT-TTTTTCTTGTT
1 ATTTCATTTTTC-TTATATTACTTGTT
1979259 ATTT
1 ATTT
1979263 TTGGAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 5 0.19
27 20 0.74
28 2 0.07
ACGTcount: A:0.16, C:0.12, G:0.04, T:0.68
Consensus pattern (26 bp):
ATTTCATTTTTCTTATATTACTTGTT
Found at i:1981896 original size:18 final size:18
Alignment explanation
Indices: 1981867--1981901 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1981857 GTTCAAAATT
1981867 TCAAACCAATCCTAACAAG
1 TCAAACCAATCC-AACAAG
1981886 TCAAA-CAATCCAACAA
1 TCAAACCAATCCAACAA
1981902 ATAGTAGCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 6 0.38
19 5 0.31
ACGTcount: A:0.51, C:0.31, G:0.03, T:0.14
Consensus pattern (18 bp):
TCAAACCAATCCAACAAG
Found at i:1982022 original size:16 final size:17
Alignment explanation
Indices: 1981996--1982030 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1981986 TTTGATTATG
*
1981996 TATATTTAGATTTAGAT
1 TATATTTAGATTAAGAT
1982013 TATA-TTAGATTAAGAT
1 TATATTTAGATTAAGAT
1982029 TA
1 TA
1982031 GGCTTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (17 bp):
TATATTTAGATTAAGAT
Found at i:1983403 original size:43 final size:43
Alignment explanation
Indices: 1983355--1983439 Score: 170
Period size: 43 Copynumber: 2.0 Consensus size: 43
1983345 AGCAATTTAA
1983355 CCTATTGAAATAAGTTGAGGATGAGAGTTAAGATTGAGATGAT
1 CCTATTGAAATAAGTTGAGGATGAGAGTTAAGATTGAGATGAT
1983398 CCTATTGAAATAAGTTGAGGATGAGAGTTAAGATTGAGATGA
1 CCTATTGAAATAAGTTGAGGATGAGAGTTAAGATTGAGATGA
1983440 AGTGTGAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.29
Consensus pattern (43 bp):
CCTATTGAAATAAGTTGAGGATGAGAGTTAAGATTGAGATGAT
Found at i:1989284 original size:18 final size:18
Alignment explanation
Indices: 1989258--1989293 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1989248 GTCTAGGTAG
* *
1989258 GCCATGCAGCCTAAGCAA
1 GCCAAGCAGCCCAAGCAA
1989276 GCCAAGCAGCCCAAGCAA
1 GCCAAGCAGCCCAAGCAA
1989294 CCTAGGCGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.36, G:0.22, T:0.06
Consensus pattern (18 bp):
GCCAAGCAGCCCAAGCAA
Found at i:1989408 original size:21 final size:20
Alignment explanation
Indices: 1989361--1989408 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
1989351 TGAACTTTTG
* *
1989361 GATTTGATTATATACATTTA
1 GATTAGATTATATACATTAA
*
1989381 GATTTAGATTATATTATATTAA
1 GA-TTAGATTATA-TACATTAA
1989403 GATTAG
1 GATTAG
1989409 GATTTGGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 2 0.09
21 13 0.57
22 8 0.35
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (20 bp):
GATTAGATTATATACATTAA
Found at i:1989480 original size:13 final size:13
Alignment explanation
Indices: 1989464--1989496 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
1989454 CATTATCTCT
1989464 ATCTTATAACTTA
1 ATCTTATAACTTA
1989477 ATCTTATAACTTA
1 ATCTTATAACTTA
1989490 ATCTTAT
1 ATCTTAT
1989497 TTAACAAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
ATCTTATAACTTA
Found at i:1991807 original size:15 final size:16
Alignment explanation
Indices: 1991776--1991808 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1991766 AACATATCAC
1991776 ATCATCATATTACATT
1 ATCATCATATTACATT
*
1991792 ATCATC-TATTATATT
1 ATCATCATATTACATT
1991807 AT
1 AT
1991809 ATTAATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (16 bp):
ATCATCATATTACATT
Found at i:1991920 original size:30 final size:30
Alignment explanation
Indices: 1991879--1991935 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1991869 CTATTAGTTA
1991879 TAAAAATTTATTTGAATTAAAATAAAAGTG
1 TAAAAATTTATTTGAATTAAAATAAAAGTG
* *
1991909 TAAAGATTTATTTGATTTAAAATAAAA
1 TAAAAATTTATTTGAATTAAAATAAAA
1991936 ATATATTAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.39
Consensus pattern (30 bp):
TAAAAATTTATTTGAATTAAAATAAAAGTG
Found at i:2000060 original size:20 final size:20
Alignment explanation
Indices: 2000037--2000077 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
2000027 CCACCGAAAG
2000037 AAAAACCCCTGTTGTTACCT
1 AAAAACCCCTGTTGTTACCT
2000057 AAAAACCCCTGTTGTTACCT
1 AAAAACCCCTGTTGTTACCT
2000077 A
1 A
2000078 TCTTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
AAAAACCCCTGTTGTTACCT
Found at i:2001019 original size:24 final size:24
Alignment explanation
Indices: 2000987--2001085 Score: 99
Period size: 24 Copynumber: 3.8 Consensus size: 24
2000977 TGTTACATGT
*
2000987 CACGTCATGTATAAAAATATGTTA
1 CACGTCATGTAAAAAAATATGTTA
*
2001011 CACATCATGTTAAAAAAAATATTATTGTTA
1 CACGTCATG-T--AAAAAA-A-TA-TGTTA
*
2001041 CACGTCATGTAAAAAAACATGTTA
1 CACGTCATGTAAAAAAATATGTTA
2001065 CACGTCATGTTAAAATAAATA
1 CACGTCATG-TAAAA-AAATA
2001086 CTATTGTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
24 22 0.35
25 7 0.11
26 5 0.08
27 11 0.18
28 1 0.02
29 3 0.05
30 13 0.21
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (24 bp):
CACGTCATGTAAAAAAATATGTTA
Found at i:2001057 original size:54 final size:54
Alignment explanation
Indices: 2000987--2001143 Score: 206
Period size: 54 Copynumber: 2.9 Consensus size: 54
2000977 TGTTACATGT
* * * *
2000987 CACGTCATGTATAAAAATATGTTACACATCATGTTAAAAAAAATATTATTGTTA
1 CACGTCATGTAAAAAAACATGTTACACGTCATGTTAAAAAAAATACTATTGTTA
*
2001041 CACGTCATGTAAAAAAACATGTTACACGTCATGTTAAAATAAATACTATTGTTA
1 CACGTCATGTAAAAAAACATGTTACACGTCATGTTAAAAAAAATACTATTGTTA
* ** * *
2001095 TACACCATGTACAAAAACATGTTACACGCCATGTTGAAAAACAAATACT
1 CACGTCATGTAAAAAAACATGTTACACGTCATGTT-AAAAA-AAATACT
2001144 GTTATAACAT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 79 0.88
55 4 0.04
56 7 0.08
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (54 bp):
CACGTCATGTAAAAAAACATGTTACACGTCATGTTAAAAAAAATACTATTGTTA
Done.