Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold247
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: 4737410
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 10 of 29
Found at i:1314468 original size:38 final size:39
Alignment explanation
Indices: 1314418--1314530 Score: 119
Period size: 38 Copynumber: 2.9 Consensus size: 39
1314408 TGATATAAAA
1314418 ATAAT-TAAATATAATATAATATA-AAAATATTAT-GAAT
1 ATAATATAAATATAATATAATATATAAAAT-TTATAGAAT
*
1314455 ATAATATAAATATAA-A-AATATATTAAAATTTATATAAT
1 ATAATATAAATATAATATAATATA-TAAAATTTATAGAAT
* *
1314493 ATCATATATATATATATATTAATATATTAAAATTTATA
1 ATAATATAAATATA-ATA-TAATATA-TAAAATTTATA
1314531 TAAATATATA
Statistics
Matches: 65, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
36 6 0.09
37 10 0.15
38 29 0.45
39 1 0.02
40 1 0.02
42 18 0.28
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (39 bp):
ATAATATAAATATAATATAATATATAAAATTTATAGAAT
Found at i:1314475 original size:28 final size:25
Alignment explanation
Indices: 1314404--1314475 Score: 99
Period size: 26 Copynumber: 2.7 Consensus size: 25
1314394 TTTTATAAAA
*
1314404 AATATGATATAAAAATAATTAAATAT
1 AATATAATATAAAAAT-ATTAAATAT
1314430 AATATAATATAAAAATATTATGAATAT
1 AATATAATATAAAAATATTA--AATAT
1314457 AATATAAATATAAAAATAT
1 AATAT-AATATAAAAATAT
1314476 ATTAAAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 4 0.10
26 15 0.36
27 10 0.24
28 13 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (25 bp):
AATATAATATAAAAATATTAAATAT
Found at i:1314489 original size:14 final size:14
Alignment explanation
Indices: 1314472--1314532 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
1314462 AAATATAAAA
1314472 ATATATTAAAATTT
1 ATATATTAAAATTT
* ** *
1314486 ATATAATATCATAT
1 ATATATTAAAATTT
* *
1314500 ATATA-TATATATTA
1 ATATATTA-AAATTT
1314514 ATATATTAAAATTT
1 ATATATTAAAATTT
1314528 ATATA
1 ATATA
1314533 AATATATAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
13 2 0.06
14 31 0.89
15 2 0.06
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:1314493 original size:27 final size:27
Alignment explanation
Indices: 1314404--1314494 Score: 98
Period size: 28 Copynumber: 3.4 Consensus size: 27
1314394 TTTTATAAAA
*
1314404 AATATGATATAAAAATA-ATT-AAATAT
1 AATATAATATAAAAATATATTAAAAT-T
* *
1314430 AATATAATATAAAAATATTATGAATA-T
1 AATATAATATAAAAATA-TATTAAAATT
1314457 AATATAAATATAAAAATATATTAAAATT
1 AATAT-AATATAAAAATATATTAAAATT
*
1314485 TATATAATAT
1 AATATAATAT
1314495 CATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
26 16 0.30
27 17 0.31
28 19 0.35
29 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (27 bp):
AATATAATATAAAAATATATTAAAATT
Found at i:1314500 original size:12 final size:11
Alignment explanation
Indices: 1314425--1314540 Score: 73
Period size: 11 Copynumber: 10.7 Consensus size: 11
1314415 AAAATAATTA
1314425 AATATA-ATAT
1 AATATATATAT
* *
1314435 AATATAAAAAT
1 AATATATATAT
*
1314446 ATTATGA-ATAT
1 AATAT-ATATAT
*
1314457 AATATAAATAT
1 AATATATATAT
*
1314468 AA-AAATATATT
1 AATATATATA-T
* *
1314479 AAAATTTATAT
1 AATATATATAT
1314490 AATATCATATAT
1 AATAT-ATATAT
1314502 -ATATATATATT
1 AATATATATA-T
*
1314513 AATATAT-TAA
1 AATATATATAT
*
1314523 AATTTATATA-
1 AATATATATAT
1314533 AATATATA
1 AATATATA
1314541 ATATTTATAA
Statistics
Matches: 84, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
10 30 0.36
11 37 0.44
12 17 0.20
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (11 bp):
AATATATATAT
Found at i:1314517 original size:42 final size:40
Alignment explanation
Indices: 1314452--1314550 Score: 130
Period size: 42 Copynumber: 2.5 Consensus size: 40
1314442 AAATATTATG
*
1314452 AATATA-ATATAAATATAAAAATATATTAAAATTTATATA
1 AATATATATATATATATAAAAATATATTAAAATTTATATA
**
1314491 ATATCATATATATATATATATTAATATATTAAAATTTATATA
1 A-AT-ATATATATATATATAAAAATATATTAAAATTTATATA
*
1314533 AATATATA-ATATTTATAA
1 AATATATATATATATATAA
1314551 TTATAATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
39 9 0.17
40 7 0.13
41 5 0.10
42 31 0.60
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (40 bp):
AATATATATATATATATAAAAATATATTAAAATTTATATA
Found at i:1314537 original size:26 final size:26
Alignment explanation
Indices: 1314499--1314552 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 26
1314489 TAATATCATA
*
1314499 TATATATATATATTAATATATTAAAATT
1 TATATAAATATA-TAATAT-TTAAAATT
*
1314527 TATATAAATATATAATATTTATAATT
1 TATATAAATATATAATATTTAAAATT
1314553 ATAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 7 0.29
27 6 0.25
28 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATATAAATATATAATATTTAAAATT
Found at i:1315574 original size:24 final size:25
Alignment explanation
Indices: 1315547--1315596 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1315537 TTAGTGAAAA
1315547 ATTT-AAAATATTATAAAAAA-TGAT
1 ATTTCAAAA-ATTATAAAAAATTGAT
*
1315571 ATTTCAAAAATTTTAAAAAATTGAT
1 ATTTCAAAAATTATAAAAAATTGAT
1315596 A
1 A
1315597 AATCGAATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
ATTTCAAAAATTATAAAAAATTGAT
Found at i:1315766 original size:29 final size:29
Alignment explanation
Indices: 1315711--1315770 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
1315701 GTTAATTGTA
* *
1315711 TATTTTTTAAAATCAAATTAAAATATTAT
1 TATTTTTAAAAATCAAATCAAAATATTAT
* * *
1315740 TATTTTTAAAAATCGAATCGAATTATTAT
1 TATTTTTAAAAATCAAATCAAAATATTAT
1315769 TA
1 TA
1315771 CTCTAAGATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (29 bp):
TATTTTTAAAAATCAAATCAAAATATTAT
Found at i:1316424 original size:37 final size:36
Alignment explanation
Indices: 1316383--1316454 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 36
1316373 AAAATTAAAA
1316383 TATTTAAATATTT-T-TAATTTATTTTATATTATAATTT
1 TATTTAAATATTTATATAATTT-TTTTA-ATTA-AATTT
*
1316420 TATTTTAATATTTATATAATTTTTTTAATTAAATT
1 TATTTAAATATTTATATAATTTTTTTAATTAAATT
1316455 AACATTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 16 0.50
38 6 0.19
39 6 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (36 bp):
TATTTAAATATTTATATAATTTTTTTAATTAAATTT
Found at i:1317396 original size:13 final size:14
Alignment explanation
Indices: 1317380--1317408 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1317370 ATAATTATAG
1317380 AATATAAA-ATATT
1 AATATAAATATATT
1317393 AATATAAATATATT
1 AATATAAATATATT
1317407 AA
1 AA
1317409 AATTTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATAAATATATT
Found at i:1317427 original size:21 final size:22
Alignment explanation
Indices: 1317384--1317428 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1317374 TTATAGAATA
1317384 TAAAATATTAATATAAATATAT
1 TAAAATATTAATATAAATATAT
1317406 TAAAAT-TT-ATATAACATATAT
1 TAAAATATTAATATAA-ATATAT
1317427 TA
1 TA
1317429 TTAACGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 6 0.27
21 10 0.45
22 6 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAAATATTAATATAAATATAT
Found at i:1317471 original size:52 final size:52
Alignment explanation
Indices: 1317415--1317527 Score: 174
Period size: 52 Copynumber: 2.2 Consensus size: 52
1317405 TTAAAATTTA
* *
1317415 TATAACATATATTATTAACGTATCATATAATACATAACATAATAAATATAAT
1 TATAAAATATATTATTAACATATCATATAATACATAACATAATAAATATAAT
* *
1317467 TATAAAATTTATTATTAACATATCATATAATACATAACATAATAAATA-AGGT
1 TATAAAATATATTATTAACATATCATATAATACATAACATAATAAATATA-AT
1317519 TATAAAATA
1 TATAAAATA
1317528 AAAAATAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
51 1 0.02
52 54 0.98
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.36
Consensus pattern (52 bp):
TATAAAATATATTATTAACATATCATATAATACATAACATAATAAATATAAT
Found at i:1318806 original size:21 final size:21
Alignment explanation
Indices: 1318766--1318804 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1318756 ATTTCTAAGA
*
1318766 TATATTTAATATTAAATTTAT
1 TATAATTAATATTAAATTTAT
1318787 TATAATTAA-ATTAAATTT
1 TATAATTAATATTAAATTT
1318805 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATAATTAATATTAAATTTAT
Found at i:1323354 original size:2 final size:2
Alignment explanation
Indices: 1323347--1323392 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1323337 ATGCATAATT
*
1323347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1323389 TA TA
1 TA TA
1323393 AGTGGTTTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1324035 original size:20 final size:20
Alignment explanation
Indices: 1324002--1324041 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1323992 ACAAAGGTCA
1324002 AAACCCTAGAATGTATCGAT
1 AAACCCTAGAATGTATCGAT
*
1324022 AAACACCTAG-ATGTTTCGAT
1 AAAC-CCTAGAATGTATCGAT
1324042 GCGTATTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
AAACCCTAGAATGTATCGAT
Found at i:1324219 original size:13 final size:13
Alignment explanation
Indices: 1324201--1324242 Score: 75
Period size: 13 Copynumber: 3.2 Consensus size: 13
1324191 TTACTGTTCA
1324201 TGTATCGATACAG
1 TGTATCGATACAG
1324214 TGTATCGATACAG
1 TGTATCGATACAG
*
1324227 TGCATCGATACAG
1 TGTATCGATACAG
1324240 TGT
1 TGT
1324243 GAATAATATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1324361 original size:20 final size:20
Alignment explanation
Indices: 1324298--1324351 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1324288 TTCAAATGCA
1324298 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
1324318 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
1324338 TGTATCGATACATT
1 TGTATCGATACATT
1324352 GGAGCATGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTATGAAT
Found at i:1329046 original size:52 final size:51
Alignment explanation
Indices: 1328968--1329116 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
1328958 CGAAATATGA
1328968 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1329020 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
1329072 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1329117 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1329123 original size:13 final size:13
Alignment explanation
Indices: 1329105--1329129 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1329095 CAAAGATCAG
1329105 TGTATCGATACAA
1 TGTATCGATACAA
1329118 TGTATCGATACA
1 TGTATCGATACA
1329130 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1329197 original size:20 final size:20
Alignment explanation
Indices: 1329168--1329225 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1329158 GCAGTAGCTT
1329168 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1329187 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1329207 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1329226 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1329968 original size:21 final size:20
Alignment explanation
Indices: 1329922--1329976 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
1329912 ATTCTTGAAA
* * *
1329922 AGAAATTAAGTGAATTAGAT
1 AGAAAATAAATGAATTAGAG
1329942 ATGAAAATAAATGAATTAGAGG
1 A-GAAAATAAATGAATTAGA-G
*
1329964 AGAAAAGAAATGA
1 AGAAAATAAATGA
1329977 GTTGCAAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (20 bp):
AGAAAATAAATGAATTAGAG
Found at i:1333869 original size:52 final size:51
Alignment explanation
Indices: 1333779--1333948 Score: 187
Period size: 52 Copynumber: 3.3 Consensus size: 51
1333769 GAAATAACGA
* * ** * *
1333779 GGTTGGAGTATCCTCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCAG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTG-TTTTGGAAATAAAACCAG
* * *
1333831 AGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAGCCAG
1 GGTTGGAGTATCCCCGATT-AAGGAAAATTGGTGTTTTGGAAATAAAACCAG
** * * * *
1333883 GGTTGGAGTATCCCCGATTGTGGGAAATCGATGATTTGGAAATAAAACCAG
1 GGTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTTGGAAATAAAACCAG
1333934 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1333949 TCGGAGATAA
Statistics
Matches: 99, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
51 39 0.39
52 49 0.49
53 11 0.11
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTAAGGAAAATTGGTGTTTTGGAAATAAAACCAG
Found at i:1333945 original size:51 final size:52
Alignment explanation
Indices: 1333814--1333948 Score: 173
Period size: 51 Copynumber: 2.6 Consensus size: 52
1333804 AATTGGTGTT
* * * * *
1333814 TTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGT
1 TTTGGAAATAAAACCAGGGTTGGAGTATCCCCGATTAAAGGAAAATCGATGA
* * ** *
1333866 TTTGAAAATAAAGCCAGGGTTGGAGTATCCCCGATT-GTGGGAAATCGATGA
1 TTTGGAAATAAAACCAGGGTTGGAGTATCCCCGATTAAAGGAAAATCGATGA
1333917 TTTGGAAATAAAACCAGGGTTGGAGTATCCCC
1 TTTGGAAATAAAACCAGGGTTGGAGTATCCCC
1333949 TCGGAGATAA
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 39 0.55
52 32 0.45
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (52 bp):
TTTGGAAATAAAACCAGGGTTGGAGTATCCCCGATTAAAGGAAAATCGATGA
Found at i:1334047 original size:80 final size:79
Alignment explanation
Indices: 1333882--1334059 Score: 241
Period size: 80 Copynumber: 2.2 Consensus size: 79
1333872 AATAAAGCCA
* * * **
1333882 GGGTTGGAGTATCCCCGATTGTGGGAAATCGATGATTTGGAAATAAAACCAGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCCGATTATGAGAAATCAATGATTTAAAAATAAAACCAGGGTTGGAGTATCC
* *
1333947 CCTCGGAGATAACG
66 CCTCGAAAATAACG
* * *
1333961 GGGTTGGAGTATCCCCGATTATGAGAAATTAAT-ATTTTAAAAATAAAGCCGGGGGTTGGAGTAT
1 GGGTTGGAGTATCCCCGATTATGAGAAATCAATGA-TTTAAAAATAAAACC-AGGGTTGGAGTAT
1334025 CCCCTCGAAAATAACG
64 CCCCTCGAAAATAACG
1334041 GGGTTGGAGTATCCCCGAT
1 GGGTTGGAGTATCCCCGAT
1334060 GATTAACGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
78 1 0.01
79 41 0.47
80 45 0.52
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCGATTATGAGAAATCAATGATTTAAAAATAAAACCAGGGTTGGAGTATCC
CCTCGAAAATAACG
Found at i:1334074 original size:27 final size:27
Alignment explanation
Indices: 1334012--1334089 Score: 113
Period size: 27 Copynumber: 2.9 Consensus size: 27
1334002 AATAAAGCCG
*
1334012 GGGGTTGGAGTATCCCCTCGA-AAATAAC
1 GGGGTTGGAGTAT-CCC-CGATGAATAAC
*
1334040 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCGATGAATAAC
1334067 GGGGTTGGAGTATCCCCGATGAA
1 GGGGTTGGAGTATCCCCGATGAA
1334090 AAATTGATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.07
27 30 0.65
28 13 0.28
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.23
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCGATGAATAAC
Found at i:1334153 original size:51 final size:51
Alignment explanation
Indices: 1334089--1334186 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
1334079 TCCCCGATGA
1334089 AAAATTGATGTTTT-AGAAATAAAATCGGAGTTGA-AGTATCCCCGATTATAG
1 AAAATTGATGTTTTGA-AAATAAAATCGGAGTTGAGA-TATCCCCGATTATAG
* *
1334140 AAAATT-AGTGTTTTGAAAATGAAATCGGAGTTGGGATATCCCCGATT
1 AAAATTGA-TGTTTTGAAAATAAAATCGGAGTTGAGATATCCCCGATT
1334187 GCGGAGAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
50 1 0.02
51 39 0.93
52 2 0.05
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (51 bp):
AAAATTGATGTTTTGAAAATAAAATCGGAGTTGAGATATCCCCGATTATAG
Found at i:1336565 original size:13 final size:13
Alignment explanation
Indices: 1336547--1336572 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1336537 ACAAAGATCC
1336547 ATGTATCGATACA
1 ATGTATCGATACA
1336560 ATGTATCGATACA
1 ATGTATCGATACA
1336573 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1336568 original size:33 final size:33
Alignment explanation
Indices: 1336526--1336592 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1336516 AAAATTTCCA
***
1336526 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1336559 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1336592 A
1 A
1336593 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1336636 original size:19 final size:18
Alignment explanation
Indices: 1336612--1336679 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1336602 CAGTAGCTAA
1336612 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1336631 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1336646 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1336663 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1336680 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1336652 original size:13 final size:13
Alignment explanation
Indices: 1336634--1336658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1336624 ACAATACTTA
1336634 TGTATCGATACAT
1 TGTATCGATACAT
1336647 TGTATCGATACA
1 TGTATCGATACA
1336659 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1336656 original size:32 final size:32
Alignment explanation
Indices: 1336615--1336677 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1336605 TAGCTAATTA
*
1336615 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1336647 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1336678 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1337610 original size:13 final size:13
Alignment explanation
Indices: 1337588--1337638 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
1337578 TCACTGTTTA
1337588 TGTATCGATACAG
1 TGTATCGATACAG
*
1337601 TGTATTGATACAG
1 TGTATCGATACAG
*
1337614 TGCATCGATACAG
1 TGTATCGATACAG
1337627 TGTATCGATACA
1 TGTATCGATACA
1337639 ATGTGAATAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1337724 original size:20 final size:20
Alignment explanation
Indices: 1337699--1337752 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1337689 TTCAAGTACA
1337699 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
1337719 TGTATCGATACATTATGAAT
1 TGTATCGATACATTATGAAT
1337739 TGTATCGATACATT
1 TGTATCGATACATT
1337753 GGAGCGTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTATGAAT
Found at i:1348192 original size:33 final size:33
Alignment explanation
Indices: 1348133--1348228 Score: 106
Period size: 33 Copynumber: 2.9 Consensus size: 33
1348123 ATTTTGTGGT
* * *
1348133 GTATCAATACAAAG-AACATGTATCGATACAAC
1 GTATTAATACTAAGCAATATGTATCGATACAAC
* * *
1348165 GTA-TAGATACTAAGTAATATGTATCGATGCAAT
1 GTATTA-ATACTAAGCAATATGTATCGATACAAC
*
1348198 GTATTAATACTAAGCAATATGTATTGATACA
1 GTATTAATACTAAGCAATATGTATCGATACA
1348229 TCTGGGTGTG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
31 1 0.02
32 10 0.19
33 40 0.75
34 2 0.04
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (33 bp):
GTATTAATACTAAGCAATATGTATCGATACAAC
Found at i:1348363 original size:23 final size:24
Alignment explanation
Indices: 1348319--1348369 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
1348309 GTATTGATAC
1348319 TTTGAATTATTTTACTTGAAAAACA
1 TTTGAATTA-TTTACTTGAAAAACA
* *
1348344 TTTGAATTA-TTGCTTGAAAAATA
1 TTTGAATTATTTACTTGAAAAACA
1348367 TTT
1 TTT
1348370 AAACTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 15 0.62
25 9 0.38
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (24 bp):
TTTGAATTATTTACTTGAAAAACA
Found at i:1348377 original size:24 final size:23
Alignment explanation
Indices: 1348333--1348377 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
1348323 AATTATTTTA
*
1348333 CTTGAAAAACATTTGAATTATTG
1 CTTGAAAAACATTTAAATTATTG
*
1348356 CTTGAAAAATATTTAAACTTAT
1 CTTGAAAAACATTTAAA-TTAT
1348378 CTCTAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (23 bp):
CTTGAAAAACATTTAAATTATTG
Found at i:1356373 original size:19 final size:19
Alignment explanation
Indices: 1356349--1356387 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1356339 AAAGGTATAA
*
1356349 CCTTACAATACTATCTTTT
1 CCTTACAACACTATCTTTT
1356368 CCTTACAACACTATCTTTT
1 CCTTACAACACTATCTTTT
1356387 C
1 C
1356388 AAAGGCTAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.44
Consensus pattern (19 bp):
CCTTACAACACTATCTTTT
Found at i:1356430 original size:35 final size:34
Alignment explanation
Indices: 1356378--1356443 Score: 123
Period size: 35 Copynumber: 1.9 Consensus size: 34
1356368 CCTTACAACA
1356378 CTATCTTTTCAAAGGCTAAGATAGAACCTCTTTC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTTTC
1356412 CTATCTTTTACAAAGGCTAAGATAGAACCTCT
1 CTATCTTTT-CAAAGGCTAAGATAGAACCTCT
1356444 CAATCACTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.33
Consensus pattern (34 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTTTC
Found at i:1357126 original size:23 final size:22
Alignment explanation
Indices: 1357076--1357157 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 22
1357066 GTATCGATAC
* *
1357076 TTTGAATTATTTTACTTGAAAAACA
1 TTTGAATTA--TT-CTTTAAAAATA
1357101 TTTGAATTATTGCTTTAAAAATA
1 TTTGAATTATT-CTTTAAAAATA
* *
1357124 TTTAAAATTA-TCTATAAAACATA
1 TTT-GAATTATTCTTTAAAA-ATA
1357147 TTTGATATTAT
1 TTTGA-ATTAT
1357158 AAAATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
22 8 0.17
23 25 0.53
24 5 0.11
25 9 0.19
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (22 bp):
TTTGAATTATTCTTTAAAAATA
Found at i:1358335 original size:23 final size:24
Alignment explanation
Indices: 1358291--1358336 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1358281 ATATTTAATT
*
1358291 TTTAAAAATTAAATTAAAAATATA
1 TTTAAAAATTAAATAAAAAATATA
1358315 TTTAAAAA-TAAA-AAAATAATAT
1 TTTAAAAATTAAATAAAA-AATAT
1358337 GACAGGTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 9 0.45
24 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TTTAAAAATTAAATAAAAAATATA
Found at i:1359126 original size:762 final size:761
Alignment explanation
Indices: 1357803--1361601 Score: 5436
Period size: 754 Copynumber: 5.0 Consensus size: 761
1357793 TAGTCGGTGT
* * * * *
1357803 CACTTGACTCGTGAAACTAGCTCAGCCACT-CCTGTTATAAATAGTATAGATTACTAAAGTTACA
1 CACTTGACTCATGATACTAGCTCAGCCACTCCCT-TTATAATTAGTATAGATTAGTAAGGTTACA
** *
1357867 TTAGTAATCTAAATTTTTACTAAAAAAAAAAACCTACCTTTTTTCTATTTGAAAAATCTATAATC
65 TTAGTAATCT-AATTTTT--T-TTAAAAAAAACCT-TCTTTTTTCTATTTGAAAAATCTATAATC
* * * * *
1357932 ATAACTTCTTTCTTTCAC-TTTTTTATGATTAAACCTATTTAAAGGTCGGGTTACTTACATAAGC
125 ATAACTTCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAACGGTCGGGTTACTTGCTTAAGC
* * * * * **
1357996 TTGAAGGCCTATACGATATTTAAAAAAGTTTTGACAAAAATAATAAGTTCAAAAAATAGGCTAAA
190 TTGAAGGCCTATACGATATTTGAGAAGGTTTTGACAAAAATATTAAGCTCAAAAAATAGGCTTGA
* *
1358061 GCAAAAAATGAAGGTTGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACAAACTC
255 GCAAAAAATGAAGGTCGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTC
* * *
1358126 AGCTCGACCAATTCGAATATAATATTTTATTATAAATTTATAATTTATAATAATAGTTGTAATTT
320 AGCTCGGCCAACTCGAATATAATATTTTATTATAAATTTATATTTTATAATAATAGTTGTAATTT
* * * * *
1358191 TATTTTTTACTTGTTAAGTTATTAGAACGCTTTTACAATAGAAGTCATACTATACA-TTTAAAAA
385 TATTTTTTAGTTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTAAAAA
1358255 -AATATTAAAAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTA
450 GAATATT--AAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTA
*** * *
1358319 AAAATAAAAAAATAATATGACAGGTCTAAATAAACTTGGACCACCCATTCGCAATATAAGCAAGC
513 AAAATAAAAAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGC
* * * *
1358384 TTATATTACTCATTTAAAAATATGGATAGGCTAGGACAAAAATAACTACCTATATTTCAAGTTTG
578 TTATATTACTCATTTAAAAATATGGATAGGCTTGGACAAAAACAACTACCTATATTTCGAGCTTG
* * * *
1358449 GACAAACTCATAGTGCGTTAATAACCTATCTGACCCAAATCAACTTGTAAACAACTCTAGTCATG
643 GACAAACTCATAGTGTGTTAATAACCTATCTGACCCAACTCAACTCGTAAACAAGTCTAGTCATG
* * * *
1358514 ATCTAGCATACTTAATTTCTTTCGATTAATGTATATATTAATTTAGATATGTAA
708 ATCTAGTATACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
* * * * *
1358568 TATTTGACTTATGATATTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTAGCAAGGTTACAT
1 CACTTGACTCATGATACTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTAGTAAGGTTACAT
*
1358633 TAGTAATCTACTTTTTTTTAAAAAAAAGCCTTCTTTTTTCTATTTGAAAAATCTATAATCATAAC
66 TAGTAATCTAATTTTTTTTAAAAAAAA-CCTTCTTTTTTCTATTTGAAAAATCTATAATCATAAC
* * * * *
1358698 TTTTTTCTCTCATTTTTTTTATGATTAAACTTGTTTAACGGTTGGGTTACTTGCTTAAGCTTAAA
130 TTCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAACGGTCGGGTTACTTGCTTAAGCTTGAA
* * *
1358763 AGCCTATACGATATTTGAAAAGGTTTTGACAAAAATATTAAACTCAAAAAATAGGCTTGAGCAAA
195 GGCCTATACGATATTTGAGAAGGTTTTGACAAAAATATTAAGCTCAAAAAATAGGCTTGAGCAAA
** * * * * *
1358828 AAATGAAGGTCGTTTAAAAAATAAGTTGTGCCTTGGGCAAAGAAATTTAAACACGGACTCAACTC
260 AAATGAAGGTCGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTCAGCTC
* * * * * *
1358893 GACCAGC-CTGAATGTAATATTTCATTATAAATTTGTATTTTATAATAATAGTTGAAATTTTATT
325 GGCCAACTC-GAATATAATATTTTATTATAAATTTATATTTTATAATAATAGTTGTAATTTTATT
*
1358957 TTTTAATTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTTAAAAA-AT
389 TTTTAGTTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACA-TTTTAAAAAGA-
1359021 ATATTAAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTAAAAA
452 ATATTAAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTAAAAA
* *
1359086 T-AAAAAATAATATGGTGGGTCTAACTAAGCTTGAACCACCCATTCGCAATATAAACAAGCTTAT
517 TAAAAAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTAT
* * * * * *
1359150 ATTACTCATTTAAAAATATGGATAGGTTTTGACAAAATCAACTACCTATATTTTGCGCTTAGACA
582 ATTACTCATTTAAAAATATGGATAGGCTTGGACAAAAACAACTACCTATATTTCGAGCTTGGACA
*
1359215 AACTCATAGTGTGTTAATAACCTATCTCACCCAACTCAACTCGT--A-AA--C-A-TCATGATCT
647 AACTCATAGTGTGTTAATAACCTATCTGACCCAACTCAACTCGTAAACAAGTCTAGTCATGATCT
* *
1359273 AGTATACTTAATTTCTTTAGATGAATGCATATATTAAGTTAGATATGTAA
712 AGTATACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
* * * *
1359323 CACTTCACTCGTGATACTAGATCAGCCATTCCCTTTATAATTAGTATAGATTAGTAAGGTTACAT
1 CACTTGACTCATGATACTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTAGTAAGGTTACAT
* * *
1359388 TAGTAATCTAAATTGTTTT-AAAAAAACCTTCTTTTTTCTTTTTGAAAAATCTATAATCATAACT
66 TAGTAATCTAATTTTTTTTAAAAAAAACCTTCTTTTTTCTATTTGAAAAATCTATAATCATAACT
* ** * * * *
1359452 TCTTTCTCTCTTTTTTTTTATGATTAAACCTGTTTAACAGTCGGGTTACTTACATAAGCTTGAAG
131 TCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAACGGTCGGGTTACTTGCTTAAGCTTGAAG
* * * *
1359517 GCTTATACGATATTGGAGAAGGTTTTGACAAAAATATTAGGCTCAAAAAATAGGCTAGAGCAAAA
196 GCCTATACGATATTTGAGAAGGTTTTGACAAAAATATTAAGCTCAAAAAATAGGCTTGAGCAAAA
* **
1359582 AATGAAGGTCGTTTAAAAAATGAGCTATGCCTTGGAAAAAGAAATTTAAGCACGAACTCAGCTCG
261 AATGAAGGTCGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTCAGCTCG
* * * *
1359647 GCCAAGTCGAATATAATATTTTATTGTAAATTTATAATTTATAATAATAGTTGCAATTTTATTTT
326 GCCAACTCGAATATAATATTTTATTATAAATTTATATTTTATAATAATAGTTGTAATTTTATTTT
* *
1359712 TTAGTTATTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTAAAAAGAATGT
391 TTAGTTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTAAAAAGAATAT
*
1359777 TAAAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTACAAATATATTTAAAAATAA
456 T-AAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTAAAAATAA
* * *
1359842 AAAAATAATATGGTGAGTTTAAATAAGCTTGAACCACCTATTCGCAATATAAGCAAGCTTATATT
520 AAAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTATATT
* * * * * * *
1359907 ACACAATTAAAAATATGGACAGGCTTTGACTAAAACAACTATCTATATTTTGAGCTTGGACAAAC
585 ACTCATTTAAAAATATGGATAGGCTTGGACAAAAACAACTACCTATATTTCGAGCTTGGACAAAC
* * ** * *
1359972 TCATAGTATGTTAATAACCTATTTGACTTAACTTAACTCGTAAACAAGTCTAGTCATGACCTAGT
650 TCATAGTGTGTTAATAACCTATCTGACCCAACTCAACTCGTAAACAAGTCTAGTCATGATCTAGT
1360037 ATACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
715 ATACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
* * *
1360084 CACTTGACTCGTGATACTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTGGTAAGGTTATAT
1 CACTTGACTCATGATACTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTAGTAAGGTTACAT
* * ** * *
1360149 TAGTAATCTACA-TTTTCTT--AAAAAACTTTCTTTTTTCTACCTAAAAAATTTATAATCATAAC
66 TAGTAATCTA-ATTTTTTTTAAAAAAAACCTTCTTTTTTCTATTTGAAAAATCTATAATCATAAC
* * * * * *
1360211 TTCTTTCTTTCACCTTTTTTATGACTAACCTTGTTTAACGATCGGGTTACCTGCTTAAGTTTGAA
130 TTCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAACGGTCGGGTTACTTGCTTAAGCTTGAA
** * * *
1360276 GGCCTATACGATATTTGAGAAGCCTCTGACAAAAATATTAAGCTCAAAAGATAAGCTTGAGCAAA
195 GGCCTATACGATATTTGAGAAGGTTTTGACAAAAATATTAAGCTCAAAAAATAGGCTTGAGCAAA
* *
1360341 AAATGAAGGTCATTTAAAAAATGGGCTATGCCTTGGGTAAAGAAATTTAAGCACGAACTCAGCTC
260 AAATGAAGGTCGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTCAGCTC
* * *
1360406 GGCCAACTCAAATACAATATTTTATTATAAATTTATATTTTATGATAATAGTTGTAATTTTATTT
325 GGCCAACTCGAATATAATATTTTATTATAAATTTATATTTTATAATAATAGTTGTAATTTTATTT
*
1360471 TTTAGTTGTTAACTTGTTAAAACACTTTTATAATAGAAGTCATACTATACATTTTAAAAAGAATA
390 TTTAGTTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTAAAAAGAATA
1360536 TTAAAAAACTTAATCAAAATATATTTAA-TTTTAAAAATTAAATTAAAAATATA-TT-----TAA
455 TTAAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTAAAAATAA
1360594 AAAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTATATT
520 AAAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTATATT
* **
1360659 ACTCATTTAAAAATATGTATAAACTTGGACAAAAACAACTACCTATATTTCGAGCTTGGACAAAC
585 ACTCATTTAAAAATATGGATAGGCTTGGACAAAAACAACTACCTATATTTCGAGCTTGGACAAAC
* * *
1360724 TCATAGTGTGTTAATAACCTATCTGACTCAGCTCAACTCGTAAACAAGTCTAGTCGTGATCTAGT
650 TCATAGTGTGTTAATAACCTATCTGACCCAACTCAACTCGTAAACAAGTCTAGTCATGATCTAGT
*
1360789 ATACTTAATTTCTTTGGATTAATGCATATATGAAGTTAGATATGTAA
715 ATACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
*
1360836 CACTTGACTCATGATACTAGCTCAGCCACTCCCTTAATAATTAGTATAGATTAGTAAGGTTACAT
1 CACTTGACTCATGATACTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTAGTAAGGTTACAT
* **** * * *
1360901 TAGTAATCTAAATTTTTTTAAAAAAAAAAACCTTTTTTTTGTCTGAAAAATCTATAATCATAACT
66 TAGTAATCTAATTTTTTTTAAAAAAAACCTTCTTTTTTCTATTTGAAAAATCTATAATCATAACT
* * **** *
1360966 TCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAAAGCTTAAATTACCTGCTTAAGCTTGAAG
131 TCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAACGGTCGGGTTACTTGCTTAAGCTTGAAG
* * * * * *
1361031 GCCTATATGATATTTGAGAAGGTTTTGACAAAAATATT-GGGTCAAAAAAATAAGCTTAAGCCAA
196 GCCTATACGATATTTGAGAAGGTTTTGACAAAAATATTAAGCTC-AAAAAATAGGCTTGAGCAAA
*
1361095 AAATGAAGGTCGTCTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTCAGCTC
260 AAATGAAGGTCGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTCAGCTC
** * *
1361160 GGCCAACTCGAATACGATATTTTATTATAAATTTATATTTTATAATAATAATTGTAATTCTATTT
325 GGCCAACTCGAATATAATATTTTATTATAAATTTATATTTTATAATAATAGTTGTAATTTTATTT
* * *
1361225 TTTATTTGTTAACTTGTTAAAACACTTTTACAATAAAAGTCATACTATGCATTTTAAAAAGAATA
390 TTTAGTTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTAAAAAGAATA
*
1361290 TTATAAAAACTTAATCAAAATATATTTAATGTTTAAAAATTAAATTAAAAATATATTTAAAAATA
455 TTA-AAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTAAAAAT-
*
1361355 AAAAAAATAATATGGTGAGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTATA
518 AAAAAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTATA
* * * *
1361420 TTATTCATTTAAAAATATAGATAGGCTTGGACAAAAACAACTACTTATATTTCGAGTTTGGACAA
583 TTACTCATTTAAAAATATGGATAGGCTTGGACAAAAACAACTACCTATATTTCGAGCTTGGACAA
* * *
1361485 ACTTATAGTGTGTTAATAACCTATCTAACCCAATTCAACTCGTAAACAAGTCTAGTCATGATCTA
648 ACTCATAGTGTGTTAATAACCTATCTGACCCAACTCAACTCGTAAACAAGTCTAGTCATGATCTA
1361550 GTATGACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
713 GTAT-ACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
1361600 CA
1 CA
1361602 AAACACTCGA
Statistics
Matches: 2718, Mismatches: 283, Indels: 67
0.89 0.09 0.02
Matches are distributed among these distances:
751 1 0.00
752 314 0.12
753 375 0.14
754 487 0.18
755 151 0.06
756 26 0.01
757 7 0.00
758 24 0.01
759 29 0.01
760 330 0.12
761 183 0.07
762 416 0.15
763 246 0.09
764 61 0.02
765 65 0.02
766 3 0.00
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.36
Consensus pattern (761 bp):
CACTTGACTCATGATACTAGCTCAGCCACTCCCTTTATAATTAGTATAGATTAGTAAGGTTACAT
TAGTAATCTAATTTTTTTTAAAAAAAACCTTCTTTTTTCTATTTGAAAAATCTATAATCATAACT
TCTTTCTTTCACTTTTTTTATGATTAAACTTGTTTAACGGTCGGGTTACTTGCTTAAGCTTGAAG
GCCTATACGATATTTGAGAAGGTTTTGACAAAAATATTAAGCTCAAAAAATAGGCTTGAGCAAAA
AATGAAGGTCGTTTAAAAAATGGGCTATGCCTTGGGCAAAGAAATTTAAGCACGAACTCAGCTCG
GCCAACTCGAATATAATATTTTATTATAAATTTATATTTTATAATAATAGTTGTAATTTTATTTT
TTAGTTGTTAACTTGTTAAAACACTTTTACAATAGAAGTCATACTATACATTTTAAAAAGAATAT
TAAAAAACTTAATCAAAATATATTTAATTTTTAAAAATTAAATTAAAAATATATTTAAAAATAAA
AAAATAATATGGTGGGTCTAAATAAGCTTGAACCACCCATTCGCAATATAAGCAAGCTTATATTA
CTCATTTAAAAATATGGATAGGCTTGGACAAAAACAACTACCTATATTTCGAGCTTGGACAAACT
CATAGTGTGTTAATAACCTATCTGACCCAACTCAACTCGTAAACAAGTCTAGTCATGATCTAGTA
TACTTAATTTCTTTGGATTAATGCATATATTAAGTTAGATATGTAA
Found at i:1361366 original size:24 final size:24
Alignment explanation
Indices: 1361321--1361367 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1361311 ATATTTAATG
**
1361321 TTTAAAAATTAAATTAAAAATATA
1 TTTAAAAATTAAAAAAAAAATATA
1361345 TTTAAAAA-TAAAAAAAATAATAT
1 TTTAAAAATTAAAAAAAA-AATAT
1361368 GGTGAGTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TTTAAAAATTAAAAAAAAAATATA
Found at i:1362648 original size:26 final size:24
Alignment explanation
Indices: 1362619--1362679 Score: 61
Period size: 26 Copynumber: 2.5 Consensus size: 24
1362609 TGATTAAAAA
1362619 TTTTAAATTAAATATCAAATAAATTT
1 TTTTAAATTAAATAT--AATAAATTT
* * **
1362645 TTTTATATTTAATATAATATGTTT
1 TTTTAAATTAAATATAATAAATTT
1362669 TTTT-AATTAAA
1 TTTTAAATTAAA
1362680 AAAAGTGCTC
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
23 5 0.17
24 11 0.38
26 13 0.45
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTAAATTAAATATAATAAATTT
Found at i:1362792 original size:23 final size:21
Alignment explanation
Indices: 1362750--1362792 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1362740 ATATGATTAG
*
1362750 ATAATATTTTTTATATTTAAT
1 ATAATATTTTTTATAATTAAT
1362771 ATAATATTTTGATTATAATTAA
1 ATAATATTTT--TTATAATTAA
1362793 ATTATGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATAATATTTTTTATAATTAAT
Found at i:1365669 original size:22 final size:22
Alignment explanation
Indices: 1365624--1365669 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1365614 TTAAATTAAT
*
1365624 ATTTAATTAATAAAAAATATAA
1 ATTTAATTAATAAAAAATAAAA
*
1365646 ATTTAATTAGA-AAAAGATAAAA
1 ATTTAATTA-ATAAAAAATAAAA
1365668 AT
1 AT
1365670 AAAAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
ATTTAATTAATAAAAAATAAAA
Found at i:1370029 original size:23 final size:25
Alignment explanation
Indices: 1370003--1370066 Score: 62
Period size: 23 Copynumber: 2.6 Consensus size: 25
1369993 CTTTTTATTT
1370003 TTTTATTTTTTTCTTTTTCT-C-TC
1 TTTTATTTTTTTCTTTTTCTCCTTC
**
1370026 TTTT-TTCCTTTCTTTTTTCTCCTTC
1 TTTTATTTTTTTC-TTTTTCTCCTTC
* *
1370051 ATTTAATTTTTTCTTT
1 TTTTATTTTTTTCTTT
1370067 CTTTCTTTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
22 6 0.19
23 11 0.35
24 1 0.03
25 8 0.26
26 5 0.16
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTATTTTTTTCTTTTTCTCCTTC
Found at i:1370042 original size:30 final size:30
Alignment explanation
Indices: 1369975--1370043 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
1369965 AAAATTCTTC
**
1369975 TTCTTTTTTTCATTATCTCTTTTTATTTTT
1 TTCTTTTTTTCATTATCTCTTTTTATTCCT
* * *
1370005 TTATTTTTTTCTTTTTCTCTCTTTT-TTCCT
1 TTCTTTTTTTCATTATCTCT-TTTTATTCCT
1370035 TTCTTTTTT
1 TTCTTTTTT
1370044 CTCCTTCATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (30 bp):
TTCTTTTTTTCATTATCTCTTTTTATTCCT
Found at i:1370264 original size:19 final size:19
Alignment explanation
Indices: 1370240--1370277 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
1370230 CTCCTTTTTC
1370240 CTCTTA-TTTTCTCTTCTCT
1 CTCTTACTTTTCTC-TCTCT
1370259 CTCTTACTTTTCTCTCTCT
1 CTCTTACTTTTCTCTCTCT
1370278 TATCTTCACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (19 bp):
CTCTTACTTTTCTCTCTCT
Found at i:1370283 original size:20 final size:19
Alignment explanation
Indices: 1370241--1370283 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1370231 TCCTTTTTCC
*
1370241 TCTTATTTTCTCTTCTCTC
1 TCTTATTTTCTCTTCTCTA
1370260 TCTTACTTTTCTC-TCTCTTA
1 TCTTA-TTTTCTCTTCTC-TA
1370280 TCTT
1 TCTT
1370284 CACAAGCCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.07, C:0.30, G:0.00, T:0.63
Consensus pattern (19 bp):
TCTTATTTTCTCTTCTCTA
Found at i:1371533 original size:5 final size:5
Alignment explanation
Indices: 1371518--1371667 Score: 55
Period size: 5 Copynumber: 30.2 Consensus size: 5
1371508 TTAAAATTTG
* * * * *
1371518 TATAT TTTAT TATAT TATAAC TATATT TAAAA TATTT TATAT TGATAT
1 TATAT TATAT TATAT TAT-AT TATA-T TATAT TATAT TATAT T-ATAT
* * * * *
1371566 AAAAT T-TAA TATAT TA-AT AAT-T TATAT TATA- TAAATT TATATT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA-T TATA-T TATAT
* * * *
1371614 T-T-T TAAAT TATAT TATAT TTTAAT TATTTT TTTAT TATA- TA-AT TATAT
1 TATAT TATAT TATAT TATAT TAT-AT TA-TAT TATAT TATAT TATAT TATAT
1371662 TATAT T
1 TATAT T
1371668 TAAAATTTTC
Statistics
Matches: 103, Mismatches: 28, Indels: 28
0.65 0.18 0.18
Matches are distributed among these distances:
3 3 0.03
4 16 0.16
5 58 0.56
6 25 0.24
7 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:1371577 original size:18 final size:16
Alignment explanation
Indices: 1371553--1371612 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 16
1371543 TTTAAAATAT
1371553 TTTATATTGATATAAAA
1 TTTATATT-ATATAAAA
1371570 TTTA-A-TATATTAATAA
1 TTTATATTATA-TAA-AA
1371586 TTTATATTATAT-AAA
1 TTTATATTATATAAAA
1371601 TTTATATT-TATA
1 TTTATATTATATA
1371613 TTTTTAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
14 6 0.16
15 14 0.37
16 8 0.21
17 6 0.16
18 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TTTATATTATATAAAA
Found at i:1371593 original size:13 final size:15
Alignment explanation
Indices: 1371575--1371626 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 15
1371565 TAAAATTTAA
1371575 TATATTA-AT-AATT
1 TATATTATATAAATT
1371588 TATATTATATAAATT
1 TATATTATATAAATT
**
1371603 TATATT-TATATTTT
1 TATATTATATAAATT
*
1371617 TAAATTATAT
1 TATATTATAT
1371627 TATATTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 7 0.21
14 13 0.39
15 13 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:1371623 original size:29 final size:28
Alignment explanation
Indices: 1371586--1371668 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
1371576 ATATTAATAA
1371586 TTTATATTATATAAATTTATATTTATATT
1 TTTATATTATATAAATTTATA-TTATATT
* *
1371615 TTTAAATTATATTATATTT-TAATTAT-TT
1 TTTATATTATA-TAAATTTAT-ATTATATT
1371643 TTT-TATTATAT-AA-TTATATTATATT
1 TTTATATTATATAAATTTATATTATATT
1371668 T
1 T
1371669 AAAATTTTCA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
24 7 0.15
25 5 0.11
26 1 0.02
27 6 0.13
28 5 0.11
29 15 0.33
30 7 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTATATTATATAAATTTATATTATATT
Found at i:1371834 original size:22 final size:22
Alignment explanation
Indices: 1371786--1371835 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
1371776 ATATCGTATG
*
1371786 ATTATATCATATTTATATTATT
1 ATTATATCATATATATATTATT
* *
1371808 TTTATATCATATCATATTTTA-T
1 ATTATATCATAT-ATATATTATT
1371830 ATTATA
1 ATTATA
1371836 ATTTAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTATATCATATATATATTATT
Found at i:1372441 original size:16 final size:15
Alignment explanation
Indices: 1372410--1372443 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1372400 AATTCAGTCA
1372410 TTTCCTTTATTTTCT
1 TTTCCTTTATTTTCT
*
1372425 TTTCCTTTTTCTTTCT
1 TTTCCTTTAT-TTTCT
1372441 TTT
1 TTT
1372444 TTGTTGCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCCTTTATTTTCT
Found at i:1373911 original size:21 final size:21
Alignment explanation
Indices: 1373887--1373926 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1373877 AAGAAAAAGT
* *
1373887 TATATTTAAATATAATAAATA
1 TATAGTTAAATAAAATAAATA
*
1373908 TATAGTTAATTAAAATAAA
1 TATAGTTAAATAAAATAAA
1373927 GGGTTAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
TATAGTTAAATAAAATAAATA
Found at i:1374573 original size:2 final size:2
Alignment explanation
Indices: 1374560--1374589 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1374550 TCCTTGGAAA
*
1374560 AT AT AT AC 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
1374590 TTGTTGAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1374794 original size:17 final size:17
Alignment explanation
Indices: 1374763--1374806 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 17
1374753 TATTTTTTAC
1374763 TTATAAAT-TATATAAA
1 TTATAAATATATATAAA
1374779 -TATAAATATAATATAAA
1 TTATAAATAT-ATATAAA
1374796 TTATTAAATAT
1 TTA-TAAATAT
1374807 TTTAAAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 7 0.29
16 1 0.04
17 7 0.29
18 2 0.08
19 7 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTATAAATATATATAAA
Found at i:1381808 original size:14 final size:12
Alignment explanation
Indices: 1381781--1381819 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1381771 AAAATTTATT
1381781 ATTTAAATAATA
1 ATTTAAATAATA
1381793 ATTTAAATCAAATA
1 ATTTAAAT--AATA
*
1381807 ATTTAAATTATA
1 ATTTAAATAATA
1381819 A
1 A
1381820 AAAATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTTAAATAATA
Found at i:1388973 original size:9 final size:9
Alignment explanation
Indices: 1388959--1388984 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1388949 GTTCTCACTT
1388959 TCTCTTTTA
1 TCTCTTTTA
1388968 TCTCTTTTA
1 TCTCTTTTA
1388977 TCTCTTTT
1 TCTCTTTT
1388985 CCCATTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.23, G:0.00, T:0.69
Consensus pattern (9 bp):
TCTCTTTTA
Found at i:1393784 original size:7 final size:8
Alignment explanation
Indices: 1393760--1393786 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1393750 ATTAGAGGCT
1393760 AAATTAAA
1 AAATTAAA
1393768 AAATTAAA
1 AAATTAAA
1393776 AAATTAAA
1 AAATTAAA
1393784 AAA
1 AAA
1393787 GAAAAAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (8 bp):
AAATTAAA
Found at i:1402068 original size:22 final size:22
Alignment explanation
Indices: 1402036--1402107 Score: 81
Period size: 22 Copynumber: 3.3 Consensus size: 22
1402026 TGAATTTGTG
* *
1402036 ATATATACATACTATTATAATA
1 ATATGTACATACTATCATAATA
* * * *
1402058 ATATGTGCATACAATCATAGTG
1 ATATGTACATACTATCATAATA
*
1402080 ATATGTACATACTACCATAATA
1 ATATGTACATACTATCATAATA
1402102 ATATGT
1 ATATGT
1402108 CTGTATTGTT
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.36
Consensus pattern (22 bp):
ATATGTACATACTATCATAATA
Found at i:1404162 original size:22 final size:20
Alignment explanation
Indices: 1404107--1404163 Score: 51
Period size: 22 Copynumber: 2.8 Consensus size: 20
1404097 AAATTATATG
* *
1404107 TACATATGACTATAACAATA
1 TACATATCACAATAACAATA
* * *
1404127 TATATGTCATAATAACAAAATA
1 TACATATCACAATAAC--AATA
1404149 TACATATCACAATAA
1 TACATATCACAATAA
1404164 TTAAGAGAAC
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
20 11 0.41
22 16 0.59
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (20 bp):
TACATATCACAATAACAATA
Found at i:1404316 original size:22 final size:21
Alignment explanation
Indices: 1404291--1404364 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
1404281 TAATAGTGTG
1404291 TACATATCTTTACAATAATATA
1 TACATATCTTTA-AATAATATA
* *
1404313 TACATATTACTTTAACT-ATATG
1 TACATA-T-CTTTAAATAATATA
* *
1404335 TGCATATCATTATAATAATATA
1 TACATATCTTTA-AATAATATA
*
1404357 AACATATC
1 TACATATC
1404365 ACAAACTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
20 4 0.10
21 3 0.08
22 25 0.62
23 3 0.08
24 5 0.12
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.41
Consensus pattern (21 bp):
TACATATCTTTAAATAATATA
Found at i:1405179 original size:9 final size:9
Alignment explanation
Indices: 1405160--1405229 Score: 72
Period size: 9 Copynumber: 7.6 Consensus size: 9
1405150 GGTTTTCAAC
1405160 ATAAAAA-A
1 ATAAAAATA
1405168 ATAAAAATA
1 ATAAAAATA
1405177 ATAAAAATAA
1 ATAAAAAT-A
*
1405187 AAAATAAATTA
1 ATAA-AAA-TA
1405198 ATAAAAAATA
1 AT-AAAAATA
*
1405208 AAAAAAATA
1 ATAAAAATA
1405217 A-AAAAATA
1 ATAAAAATA
1405225 ATAAA
1 ATAAA
1405230 GTAAAGAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
8 15 0.28
9 20 0.38
10 7 0.13
11 8 0.15
12 3 0.06
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
ATAAAAATA
Found at i:1405199 original size:21 final size:23
Alignment explanation
Indices: 1405163--1405234 Score: 78
Period size: 22 Copynumber: 3.1 Consensus size: 23
1405153 TTTCAACATA
1405163 AAAAAATAAAAATAAT-AAAAAT
1 AAAAAATAAAAATAATAAAAAAT
*
1405185 AAAAAAT-AAATTAATAAAAAAT
1 AAAAAATAAAAATAATAAAAAAT
*
1405207 AAAAAAAATAAAAA-AATAATAAAGT
1 --AAAAAATAAAAATAATAA-AAAAT
1405232 AAA
1 AAA
1405235 GAAAAAAGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
21 7 0.17
22 13 0.31
23 3 0.07
24 12 0.29
25 7 0.17
ACGTcount: A:0.81, C:0.00, G:0.01, T:0.18
Consensus pattern (23 bp):
AAAAAATAAAAATAATAAAAAAT
Found at i:1405239 original size:20 final size:17
Alignment explanation
Indices: 1405200--1405251 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
1405190 ATAAATTAAT
*
1405200 AAAAAATAAAAAAAATA
1 AAAAAATAAAAAAAAGA
1405217 AAAAAATAATAAAGTAAAGA
1 AAAAAATAA-AAA--AAAGA
**
1405237 AAAAAGCAAAAAAAA
1 AAAAAATAAAAAAAA
1405252 AAGTAAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 12 0.41
18 3 0.10
19 3 0.10
20 11 0.38
ACGTcount: A:0.83, C:0.02, G:0.06, T:0.10
Consensus pattern (17 bp):
AAAAAATAAAAAAAAGA
Found at i:1405241 original size:37 final size:37
Alignment explanation
Indices: 1405162--1405251 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 37
1405152 TTTTCAACAT
* *
1405162 AAAAAAATAAAAATAATAAAAATAAAAAATAAATTAA
1 AAAAAAATAAAAAAAATAAAAATAAAAAATAAATAAA
* *
1405199 TAAAAAATAAAAAAAAT-AAAA-AAATAATAAAGTAAA
1 AAAAAAATAAAAAAAATAAAAATAAAAAATAAA-TAAA
**
1405235 GAAAAAAGCAAAAAAAA
1 -AAAAAAATAAAAAAAA
1405252 AAGTAAAATG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
35 9 0.20
36 7 0.16
37 28 0.64
ACGTcount: A:0.81, C:0.01, G:0.03, T:0.14
Consensus pattern (37 bp):
AAAAAAATAAAAAAAATAAAAATAAAAAATAAATAAA
Found at i:1405259 original size:9 final size:8
Alignment explanation
Indices: 1405160--1405239 Score: 69
Period size: 8 Copynumber: 10.1 Consensus size: 8
1405150 GGTTTTCAAC
1405160 ATAAAAAA
1 ATAAAAAA
1405168 AT--AAAA
1 ATAAAAAA
1405174 ATAATAAAA
1 ATAA-AAAA
1405183 AT-AAAAA
1 ATAAAAAA
**
1405190 ATAAATTA
1 ATAAAAAA
1405198 AT-AAAAA
1 ATAAAAAA
1405205 ATAAAAAAA
1 AT-AAAAAA
1405214 ATAAAAAA
1 ATAAAAAA
*
1405222 ATAATAAA
1 ATAAAAAA
*
1405230 GTAAAGAAA
1 ATAAA-AAA
1405239 A
1 A
1405240 AAGCAAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
6 6 0.11
7 11 0.19
8 24 0.42
9 16 0.28
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (8 bp):
ATAAAAAA
Found at i:1405578 original size:28 final size:28
Alignment explanation
Indices: 1405546--1405601 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1405536 TAAAGTAGCC
*
1405546 ACATGGACACGTGAAGAAACAAGCAGCT
1 ACATGGACACATGAAGAAACAAGCAGCT
1405574 ACATGGACACATGAAGAAACAAGCAGCT
1 ACATGGACACATGAAGAAACAAGCAGCT
1405602 GTATCGAAAC
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:0.45, C:0.21, G:0.23, T:0.11
Consensus pattern (28 bp):
ACATGGACACATGAAGAAACAAGCAGCT
Found at i:1408600 original size:155 final size:154
Alignment explanation
Indices: 1408139--1408627 Score: 608
Period size: 156 Copynumber: 3.1 Consensus size: 154
1408129 ATATCCCCTT
* * * **
1408139 AGGGCATTTTGGTAATTTTTCTTAGAACCGAGTCCT-GGCTATCACCGGGTCTGCTTTTATGCCG
1 AGGGCATTTTCGT-ACTTTT-TTAGAACTGAGTCCTAGGCTATCACCGGGTCCACTTTTATGCCG
* *
1408203 AAGGTGGGCATTTAGGATAGGTTCATTGTATTTCTAGTCTTTTTAAGTCCTTTAAGGTTGCCGGG
64 AAGGTCGGCATTTAGGATAGGTTCATTGTATTTCTAGTCTTTTTAAGTCCTTT-AGGTTGTC-GG
*
1408268 GTATTTTTACGTCGAAAGTATACCTATA
127 GTACTTTTACGTCGAAAGTATACCTATA
* * * * * * *
1408296 GGGGCATTTTCGTACTTTCTTAAAAATGAGTCTTAGGCTATCACCGGGT-CATCTTTTATACTGA
1 AGGGCATTTTCGTACTTTTTTAGAACTGAGTCCTAGGCTATCACCGGGTCCA-CTTTTATGCCGA
* *
1408360 AGGTCGGTAATTAGGATAGGTTCATTGTATTTCTAGTCTTTTTAAGTCCTTTAGGGTTGTCTGGG
65 AGGTCGGCATTTAGGATAGGTTCATTGTATTTCTAGTCTTTTTAAGTCCTTTA-GGTTGTC-GGG
* *
1408425 TACTTTTACGTTGAAGGTATACCTATA
128 TACTTTTACGTCGAAAGTATACCTATA
* * *
1408452 AGGGCATTTTCGTACTTTTTTAGAACTGAGTCCTAGGTTGTCACCAGGTCCACTTTTATGCCGAA
1 AGGGCATTTTCGTACTTTTTTAGAACTGAGTCCTAGGCTATCACCGGGTCCACTTTTATGCCGAA
* *
1408517 GGT-GGCATTTAGGATAGGTTCATTGCATTTCTAGTCTTTTTAAGTCCTTTAGGATTATCGGGAT
66 GGTCGGCATTTAGGATAGGTTCATTGTATTTCTAGTCTTTTTAAGTCCTTTAGG-TTGTCGGG-T
*
1408581 ACTTTCACGTCGAAAGTATATCCT-TA
129 ACTTTTACGTCGAAAGTATA-CCTATA
* * *
1408607 TGGGCATTTTCATAATTTTTT
1 AGGGCATTTTCGTACTTTTTT
1408628 CTTGAACTTA
Statistics
Matches: 285, Mismatches: 40, Indels: 16
0.84 0.12 0.05
Matches are distributed among these distances:
154 5 0.02
155 99 0.35
156 168 0.59
157 13 0.05
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (154 bp):
AGGGCATTTTCGTACTTTTTTAGAACTGAGTCCTAGGCTATCACCGGGTCCACTTTTATGCCGAA
GGTCGGCATTTAGGATAGGTTCATTGTATTTCTAGTCTTTTTAAGTCCTTTAGGTTGTCGGGTAC
TTTTACGTCGAAAGTATACCTATA
Found at i:1411976 original size:141 final size:141
Alignment explanation
Indices: 1411790--1412050 Score: 416
Period size: 141 Copynumber: 1.9 Consensus size: 141
1411780 ATACAATATA
* * * * **
1411790 TGGAGGTCTTTCCGGGGTAATGATTTAGTAATTCCTAATTTAGAGGGGGTTAGTCTCTAAGTAAC
1 TGGAGGTCTATCCGGGGTAATGATTTAGTAATTCCTAATGTAGAGGGGGTTAATCTCCAAACAAC
* *
1411855 CATCCAGTTGAAACCTCTTATGCCATCTAAGGTTGTA-TTAATCAAGGAAGAGGCTGGACGAGAT
66 CATCCAGCTCAAACCTCTTATGCCATCTAAGGTTG-AGTTAATCAAGGAAGAGGCTGGACGAGAT
1411919 TGAAAAAGGTTG
130 TGAAAAAGGTTG
1411931 TGGAGGTCTATCCGGGGTAATGATTTAGTAATTCCTAATGTAGAGGGGGTTAATCTCCAAACAAC
1 TGGAGGTCTATCCGGGGTAATGATTTAGTAATTCCTAATGTAGAGGGGGTTAATCTCCAAACAAC
* *
1411996 CATCTAGCTCAAACCTCTTATGCCATCTGAGGTTGAGTTAATCAAGGAAGAGGCT
66 CATCCAGCTCAAACCTCTTATGCCATCTAAGGTTGAGTTAATCAAGGAAGAGGCT
1412051 AAACAAGATC
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
140 1 0.01
141 108 0.99
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (141 bp):
TGGAGGTCTATCCGGGGTAATGATTTAGTAATTCCTAATGTAGAGGGGGTTAATCTCCAAACAAC
CATCCAGCTCAAACCTCTTATGCCATCTAAGGTTGAGTTAATCAAGGAAGAGGCTGGACGAGATT
GAAAAAGGTTG
Found at i:1421481 original size:83 final size:83
Alignment explanation
Indices: 1421337--1422025 Score: 1035
Period size: 83 Copynumber: 8.3 Consensus size: 83
1421327 CTATTTGTCT
* *
1421337 GACGAAATGGTTACCACCCTGGTCAGCTTCTTTCCATTT-AATGTATGGTTACCACCCTAGTCAA
1 GACG-AATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACT-TATGGTTACCACCCTAGTCAA
* *
1421401 ACTCTTCTTATTTTAGGAAT
64 ACTCTTCTCATTTTAGGAAC
* ** *
1421421 GACGAATGGTTACCACCTTTTTCAATTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAAC
1 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAAC
1421486 TCTTCTCATTTTAGGAAC
66 TCTTCTCATTTTAGGAAC
* *
1421504 GACGAATGGTTAACACCC-GAGTCAGTTTCTTTCCATTTGACTTATGGTTACTACCCTAGTCAAA
1 GACGAATGGTTACCACCCTG-GTCAGTTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAA
*
1421568 CTCTTCTCATTTTAGAAAC
65 CTCTTCTCATTTTAGGAAC
* * *
1421587 GAAGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGGTTACCACCCTGGTCAAAC
1 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAAC
1421652 TCTTCTCATTTTAGGAAC
66 TCTTCTCATTTTAGGAAC
* * * *
1421670 GACGAATGGTTACCACCCTGGTCAATTTCTTTCCATTTAACCTATGGTTACCACCCTGGTCAAAC
1 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAAC
*
1421735 TCTTCTCATTTTAGAAAC
66 TCTTCTCATTTTAGGAAC
* * *
1421753 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGA-TGTATAGTTACCACCATGGTCAAA
1 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACT-TATGGTTACCACCCTAGTCAAA
1421817 CTCTTCTCATTTTAGGAAC
65 CTCTTCTCATTTTAGGAAC
* * * *
1421836 GATGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACTTATTGTTACTACCCTAGTCCAAC
1 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAAC
*
1421901 TCTTCTCATTTTAGGAAT
66 TCTTCTCATTTTAGGAAC
* * *
1421919 GACGATTGGTTATCACCCTGGTCAGTTTCTTTCCATTTGA-TGTATGGTTACCACCCTGGTCAAA
1 GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACT-TATGGTTACCACCCTAGTCAAA
1421983 CTCTTCTCATTTTAGGAAC
65 CTCTTCTCATTTTAGGAAC
1422002 GACGAATGGTTACCACCCTGGTCA
1 GACGAATGGTTACCACCCTGGTCA
1422026 AACTCTTCTC
Statistics
Matches: 550, Mismatches: 49, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
82 1 0.00
83 541 0.98
84 8 0.01
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.36
Consensus pattern (83 bp):
GACGAATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACTTATGGTTACCACCCTAGTCAAAC
TCTTCTCATTTTAGGAAC
Found at i:1422102 original size:83 final size:83
Alignment explanation
Indices: 1422007--1423056 Score: 1451
Period size: 83 Copynumber: 12.8 Consensus size: 83
1421997 GGAACGACGA
*
1422007 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAATGGTTACCACCCTGGTCAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
* * *
1422072 TTTTTTTCTATTTGACTA
66 TTTCTTTCCATTTGACTT
*
1422090 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCTTGGTCAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422155 TTTCTTTCC-----ACAT
66 TTTCTTTCCATTTGACTT
** * *
1422168 ATGGTTACCACATTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCTTGGTTAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422233 TTTCTTACCATTTGACTT
66 TTTCTTTCCATTTGACTT
** * * *
1422251 ATGGTTACCACATTGGTCAAGCTCTTCTCATTTTAGGAATGACGAATGGTTACCACCTTGGTTAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422316 TTTCTTACCATTTGACTT
66 TTTCTTTCCATTTGACTT
* ** *
1422334 ATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAACAACGAATGGTTACCACCCTGGTCAA
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
1422399 TTTCTTTCCATTTGACTT
66 TTTCTTTCCATTTGACTT
* * * *
1422417 ATGGTTACCACCTTGGTCAAACTCTTTTCATTTTAGGAATGGCGAATGGTTATCACCCTGGTCAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422482 TTTCTTTCCATTTTA-TGT
66 TTTCTTTCCATTTGACT-T
* * * * *
1422500 ATGGTTACTACCCTGGTCAAACTCTTCTCATTTTAGAAACGATGAATGGTTACCACCCTGGTCGG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
* *
1422565 TTTTTTTCTATTTGACTT
66 TTTCTTTCCATTTGACTT
* * *
1422583 ATGGTTAACACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAATGGTTACCACCCTGGTTAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
1422648 TTTCTTTCCATTTGACTT
66 TTTCTTTCCATTTGACTT
* * * *
1422666 ATGGTTACCACCTTAGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCA--TTGGTTAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422729 TTTCTTTCCATTTGACGT
66 TTTCTTTCCATTTGACTT
* *
1422747 ATGGTTACCACCCTGGTCAAACTCTTCTCA--TT-GGAATGATGAATGGTTACCACCCT-ATCCA
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGT-CA
* *
1422808 GTTTCTTTCCATTTAACCT
65 GTTTCTTTCCATTTGACTT
* * * *
1422827 ATGGTTACCACCCTGGTCAAACTTTTCTCATTTTAGGAATGACGAAAGGTTTCCACCCTGGTTAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422892 TTTCTTTTCATTTGA-TGT
66 TTTCTTTCCATTTGACT-T
* * * *
1422910 ATGGTTACCACCATGGTCAAACTCTTCTCATTTTAAGAATGATGAATGGTTACCACCCCGGTCAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
*
1422975 TTTCTTTCCATTTGACAT
66 TTTCTTTCCATTTGACTT
* * * *
1422993 ATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAATGATGAATGGTTACCAACTTGGTCA
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCA
1423057 AACTCTTCTC
Statistics
Matches: 861, Mismatches: 90, Indels: 32
0.88 0.09 0.03
Matches are distributed among these distances:
78 91 0.11
79 3 0.00
80 48 0.06
81 52 0.06
82 3 0.00
83 662 0.77
84 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (83 bp):
ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAATGGTTACCACCCTGGTCAG
TTTCTTTCCATTTGACTT
Found at i:1422267 original size:38 final size:38
Alignment explanation
Indices: 1422213--1422345 Score: 126
Period size: 38 Copynumber: 3.3 Consensus size: 38
1422203 GGAATGACGA
1422213 ATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTT
1 ATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTT
* * * **
1422251 ATGGTTACCACATTGGTCAAG-CTCTT-CTCATTTTAGGAATGACGA
1 ATGGTTACCACCTTGGT-TAGTTTCTTAC-CA--TT-----TGACTT
1422296 ATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTT
1 ATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTT
1422334 ATGGTTACCACC
1 ATGGTTACCACC
1422346 CTAGTCAAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
37 1 0.01
38 38 0.51
39 2 0.03
40 2 0.03
43 2 0.03
44 2 0.03
45 26 0.35
46 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (38 bp):
ATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTT
Found at i:1422921 original size:38 final size:38
Alignment explanation
Indices: 1422722--1423011 Score: 116
Period size: 38 Copynumber: 7.2 Consensus size: 38
1422712 TGGTTACCAT
* * *
1422722 TGGTTAGTTTCTTTCCATTTGACGTATGGTTACCACCC
1 TGGTCAGTTTCTTTTCATTTGATGTATGGTTACCACCC
*** * *
1422760 TGGTCAAACTCTTCTCATTGGAATGATGAATGGTTACCACCC
1 TGGTCAGTTTCTTTTCATT----TGATGTATGGTTACCACCC
* * * **
1422802 T-ATCCAGTTTCTTTCCATTTAACCTATGGTTACCACCC
1 TGGT-CAGTTTCTTTTCATTTGATGTATGGTTACCACCC
** * * * *
1422840 TGGTCAAACTT-TTCTCATTTTAGGAATGACGAAAGGTTTCCACCC
1 TGGTC-AGTTTCTTTTCA-TTT--G-AT---GTATGGTTACCACCC
* *
1422885 TGGTTAGTTTCTTTTCATTTGATGTATGGTTACCACCA
1 TGGTCAGTTTCTTTTCATTTGATGTATGGTTACCACCC
*** *
1422923 TGGTCAAACTCTTCTCATTTTAAGAATGATGAATGGTTACCACCC
1 TGGTCAGTTTCTTTTCA-TTT--G-ATG-T--ATGGTTACCACCC
* * **
1422968 CGGTCAGTTTCTTTCCATTTGACATATGGTTACCACCC
1 TGGTCAGTTTCTTTTCATTTGATGTATGGTTACCACCC
*
1423006 TAGTCA
1 TGGTCA
1423012 AACTCTTCTC
Statistics
Matches: 177, Mismatches: 53, Indels: 44
0.65 0.19 0.16
Matches are distributed among these distances:
38 74 0.42
39 10 0.06
40 1 0.01
41 5 0.03
42 34 0.19
43 1 0.01
44 9 0.05
45 43 0.24
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (38 bp):
TGGTCAGTTTCTTTTCATTTGATGTATGGTTACCACCC
Found at i:1422933 original size:493 final size:491
Alignment explanation
Indices: 1422007--1423056 Score: 1561
Period size: 493 Copynumber: 2.1 Consensus size: 491
1421997 GGAACGACGA
*
1422007 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAATGGTTACCACCCTGGTCAG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGATGAATGGTTACCACCCTGGTCAG
* *
1422072 TTTTTTTCTATTTGACTAATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGAAT
66 TTTTTTTCTATTTGACTAATGGTTAACACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAAT
* *
1422137 GGTTACCACCTTGGTCAGTTTCTTTCCACATATGGTTACCACATTGGTCAAACTCTTCTCATTTT
131 GGTTACCACCCTGGTCAGTTTCTTTCCACATATGGTTACCACATTAGTCAAACTCTTCTCATTTT
* *
1422202 AGGAATGACGAATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTTATGGTTACCACATTGG
196 AGGAATGACGAATGGTTACCA-CTTGGTTAGTTTCTTACCATTTGACGTATGGTTACCACACTGG
* * * * *
1422267 TCAAGCTCTTCTCATTTTAGGAATGACGAATGGTTACCACCTTGGTTAGTTTCTTACCATTTGAC
260 TCAAACTCTTCTCA-TTTAGGAATGACGAATGGTTACCACCCTGATCAGTTTCTTACCATTTAAC
* *
1422332 TTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAACAACGAATGGTTACCACCCTGGTC
324 CTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAACAACGAAAGGTTACCACCCTGGTC
* * * *
1422397 AATTTCTTTCCATTTGACTTATGGTTACCACCTTGGTCAAACTCTTTTCATTTTAGGAATGGCGA
389 AATTTCTTTCCATTTGACTTATGGTTACCACCATGGTCAAACTCTTCTCATTTTAAGAATGACGA
* * * **
1422462 ATGGTTATCACCCTGGTCAGTTTCTTTCCATTTTATGT
454 ATGGTTACCACCCCGGTCAGTTTCTTTCCATTTGACAT
* * *
1422500 ATGGTTACTACCCTGGTCAAACTCTTCTCATTTTAGAAACGATGAATGGTTACCACCCTGGTCGG
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGATGAATGGTTACCACCCTGGTCAG
*
1422565 TTTTTTTCTATTTGACTTATGGTTAACACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAAT
66 TTTTTTTCTATTTGACTAATGGTTAACACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAAT
* * *
1422630 GGTTACCACCCTGGTTAGTTTCTTTCCATTTGACTTATGGTTACCACCTTAGTCAAACTCTTCTC
131 GGTTACCACCCTGGTCAGTTTCTTTCC-----ACATATGGTTACCACATTAGTCAAACTCTTCTC
* *
1422695 ATTTTAGGAATGACGAATGGTTACCA-TTGGTTAGTTTCTTTCCATTTGACGTATGGTTACCACC
191 ATTTTAGGAATGACGAATGGTTACCACTTGGTTAGTTTCTTACCATTTGACGTATGGTTACCACA
* *
1422759 CTGGTCAAACTCTTCTCA-TT-GGAATGATGAATGGTTACCACCCT-ATCCAGTTTCTTTCCATT
256 CTGGTCAAACTCTTCTCATTTAGGAATGACGAATGGTTACCACCCTGAT-CAGTTTCTTACCATT
* * ** *
1422821 TAACCTATGGTTACCACCCTGGTCAAACTTTTCTCATTTTAGGAATGACGAAAGGTTTCCACCCT
320 TAACCTATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAACAACGAAAGGTTACCACCCT
* * *
1422886 GGTTAGTTTCTTTTCATTTGA-TGTATGGTTACCACCATGGTCAAACTCTTCTCATTTTAAGAAT
385 GGTCAATTTCTTTCCATTTGACT-TATGGTTACCACCATGGTCAAACTCTTCTCATTTTAAGAAT
*
1422950 GATGAATGGTTACCACCCCGGTCAGTTTCTTTCCATTTGACAT
449 GACGAATGGTTACCACCCCGGTCAGTTTCTTTCCATTTGACAT
* * * *
1422993 ATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAATGATGAATGGTTACCAACTTGGTCA
1 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGATGAATGGTTACCACCCTGGTCA
1423057 AACTCTTCTC
Statistics
Matches: 500, Mismatches: 50, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
492 2 0.00
493 389 0.78
494 2 0.00
496 51 0.10
498 56 0.11
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (491 bp):
ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGATGAATGGTTACCACCCTGGTCAG
TTTTTTTCTATTTGACTAATGGTTAACACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGAAT
GGTTACCACCCTGGTCAGTTTCTTTCCACATATGGTTACCACATTAGTCAAACTCTTCTCATTTT
AGGAATGACGAATGGTTACCACTTGGTTAGTTTCTTACCATTTGACGTATGGTTACCACACTGGT
CAAACTCTTCTCATTTAGGAATGACGAATGGTTACCACCCTGATCAGTTTCTTACCATTTAACCT
ATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAACAACGAAAGGTTACCACCCTGGTCAA
TTTCTTTCCATTTGACTTATGGTTACCACCATGGTCAAACTCTTCTCATTTTAAGAATGACGAAT
GGTTACCACCCCGGTCAGTTTCTTTCCATTTGACAT
Found at i:1423128 original size:83 final size:83
Alignment explanation
Indices: 1423038--1423390 Score: 422
Period size: 83 Copynumber: 4.3 Consensus size: 83
1423028 GGAATGATGA
* *
1423038 ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGATGAATGGTTACCACCCTGGTCAG
1 ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGACGAATGGTTACCACCCTAGTCAG
* *
1423103 TTTCTTACCATTTGACTT
66 TTTCTTTCCATTTGACGT
* * * *
1423121 ATAGTTACC-ACTCTGGTTAAACTTTTCTCATTTTAGAAACGACGAATGGTTAACACCCTAGTCA
1 ATGGTTACCAACT-TGGTCAAACTCTTCTCATTTTAGAAACGACGAATGGTTACCACCCTAGTCA
*
1423185 GTTTCTTTCCATTTGATGT
65 GTTTCTTTCCATTTGACGT
* * * * * * * * *
1423204 ATGGTTACCACCCTGGTCAAACTCTACTCATTTTAGGAACGATGAATGGTTACAACCTTGGTCAA
1 ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGACGAATGGTTACCACCCTAGTCAG
1423269 TTTCTTTCCATTTGACGT
66 TTTCTTTCCATTTGACGT
* * * * * * ** *
1423287 ATGGTTACCACCCTAGTTAAACTCTTTTCATTTTAGGAATAACGAATGGTTACCACCCTAGTCAT
1 ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGACGAATGGTTACCACCCTAGTCAG
1423352 TTTCTTTCCATTTGACGT
66 TTTCTTTCCATTTGACGT
*
1423370 ACGGTTA-CAACCTTGGTCAAA
1 ATGGTTACCAA-CTTGGTCAAA
1423391 TCTGCTTCCT
Statistics
Matches: 228, Mismatches: 39, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
82 5 0.02
83 222 0.97
84 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (83 bp):
ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGACGAATGGTTACCACCCTAGTCAG
TTTCTTTCCATTTGACGT
Found at i:1423130 original size:166 final size:162
Alignment explanation
Indices: 1421547--1423137 Score: 803
Period size: 166 Copynumber: 9.6 Consensus size: 162
1421537 CATTTGACTT
* * * * *
1421547 ATGGTTACTACCCTAGTCAAACTCTTCTCATTTTAGAAACGAAGAATGGTTACCACCCTGGTCAG
1 ATGGTTACCACCCTGGTCAAATTCTTCTCATTTT-G--ACGATGAATGGTTACCACCCTGGTCAA
** * *** *
1421612 TTTCTTTCCATTTGACATATGGTTACCACCCTGGTCAAACTC-TTCTCATTTTAGGAACGACGAA
63 ACTC-TTCCATTTGACGTATGGTTACCACCCTGGTCAGTTTCTTTC-CA-TTT--G-AC-A--TA
** **
1421676 TGGTTACCACCCTGGTCAATTTCTT-TCCA-TTT----A--ACCT
119 TGGTTACCACCCTGGTCAAACTCTTCT-CATTTTAGGAATGACGA
* * *
1421713 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGAAACGACGAATGGTTACCACCCTGGTCAG
1 ATGGTTACCACCCTGGTCAAATTCTTCTCATTTT-G--ACGATGAATGGTTACCACCCTGGTCAA
** * * * ***
1421778 TTTCTTTCCATTTGATGTATAGTTACCACCATGGTCAAACTC-TTCTCATTTTAGGAACGATGAA
63 ACTC-TTCCATTTGACGTATGGTTACCACCCTGGTCAGTTTCTTTC-CA-TTT--G-AC-AT--A
*** **
1421842 TGGTTACCACCCTGGTCAGTTTCTT-TCCA--TT-----TGACTT
119 TGGTTACCACCCTGGTCAAACTCTTCT-CATTTTAGGAATGACGA
* * * * * * *
1421879 ATTGTTACTACCCTAGTCCAACTCTTCTCATTTT-AGGAATGACGATTGGTTATCACCCTGGTCA
1 ATGGTTACCACCCTGGTCAAATTCTTCTCATTTTGACG-ATGA--A-TGGTTACCACCCTGGTCA
*** * *** *
1421943 GTTTCTTTCCATTTGATGTATGGTTACCACCCTGGTCAAACTC-TTCTCATTTTAGGAACGACGA
62 AACTC-TTCCATTTGACGTATGGTTACCACCCTGGTCAGTTTCTTTC-CA-TTT--G-AC-A--T
*
1422007 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAACGACGA
118 ATGGTTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
* * *
1422052 ATGGTTACCACCCTGGTC-AGTTTTTTTC-TATTTGAC--T-AATGGTTACCACCCTGGTCAAAC
1 ATGGTTACCACCCTGGTCAAATTCTTCTCAT-TTTGACGATGAATGGTTACCACCCTGGTCAAAC
* *
1422112 TCTTCTCATTTTAGGAATGACGAATGGTTACCACCTTGGTCAGTTTCTTTCC-----ACATATGG
65 TCTTC-CA--TT-----TGACGTATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGG
**
1422172 TTACCACATTGGTCAAACTCTTCTCATTTTAGGAATGACGA
122 TTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
* * ** * ** *
1422213 ATGGTTACCACCTTGGTTAGTTTCTTAC-CA-TTTGAC--T-TATGGTTACCACATTGGTCAAGC
1 ATGGTTACCACCCTGGTCAAATTCTT-CTCATTTTGACGATGAATGGTTACCACCCTGGTCAAAC
* * * * *
1422273 TCTTCTCATTTTAGGAATGACGAATGGTTACCACCTTGGTTAGTTTCTTACCATTTGACTTATGG
65 TCTTC-CA--TT-----TGACGTATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGG
* **
1422338 TTACCACCCTAGTCAAACTCTTCTCATTTTAGGAACAACGA
122 TTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
* * *
1422379 ATGGTTACCACCCTGGTCAATTTCTT-TCCA-TTTGAC--T-TATGGTTACCACCTTGGTCAAAC
1 ATGGTTACCACCCTGGTCAAATTCTTCT-CATTTTGACGATGAATGGTTACCACCCTGGTCAAAC
* * * * **
1422439 TCTTTTCATTTTAGGAATGGCGAATGGTTATCACCCTGGTCAGTTTCTTTCCATTTTATGTATGG
65 TC-TTCCA-TTT--G-A---CGTATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGG
* * * *
1422504 TTACTACCCTGGTCAAACTCTTCTCATTTTAGAAACGATGA
122 TTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
** * * * *
1422545 ATGGTTACCACCCTGGTC-GGTTTTTTTC-TATTTGAC--T-TATGGTTAACACCCTGGTCAAAC
1 ATGGTTACCACCCTGGTCAAATTCTTCTCAT-TTTGACGATGAATGGTTACCACCCTGGTCAAAC
* * *
1422605 TCTTCTCATTTTAGGAACGACGAATGGTTACCACCCTGGTTAGTTTCTTTCCATTTGACTTATGG
65 TCTTC-CA-TTT------GACGTATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGG
* *
1422670 TTACCACCTTAGTCAAACTCTTCTCATTTTAGGAATGACGA
122 TTACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
* * **
1422711 ATGGTTACCA--TTGGTTAGTTTCTT-TCCA-TTTGACG-T--ATGGTTACCACCCTGGTCAAAC
1 ATGGTTACCACCCTGGTCAAATTCTTCT-CATTTTGACGATGAATGGTTACCACCCTGGTCAAAC
* * * * *
1422769 TCTTCTCATTGGAATGATGAATGGTTACCACCCT-ATCCAGTTTCTTTCCATTTAACCTATGGTT
65 TCTTC-CATT----TGACGTATGGTTACCACCCTGGT-CAGTTTCTTTCCATTTGACATATGGTT
*
1422833 ACCACCCTGGTCAAACTTTTCTCATTTTAGGAATGACGA
124 ACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
* * * ** * * *
1422872 AAGGTTTCCACCCTGGTTAGTTTCTTTTCA-TTT---GATGTATGGTTACCACCATGGTCAAACT
1 ATGGTTACCACCCTGGTCAAATTCTTCTCATTTTGACGATGAATGGTTACCACCCTGGTCAAACT
* *
1422933 CTTCTCATTTTAAGAATGATGAATGGTTACCACCCCGGTCAGTTTCTTTCCATTTGACATATGGT
66 CTTC-CA-TTT--G-ACG-T--ATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGGT
* *
1422998 TACCACCCTAGTCAAACTCTTCTCATTTTAGGAATGATGA
123 TACCACCCTGGTCAAACTCTTCTCATTTTAGGAATGACGA
* * * *
1423038 ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGATGAATGGTTACCACCCTGGTCAG
1 ATGGTTACCACCCTGGTCAAATTCTTCTCATTTT-G--ACGATGAATGGTTACCACCCTGGTCAA
** * * *
1423103 TTTCTTACCATTTGACTTATAGTTACCACTCTGGT
63 ACTCTT-CCATTTGACGTATGGTTACCACCCTGGT
1423138 TAAACTTTTC
Statistics
Matches: 1194, Mismatches: 146, Indels: 170
0.79 0.10 0.11
Matches are distributed among these distances:
160 4 0.00
161 221 0.19
162 9 0.01
163 57 0.05
164 45 0.04
165 23 0.02
166 725 0.61
167 9 0.01
168 5 0.00
169 3 0.00
170 4 0.00
171 1 0.00
172 12 0.01
173 72 0.06
174 4 0.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (162 bp):
ATGGTTACCACCCTGGTCAAATTCTTCTCATTTTGACGATGAATGGTTACCACCCTGGTCAAACT
CTTCCATTTGACGTATGGTTACCACCCTGGTCAGTTTCTTTCCATTTGACATATGGTTACCACCC
TGGTCAAACTCTTCTCATTTTAGGAATGACGA
Found at i:1423130 original size:294 final size:291
Alignment explanation
Indices: 1422747--1423350 Score: 859
Period size: 294 Copynumber: 2.1 Consensus size: 291
1422737 CATTTGACGT
* * *
1422747 ATGGTTACCACCCTGGTCAAACTCTTCTCATTGGAATGATGAATGGTTACCACCCTATCCAGTTT
1 ATGGTTACCAACCTGGTCAAACTCTTCTCATTGAAACGATGAATGGTTACCACCCTATCCAGTTT
* * * *
1422812 CTTTCCATTTAACCTATGGTTACCACCCTGGTCAAACTTTTCTCATTTTAGGAATGACGAAAGGT
66 CTTACCATTTAACCTATAGTTACCACCCTGGTCAAACTTTTCTCATTTTAGAAACGACGAAAGGT
** * * * *
1422877 TTCCACCCTGGTTAGTTTCTTTTCATTTGATGTATGGTTACCACCATGGTCAAACTCTTCTCATT
131 TAACACCCTAGTCAGTTTCTTTCCATTTGATGTATGGTTACCACCATGGTCAAACTCTACTCATT
* * *
1422942 TTAAGAATGATGAATGGTTACCACCCCGGTCAGTTTCTTTCCATTTGACATATGGTTACCACCCT
196 TTAAGAACGATGAATGGTTACAACCCCGGTCAATTTCTTTCCATTTGACATATGGTTACCACCCT
* *
1423007 AGTCAAACTCTTCTCATTTTAGGAATGATGA
261 AGTCAAACTCTTCTCATTTTAGGAATAACGA
* *
1423038 ATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGATGAATGGTTACCACCCTGGT-CA
1 ATGGTTACCAACCTGGTCAAACTCTTCTCA--TT-GAAACGATGAATGGTTACCACCCT-ATCCA
* * * *
1423102 GTTTCTTACCATTTGACTTATAGTTACCACTCTGGTTAAACTTTTCTCATTTTAGAAACGACGAA
62 GTTTCTTACCATTTAACCTATAGTTACCACCCTGGTCAAACTTTTCTCATTTTAGAAACGACGAA
* *
1423167 TGGTTAACACCCTAGTCAGTTTCTTTCCATTTGATGTATGGTTACCACCCTGGTCAAACTCTACT
127 AGGTTAACACCCTAGTCAGTTTCTTTCCATTTGATGTATGGTTACCACCATGGTCAAACTCTACT
* ** *
1423232 CATTTTAGGAACGATGAATGGTTACAACCTTGGTCAATTTCTTTCCATTTGACGTATGGTTACCA
192 CATTTTAAGAACGATGAATGGTTACAACCCCGGTCAATTTCTTTCCATTTGACATATGGTTACCA
* *
1423297 CCCTAGTTAAACTCTTTTCATTTTAGGAATAACGA
257 CCCTAGTCAAACTCTTCTCATTTTAGGAATAACGA
* *
1423332 ATGGTTACCACCCTAGTCA
1 ATGGTTACCAACCTGGTCA
1423351 TTTTCTTTCC
Statistics
Matches: 274, Mismatches: 35, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
291 28 0.10
293 2 0.01
294 243 0.89
295 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (291 bp):
ATGGTTACCAACCTGGTCAAACTCTTCTCATTGAAACGATGAATGGTTACCACCCTATCCAGTTT
CTTACCATTTAACCTATAGTTACCACCCTGGTCAAACTTTTCTCATTTTAGAAACGACGAAAGGT
TAACACCCTAGTCAGTTTCTTTCCATTTGATGTATGGTTACCACCATGGTCAAACTCTACTCATT
TTAAGAACGATGAATGGTTACAACCCCGGTCAATTTCTTTCCATTTGACATATGGTTACCACCCT
AGTCAAACTCTTCTCATTTTAGGAATAACGA
Found at i:1423143 original size:128 final size:128
Alignment explanation
Indices: 1422904--1423172 Score: 387
Period size: 128 Copynumber: 2.1 Consensus size: 128
1422894 TCTTTTCATT
* * *
1422904 TGATGTATGGTTACCACCATGGTCAAACTCTTCTCATTTTAAGAATGATGAATGGTTACCACCCC
1 TGATGAATGGTTACCAACATGGTCAAACTCTTCTCATTTTAAGAACGATGAATGGTTACCACCCC
* * *
1422969 GGTCAGTTTCTTTCCATTTGACATATGGTTACCACCCTAGTCAAACTCTTCTCATTTTAGGAA
66 GGTCAGTTTCTTACCATTTGACATATAGTTACCACCCTAGTCAAACTCTTCTCATTTTAGAAA
*
1423032 TGATGAATGGTTACCAACTTGGTCAAACTCTTCTCATTTT-AGAAACGATGAATGGTTACCACCC
1 TGATGAATGGTTACCAACATGGTCAAACTCTTCTCATTTTAAG-AACGATGAATGGTTACCACCC
* * * * * *
1423096 TGGTCAGTTTCTTACCATTTGACTTATAGTTACCACTCTGGTTAAACTTTTCTCATTTTAGAAA
65 CGGTCAGTTTCTTACCATTTGACATATAGTTACCACCCTAGTCAAACTCTTCTCATTTTAGAAA
* *
1423160 CGACGAATGGTTA
1 TGATGAATGGTTA
1423173 ACACCCTAGT
Statistics
Matches: 125, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
127 2 0.02
128 123 0.98
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (128 bp):
TGATGAATGGTTACCAACATGGTCAAACTCTTCTCATTTTAAGAACGATGAATGGTTACCACCCC
GGTCAGTTTCTTACCATTTGACATATAGTTACCACCCTAGTCAAACTCTTCTCATTTTAGAAA
Found at i:1423228 original size:166 final size:166
Alignment explanation
Indices: 1423032--1423390 Score: 513
Period size: 166 Copynumber: 2.2 Consensus size: 166
1423022 ATTTTAGGAA
* * * *
1423032 TGATGAATGGTTACCAACTTGGTCAAACTCTTCTCATTTTAGAAACGATGAATGGTTACCACCCT
1 TGATGTATGGTTACCACCTTGGTCAAACTCTACTCATTTTAGAAACGATGAATGGTTACAACCCT
* * * *
1423097 GGTCAGTTTCTTACCATTTGACTTATAGTTACCACTCTGGTTAAACT-TTTCTCATTTTAGAAAC
66 GGTCAATTTCTTACCATTTGACGTATAGTTACCACCCTAGTTAAACTCTTT-TCATTTTAGAAAC
*
1423161 GACGAATGGTTAACACCCTAGTCAGTTTCTTTCCATT
130 AACGAATGGTTAACACCCTAGTCAGTTTCTTTCCATT
* * *
1423198 TGATGTATGGTTACCACCCTGGTCAAACTCTACTCATTTTAGGAACGATGAATGGTTACAACCTT
1 TGATGTATGGTTACCACCTTGGTCAAACTCTACTCATTTTAGAAACGATGAATGGTTACAACCCT
* * * *
1423263 GGTCAATTTCTTTCCATTTGACGTATGGTTACCACCCTAGTTAAACTCTTTTCATTTTAGGAATA
66 GGTCAATTTCTTACCATTTGACGTATAGTTACCACCCTAGTTAAACTCTTTTCATTTTAGAAACA
* *
1423328 ACGAATGGTTACCACCCTAGTCATTTTCTTTCCATT
131 ACGAATGGTTAACACCCTAGTCAGTTTCTTTCCATT
* * *
1423364 TGACGTACGGTTACAACCTTGGTCAAA
1 TGATGTATGGTTACCACCTTGGTCAAA
1423391 TCTGCTTCCT
Statistics
Matches: 170, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
166 167 0.98
167 3 0.02
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (166 bp):
TGATGTATGGTTACCACCTTGGTCAAACTCTACTCATTTTAGAAACGATGAATGGTTACAACCCT
GGTCAATTTCTTACCATTTGACGTATAGTTACCACCCTAGTTAAACTCTTTTCATTTTAGAAACA
ACGAATGGTTAACACCCTAGTCAGTTTCTTTCCATT
Found at i:1423592 original size:45 final size:44
Alignment explanation
Indices: 1423562--1423754 Score: 142
Period size: 44 Copynumber: 4.4 Consensus size: 44
1423552 TTTATCTTTT
* * *
1423562 AGTCTACTTGTCAGTTTTGACCTTGGAGACTTTCATTACCCTTA
1 AGTCTACCTGTCAGCTTTGACCCTGGAGACTTTCATTACCCTTA
* * *
1423606 AGTCTGCCTGTCAGCTTTGACCCTGGAAACTTT-ATTACTCTTA
1 AGTCTACCTGTCAGCTTTGACCCTGGAGACTTTCATTACCCTTA
* * * ** * * **
1423649 AGTATGCCTATC-GACTTTGACCCTAAAGACTTCCTTTATTCTTA
1 AGTCTACCTGTCAG-CTTTGACCCTGGAGACTTTCATTACCCTTA
* * * *
1423693 AGTCTGCCTGTCGGCTTTTGACCCTGGAGA-TTTCCTTTCCCTT-
1 AGTCTACCTGTCAGC-TTTGACCCTGGAGACTTTCATTACCCTTA
* * *
1423736 TGTTTACCTGTCGGCTTTG
1 AGTCTACCTGTCAGCTTTG
1423755 TCCTCAGTAA
Statistics
Matches: 119, Mismatches: 26, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
42 5 0.04
43 46 0.39
44 55 0.46
45 13 0.11
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (44 bp):
AGTCTACCTGTCAGCTTTGACCCTGGAGACTTTCATTACCCTTA
Found at i:1423625 original size:44 final size:44
Alignment explanation
Indices: 1423570--1423735 Score: 158
Period size: 44 Copynumber: 3.8 Consensus size: 44
1423560 TTAGTCTACT
* *
1423570 TGTCAGTTTTGACCTTGGAGACTTTCATTACCCTTAAGTCTGCC
1 TGTCAGCTTTGACCCTGGAGACTTTCATTACCCTTAAGTCTGCC
* * *
1423614 TGTCAGCTTTGACCCTGGAAACTTT-ATTACTCTTAAGTATGCC
1 TGTCAGCTTTGACCCTGGAGACTTTCATTACCCTTAAGTCTGCC
* ** * * **
1423657 TATC-GACTTTGACCCTAAAGACTTCCTTTATTCTTAAGTCTGCC
1 TGTCAG-CTTTGACCCTGGAGACTTTCATTACCCTTAAGTCTGCC
* * *
1423701 TGTCGGCTTTTGACCCTGGAGA-TTTCCTTTCCCTT
1 TGTCAGC-TTTGACCCTGGAGACTTTCATTACCCTT
1423736 TGTTTACCTG
Statistics
Matches: 97, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
42 1 0.01
43 34 0.35
44 49 0.51
45 13 0.13
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.39
Consensus pattern (44 bp):
TGTCAGCTTTGACCCTGGAGACTTTCATTACCCTTAAGTCTGCC
Found at i:1424284 original size:11 final size:10
Alignment explanation
Indices: 1424252--1424331 Score: 64
Period size: 11 Copynumber: 8.2 Consensus size: 10
1424242 TTTTCAGCAT
1424252 AAAA-AATAA
1 AAAATAATAA
1424261 AAAAT-AT-A
1 AAAATAATAA
1424269 AAAATAAGTAA
1 AAAATAA-TAA
1424280 AAAATAATAA
1 AAAATAATAA
*
1424290 ATTAATAA-AA
1 A-AAATAATAA
*
1424300 AAAATCA-AA
1 AAAATAATAA
1424309 AAAATCAA-AA
1 AAAAT-AATAA
1424319 AAGAATAATAA
1 AA-AATAATAA
1424330 AA
1 AA
1424332 TAAAGTGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
8 6 0.10
9 18 0.31
10 15 0.25
11 20 0.34
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (10 bp):
AAAATAATAA
Found at i:1424300 original size:19 final size:17
Alignment explanation
Indices: 1424252--1424320 Score: 54
Period size: 18 Copynumber: 3.8 Consensus size: 17
1424242 TTTTCAGCAT
1424252 AAAA-AATAAAAAATATA
1 AAAATAATAAAAAA-ATA
1424269 AAAATAAGT-AAAAAATA
1 AAAATAA-TAAAAAAATA
1424286 ATAAATTAATAAAAAAAATCA
1 A-AAA-TAAT-AAAAAAAT-A
1424307 AAAA-AATCAAAAAA
1 AAAATAAT-AAAAAA
1424321 GAATAATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 8 0.18
18 20 0.45
19 4 0.09
20 10 0.23
21 2 0.05
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.17
Consensus pattern (17 bp):
AAAATAATAAAAAAATA
Found at i:1424334 original size:37 final size:36
Alignment explanation
Indices: 1424250--1424335 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 36
1424240 AGTTTTCAGC
* *
1424250 ATAAAAAATAAAAAATATAAAAATAAGTAAAAAATA
1 ATAAAAAATAAAAAAAATAAAAATAAGTAAAAAAGA
*
1424286 ATAAATTAATAAAAAAAATCAAAAA-AA-TCAAAAAAGA
1 ATAAA-AAATAAAAAAAAT-AAAAATAAGT-AAAAAAGA
1424323 ATAATAAAATAAA
1 ATAA-AAAATAAA
1424336 GTGAAAAGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
36 6 0.14
37 30 0.71
38 6 0.14
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (36 bp):
ATAAAAAATAAAAAAAATAAAAATAAGTAAAAAAGA
Found at i:1424682 original size:28 final size:28
Alignment explanation
Indices: 1424650--1424717 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1424640 TGAAAATCTA
* *
1424650 AAGCAGCCATATGGACACGTGAAGAAAC
1 AAGCAGCTATATGGACACATGAAGAAAC
* *
1424678 AAGCAGCTACATGGGCACATGAAGAAAC
1 AAGCAGCTATATGGACACATGAAGAAAC
1424706 AAGCAGCTATAT
1 AAGCAGCTATAT
1424718 CGAAACAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (28 bp):
AAGCAGCTATATGGACACATGAAGAAAC
Found at i:1426784 original size:160 final size:162
Alignment explanation
Indices: 1426503--1426803 Score: 423
Period size: 161 Copynumber: 1.9 Consensus size: 162
1426493 ATTGCAAAAT
*
1426503 TAAACTTTAATCATTCTTTTTAATCTTTTATATTCCTATGAGCATCCGTAGAGGTATAAAAGATT
1 TAAACTTTAATCATTCTTTTTAATCTTTTATATTCCTATGAGCATCCATAGAGGTATAAAAGATT
**
1426568 TTCAAAAACTTTTAGTATCTTTTCGAACTTCCATTAAGGTACAAAATAGTATTTTCAA-AAATAA
66 TTCAAAAACTTTTAGTATCTTTTCGAACTTCCATTAAGACACAAAATAGTATTTTCAAGAAATAA
*
1426632 ATTAAATTAAATTAACACTTTCATAAAAAAGA
131 ATAAAATTAAATTAACACTTTCATAAAAAAGA
* * *
1426664 TAAATTTTAATC-TTTTTTTCTAATCTTTTATATTCCTATGGGCATCCATA-AGGGTATAAAAGA
1 TAAACTTTAATCATTCTTTT-TAATCTTTTATATTCCTATGAGCATCCATAGA-GGTATAAAAGA
* * ** *
1426727 -TTTCAAAAACTTTTCGTATCTTTTTGAGTTTCCATTAAGACACGAAAT-GATATTTTCAAGAAA
64 TTTTCAAAAACTTTTAGTATCTTTTCGAACTTCCATTAAGACACAAAATAG-TATTTTCAAGAAA
*
1426790 TGAATAAAATTAAA
128 TAAATAAAATTAAA
1426804 CATAACATTA
Statistics
Matches: 123, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
159 1 0.01
160 57 0.46
161 65 0.53
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (162 bp):
TAAACTTTAATCATTCTTTTTAATCTTTTATATTCCTATGAGCATCCATAGAGGTATAAAAGATT
TTCAAAAACTTTTAGTATCTTTTCGAACTTCCATTAAGACACAAAATAGTATTTTCAAGAAATAA
ATAAAATTAAATTAACACTTTCATAAAAAAGA
Found at i:1428050 original size:155 final size:156
Alignment explanation
Indices: 1427458--1428051 Score: 729
Period size: 155 Copynumber: 3.8 Consensus size: 156
1427448 CTATCACTGG
* * *
1427458 GTCCGTTTTTATGCCGAAAGTGGGCATTTAGGATAGGTTCAAT-GCATTTCTAGTCTTTTAAAGT
1 GTCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTC-ATCGCATTTCTAGTCTTTTTAAGT
* * *
1427522 CCTTTAGGGTTGGCAGA-GTACTTTTACGTCGAAGGTATACCCACAAAGGCATTTTCGTACTTTT
65 CCTTTAGGGTT-GCTGAGGTACTTTTACGTCGAAGGTATACCCATAAGGGCATTTTCGTACTTTT
* * **
1427586 TTAGAACTAAGTCCTAGGTTGTCATCGG
129 TTAGAACTAAGTCCTAGGCTGTCACCAA
* * ** * *
1427614 GTCTGCTTTTATGCCGAAGGTGGGAAACTAGGATAGGTTCATCACATTTCTAGTCTTTTTAAGTT
1 GTCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCGCATTTCTAGTCTTTTTAAGTC
* * * * *
1427679 CTTTAAGATTG-TCGAGGTACTTTTACGTTGAAGGTATACCCATAA-GGCATCTTCGTACTTTCT
66 CTTTAGGGTTGCT-GAGGTACTTTTACGTCGAAGGTATACCCATAAGGGCATTTTCGTACTTTTT
* *
1427742 TAGAA-TCGAGTCCTAGGCTGTCACCAT
130 TAGAACT-AAGTCCTAGGCTGTCACCAA
*
1427769 GTCCGCTTTTATGCCGAAGGTGGGC-TATTAGGATAGGTTC--CACATTTCTAGTCTTTTTAAGT
1 GTCCGCTTTTATGCCGAAGGTGGGCAT-TTAGGATAGGTTCATCGCATTTCTAGTCTTTTTAAGT
* * * * * *
1427831 TCTTTAGGGTTGTTGGGGTACTTTTACGTCGAAGGTATACCTATAAGGGTATTTTCATACTTTTT
65 CCTTTAGGGTTGCTGAGGTACTTTTACGTCGAAGGTATACCCATAAGGGCATTTTCGTACTTTTT
1427896 TAGAACTAAGTCCTAGGCTGTCACCAA
130 TAGAACTAAGTCCTAGGCTGTCACCAA
* *
1427923 GTCCACTTTTATGCCGAAGGT-GGCATTTAGGATAGGTTCATCGTATTTCTAGTCTTTTTAAGTC
1 GTCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCGCATTTCTAGTCTTTTTAAGTC
* * * * * * *
1427987 CTTTAGGGTTACTGAGATACTTTCACGTCGAAAGTATACCCTTAAGGGTATTTTCGTAATTTTTT
66 CTTTAGGGTTGCTGAGGTACTTTTACGTCGAAGGTATACCCATAAGGGCATTTTCGTACTTTTTT
1428052 CTTGCACTTA
Statistics
Matches: 377, Mismatches: 50, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
153 77 0.20
154 60 0.16
155 152 0.40
156 88 0.23
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (156 bp):
GTCCGCTTTTATGCCGAAGGTGGGCATTTAGGATAGGTTCATCGCATTTCTAGTCTTTTTAAGTC
CTTTAGGGTTGCTGAGGTACTTTTACGTCGAAGGTATACCCATAAGGGCATTTTCGTACTTTTTT
AGAACTAAGTCCTAGGCTGTCACCAA
Found at i:1429890 original size:2 final size:2
Alignment explanation
Indices: 1429878--1429911 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1429868 ATTTTTCTTA
*
1429878 AT AT TT 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
1429912 CCAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1443951 original size:14 final size:14
Alignment explanation
Indices: 1443932--1443959 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1443922 AAATTATCCC
1443932 TTTAGTTTTAGATA
1 TTTAGTTTTAGATA
1443946 TTTAGTTTTAGATA
1 TTTAGTTTTAGATA
1443960 ACATAGTAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
TTTAGTTTTAGATA
Found at i:1445761 original size:32 final size:32
Alignment explanation
Indices: 1445725--1445795 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
1445715 TTCAACGATT
*
1445725 TGTATTGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1445757 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1445789 TGTATCG
1 TGTATCG
1445796 CTACGAAGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1445762 original size:13 final size:13
Alignment explanation
Indices: 1445744--1445768 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1445734 ACATAAGTGT
1445744 TGTATCGATACAA
1 TGTATCGATACAA
1445757 TGTATCGATACA
1 TGTATCGATACA
1445769 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1445781 original size:19 final size:19
Alignment explanation
Indices: 1445723--1445787 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
1445713 ATTTCAACGA
*
1445723 TTTGTATTGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1445742 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1445757 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1445774 TTTGTATCGATACA
1 TTTGTATCGATACA
1445788 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1445858 original size:13 final size:13
Alignment explanation
Indices: 1445840--1445864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1445830 ATTACTCAAA
1445840 TGTATCGATACAT
1 TGTATCGATACAT
1445853 TGTATCGATACA
1 TGTATCGATACA
1445865 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1445917 original size:52 final size:52
Alignment explanation
Indices: 1445873--1446001 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1445863 CACTAATCTT
1445873 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
1445925 TGTATCGATACATACAGGCAATTTTGCCCAGATGTATCGATACACCATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1445977 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1446002 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:1451413 original size:22 final size:22
Alignment explanation
Indices: 1451385--1451439 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1451375 TGGACATGTT
*
1451385 AAAAATGTATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1451407 AAAAATGCATGAAACATAATAA
1 AAAAATGCATGAAACATAATAA
1451429 AAAAATGCATG
1 AAAAATGCATG
1451440 GTCAAAGGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAAATGCATGAAACATAATAA
Found at i:1452397 original size:20 final size:20
Alignment explanation
Indices: 1452350--1452424 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
1452340 AAAAAGACAT
*
1452350 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1452369 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1452390 CATGTATCGATATATTAAAA
1 AATGTATCGATACATTCATA
*
1452410 AATGCATCGATACAT
1 AATGTATCGATACAT
1452425 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:1458045 original size:19 final size:20
Alignment explanation
Indices: 1458012--1458052 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1458002 GAAAATTTAA
**
1458012 AGAAAAAAAGGTAAAA-TAT
1 AGAAAAAAAAATAAAATTAT
1458031 AGAAAAAAAAATAAAATTAT
1 AGAAAAAAAAATAAAATTAT
1458051 AG
1 AG
1458053 GAACGATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.71, C:0.00, G:0.12, T:0.17
Consensus pattern (20 bp):
AGAAAAAAAAATAAAATTAT
Found at i:1460143 original size:97 final size:97
Alignment explanation
Indices: 1459972--1460160 Score: 299
Period size: 97 Copynumber: 1.9 Consensus size: 97
1459962 CAATAATAGG
* *
1459972 TTAAAGGCGATTATAGGAAGTTACAATATTATGAATGTTTTGGTAACATACGATGAATATTGATT
1 TTAAAGGCGATTATAGGAAGTTACAACATTATGAATGTTTTGGTAACATACGATGAATATTAATT
1460037 ATATAACAGCACGTTTGAA-GGTGTATTGCTTA
66 ATATAACAGCACGTTT-AAGGGTGTATTGCTTA
* ** *
1460069 TTAAGGGCGATTATAGGAAGTTACAACATTATGAATGTTTTGGTAACATATTATGGATATTAATT
1 TTAAAGGCGATTATAGGAAGTTACAACATTATGAATGTTTTGGTAACATACGATGAATATTAATT
*
1460134 ATATGACAGCACGTTTAAGGGTGTATT
66 ATATAACAGCACGTTTAAGGGTGTATT
1460161 ACCTATTCAA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
96 2 0.02
97 82 0.98
ACGTcount: A:0.34, C:0.08, G:0.21, T:0.37
Consensus pattern (97 bp):
TTAAAGGCGATTATAGGAAGTTACAACATTATGAATGTTTTGGTAACATACGATGAATATTAATT
ATATAACAGCACGTTTAAGGGTGTATTGCTTA
Found at i:1460446 original size:29 final size:29
Alignment explanation
Indices: 1460413--1460475 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
1460403 ACCTCTGTCA
1460413 AAAGTACTTATGCT-AAAGTACTTATGCCC
1 AAAGTACTTATGCTAAAAGTACTTATG-CC
* *
1460442 AAAGTATTTGTGCTAAAAGTACTTATGCC
1 AAAGTACTTATGCTAAAAGTACTTATGCC
1460471 AAAGT
1 AAAGT
1460476 GCCTGTGCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 19 0.61
30 12 0.39
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (29 bp):
AAAGTACTTATGCTAAAAGTACTTATGCC
Found at i:1460447 original size:15 final size:14
Alignment explanation
Indices: 1460413--1460475 Score: 72
Period size: 15 Copynumber: 4.4 Consensus size: 14
1460403 ACCTCTGTCA
*
1460413 AAAGTACTTATGCT
1 AAAGTACTTATGCC
1460427 AAAGTACTTATGCCC
1 AAAGTACTTATG-CC
* * *
1460442 AAAGTATTTGTGCTA
1 AAAGTACTTATGC-C
1460457 AAAGTACTTATGCC
1 AAAGTACTTATGCC
1460471 AAAGT
1 AAAGT
1460476 GCCTGTGCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
14 18 0.45
15 22 0.55
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (14 bp):
AAAGTACTTATGCC
Found at i:1460482 original size:29 final size:29
Alignment explanation
Indices: 1460413--1460483 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
1460403 ACCTCTGTCA
* *
1460413 AAAGTACTTATGCTAAAGTACTTATGCCC
1 AAAGTACCTGTGCTAAAGTACTTATGCCC
**
1460442 AAAGTATTTGTGCTAAAAGTACTTATG-CC
1 AAAGTACCTGTGCT-AAAGTACTTATGCCC
*
1460471 AAAGTGCCTGTGC
1 AAAGTACCTGTGC
1460484 CATAGAGTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (29 bp):
AAAGTACCTGTGCTAAAGTACTTATGCCC
Found at i:1462446 original size:3 final size:3
Alignment explanation
Indices: 1462440--1462491 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
1462430 TATTAATGCT
1462440 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1462488 ATA A
1 ATA A
1462492 ATATTAAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1462499 original size:7 final size:7
Alignment explanation
Indices: 1462442--1462499 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 7
1462432 TTAATGCTAT
1462442 AATAAT-
1 AATAATA
1462448 AATAAT-
1 AATAATA
1462454 AATAAT-
1 AATAATA
1462460 AATAAT-
1 AATAATA
1462466 AATAAT-
1 AATAATA
1462472 AATAAT-
1 AATAATA
1462478 AATAAT-
1 AATAATA
1462484 AATAATA
1 AATAATA
*
1462491 AATATTA
1 AATAATA
1462498 AA
1 AA
1462500 AAAAGTAAGT
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
6 42 0.84
7 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (7 bp):
AATAATA
Found at i:1464412 original size:14 final size:14
Alignment explanation
Indices: 1464388--1464429 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1464378 AAAGCATTTT
1464388 TGCTAAAAGTACTTG
1 TGCT-AAAGTACTTG
*
1464403 TGCTAAAGTATTTG
1 TGCTAAAGTACTTG
*
1464417 TGATAAAGTACTT
1 TGCTAAAGTACTT
1464430 ATGTCAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (14 bp):
TGCTAAAGTACTTG
Found at i:1464509 original size:14 final size:15
Alignment explanation
Indices: 1464488--1464526 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1464478 TAAAAGTACC
*
1464488 TATGCCAAAA-TACT
1 TATGCCAAAAGTAAT
*
1464502 TCTGCCAAAAGTAAT
1 TATGCCAAAAGTAAT
1464517 TATGCCAAAA
1 TATGCCAAAA
1464527 AGTGTTATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (15 bp):
TATGCCAAAAGTAAT
Found at i:1465104 original size:83 final size:82
Alignment explanation
Indices: 1464979--1465144 Score: 253
Period size: 83 Copynumber: 2.0 Consensus size: 82
1464969 TGAAAAGTTG
* * * *
1464979 AAAATGAACATTTCTTTTTACTAAAACTTTCATTTGATAGAAAATATAAAGTTGTCATAAGATTA
1 AAAATGAACATTTCTTCTCACTAAAACTTTCATTTGATAGAAAATACAAAGTTGCCATAAGATTA
*
1465044 TATAAAAGAAATGCAAT
66 TATAAAAGAAAAGCAAT
1465061 AAAATTGAACATTTCTTCTCACCT-AAACTTTCATTTGATAGAAAATACAAAGTTGCCATAAGAT
1 AAAA-TGAACATTTCTTCTCA-CTAAAACTTTCATTTGATAGAAAATACAAAGTTGCCATAAGAT
*
1465125 TATATAGAAGAAAAGCAAT
64 TATATAAAAGAAAAGCAAT
1465144 A
1 A
1465145 TAATAAGTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
82 4 0.05
83 70 0.92
84 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (82 bp):
AAAATGAACATTTCTTCTCACTAAAACTTTCATTTGATAGAAAATACAAAGTTGCCATAAGATTA
TATAAAAGAAAAGCAAT
Found at i:1466665 original size:16 final size:16
Alignment explanation
Indices: 1466646--1466689 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 16
1466636 AACAAATCAT
*
1466646 TAAATGAATAATTACA
1 TAAATGAATAATTAAA
1466662 TAAATGATGAATAATTAAA
1 T-AA--ATGAATAATTAAA
1466681 TAAATGAAT
1 TAAATGAAT
1466690 GATGAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 2 0.08
19 13 0.54
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (16 bp):
TAAATGAATAATTAAA
Found at i:1466673 original size:19 final size:19
Alignment explanation
Indices: 1466649--1466687 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1466639 AAATCATTAA
*
1466649 ATGAATAATTACATAAATG
1 ATGAATAATTAAATAAATG
1466668 ATGAATAATTAAATAAATG
1 ATGAATAATTAAATAAATG
1466687 A
1 A
1466688 ATGATGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.31
Consensus pattern (19 bp):
ATGAATAATTAAATAAATG
Found at i:1468842 original size:3 final size:3
Alignment explanation
Indices: 1468836--1468869 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1468826 CTTCTTCTTC
1468836 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1468870 AATTCTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1469036 original size:78 final size:78
Alignment explanation
Indices: 1468907--1469061 Score: 310
Period size: 78 Copynumber: 2.0 Consensus size: 78
1468897 TCTTCCCTTC
1468907 GAAGAAAAAAAAATTAAAAGAAATTTAACTAAAGATAAAAATATAGATAATTAAAATAAAAACGA
1 GAAGAAAAAAAAATTAAAAGAAATTTAACTAAAGATAAAAATATAGATAATTAAAATAAAAACGA
1468972 AATAAAAGAAAGG
66 AATAAAAGAAAGG
1468985 GAAGAAAAAAAAATTAAAAGAAATTTAACTAAAGATAAAAATATAGATAATTAAAATAAAAACGA
1 GAAGAAAAAAAAATTAAAAGAAATTTAACTAAAGATAAAAATATAGATAATTAAAATAAAAACGA
1469050 AATAAAAGAAAG
66 AATAAAAGAAAG
1469062 TGGGCCGATA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.68, C:0.03, G:0.11, T:0.18
Consensus pattern (78 bp):
GAAGAAAAAAAAATTAAAAGAAATTTAACTAAAGATAAAAATATAGATAATTAAAATAAAAACGA
AATAAAAGAAAGG
Found at i:1470114 original size:20 final size:21
Alignment explanation
Indices: 1470081--1470120 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1470071 TTTTATATTT
1470081 TTTAAATTATAAAAAAAATTA
1 TTTAAATTATAAAAAAAATTA
1470102 TTT-AATT-TAAAAAATAATT
1 TTTAAATTATAAAAAA-AATT
1470121 TCAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 8 0.44
21 3 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAATTATAAAAAAAATTA
Found at i:1470115 original size:17 final size:17
Alignment explanation
Indices: 1470093--1470130 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1470083 TAAATTATAA
*
1470093 AAAAAATTATTT-AATTT
1 AAAAAATAATTTCAA-TT
1470110 AAAAAATAATTTCAATT
1 AAAAAATAATTTCAATT
1470127 AAAA
1 AAAA
1470131 TAAGAGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAAATAATTTCAATT
Found at i:1471697 original size:12 final size:12
Alignment explanation
Indices: 1471682--1471722 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1471672 AAAAAAATTC
1471682 AAAAAATTAGAA
1 AAAAAATTAGAA
1471694 AAAAAATT-GAA
1 AAAAAATTAGAA
*
1471705 AATGAAATTA-AA
1 AA-AAAATTAGAA
1471717 AAAAAA
1 AAAAAA
1471723 GAGAGGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
AAAAAATTAGAA
Found at i:1471851 original size:9 final size:9
Alignment explanation
Indices: 1471837--1471946 Score: 52
Period size: 9 Copynumber: 12.2 Consensus size: 9
1471827 ATATTTAATG
1471837 ATTAAAAAA
1 ATTAAAAAA
1471846 ATTAAAAATA
1 ATTAAAAA-A
1471856 ATT-AAAAA
1 ATTAAAAAA
* *
1471864 TTTAAGAAATT
1 ATTAA-AAA-A
1471875 ATTAAAAAA
1 ATTAAAAAA
* *
1471884 A-GAGAAAA
1 ATTAAAAAA
*
1471892 A-TCAAAAA
1 ATTAAAAAA
1471900 A-TAAGGAAAA
1 ATTAA--AAAA
1471910 A-TAAAAAA
1 ATTAAAAAA
**
1471918 ATTCTAAAA
1 ATTAAAAAA
*
1471927 ATTAGAAAA
1 ATTAAAAAA
1471936 A-TAAAATAA
1 ATTAAAA-AA
1471945 AT
1 AT
1471947 AATATAAATA
Statistics
Matches: 77, Mismatches: 15, Indels: 17
0.71 0.14 0.16
Matches are distributed among these distances:
8 25 0.32
9 30 0.39
10 18 0.23
11 4 0.05
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:1471861 original size:19 final size:20
Alignment explanation
Indices: 1471837--1471884 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
1471827 ATATTTAATG
1471837 ATTAAAAAAATTAA-AAATA
1 ATTAAAAAAATTAAGAAATA
* *
1471856 ATT-AAAAATTTAAGAAATT
1 ATTAAAAAAATTAAGAAATA
1471875 ATTAAAAAAA
1 ATTAAAAAAA
1471885 GAGAAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 9 0.38
19 10 0.42
20 5 0.21
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
ATTAAAAAAATTAAGAAATA
Found at i:1471864 original size:10 final size:10
Alignment explanation
Indices: 1471837--1471882 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
1471827 ATATTTAATG
1471837 ATTAAAAA-A
1 ATTAAAAATA
1471846 ATTAAAAATA
1 ATTAAAAATA
1471856 ATTAAAAAT-
1 ATTAAAAATA
*
1471865 -TTAAGAAATT
1 ATTAA-AAATA
1471875 ATTAAAAA
1 ATTAAAAA
1471883 AAGAGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
8 4 0.12
9 12 0.36
10 13 0.39
11 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
ATTAAAAATA
Done.