Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold341
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: 1349338
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 9 of 9
Found at i:1237179 original size:27 final size:28
Alignment explanation
Indices: 1237117--1237191 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
1237107 GAATAAAGCA
* *
1237117 GGGGTTGGAGTATCCCCTAGGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
* *
1237145 GGAGTTGGAGTATCCCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
1237172 GGGGTTGGAGTATCTCCGAT
1 GGGGTTGGAGTATCCCCGAT
1237192 TGTGAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
27 23 0.56
28 18 0.44
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.25
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:1239679 original size:34 final size:33
Alignment explanation
Indices: 1239641--1239707 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
1239631 AACTTCCTAG
*
1239641 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAA-AAATGTATCGATACA
*
1239675 ATGTATCGATACACAGAAAAATGTATCGATACA
1 ATGTATCGATACAAAGAAAAATGTATCGATACA
1239708 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 14 0.45
34 17 0.55
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.25
Consensus pattern (33 bp):
ATGTATCGATACAAAGAAAAATGTATCGATACA
Found at i:1239680 original size:13 final size:13
Alignment explanation
Indices: 1239662--1239687 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1239652 CAAAGAATAG
1239662 ATGTATCGATACA
1 ATGTATCGATACA
1239675 ATGTATCGATACA
1 ATGTATCGATACA
1239688 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:1239749 original size:13 final size:13
Alignment explanation
Indices: 1239731--1239782 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
1239721 AGCTTCCTAG
1239731 CGATACATTGTAT
1 CGATACATTGTAT
1239744 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1239763 CGATACATTGTAT
1 CGATACATTGTAT
1239776 CGATACA
1 CGATACA
1239783 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1239763 original size:19 final size:19
Alignment explanation
Indices: 1239739--1239824 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
1239729 AGCGATACAT
1239739 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
1239758 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
1239771 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
** *
1239790 TGTATCGATACATTTACTGAA
1 TGTATCGATACA-AAACT-TA
1239811 TGTATCGATACAAA
1 TGTATCGATACAAA
1239825 TTATTGGAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
13 11 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:1239772 original size:32 final size:32
Alignment explanation
Indices: 1239731--1239803 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1239721 AGCTTCCTAG
1239731 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
1239763 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
1239795 CGATACATT
1 CGATACATT
1239804 TACTGAATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:1241491 original size:17 final size:20
Alignment explanation
Indices: 1241455--1241496 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 20
1241445 ACAAAAAAAT
1241455 TTTATAAATTACAGATTTAA
1 TTTATAAATTACAGATTTAA
1241475 TTTATAAA-TA-A-ATTTAA
1 TTTATAAATTACAGATTTAA
1241492 TTTAT
1 TTTAT
1241497 GATTATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 1 0.05
19 2 0.09
20 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTATAAATTACAGATTTAA
Found at i:1241574 original size:20 final size:20
Alignment explanation
Indices: 1241551--1241588 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1241541 AATTTAATTT
1241551 TTAAT-ATAATATATATTTTA
1 TTAATCATAAT-TATATTTTA
1241571 TTAATCATAATTATATTT
1 TTAATCATAATTATATTT
1241589 AATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TTAATCATAATTATATTTTA
Found at i:1242603 original size:20 final size:20
Alignment explanation
Indices: 1242528--1242622 Score: 56
Period size: 20 Copynumber: 4.8 Consensus size: 20
1242518 TAATTTGATT
*
1242528 TTTAATT-TTTTATTTA-TA
1 TTTAATTATTATATTTATTA
* *
1242546 TATTAATAATTATA-TCATTAA
1 T-TTAATTATTATATTTATT-A
* *
1242567 ATTAAATA-TATATTTTATTA
1 TTTAATTATTATA-TTTATTA
*
1242587 TTTAATTATTATATTTAATA
1 TTTAATTATTATATTTATTA
* *
1242607 TTTCACTA-TATATTTA
1 TTTAATTATTATATTTA
1242623 ATATATTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.02
19 19 0.33
20 29 0.50
21 9 0.16
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATTATTATATTTATTA
Found at i:1242620 original size:19 final size:19
Alignment explanation
Indices: 1242568--1242626 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
1242558 TATCATTAAA
* *
1242568 TTAAATATATATTTTATTAT
1 TTAACTATATA-TTTAATAT
*
1242588 TTAATTATTATATTTAATAT
1 TTAACTA-TATATTTAATAT
*
1242608 TTCACTATATATTTAATAT
1 TTAACTATATATTTAATAT
1242627 ATTTTTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.35
20 18 0.53
21 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TTAACTATATATTTAATAT
Found at i:1242670 original size:13 final size:13
Alignment explanation
Indices: 1242652--1242676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1242642 ATCTTAATAA
1242652 AATATATTTAATT
1 AATATATTTAATT
1242665 AATATATTTAAT
1 AATATATTTAAT
1242677 ATTTAATATA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATATTTAATT
Found at i:1244093 original size:20 final size:20
Alignment explanation
Indices: 1244068--1244105 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1244058 TACAATCTTA
*
1244068 TAATTATTTAATCATAGTAT
1 TAATTATTTAACCATAGTAT
1244088 TAATTATTTAACCATAGT
1 TAATTATTTAACCATAGT
1244106 GTAAAATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (20 bp):
TAATTATTTAACCATAGTAT
Found at i:1253608 original size:24 final size:22
Alignment explanation
Indices: 1253574--1253618 Score: 63
Period size: 24 Copynumber: 2.0 Consensus size: 22
1253564 AAAATTTAAA
1253574 TTTTTTTATTATAATTTTTTTT
1 TTTTTTTATTATAATTTTTTTT
*
1253596 TTTTTTTAAATTATGATTTTTTT
1 TTTTTTT--ATTATAATTTTTTT
1253619 CCTTGTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTTTTTATTATAATTTTTTTT
Found at i:1256048 original size:3 final size:3
Alignment explanation
Indices: 1256040--1256081 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1256030 ATCAGCTCAA
1256040 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1256082 TGTTAATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1258108 original size:21 final size:21
Alignment explanation
Indices: 1258066--1258108 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1258056 GTGTATAAAA
* * *
1258066 TTATTTATTTTTAATTTTTAT
1 TTATTTATTTTCAATATATAT
1258087 TTATTTATTTTCAATATATAT
1 TTATTTATTTTCAATATATAT
1258108 T
1 T
1258109 ATCATTATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTATTTATTTTCAATATATAT
Found at i:1260412 original size:2 final size:2
Alignment explanation
Indices: 1260405--1260436 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1260395 AAATATTTCA
1260405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1260437 CGTTGCAGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1261289 original size:25 final size:25
Alignment explanation
Indices: 1261241--1261289 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1261231 TCTATCACCA
* * *
1261241 ACACTACACGAAATATTAACTACTT
1 ACACTACACAAAAAAATAACTACTT
*
1261266 ACACTACACAAAAAAATAATTACT
1 ACACTACACAAAAAAATAACTACT
1261290 ATAATTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.51, C:0.22, G:0.02, T:0.24
Consensus pattern (25 bp):
ACACTACACAAAAAAATAACTACTT
Found at i:1261799 original size:14 final size:14
Alignment explanation
Indices: 1261777--1261806 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1261767 TTGCAGACGG
1261777 GTTAGTGATTATTA
1 GTTAGTGATTATTA
*
1261791 GTTATTGATTATTA
1 GTTAGTGATTATTA
1261805 GT
1 GT
1261807 GTTTTCTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (14 bp):
GTTAGTGATTATTA
Found at i:1264800 original size:16 final size:20
Alignment explanation
Indices: 1264751--1264795 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
1264741 ATTTAATACT
1264751 TTTAATATTAAAATTATTTA
1 TTTAATATTAAAATTATTTA
1264771 TTTAATATTAAAATTATTT-
1 TTTAATATTAAAATTATTTA
1264790 TTTAAT
1 TTTAAT
1264796 TAAATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.24
20 19 0.76
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTAATATTAAAATTATTTA
Found at i:1264804 original size:19 final size:20
Alignment explanation
Indices: 1264751--1264804 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
1264741 ATTTAATACT
*
1264751 TTTAATATTAAAATTATTTA
1 TTTAATATAAAAATTATTTA
*
1264771 TTTAATATTAAAATTATTT-
1 TTTAATATAAAAATTATTTA
1264790 TTTAAT-TAAATAATT
1 TTTAATATAAA-AATT
1264805 TAATTCAACT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
18 3 0.09
19 10 0.31
20 19 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATATAAAAATTATTTA
Found at i:1265460 original size:17 final size:17
Alignment explanation
Indices: 1265440--1265472 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1265430 ATATAAGTAT
1265440 ATTATATATATTAAAAA
1 ATTATATATATTAAAAA
1265457 ATTATATATATTAAAA
1 ATTATATATATTAAAA
1265473 TCATGTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATTATATATATTAAAAA
Found at i:1266368 original size:3 final size:3
Alignment explanation
Indices: 1266360--1266391 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1266350 TAATAGTTAA
1266360 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1266392 AGCAAGGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1268469 original size:3 final size:3
Alignment explanation
Indices: 1268463--1268521 Score: 109
Period size: 3 Copynumber: 19.7 Consensus size: 3
1268453 AATAAGAACA
*
1268463 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG TAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1268511 AAG AAG AAG AA
1 AAG AAG AAG AA
1268522 AGGGGTTGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:1272775 original size:14 final size:14
Alignment explanation
Indices: 1272756--1272784 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1272746 CATGATTTTT
1272756 AAATGAATGTATTA
1 AAATGAATGTATTA
1272770 AAATGAATGTATTA
1 AAATGAATGTATTA
1272784 A
1 A
1272785 TACTTTCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (14 bp):
AAATGAATGTATTA
Found at i:1272961 original size:51 final size:51
Alignment explanation
Indices: 1272902--1273007 Score: 212
Period size: 51 Copynumber: 2.1 Consensus size: 51
1272892 AGCTTTACAC
1272902 GTATTGATACCATTGCTTCCAAAGGTCATATTTTGTTATTTTAAATGCAAT
1 GTATTGATACCATTGCTTCCAAAGGTCATATTTTGTTATTTTAAATGCAAT
1272953 GTATTGATACCATTGCTTCCAAAGGTCATATTTTGTTATTTTAAATGCAAT
1 GTATTGATACCATTGCTTCCAAAGGTCATATTTTGTTATTTTAAATGCAAT
1273004 GTAT
1 GTAT
1273008 CAATATTCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (51 bp):
GTATTGATACCATTGCTTCCAAAGGTCATATTTTGTTATTTTAAATGCAAT
Found at i:1280585 original size:21 final size:20
Alignment explanation
Indices: 1280558--1280605 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1280548 GTGATAATTT
*
1280558 ATAATTTTATTTTATTTTTC
1 ATAATTTTATATTATTTTTC
* *
1280578 ATATATTTTATATTGTTTTTT
1 ATA-ATTTTATATTATTTTTC
1280599 ATAATTT
1 ATAATTT
1280606 GTATGACAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
ATAATTTTATATTATTTTTC
Found at i:1281177 original size:21 final size:20
Alignment explanation
Indices: 1281137--1281177 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1281127 TTTTAGTAAT
* *
1281137 ATTTATATCTATAATTTATA
1 ATTTATATCTACAATATATA
1281157 ATTTATAATCTACAATATATA
1 ATTTAT-ATCTACAATATATA
1281178 CAAGCATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATATCTACAATATATA
Found at i:1283370 original size:20 final size:19
Alignment explanation
Indices: 1283347--1283385 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1283337 CTAAAGCACT
*
1283347 TAAAAGGCATTAAAAGCATC
1 TAAAAGGCATGAAAA-CATC
*
1283367 TAAAATGCATGAAAACATC
1 TAAAAGGCATGAAAACATC
1283386 CCGAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (19 bp):
TAAAAGGCATGAAAACATC
Found at i:1283520 original size:21 final size:20
Alignment explanation
Indices: 1283492--1283531 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1283482 GGTCCCTAAA
*
1283492 ATGCTAAAAATGCTTGAAAT
1 ATGCTAAAAATGCATGAAAT
*
1283512 ATGCTTAAATATGCATGAAA
1 ATGC-TAAAAATGCATGAAA
1283532 CACTCATCCT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGCTAAAAATGCATGAAAT
Found at i:1285038 original size:153 final size:151
Alignment explanation
Indices: 1284628--1285076 Score: 407
Period size: 154 Copynumber: 2.9 Consensus size: 151
1284618 TGTTATATAT
* * * * *
1284628 AAAAAAA-TGTAAAACTCATAAAA-AATTGAA-TCTCCAAAAATTGATTTAATATGAATTTAAAT
1 AAAAAAATTATAAAACTCATAAAATAAATGAATTCTTC-AAAACT-ATTTTATATGAA-TTAAAT
* ** * * **
1284690 GAA-AATATTTAATGAATTTTAAAAATTATAAACTTAGAAAAATCCCATTGAAAAAATTTACAGA
63 -AATAATATTTAAAGAATTTTGGAAATTATAAACTTTGAAAAATCCTATT-AAAAAATTTATGGA
**
1284754 GTAGAAAACCTT-GTAACTTGGTAATAG
126 GTAGAAAA--TTCGTATTTTGGTAATAG
* * * * * * * *
1284781 AAAAAAATTATAAAACTTATAAAATGAATTAATTGTTTTAAAACTGTTTTAATATGAACTAAACA
1 AAAAAAATTATAAAACTCATAAAATAAATGAATT-CTTCAAAACTATTTT-ATATGAATTAAATA
* *
1284846 ATAATATCTGAAA-AA-ATTGGAAATTATAAAC-TTGAAAAAATCCTATTAAAAAAATTTATGGA
64 ATAATAT-TTAAAGAATTTTGGAAATTATAAACTTTG-AAAAATCCTATT-AAAAAATTTATGGA
*
1284908 GTAGAAAATTTCGTATTTTGGTAA-CG
126 GTAGAAAA-TTCGTATTTTGGTAATAG
* * * *
1284934 GAAAAAATTTTAAAACTCATAAAATAAATGAATTCTTCAAAACTAATTTTCTATGAATTGAATAA
1 AAAAAAATTATAAAACTCATAAAATAAATGAATTCTTCAAAACT-ATTTTATATGAATTAAATAA
*
1284999 TAATATTTAAAGAATTTTGGAAGTTATAAACTTTGAAAAA-CCTTATT-AAAAATTTATGGAGTA
65 TAATATTTAAAGAATTTTGGAAATTATAAACTTTGAAAAATCC-TATTAAAAAATTTATGGAGTA
1285062 GAAAATTCTGTATTT
129 GAAAATTC-GTATTT
1285077 CAAAAATAGA
Statistics
Matches: 239, Mismatches: 42, Indels: 32
0.76 0.13 0.10
Matches are distributed among these distances:
150 3 0.01
151 31 0.13
152 29 0.12
153 68 0.28
154 73 0.31
155 18 0.08
156 16 0.07
157 1 0.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (151 bp):
AAAAAAATTATAAAACTCATAAAATAAATGAATTCTTCAAAACTATTTTATATGAATTAAATAAT
AATATTTAAAGAATTTTGGAAATTATAAACTTTGAAAAATCCTATTAAAAAATTTATGGAGTAGA
AAATTCGTATTTTGGTAATAG
Found at i:1286298 original size:43 final size:43
Alignment explanation
Indices: 1286150--1286299 Score: 120
Period size: 43 Copynumber: 3.5 Consensus size: 43
1286140 AGAAAGGTGT
* * ** * * *
1286150 AAACCATGCAAATCAATGAGTCAGTAAGGTATTGGCTGGGATG
1 AAACCATACAAACCAACAAGTCAGTAAGGTGTTGGCCGAGATG
** * * * * **
1286193 AAATTATACAAACCAACAAGTTAGAAAGGAGTTGGTCGAGACA
1 AAACCATACAAACCAACAAGTCAGTAAGGTGTTGGCCGAGATG
****
1286236 AAACCATGTTTACCAACAAGTCAGTAAGGTGTTGGCCGAGATG
1 AAACCATACAAACCAACAAGTCAGTAAGGTGTTGGCCGAGATG
*
1286279 AAACCATACAAACCTACAAGT
1 AAACCATACAAACCAACAAGT
1286300 TAGAAGGGAG
Statistics
Matches: 75, Mismatches: 32, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.40, C:0.17, G:0.22, T:0.21
Consensus pattern (43 bp):
AAACCATACAAACCAACAAGTCAGTAAGGTGTTGGCCGAGATG
Found at i:1286313 original size:43 final size:42
Alignment explanation
Indices: 1286189--1286809 Score: 221
Period size: 43 Copynumber: 14.8 Consensus size: 42
1286179 TATTGGCTGG
** *
1286189 GATGAAATTATACAAACCAACAAGTTAGAAAGGAGTTGGTCGA
1 GATGAAACCATACAAACCAACAAGTTAG-AAGGAGTTGGCCGA
** **** * *
1286232 GACAAAACCATGTTTACCAACAAGTCAGTAAGGTGTTGGCCGA
1 GATGAAACCATACAAACCAACAAGTTAG-AAGGAGTTGGCCGA
* *
1286275 GATGAAACCATACAAACCTACAAGTTAGAAGGGAGTTGG-GGAA
1 GATGAAACCATACAAACCAACAAGTTAGAA-GGAGTTGGCCG-A
** * ** *
1286318 GACAAAATCATATTTAA-CAACGAA-TTAGAA-G-G-T---CAA
1 GATGAAACCATA-CAAACCAAC-AAGTTAGAAGGAGTTGGCCGA
** ** * * * * *
1286354 GACAAAACTGTACGAACTAATAAGTTAGAAGGAAGTTGGTCGG
1 GATGAAACCATACAAACCAACAAGTTAGAAGG-AGTTGGCCGA
** * ** *
1286397 GATGAAACCATACTTACTAATGAGTTAGAAGGTGTTGGCC-A
1 GATGAAACCATACAAACCAACAAGTTAGAAGGAGTTGGCCGA
** * * * *
1286438 GGATGAAACCATATGAACCAACGAGTTAGTAGGGTGTTGGTCGA
1 -GATGAAACCATACAAACCAACAAGTTAG-AAGGAGTTGGCCGA
* * * * ** *
1286482 GATAAAACCATACTAACCAATAAGTTAGAAGGGTGTTGGTTGG
1 GATGAAACCATACAAACCAACAAGTTAGAA-GGAGTTGGCCGA
* ** ** * * *
1286525 GACGAAACCATACGTACCAATGAGTTAAAAGGTGCTGGCCGA
1 GATGAAACCATACAAACCAACAAGTTAGAAGGAGTTGGCCGA
** * * * * *
1286567 GACAAAACTAT-CGAACCAATAAG-TAG--GGTGTTGGCCAA
1 GATGAAACCATACAAACCAACAAGTTAGAAGGAGTTGGCCGA
* *
1286605 GACGAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCG-
1 GATGAAACCATACAAACCAACAAGTTAG-AAGGAGTTGGCCGA
* * * * *
1286647 GCATGAAACCATATAAACCAACGAGTTCGAAGGTGTTGGCCGG
1 G-ATGAAACCATACAAACCAACAAGTTAGAAGGAGTTGGCCGA
* * * * * ** *
1286690 GATAAAACCATACAAACCAATAAGTAAGTAGGGTGTTGGTTGG
1 GATGAAACCATACAAACCAACAAGTTAG-AAGGAGTTGGCCGA
** * ** *
1286733 GATGAAACCATATGAACCAATAAGTTAGAAAAGGTTTTTGCCCGA
1 GATGAAACCATACAAACCAACAAGTTAG--AAGG-AGTTGGCCGA
*
1286778 GATGAAACCATA-AGAACCAACAAGTTCGAAGG
1 GATGAAACCATACA-AACCAACAAGTTAGAAGG
1286810 TGTCGGCTAG
Statistics
Matches: 437, Mismatches: 113, Indels: 56
0.72 0.19 0.09
Matches are distributed among these distances:
35 4 0.01
36 18 0.04
37 1 0.00
38 19 0.04
39 12 0.03
40 7 0.02
41 11 0.03
42 85 0.19
43 243 0.56
44 8 0.02
45 29 0.07
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (42 bp):
GATGAAACCATACAAACCAACAAGTTAGAAGGAGTTGGCCGA
Found at i:1286493 original size:85 final size:85
Alignment explanation
Indices: 1286175--1289190 Score: 403
Period size: 85 Copynumber: 36.0 Consensus size: 85
1286165 ATGAGTCAGT
* * ** * * **
1286175 AAGGTATTGGCTGGGATGAAATTATACAAACCAACAAGTTAGAAAGGAGTTGGTCGAGACAAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
* ** * *
1286240 CATGTTTACCAACAAGTCAG
66 CATATGAACCAATAAGTTAG
* * * * * * **
1286260 TAAGGTGTTGGCCGAGATGAAACCATACAAACCTACAAGTTAGAAGGGAGTTGG-GGAAGACAAA
1 -AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCG-AGATGAA
* * *
1286324 ATCATATTTAA-CAACGAA-TTAG
64 ACCATA-TGAACCAA-TAAGTTAG
** ** ** * * * *
1286346 AA-G-G-T---CAAGACAAAACTGTACGAACTAATAAGTTAG-AAGGAAGTTGGTCGGGATGAAA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGG-TGTTGGTCGAGATGAAA
* * *
1286404 CCATACT-TACTAATGAGTTAG
65 CCATA-TGAACCAATAAGTTAG
* * * * * *
1286425 AAGGTGTTGGCCAGGATGAAACCATATGAACCAACGAGTTAGTAGGGTGTTGGTCGAGATAAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
1286490 CATACT-AACCAATAAGTTAG
66 CATA-TGAACCAATAAGTTAG
** * * ** * * *
1286510 AAGGGTGTTGGTTGGGACGAAACCATACGTACCAATGAGTTA-AAAGGTGCTGGCCGAGA-CAAA
1 AA-GGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAA
*
1286573 AC-TATCGAACCAATAAG-TAG
65 CCATAT-GAACCAATAAGTTAG
** * * *
1286593 --GGTGTTGGCCAAGACGAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCG-GCATGAAA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAG-ATGAAA
* ** *
1286655 CCATATAAACCAACGAGTTCG
65 CCATATGAACCAATAAGTTAG
* * * * * * * *
1286676 AAGGTGTTGGCCGGGATAAAACCATACAAACCAATAAGTAAGTAGGGTGTTGGTTGGGATGAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
1286741 CATATGAACCAATAAGTTAG
66 CATATGAACCAATAAGTTAG
* * * * * * *
1286761 AAAAGGTTTTTGCCCGAGATGAAACCATAAGAACCAACAAGTTCG-AAGGTGTCGG-CTAGGATG
1 --AAGG-TGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGA-GATG
* * *
1286824 AAATCATATGAACTAATGAGTTAG
62 AAACCATATGAACCAATAAGTTAG
* * ** * * * * * *
1286848 TAAAGTGTTAGTTGGGATGAAACCATATGAACCAAAAAATAAGAAGGGTAAGAAGGGCATTGGCC
1 -AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAG-A----AAG--GTG--TTGGTC
* * *
1286913 AAGAT-AAGACCATA-CATACCAACAAGTTAG
56 GAGATGAA-ACCATATGA-ACCAATAAGTTAG
* * ** * * * *
1286943 AAGGTGTTGGTCGGGATGAAACCATACGAACTAATGAGTTA-ATAGGTATTGGCCGCGATGAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
* **
1287007 CATACGAACCAACGAGTTAG
66 CATATGAACCAATAAGTTAG
** * * * * * * * * * **
1287027 AAGGGTGTTGGTTGGGATAAAACCAGACGAATCAATAATTTAGTAGGGTGTTAG-CTGGGACAAA
1 AA-GGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTC-GAGATGAA
* * ** *
1287091 ACCATACGAGCCAACGAGTTAA
64 ACCATATGAACCAATAAGTTAG
** ** * * * * * *
1287113 AAGGGTGTT-AACGGAGACAAAACCATACGTACCAACAAGTTA-AAAAGTGTTTGTTGCGACGAA
1 AA-GGTGTTGGCCGG-GATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAA
* *
1287176 ACCATA-CATACCAACAA---AG
64 ACCATATGA-ACCAATAAGTTAG
*** ** * * * * ** * * *
1287195 AA-AAATTAACTGGGATGAAACTAGATGAGTCAATGAA--T-G-AAGAGTGATGG-CTAGGATGA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAA-CAAGTTAGAAAG-GTGTTGGTCGA-GATGA
*
1287254 AACCATACGAACCAATGAAG---G
63 AACCATATGAACCAAT-AAGTTAG
* * *** * * * * * *
1287275 AA--AGTTGACTAAGATGAAACTATA-TAAGTCAACGAAG---GAAGGGTATTGG-CCAGAATGA
1 AAGGTGTTGGCCGGGATGAAACCATACGAA-CCAAC-AAGTTAGAAAGGTGTTGGTCGAG-ATGA
* * *
1287333 AACCATATGAACCAACGAA--AAA
63 AACCATATGAACCAA-TAAGTTAG
* ** *** *** * ** * *
1287355 AAGTTGATT----GGGATGAAACCATAC-AAGTAGGTA-TT-GGTCGG-GATGAAACCATATG-A
1 AAGGTG-TTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTG-GTCGAGATGAA
*
1287411 A-C---T-AA-C--T-AGTCAG
64 ACCATATGAACCAATAAGTTAG
* * ** ** * ** * * * *
1287424 AAAAGTATTGGCTAGGACAAAACCATACGTACCAATGAGTTAG-AAGGTATTGGTTGGGATGAAG
1 -AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAA
* *
1287488 CCATATGAACTAATGAGTTAG
65 CCATATGAACCAATAAGTTAG
** ** * *
1287509 CAAGGTGTCAAG-TAGGATGAAACCATGCGAACCAAC-AGTTAGAAAGGTGTTGG-CTAGGATGA
1 -AAGGTGT-TGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGA-GATGA
* *
1287571 AAACATACGAACCAATAAGTTAG
63 AACCATATGAACCAATAAGTTAG
* * ** * * * * *
1287594 AAGGTGTTGGCAGAGACAAAACCATACAAACCAACGAGTTAGTAAGGTGTTAG-CCAGGATGAAA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGA-GATGAAA
* * **
1287658 CCATACGAAGCAACGAGTTAG
65 CCATATGAACCAATAAGTTAG
* * * **
1287679 TAGG-GCATTGGCCGGGATGAAACTATACGAACCAACAAGTTAG-AAGAGTGTTGG-CCAGGACA
1 AAGGTG--TTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAG-GTGTTGGTCGA-GATG
* * *
1287741 AAACCATACGTACCAATGAGTTA-
62 AAACCATATGAACCAATAAGTTAG
* * * ** * *
1287764 AAGGTATTAGCTGGGACAAAACCATATGAACCAACAAGTTAG-AAGAGTGTTGGTCGAGACGAAA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAG-GTGTTGGTCGAGATGAAA
** *
1287828 CCATATTTACCAATGAGTTAG
65 CCATATGAACCAATAAGTTAG
** * * * * * * * **
1287849 AAGGTGTTGATCGAGATGAAACCAAATGAACCAACGAGTTAGTAAA-GTGTTAGCCGGGACAAAA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAG-AAAGGTGTTGGTCGAGATGAAA
* *
1287913 CCATATG-ATC--TAACG-AAG
65 CCATATGAACCAATAA-GTTAG
** ** * * ** * * * * * **
1287931 AA-AAGTTAACTGGGATAAAACCATACGAGTC-A-ATGATATAAA-GTGTTGGTTGGGACAAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
* * *
1287992 CATACGAACCAACT-AGTCAA
66 CATATGAACCAA-TAAGTTAG
** ** * * * * *
1288012 AATAATGTTGGCTAGGATGAAACCATACGTACCAATAAGTTATAAA-ATGTTGG-CTATGATGAA
1 AA-GGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGA-GATGAA
* *
1288075 ACCATATGAATC---AAGTTAAT
64 ACCATATGAACCAATAAGTT-AG
** * * * * ** * *
1288095 AAGGTGTTGGCCAAGACGAAACCATATGAACCAATAAGTTAGAAAGGTATTATTTGGGATGAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
* * ** *
1288160 TATATGAACTAACGAGTTGG
66 CATATGAACCAATAAGTTAG
*** ** * * ** * * * * *
1288180 AAGGTGTTGGTTAGGACAAAACCAGACAAACCAATGAGTTAGTAGGGTATTGATCGGGATGAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
* * * *
1288245 TATACGAACTAACAAGTTAG
66 CATATGAACCAATAAGTTAG
* * * * *
1288265 AAGGGTATTAGCTGAGATGACACCATAC-ATACCAACAAGTTAG-AAGGTGTTGG-CTGAGATGA
1 AA-GGTGTTGGCCGGGATGAAACCATACGA-ACCAACAAGTTAGAAAGGTGTTGGTC-GAGATGA
*
1288327 AACCATATGAACCAACAAGTTAG
63 AACCATATGAACCAATAAGTTAG
*** ** * * **
1288350 AAGAGTGTTGATTGGGACAAAACCATAC-ATACCAACGAGTTAGAAA-GTGTTGG-CTGGGACAA
1 AAG-GTGTTGGCCGGGATGAAACCATACGA-ACCAACAAGTTAGAAAGGTGTTGGTC-GAGATGA
* **
1288412 AACCATATGAACTAACGAGTTAG
63 AACCATATGAACCAATAAGTTAG
* * ** * *** **
1288435 TAGGGTATTGGCCAAGATGAAATCATGTAAACCAACGAA---AGAAA---GTTGACCGAGATGAA
1 -AAGGTGTTGGCCGGGATGAAACCATACGAACCAAC-AAGTTAGAAAGGTGTTGGTCGAGATGAA
* **
1288494 ACCATACGAGTCAATAA---AGG
64 ACCATATGAACCAATAAGTTA-G
* * * ** * * ** *
1288514 AAGCATGTTGGCTGAGACAAAACCATACAAACTAACGAA---AGAAA---GTTGACCAAGATGAA
1 AAG-GTGTTGGCCGGGATGAAACCATACGAACCAAC-AAGTTAGAAAGGTGTTGGTCGAGATGAA
* ***
1288573 ACCACATGAGTTAATGAAG---G
64 ACCATATGAACCAAT-AAGTTAG
*** ** * * ** * * *
1288593 AAGGTGTTGGCTAAGACAAAACTATACCAACCAACTCGTTAGAAGGGTGTTGGTTGGGATGAAAC
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
* * *
1288658 CATACG-ATCAACTAA-TCAG
66 CATATGAACCAA-TAAGTTAG
* * * * * * * *
1288677 AAAGCTATT-GCCTGAGACGAAACCATACGTACCAACAAGTTA-AAAGGTGTTAGCCGGGATGAA
1 -AAGGTGTTGGCC-GGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAA
* * *
1288740 ACCCTATGAACTAACAAGTTA-
64 ACCATATGAACCAATAAGTTAG
* * * * * * *
1288761 ATAGGGTGTTGGCTGGGAAGAAACCATGCAAACTAACAAGTTAG-AAGG-GTTGG-CCAGGATAA
1 A-A-GGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGA-GATGA
* ** **
1288823 AACTATACAAACCAACGAGTTAG
63 AACCATATGAACCAATAAGTTAG
** * * * * * * * **
1288846 AAGGTGTTGATCGAGATGAAACCATATGAACGAACAAGTTTA-CAAGATGTTGGCCAAGACAAAA
1 AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAG-TTAGAAAGGTGTTGGTCGAGATGAAA
*
1288910 CCATATGAACCAACAAGTTAG
65 CCATATGAACCAATAAGTTAG
* * * ** * * * *
1288931 AAAGGTGTTAGCTGAGACAAAACCATAC-ATACTAACGAGTTAGAAA-GTATTGG-CTGGGATGA
1 -AAGGTGTTGGCCGGGATGAAACCATACGA-ACCAACAAGTTAGAAAGGTGTTGGTC-GAGATG-
* *
1288993 AAACCATACGAACCAACAAGTTAG
62 AAACCATATGAACCAATAAGTTAG
* * ** * * ** * * *
1289017 AAAGATATTGGTTGGGATGAAACCATA-TATACTAATGAGTTA-AAAGGTGTTGGCCGCGACGAA
1 -AAGGTGTTGGCCGGGATGAAACCATACGA-ACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAA
**
1289080 ACCATACAAACCAACT-AGTTAG
64 ACCATATGAACCAA-TAAGTTAG
* * ** * * *
1289102 TAGGGTGTTGGTCGGGACAAAACCATATGAACCAACTAGTTAGAAA-GTGTTGG-CTAGGATGAA
1 -AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGA-GATGAA
* * * *
1289165 ATCATACGAACGAACAAGTTAG
64 ACCATATGAACCAATAAGTTAG
1289187 AAGG
1 AAGG
1289191 GTATTGGTTA
Statistics
Matches: 2141, Mismatches: 613, Indels: 354
0.69 0.20 0.11
Matches are distributed among these distances:
67 1 0.00
69 3 0.00
70 3 0.00
71 1 0.00
72 2 0.00
73 13 0.01
74 3 0.00
75 7 0.00
76 5 0.00
77 6 0.00
78 70 0.03
79 201 0.09
80 67 0.03
81 64 0.03
82 70 0.03
83 108 0.05
84 212 0.10
85 799 0.37
86 366 0.17
87 45 0.02
88 31 0.01
91 3 0.00
92 1 0.00
93 2 0.00
94 35 0.02
95 21 0.01
96 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (85 bp):
AAGGTGTTGGCCGGGATGAAACCATACGAACCAACAAGTTAGAAAGGTGTTGGTCGAGATGAAAC
CATATGAACCAATAAGTTAG
Found at i:1286641 original size:123 final size:124
Alignment explanation
Indices: 1286465--1286715 Score: 297
Period size: 123 Copynumber: 2.0 Consensus size: 124
1286455 CCAACGAGTT
* * * * * * ** *
1286465 AGTAGGGTGTTGGTCGAGATAAAACCATACTAACCAATAAGTTAGAAGGGTGTTGGTTGGGACGA
1 AGTAGGGTGTTGGCCAAGACAAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCGGCACGA
** * * *
1286530 AACCATACGTACCAATGAGTTAAAAGGTGCTGGCCGAGACAAAACTAT-CGAACCAATA
66 AACCATACAAACCAACGAGTTAAAAGGTGCTGGCCGAGACAAAACCATACAAACCAATA
* *
1286588 AGTAGGGTGTTGGCCAAGACGAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCGGCATGA
1 AGTAGGGTGTTGGCCAAGACAAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCGGCACGA
* ** * * *
1286653 AACCATATAAACCAACGAGTTCGAAGGTGTTGGCCGGGATAAAACCATACAAACCAATA
66 AACCATACAAACCAACGAGTTAAAAGGTGCTGGCCGAGACAAAACCATACAAACCAATA
1286712 AGTA
1 AGTA
1286716 AGTAGGGTGT
Statistics
Matches: 105, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
123 92 0.88
124 13 0.12
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (124 bp):
AGTAGGGTGTTGGCCAAGACAAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCGGCACGA
AACCATACAAACCAACGAGTTAAAAGGTGCTGGCCGAGACAAAACCATACAAACCAATA
Found at i:1286856 original size:130 final size:128
Alignment explanation
Indices: 1286608--1286882 Score: 329
Period size: 130 Copynumber: 2.1 Consensus size: 128
1286598 TGGCCAAGAC
** * *
1286608 GAAACCATACAAACCAACAAGTTAGAAAGGTGTTGGCCGGCATGAAACCATATAAACCAACGAGT
1 GAAACCATATGAACCAACAAGTTAGAAAGGTGTTGCCCGGCATGAAACCATATAAACCAACAAGT
* * ** *
1286673 TCGAAGGTGTTGGCCGGGATAAAACCATACAAACCAATAAGTAAGTAGGGTGTTGGTTGGGAT
66 TCGAAGGTGTCGGCCAGGATAAAACCATACAAACCAATAAGTAAGTAAAGTGTTAGTTGGGAT
* *
1286736 GAAACCATATGAACCAATAAGTTAGAAAAGGTTTTTGCCCGAG-ATGAAACCATA-AGAACCAAC
1 GAAACCATATGAACCAACAAGTTAG-AAAGG-TGTTGCCCG-GCATGAAACCATATA-AACCAAC
* * * ** * * *
1286799 AAGTTCGAAGGTGTCGGCTAGGATGAAATCATATGAACTAATGAGTTAGTAAAGTGTTAGTTGGG
62 AAGTTCGAAGGTGTCGGCCAGGATAAAACCATACAAACCAATAAGTAAGTAAAGTGTTAGTTGGG
1286864 AT
127 AT
1286866 GAAACCATATGAACCAA
1 GAAACCATATGAACCAA
1286883 AAAATAAGAA
Statistics
Matches: 124, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
128 22 0.18
129 6 0.05
130 95 0.77
131 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.24, T:0.21
Consensus pattern (128 bp):
GAAACCATATGAACCAACAAGTTAGAAAGGTGTTGCCCGGCATGAAACCATATAAACCAACAAGT
TCGAAGGTGTCGGCCAGGATAAAACCATACAAACCAATAAGTAAGTAAAGTGTTAGTTGGGAT
Found at i:1286968 original size:42 final size:42
Alignment explanation
Indices: 1286921--1287192 Score: 158
Period size: 43 Copynumber: 6.4 Consensus size: 42
1286911 CCAAGATAAG
**
1286921 ACCATAC-ATACCAACAAGTTAGAAGGTGTTGGTCGGGATGAA
1 ACCATACGA-ACCAACAAGTTAGAAGGTGTTGGTCGGGACAAA
* ** * * * **
1286963 ACCATACGAACTAATGAGTTA-ATAGGTATTGGCCGCGATGAA
1 ACCATACGAACCAACAAGTTAGA-AGGTGTTGGTCGGGACAAA
* * *
1287005 ACCATACGAACCAACGAGTTAGAAGGGTGTTGGTTGGGATAAA
1 ACCATACGAACCAACAAGTTAGAA-GGTGTTGGTCGGGACAAA
* * * * * *
1287048 ACCAGACGAATCAATAATTTAGTAGGGTGTTAG-CTGGGACAAA
1 ACCATACGAACCAACAAGTTAG-AAGGTGTTGGTC-GGGACAAA
* * * **
1287091 ACCATACGAGCCAACGAGTTAAAAGGGTGTT-AACGGAGACAAA
1 ACCATACGAACCAACAAGTTAGAA-GGTGTTGGTCGG-GACAAA
* * * * * * *
1287134 ACCATACGTACCAACAAGTTAAAAAGTGTTTGTTGCGACGAA
1 ACCATACGAACCAACAAGTTAGAAGGTGTTGGTCGGGACAAA
1287176 ACCATAC-ATACCAACAA
1 ACCATACGA-ACCAACAA
1287193 AGAAAAATTA
Statistics
Matches: 178, Mismatches: 41, Indels: 22
0.74 0.17 0.09
Matches are distributed among these distances:
41 1 0.01
42 80 0.45
43 96 0.54
44 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.21
Consensus pattern (42 bp):
ACCATACGAACCAACAAGTTAGAAGGTGTTGGTCGGGACAAA
Found at i:1287057 original size:43 final size:43
Alignment explanation
Indices: 1286915--1287154 Score: 175
Period size: 43 Copynumber: 5.6 Consensus size: 43
1286905 CATTGGCCAA
* * *
1286915 GATAAGACCATAC-ATACCAACAAGTTAGAA-GGTGTTGGTCGG
1 GATAAAACCATACGA-ACCAACGAGTTAGAAGGGTGTTGGCCGG
* * * * *
1286957 GATGAAACCATACGAACTAATGAGTTA-ATA-GGTATTGGCCGC
1 GATAAAACCATACGAACCAACGAGTTAGA-AGGGTGTTGGCCGG
* **
1286999 GATGAAACCATACGAACCAACGAGTTAGAAGGGTGTTGGTTGG
1 GATAAAACCATACGAACCAACGAGTTAGAAGGGTGTTGGCCGG
* * ** * * * *
1287042 GATAAAACCAGACGAATCAATAATTTAGTAGGGTGTTAGCTGG
1 GATAAAACCATACGAACCAACGAGTTAGAAGGGTGTTGGCCGG
* * * **
1287085 GACAAAACCATACGAGCCAACGAGTTAAAAGGGTGTT-AACGG
1 GATAAAACCATACGAACCAACGAGTTAGAAGGGTGTTGGCCGG
* * *
1287127 AGACAAAACCATACGTACCAACAAGTTA
1 -GATAAAACCATACGAACCAACGAGTTA
1287155 AAAAGTGTTT
Statistics
Matches: 155, Mismatches: 38, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
41 1 0.01
42 58 0.37
43 96 0.62
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (43 bp):
GATAAAACCATACGAACCAACGAGTTAGAAGGGTGTTGGCCGG
Found at i:1287370 original size:79 final size:79
Alignment explanation
Indices: 1287173--1287382 Score: 210
Period size: 79 Copynumber: 2.7 Consensus size: 79
1287163 TTGTTGCGAC
* * * * * *
1287173 GAAACCATAC-ATACCAAC-AAAGAAAAATTAACTGGGATGAAACTAGATGAGTCAATGAATGAA
1 GAAACCATACGA-ACCAACGAAA-AAAAGTTGACTGGGATGAAACTATATAAGTCAACGAAGGAA
* *
1287236 GAGTGATGGCTAGGAT
64 GAGTGATGGCCAGAAT
* ** ** *
1287252 GAAACCATACGAACCAATGAAGGAAAGTTGACTAAGATGAAACTATATAAGTCAACGAAGGAAGG
1 GAAACCATACGAACCAACGAAAAAAAGTTGACTGGGATGAAACTATATAAGTCAACGAAGGAAGA
1287317 GT-ATTGGCCAGAAT
66 GTGA-TGGCCAGAAT
* * * *
1287331 GAAACCATATGAACCAACGAAAAAAAGTTGATTGGGATGAAACCATACAAGT
1 GAAACCATACGAACCAACGAAAAAAAGTTGACTGGGATGAAACTATATAAGT
1287383 AGGTATTGGT
Statistics
Matches: 105, Mismatches: 23, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
78 1 0.01
79 101 0.96
80 3 0.03
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (79 bp):
GAAACCATACGAACCAACGAAAAAAAGTTGACTGGGATGAAACTATATAAGTCAACGAAGGAAGA
GTGATGGCCAGAAT
Found at i:1287433 original size:43 final size:42
Alignment explanation
Indices: 1287385--1287505 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 42
1287375 ATACAAGTAG
1287385 GTATTGGTCGGGATGAAACCATATGAACTAACT-AGTCAGAAAA
1 GTATTGGTCGGGATGAAACCATATGAACTAA-TGAGTCAG-AAA
* ** * * * * *
1287428 GTATTGG-CTAGGACAAAACCATACGTACCAATGAGTTAGAAG
1 GTATTGGTC-GGGATGAAACCATATGAACTAATGAGTCAGAAA
* *
1287470 GTATTGGTTGGGATGAAGCCATATGAACTAATGAGT
1 GTATTGGTCGGGATGAAACCATATGAACTAATGAGT
1287506 TAGCAAGGTG
Statistics
Matches: 59, Mismatches: 16, Indels: 7
0.72 0.20 0.09
Matches are distributed among these distances:
42 31 0.53
43 28 0.47
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (42 bp):
GTATTGGTCGGGATGAAACCATATGAACTAATGAGTCAGAAA
Found at i:1287633 original size:127 final size:127
Alignment explanation
Indices: 1287395--1287807 Score: 370
Period size: 127 Copynumber: 3.2 Consensus size: 127
1287385 GTATTGGTCG
* * * * * * *
1287395 GGATGAAACCATATGAACTAACTAGTCAGAAAAGTATTGGCTAGGA-CAAAACCATACGTACCAA
1 GGATGAAACCATACGAACCAACGAGTTAGAAAGGTATTGGCTAGGATGAAAA-CATACGAACCAA
* * ** ** * * * *
1287459 TGAGTTAGAAGGTATTGGTTGGGATGAAGCCATATGAACTAATGAGTTAGCAAGGTGTCAAG-TA
65 TAAGTTAGAAGGTGTTGG-CAGGACAAAACCATACGAACCAATGAGTTAGCAAGGTGT-AAGCCA
* *
1287523 GGATGAAACCATGCGAACCAAC-AGTTAGAAAGGTGTTGGCTAGGATGAAAACATACGAACCAAT
1 GGATGAAACCATACGAACCAACGAGTTAGAAAGGTATTGGCTAGGATGAAAACATACGAACCAAT
* * * *
1287587 AAGTTAGAAGGTGTTGGCAGAGACAAAACCATACAAACCAACGAGTTAGTAAGGTGTTAGCCA
66 AAGTTAGAAGGTGTTGGCAG-GACAAAACCATACGAACCAATGAGTTAGCAAGGTGTAAGCCA
* * * * **
1287650 GGATGAAACCATACGAAGCAACGAGTTAGTAGGGCATTGGCCGGGATG-AAACTATACGAACCAA
1 GGATGAAACCATACGAACCAACGAGTTAGAAAGGTATTGGCTAGGATGAAAAC-ATACGAACCAA
* * * * **
1287714 CAAGTTAGAAGAGTGTTGGCCAGGACAAAACCATACGTACCAATGAGTTA--AAGGTATTAGCTG
65 TAAGTTAGAAG-GTGTTGG-CAGGACAAAACCATACGAACCAATGAGTTAGCAAGGTGTAAGCCA
** * *
1287777 GGACAAAACCATATGAACCAACAAGTTAGAA
1 GGATGAAACCATACGAACCAACGAGTTAGAA
1287808 GAGTGTTGGT
Statistics
Matches: 235, Mismatches: 43, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
126 3 0.01
127 135 0.57
128 63 0.27
129 31 0.13
130 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (127 bp):
GGATGAAACCATACGAACCAACGAGTTAGAAAGGTATTGGCTAGGATGAAAACATACGAACCAAT
AAGTTAGAAGGTGTTGGCAGGACAAAACCATACGAACCAATGAGTTAGCAAGGTGTAAGCCA
Found at i:1288073 original size:42 final size:43
Alignment explanation
Indices: 1287988--1288080 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 43
1287978 GGTTGGGACA
1287988 AAACCATACGAACCAACTAGTCAAAATAATGTTGGCTAGGATG
1 AAACCATACGAACCAACTAGTCAAAATAATGTTGGCTAGGATG
* * * *
1288031 AAACCATACGTACCAA-TAAGTTATAA-AATGTTGGCTATGATG
1 AAACCATACGAACCAACT-AGTCAAAATAATGTTGGCTAGGATG
1288073 AAACCATA
1 AAACCATA
1288081 TGAATCAAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 24 0.53
43 21 0.47
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (43 bp):
AAACCATACGAACCAACTAGTCAAAATAATGTTGGCTAGGATG
Found at i:1288341 original size:42 final size:42
Alignment explanation
Indices: 1287443--1289190 Score: 560
Period size: 43 Copynumber: 41.7 Consensus size: 42
1287433 GGCTAGGACA
* ** * * *
1287443 AAACCATACGTACCAATGAGTTAGAAGGTATTGGTTGGGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* * * ** **
1287485 AAGCCATATGAACTAATGAGTTAGCAAGGTGTCAAG-T-AGGATG
1 AAACCATACGAACCAACAAGTTAG-AAGGTGT-TGGCTGA-GATG
*
1287528 AAACCATGCGAACCAAC-AGTTAGAAAGGTGTTGGCT-AGGATG
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGA-GATG
* * * **
1287570 AAAACATACGAACCAATAAGTTAGAAGGTGTTGGCAGAGACA
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* * * *
1287612 AAACCATACAAACCAACGAGTTAGTAAGGTGTTAGC-CAGGATG
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGA-GATG
* * * * *
1287655 AAACCATACGAAGCAACGAGTTAGTAGG-GCATTGGCCGGGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTG--TTGGCTGAGATG
* * **
1287698 AAACTATACGAACCAACAAGTTAGAAGAGTGTTGGC-CAGGACA
1 AAACCATACGAACCAACAAGTTAGAAG-GTGTTGGCTGA-GATG
* ** * * * **
1287741 AAACCATACGTACCAATGAGTTA-AAGGTATTAGCTGGGACA
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* *
1287782 AAACCATATGAACCAACAAGTTAGAAGAGTGTTGG-TCGAGACG
1 AAACCATACGAACCAACAAGTTAGAAG-GTGTTGGCT-GAGATG
*** ** *
1287825 AAACCATATTTACCAATGAGTTAGAAGGTGTT-GATCGAGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCT-GAGATG
* * * * * * * **
1287867 AAACCAAATGAACCAACGAGTTAGTAAAGTGTTAGCCGGGACA
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGAGATG
* * * * ** * *
1287910 AAACCATATGATCTAACGAAG--A-AA--AGTTAACTGGGATA
1 AAACCATACGAACCAAC-AAGTTAGAAGGTGTTGGCTGAGATG
** ** * * **
1287948 AAACCATACGAGTCAATGA-TATA-AA-GTGTTGGTTGGGACA
1 AAACCATACGAACCAACAAGT-TAGAAGGTGTTGGCTGAGATG
* * * **
1287988 AAACCATACGAACCAACTAGTCAAAATAATGTTGGCT-AGGATG
1 AAACCATACGAACCAACAAGTTAGAA-GGTGTTGGCTGA-GATG
* * * **
1288031 AAACCATACGTACCAATAAGTTATAAAATGTTGGCT-ATGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGA-GATG
* * * ** *
1288073 AAACCATATG-A--ATCAAGTTAATAAGGTGTTGGCCAAGACG
1 AAACCATACGAACCAACAAGTT-AGAAGGTGTTGGCTGAGATG
* * * *** *
1288113 AAACCATATGAACCAATAAGTTAGAAAGGTATTATTTGGGATG
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGAGATG
* * * * * * **
1288156 AAACTATATGAACTAACGAGTTGGAAGGTGTTGG-TTAGGACA
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGA-GATG
* * ** * * * *
1288198 AAACCAGACAAACCAATGAGTTAGTAGG-GTATTGATCGGGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGT-TGGCT-GAGATG
* * * *
1288241 AAACTATACGAACTAACAAGTTAGAAGGGTATTAGCTGAGATG
1 AAACCATACGAACCAACAAGTTAGAA-GGTGTTGGCTGAGATG
*
1288284 ACACCATAC-ATACCAACAAGTTAGAAGGTGTTGGCTGAGATG
1 AAACCATACGA-ACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* ** * **
1288326 AAACCATATGAACCAACAAGTTAGAAGAGTGTTGATTGGGACA
1 AAACCATACGAACCAACAAGTTAGAAG-GTGTTGGCTGAGATG
* * * **
1288369 AAACCATAC-ATACCAACGAGTTAGAAAGTGTTGGCTGGGACA
1 AAACCATACGA-ACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* * * * * **
1288411 AAACCATATGAACTAACGAGTTAGTAGGGTATTGGCCAAGATG
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGAGATG
* *** * * *
1288454 AAATCATGTAAACCAACGAA---AGAA--AGTTGACCGAGATG
1 AAACCATACGAACCAAC-AAGTTAGAAGGTGTTGGCTGAGATG
** * * **
1288492 AAACCATACGAGTCAATAA---AGGAAGCATGTTGGCTGAGACA
1 AAACCATACGAACCAACAAGTTA-GAAG-GTGTTGGCTGAGATG
* * * * **
1288533 AAACCATACAAACTAACGAA---AGAA--AGTTGACCAAGATG
1 AAACCATACGAACCAAC-AAGTTAGAAGGTGTTGGCTGAGATG
* * *** * * **
1288571 AAACCACATGAGTTAATGAAG---GAAGGTGTTGGCTAAGACA
1 AAACCATACGAACCAA-CAAGTTAGAAGGTGTTGGCTGAGATG
* * ** * *
1288611 AAACTATACCAACCAACTCGTTAGAAGGGTGTTGGTTGGGATG
1 AAACCATACGAACCAACAAGTTAGAA-GGTGTTGGCTGAGATG
* * * * * *
1288654 AAACCATACG-ATCAACTAA-TCAGAAAGCTATTGCCTGAGACG
1 AAACCATACGAACCAAC-AAGTTAG-AAGGTGTTGGCTGAGATG
* * * * *
1288696 AAACCATACGTACCAACAAGTTAAAAGGTGTTAGCCGGGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* * * * *
1288738 AAACCCTATGAACTAACAAGTTA-ATAGGGTGTTGGCTGGGAAG
1 AAACCATACGAACCAACAAGTTAGA-A-GGTGTTGGCTGAGATG
* * * * *
1288781 AAACCATGCAAACTAACAAGTTAGAAGG-GTTGGC-CAGGATA
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGA-GATG
* * * *
1288822 AAACTATACAAACCAACGAGTTAGAAGGTGTT-GATCGAGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCT-GAGATG
* * * * ** **
1288864 AAACCATATGAACGAACAAGTTTACAAGATGTTGGCCAAGACA
1 AAACCATACGAACCAACAAG-TTAGAAGGTGTTGGCTGAGATG
* * **
1288907 AAACCATATGAACCAACAAGTTAGAAAGGTGTTAGCTGAGACA
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGAGATG
* * * * *
1288950 AAACCATAC-ATACTAACGAGTTAGAAAGTATTGGCTGGGATG
1 AAACCATACGA-ACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* * * *
1288992 AAAACCATACGAACCAACAAGTTAGAAAGATATTGGTTGGGATG
1 -AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCTGAGATG
* * ** * * * *
1289036 AAACCATA-TATACTAATGAGTTAAAAGGTGTTGGCCGCGACG
1 AAACCATACGA-ACCAACAAGTTAGAAGGTGTTGGCTGAGATG
* * * * **
1289078 AAACCATACAAACCAACTAGTTAGTAGGGTGTTGG-TCGGGACA
1 AAACCATACGAACCAACAAGTTAG-AAGGTGTTGGCT-GAGATG
* * *
1289121 AAACCATATGAACCAACTAGTTAGAAAGTGTTGGCT-AGGATG
1 AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGA-GATG
* *
1289163 AAATCATACGAACGAACAAGTTAGAAGG
1 AAACCATACGAACCAACAAGTTAGAAGG
1289191 GTATTGGTTA
Statistics
Matches: 1261, Mismatches: 358, Indels: 174
0.70 0.20 0.10
Matches are distributed among these distances:
37 4 0.00
38 69 0.05
39 10 0.01
40 70 0.06
41 101 0.08
42 428 0.34
43 548 0.43
44 29 0.02
45 2 0.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.21
Consensus pattern (42 bp):
AAACCATACGAACCAACAAGTTAGAAGGTGTTGGCTGAGATG
Found at i:1288551 original size:79 final size:78
Alignment explanation
Indices: 1288463--1288627 Score: 231
Period size: 79 Copynumber: 2.1 Consensus size: 78
1288453 GAAATCATGT
* * *
1288463 AAACCAACGAAAGAAAGTTGACCGAGATGAAACCATACGAGTCAATAAAGGAAGCATGTTGGCTG
1 AAACCAACGAAAGAAAGTTGACCAAGATGAAACCACACGAGTCAATAAAGGAAG-ATGTTGGCTA
1288528 AGACAAAACCATAC
65 AGACAAAACCATAC
* * * * *
1288542 AAACTAACGAAAGAAAGTTGACCAAGATGAAACCACATGAGTTAATGAAGGAAGGTGTTGGCTAA
1 AAACCAACGAAAGAAAGTTGACCAAGATGAAACCACACGAGTCAATAAAGGAAGATGTTGGCTAA
*
1288607 GACAAAACTATAC
66 GACAAAACCATAC
*
1288620 CAACCAAC
1 AAACCAAC
1288628 TCGTTAGAAG
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
78 27 0.36
79 48 0.64
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (78 bp):
AAACCAACGAAAGAAAGTTGACCAAGATGAAACCACACGAGTCAATAAAGGAAGATGTTGGCTAA
GACAAAACCATAC
Found at i:1289064 original size:128 final size:125
Alignment explanation
Indices: 1288769--1289267 Score: 351
Period size: 128 Copynumber: 3.9 Consensus size: 125
1288759 TAATAGGGTG
* * * * * * * * * *
1288769 TTGGCTGGGAAGAAACCATGCAAACTAACAAGTTAGAAGG-GTTGGC-CAGGATAAAACTATACA
1 TTGGCTAGGATGAAACCATACGAACGAACAAGTTAAAAGGTGTTAGCTGA-GACAAAACCATACA
* * * * ** * * * *
1288832 AACCAACGAGTTAGAAGGTGTTGATCGAGATGAAACCATATGAACGAACAAGTTTA-CAAGATG
65 AACTAACGAGTTAGAAGGTATTGGT-GGGACAAAACCATACGAACCAACAAG-TTAGAAAG-TA
* * ** * *
1288895 TTGGCCAAGACAAAACCATATGAACCAACAAGTTAGAAAGGTGTTAGCTGAGACAAAACCATACA
1 TTGGCTAGGATGAAACCATACGAACGAACAAGTTA-AAAGGTGTTAGCTGAGACAAAACCATACA
* * *
1288960 TACTAACGAGTTAGAAAGTATTGGCTGGGATGAAAACCATACGAACCAACAAGTTAGAAAGATA
65 AACTAACGAGTTAGAAGGTATTGG-TGGGA-CAAAACCATACGAACCAACAAGTTAGAAAG-TA
* * * * ** * * * *
1289024 TTGGTTGGGATGAAACCATA-TATACTAATGAGTTAAAAGGTGTTGGCCGCGACGAAACCATACA
1 TTGGCTAGGATGAAACCATACGA-ACGAACAAGTTAAAAGGTGTTAGCTGAGACAAAACCATACA
* * * * * * *
1289088 AACCAACTAGTTAGTAGGGTGTTGGTCGGGACAAAACCATATGAACCAACTAGTTAGAAAGTG
65 AACTAACGAGTTAG-AAGGTATTGGT-GGGACAAAACCATACGAACCAACAAGTTAGAAAGTA
* * * * *
1289151 TTGGCTAGGATGAAATCATACGAACGAACAAGTTAGAAGG-GTATTGGTTAGGACAAAACCATAC
1 TTGGCTAGGATGAAACCATACGAACGAACAAGTTAAAAGGTGT-TAGCTGA-GACAAAACCATAC
* *
1289215 AAACTAATGAGTTAGAAGGGTATTGGTTGGGACAAAACCATACGTACCAACAA
64 AAACTAACGAGTTAGAA-GGTATTGG-TGGGACAAAACCATACGAACCAACAA
1289268 AGGAAGGGTG
Statistics
Matches: 287, Mismatches: 72, Indels: 26
0.75 0.19 0.07
Matches are distributed among these distances:
126 28 0.10
127 38 0.13
128 161 0.56
129 60 0.21
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (125 bp):
TTGGCTAGGATGAAACCATACGAACGAACAAGTTAAAAGGTGTTAGCTGAGACAAAACCATACAA
ACTAACGAGTTAGAAGGTATTGGTGGGACAAAACCATACGAACCAACAAGTTAGAAAGTA
Found at i:1289228 original size:85 final size:85
Alignment explanation
Indices: 1288907--1289267 Score: 332
Period size: 85 Copynumber: 4.2 Consensus size: 85
1288897 GGCCAAGACA
* * * * * * *
1288907 AAACCATATGAACCAACAAGTTAGAAAGGTGTTAGCTGAGACAAAACCATACATACTAACGAGTT
1 AAACCATACGAACCAACAAGTTAGAAAGGTATTGGTTGGGACAAAACCATACAAACTAATGAGTT
* *
1288972 AGAAAGTATTGGCTGGGATG
66 AGAAAGTGTTGGCTAGGATG
* ** * *
1288992 AAAACCATACGAACCAACAAGTTAGAAAGATATTGGTTGGGATGAAACCATATATACTAATGAGT
1 -AAACCATACGAACCAACAAGTTAGAAAGGTATTGGTTGGGACAAAACCATACAAACTAATGAGT
* *
1289057 TA-AAAGGTGTTGGC-CGCGACG
65 TAGAAA-GTGTTGGCTAG-GATG
* * * * * * ** *
1289078 AAACCATACAAACCAACTAGTTAGTAGGGTGTTGGTCGGGACAAAACCATATGAACCAACT-AGT
1 AAACCATACGAACCAACAAGTTAGAAAGGTATTGGTTGGGACAAAACCATACAAACTAA-TGAGT
1289142 TAGAAAGTGTTGGCTAGGATG
65 TAGAAAGTGTTGGCTAGGATG
* * * *
1289163 AAATCATACGAACGAACAAGTTAGAAGGGTATTGGTTAGGACAAAACCATACAAACTAATGAGTT
1 AAACCATACGAACCAACAAGTTAGAAAGGTATTGGTTGGGACAAAACCATACAAACTAATGAGTT
* * * * **
1289228 AGAAGGGTATTGGTTGGGACA
66 AGAA-AGTGTTGGCTAGGATG
*
1289249 AAACCATACGTACCAACAA
1 AAACCATACGAACCAACAA
1289268 AGGAAGGGTG
Statistics
Matches: 221, Mismatches: 47, Indels: 14
0.78 0.17 0.05
Matches are distributed among these distances:
84 1 0.00
85 123 0.56
86 97 0.44
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (85 bp):
AAACCATACGAACCAACAAGTTAGAAAGGTATTGGTTGGGACAAAACCATACAAACTAATGAGTT
AGAAAGTGTTGGCTAGGATG
Found at i:1289234 original size:43 final size:43
Alignment explanation
Indices: 1288903--1289257 Score: 207
Period size: 43 Copynumber: 8.3 Consensus size: 43
1288893 TGTTGGCCAA
** ** * * * * *
1288903 GACAAAACCATATGAACCAACAAGTTAGAAAGGTGTTAGCTGA
1 GACAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
* * * * *
1288946 GACAAAACCATACATACTAACGAGTTAGAA-AGTATTGGCTGG
1 GACAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
* * ** * *
1288988 GATGAAAACCATACGAACCAACAAGTTAGAAAGATATTGGTTGG
1 GA-CAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
** * * * * * ** *
1289032 GATGAAACCATATATACTAATGAGTTA-AAAGGTGTTGGCCGC
1 GACAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
* * * *
1289074 GACGAAACCATACAAACCAACT-AGTTAGTAGGGTGTTGGTCGG
1 GACAAAACCATACAAACCAA-TGAGTTAGAAGGGTATTGGTTGG
** * * * *
1289117 GACAAAACCATATGAACCAACT-AGTTAGAA-AGTGTTGGCTAG
1 GACAAAACCATACAAACCAA-TGAGTTAGAAGGGTATTGGTTGG
** * * * ** *
1289159 GATGAAATCATACGAACGAACAAGTTAGAAGGGTATTGGTTAG
1 GACAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
*
1289202 GACAAAACCATACAAACTAATGAGTTAGAAGGGTATTGGTTGG
1 GACAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
1289245 GACAAAACCATAC
1 GACAAAACCATAC
1289258 GTACCAACAA
Statistics
Matches: 243, Mismatches: 63, Indels: 12
0.76 0.20 0.04
Matches are distributed among these distances:
42 72 0.30
43 160 0.66
44 11 0.05
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.21
Consensus pattern (43 bp):
GACAAAACCATACAAACCAATGAGTTAGAAGGGTATTGGTTGG
Found at i:1292948 original size:20 final size:20
Alignment explanation
Indices: 1292923--1292976 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1292913 GTTACAAGCA
*
1292923 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
1292943 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
1292963 ATGTATCGATACAA
1 ATGTATCGATACAA
1292977 ACAGTGGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1293641 original size:25 final size:25
Alignment explanation
Indices: 1293607--1293662 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
1293597 CCCCCTAGAT
* *
1293607 TAAAAATTCTCCCCGTTAATCAAAG
1 TAAAAATTCTCCCCCTTAAACAAAG
1293632 TAAAAATTCTCCCCCTTAAACAAAG
1 TAAAAATTCTCCCCCTTAAACAAAG
*
1293657 GAAAAA
1 TAAAAA
1293663 AATATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.23
Consensus pattern (25 bp):
TAAAAATTCTCCCCCTTAAACAAAG
Found at i:1295574 original size:13 final size:13
Alignment explanation
Indices: 1295556--1295582 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1295546 ATAGTAACCC
1295556 ATGTATCGATACA
1 ATGTATCGATACA
1295569 ATGTATCGATACA
1 ATGTATCGATACA
1295582 A
1 A
1295583 GAAATGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1301432 original size:52 final size:52
Alignment explanation
Indices: 1301362--1301482 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1301352 GAAAATTTAT
*
1301362 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1301414 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1301466 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1301483 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1301495 original size:52 final size:51
Alignment explanation
Indices: 1301362--1301502 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1301352 GAAAATTTAT
1301362 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1301414 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1301466 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1301503 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1301509 original size:13 final size:13
Alignment explanation
Indices: 1301491--1301515 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1301481 CAAAGATCAG
1301491 TGTATCGATACAA
1 TGTATCGATACAA
1301504 TGTATCGATACA
1 TGTATCGATACA
1301516 TGTGAGTAAT
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:1301601 original size:13 final size:13
Alignment explanation
Indices: 1301583--1301607 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1301573 CAAAAAAATA
1301583 TGTATCGATACAT
1 TGTATCGATACAT
1301596 TGTATCGATACA
1 TGTATCGATACA
1301608 ACATTTTGTG
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:1302643 original size:49 final size:49
Alignment explanation
Indices: 1302497--1302654 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
1302487 AAAAGTGATA
* * * * *
1302497 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
1302548 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1302601 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1302649 ATGATG
1 AAGATG
1302655 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
48 8 0.09
49 37 0.44
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:1302714 original size:170 final size:170
Alignment explanation
Indices: 1302426--1302946 Score: 961
Period size: 170 Copynumber: 3.1 Consensus size: 170
1302416 TTTTAGAGAT
* * *
1302426 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATGATGATGAGAAAA
*
1302491 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
1302556 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1302597 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
1302662 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
66 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
*
1302727 GTCAACGTGCTGATTCAAGGTCAGCTACATTGAACTTAAA
131 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1302767 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
1302832 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
66 TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
* * *
1302897 GTCAACGTGCTGATTCAAGGCCAGCAATATTGGACTTAAA
131 GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
1302937 GATGAAGATG
1 GATGAAGATG
1302947 AGAAAAGTGA
Statistics
Matches: 341, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
170 294 0.86
171 47 0.14
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (170 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGAGAAAAG
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGAT
GTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:1302813 original size:49 final size:49
Alignment explanation
Indices: 1302667--1302824 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
1302657 AAAAGTGATA
* * * *
1302667 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * * *
1302718 AAAAAGGATGTCAACGTGCTGATTCAAGGTCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1302771 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
1302819 ATGATG
1 AAGATG
1302825 AGAAAAGTGA
Statistics
Matches: 84, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
48 8 0.10
49 36 0.43
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.42
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:1302945 original size:61 final size:61
Alignment explanation
Indices: 1302880--1303068 Score: 176
Period size: 61 Copynumber: 3.1 Consensus size: 61
1302870 ATTGGGCTTA
1302880 AAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATG
1 AAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATG
** * * * * *
1302941 AAGATGAG-AAAAGTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTT----
1 AAGATGAGAAAAAG-GAT---G-T--CAACGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1303001 A--
59 ATG
* * *
1303002 AAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 AAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATG
1303063 AAGATG
1 AAGATG
1303069 CCAATATGCT
Statistics
Matches: 98, Mismatches: 16, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
55 26 0.27
57 1 0.01
58 1 0.01
59 1 0.01
60 5 0.05
61 28 0.29
62 5 0.05
63 1 0.01
64 1 0.01
65 1 0.01
67 28 0.29
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (61 bp):
AAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATG
Found at i:1303105 original size:49 final size:49
Alignment explanation
Indices: 1302959--1303537 Score: 648
Period size: 49 Copynumber: 11.6 Consensus size: 49
1302949 AAAAGTGATA
* * * * *
1302959 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT--G
* ** * *
1303010 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
*
1303063 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAA-GATG
* * * * *
1303114 ATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
*
1303163 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * * *
1303209 --G-TGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTCAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* *
1303255 AAGATGCCAATATGCTGATTCAAGGTCAGCGATATTGGACTTAAAATGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAA-GATG
* * * * *
1303306 ATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
*
1303355 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
* * * *
1303404 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G
*
1303454 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGG
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G
*
1303506 AAAAGGTGCCAATATGCTGATTCAAGGCCAGC
1 --AAGATGCCAATATGCTGATTCAAGGCCAGC
1303538 TATATTGGGC
Statistics
Matches: 450, Mismatches: 61, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
43 33 0.07
44 3 0.01
45 1 0.00
46 2 0.00
47 1 0.00
48 3 0.01
49 196 0.44
50 14 0.03
51 79 0.18
52 79 0.18
53 1 0.00
54 2 0.00
55 36 0.08
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG
Found at i:1303167 original size:100 final size:99
Alignment explanation
Indices: 1302959--1303545 Score: 823
Period size: 100 Copynumber: 5.9 Consensus size: 99
1302949 AAAAGTGATA
* * * * *
1302959 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-ATGAG---AAGG-TGCCAA
* * *
1303024 CGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
61 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
*
1303063 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGGTGCCAATGTG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGA-GAAGGTGCCAATGTG
1303128 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1303163 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T----T-A-AAGGTGCCAATGTGC
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGAGAAGGTGCCAATGTGC
* *
1303221 TGAGTCAAGGCTAGCTACATTGGACTTCAAGATG
66 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
1303255 AAGATGCCAATATGCTGATTCAAGGTCAGCGATATTGGACTTAAAATGATGATGGTGCCAATGTG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGA-GAAGGTGCCAATGTG
1303320 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1303355 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAA-GATGAAGGTGCCAATGTG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGA-GAAGGTGCCAATGTG
1303418 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* * *
1303454 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAAAAGGTGCCAAT
1 --AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA-AT-GAGAAGGTGCCAAT
* * *
1303519 ATGCTGATTCAAGGCCAGCTATATTGG
62 GTGCTGAGTCAAGGCCAGCTACATTGG
1303546 GCTTCGAAGG
Statistics
Matches: 443, Mismatches: 24, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
92 85 0.19
93 1 0.00
94 1 0.00
95 1 0.00
97 1 0.00
98 52 0.12
99 5 0.01
100 168 0.38
101 43 0.10
102 2 0.00
103 5 0.01
104 77 0.17
105 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (99 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGAGAAGGTGCCAATGTGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:1303352 original size:192 final size:194
Alignment explanation
Indices: 1303025--1303545 Score: 832
Period size: 192 Copynumber: 2.7 Consensus size: 194
1303015 GGATGTCAAC
* *
1303025 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1303090 AGCGATATTGGACTTAAAATGATGATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 AGCGATATTGGACTTAAAATGATGATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
1303155 TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-A-AAGGTGCCAAT
131 TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAAT
* * *
1303217 GTGCTGAGTCAAGGCTAGCTACATTGGACTTCAAGATGAAGATGCCAATATGCTGATTCAAGGTC
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
1303282 AGCGATATTGGACTTAAAATGATGATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
66 AGCGATATTGGACTTAAAATGATGATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
1303347 TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCC
131 TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A-GAAGGTGCC
1303412 AAT
192 AAT
*
1303415 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAG
1 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGATGCCAATATGCTGATTCAAG
* * * * * *
1303480 GCCAGCGACATTGGACTTAAAGATGGA-AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATT
63 GCCAGCGATATTGGACTTAAA-AT-GATGATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATT
1303544 GG
126 GG
1303546 GCTTCGAAGG
Statistics
Matches: 303, Mismatches: 15, Indels: 12
0.92 0.05 0.04
Matches are distributed among these distances:
192 175 0.58
196 1 0.00
198 46 0.15
199 1 0.00
201 42 0.14
202 36 0.12
203 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (194 bp):
GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCC
AGCGATATTGGACTTAAAATGATGATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAGAAGGTGCCAAT
Found at i:1303482 original size:52 final size:49
Alignment explanation
Indices: 1303026--1303545 Score: 656
Period size: 49 Copynumber: 10.5 Consensus size: 49
1303016 GATGTCAACG
* *
1303026 TGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
1303075 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAATGATGATGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTT-AAA-GATGAAGGTGCCAATA
* *
1303126 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
1303175 TGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * *
1303218 TGCTGAGTCAAGGCTAGCTACATTGGACTTCAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * * * *
1303267 TGCTGATTCAAGGTCAGCGATATTGGACTTAAAATGATGATGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTT-AAA-GATGAAGGTGCCAATA
* *
1303318 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
* * *
1303367 TGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
*
1303416 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
*
1303468 TGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
*
1303520 TGCTGATTCAAGGCCAGCTATATTGG
1 TGCTGATTCAAGGCCAGCTACATTGG
1303546 GCTTCGAAGG
Statistics
Matches: 406, Mismatches: 52, Indels: 23
0.84 0.11 0.05
Matches are distributed among these distances:
43 36 0.09
45 1 0.00
47 1 0.00
49 192 0.47
50 12 0.03
51 79 0.19
52 85 0.21
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
Found at i:1303594 original size:33 final size:32
Alignment explanation
Indices: 1303543--1303647 Score: 162
Period size: 33 Copynumber: 3.3 Consensus size: 32
1303533 CCAGCTATAT
*
1303543 TGGGC-TTCGAAG-GGTTGCCACCGACTTGTG
1 TGGGCTTTGGAAGAGGTTGCCACCGACTTGTG
1303573 TGGGCTTTGGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTGGAAG-AGGTTGCCACCGACTTGTG
1303606 TGGGCTTTAGGAAGA-GTTGCCACCGACTTGTG
1 TGGGCTTT-GGAAGAGGTTGCCACCGACTTGTG
1303638 TGGGCTTTGG
1 TGGGCTTTGG
1303648 GAAGGAAAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
30 5 0.07
31 8 0.11
32 25 0.36
33 27 0.39
34 5 0.07
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (32 bp):
TGGGCTTTGGAAGAGGTTGCCACCGACTTGTG
Found at i:1303834 original size:34 final size:32
Alignment explanation
Indices: 1303664--1304540 Score: 975
Period size: 34 Copynumber: 26.8 Consensus size: 32
1303654 AAAAAGATGT
* * *
1303664 CACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGC
1 CACGGAGTTGTGGGCTTTAAA--GAAGAAG-GTGC
* *
1303699 CACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGC
1 CACGGAGTTGTGGGCTTT-AAAGAAGAAGGTGC
*
1303732 CACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGC
1 CACGGAGTTGTGGGCTTT--AAA--GAAGAAG-GTGC
* *
1303769 CATGGAGTTGTGGGCTTTAAAAAAGAAGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
1303801 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
*
1303835 CACGGAGTTGTGGGCTTTAAAAAAGAAGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
1303867 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
*
1303901 CACGGAGTTGTGGGCTTTAAAAAAGAAGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
1303933 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
*
1303967 CACGGAGTTGTGGGCTTTAAAAAAGAAGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
1303999 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
**
1304033 CACGGAGTTGTGGGCTTTGGA-AAGAAGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
1304064 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
*
1304098 CACGGAGTTGTGGGCTTTGGAAAGAAGAAAGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
1304132 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGC
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGC
*
1304166 CACGGAGTTGTGGGCTTTAAAAAAGAAGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
*
1304198 CACGGAGTTGTGGGC-TT-AA-AAG--GATGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
*
1304225 CACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGC
1 CACGGAGTTGTGGGCTTTA-AA-GAAGAAG-GTGC
* * *
1304259 CACAGAGTTGTGGGC-TTAGGAGGAAAAAGAGTGC
1 CACGGAGTTGTGGGCTTTA--AAGAAGAAG-GTGC
*
1304293 CACAGAGTTGTGGGCTTTAAA-AAG-A-GTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
* *
1304322 CACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGC
1 CACGGAGTTGTGGGCTTT---AA-AGAAGAAG-GTGC
*
1304359 CACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGC
1 CACGGAGTTGTGGGCTTT-AA-AGAAGAAGGTGC
1304393 CACGGAGTTGTGGGCTTT---GAAG-A-GTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
* *
1304420 CACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGC
1 CACGGAGTTGTGGGCTTT---AA-AGAAGAAG-GTGC
*
1304457 CACGGAGTTGTGGGC-TTAAAGATG-AGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
* *
1304487 CACGGAATTGTGGGC-TTAAAGATG-AGGTGC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
*
1304517 CACGGAATTGTGGGCTTTAAAGAA
1 CACGGAGTTGTGGGCTTTAAAGAA
1304541 AAAATGCCAC
Statistics
Matches: 756, Mismatches: 42, Indels: 92
0.85 0.05 0.10
Matches are distributed among these distances:
27 42 0.06
28 1 0.00
29 28 0.04
30 50 0.07
31 42 0.06
32 150 0.20
33 33 0.04
34 302 0.40
35 37 0.05
36 11 0.01
37 60 0.08
ACGTcount: A:0.30, C:0.12, G:0.37, T:0.21
Consensus pattern (32 bp):
CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGC
Found at i:1303848 original size:66 final size:66
Alignment explanation
Indices: 1303695--1304534 Score: 1068
Period size: 66 Copynumber: 12.8 Consensus size: 66
1303685 GGGAAAAAGA
* * *
1303695 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAA-AAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAA--GAA
*
1303760 AAAG
63 GAAG
*
1303764 AGTGCCATGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGA
1 -GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGA
1303829 AG
65 AG
1303831 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1303896 G
66 G
1303897 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1303962 G
66 G
1303963 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1304028 G
66 G
**
1304029 GTGCCACGGAGTTGTGGGCTTT-GGAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1304093 G
66 G
* *
1304094 GTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAAAGTGCCACGGAGTTGTGGGCTTTGGAAAGAAG
1 GTGCCACGGAGTTGTGGGCTTT--AAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAG
1304159 AAG
64 AAG
1304162 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGC-TT---AA-AAG--
1 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
1304220 G
66 G
* * * *
1304221 ATGCCACGGAGTTGTGGGC-TTAGAAGGAAA-AAGAGTGCCACAGAGTTGTGGGCTTAGG-AGGA
1 GTGCCACGGAGTTGTGGGCTTTA-AA--AAAGAAG-GTGCCACGGAGTTGTGGGCTTTGGAAAGA
*
1304283 AAAAG
62 AGAAG
* * *
1304288 AGTGCCACAGAGTTGTGGGCTTT-AAAAAG-A-GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAA
1 -GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTG-GAA-AGAA
*
1304350 AAAG
63 GAAG
*
1304354 AGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-----GAA
1 -GTGCCACGGAGTTGTGGGCTTTAAA-A-AAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAA
1304414 G-A-
63 GAAG
* *
1304416 GTGCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGCCACGGAGTTGTGGGC-TT--AAAG
1 GTGCCACGGAGTTGTGGGCTTT--AAA-A-AAGAAG-GTGCCACGGAGTTGTGGGCTTTGGAAAG
*
1304478 ATG-AG
61 AAGAAG
* * * *
1304483 GTGCCACGGAATTGTGGGC-TTAAAGATG-AGGTGCCACGGAATTGTGGGCTTT
1 GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTT
1304535 AAAGAAAAAA
Statistics
Matches: 699, Mismatches: 39, Indels: 73
0.86 0.05 0.09
Matches are distributed among these distances:
58 3 0.00
59 21 0.03
60 21 0.03
61 49 0.07
62 4 0.01
63 34 0.05
64 26 0.04
65 72 0.10
66 281 0.40
67 28 0.04
68 79 0.11
69 34 0.05
70 26 0.04
71 21 0.03
ACGTcount: A:0.29, C:0.13, G:0.37, T:0.21
Consensus pattern (66 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAA
G
Found at i:1303918 original size:100 final size:98
Alignment explanation
Indices: 1303664--1304534 Score: 1002
Period size: 100 Copynumber: 8.8 Consensus size: 98
1303654 AAAAAGATGT
* * * * *
1303664 CACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAG
1 CACGGAGTTGTGGGCTTTAAA--GAAGAAG-GTGCCACGGAGTTGTGGGCTTT-AAAGAAGAAGG
*
1303729 TGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGC
62 TGCCACGGAGTTGTGGGCTTTGAAAA---AAGAAGAGTGC
* *
1303769 CATGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTG
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--AAAGAAGAAGGTG
1303834 CCACGGAGTTGTGGGCTTT-AAAAAAGAAG-GTGC
64 CCACGGAGTTGTGGGCTTTGAAAAAAGAAGAGTGC
*
1303867 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAAAGAAGGTG
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAGAAGGTG
*
1303932 CCACGGAGTTGTGGGCTTTGGAAAGAAGAAG-GTGC
64 CCACGGAGTTGTGGGCTTT-GAAAAAAGAAGAGTGC
*
1303967 CACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTG
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--AAAGAAGAAGGTG
*
1304032 CCACGGAGTTGTGGGCTTTG--GAAAGAAG-GTGC
64 CCACGGAGTTGTGGGCTTTGAAAAAAGAAGAGTGC
*
1304064 CACGGAGTTGTGGGCTTTGGAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGGAAAGAAGAAAG
1 CACGGAGTTGTGGGCTTT--AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--AAAGAAGAAGG
*
1304129 TGCCACGGAGTTGTGGGCTTTGGAAAGAAGAAG-GTGC
62 TGCCACGGAGTTGTGGGCTTT-GAAAAAAGAAGAGTGC
* *
1304166 CACGGAGTTGTGGGCTTTAAAAAAGAAGGTGCCACGGAGTTGTGGGC-TT-AA-AAG--GATGCC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCC
* *
1304226 ACGGAGTTGTGGGCTTAGAAGGAAA-AAGAGTGC
66 ACGGAGTTGTGGGCTTTGAA-AAAAGAAGAGTGC
* * * *
1304259 CACAGAGTTGTGGGC-TTAGGAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA-AAG-A-GT
1 CACGGAGTTGTGGGCTTTA--AAGAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAAGAAGAAGGT
* *
1304320 GCCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGC
63 GCCACGGAGTTGTGGGCTTTG-AAA-A-AAGAAGAGTGC
*
1304359 CACGGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTT---GAAG-A-GTG
1 CACGGAGTTGTGGGCTTT-AA-AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAGAAGGTG
* *
1304419 CCACGGAGTCGTGGGCTTTGAAAAGAGAAAAAGAGTGC
64 CCACGGAGTTGTGGGCTTTG-AAA-A-AAGAAGAGTGC
* * *
1304457 CACGGAGTTGTGGGC-TTAAAGATG-AGGTGCCACGGAATTGTGGGC-TTAAAGATG-AGGTGCC
1 CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCC
*
1304518 ACGGAATTGTGGGCTTT
66 ACGGAGTTGTGGGCTTT
1304535 AAAGAAAAAA
Statistics
Matches: 689, Mismatches: 45, Indels: 72
0.85 0.06 0.09
Matches are distributed among these distances:
92 9 0.01
93 42 0.06
94 26 0.04
95 24 0.03
96 10 0.01
97 75 0.11
98 146 0.21
99 74 0.11
100 166 0.24
101 9 0.01
102 55 0.08
103 35 0.05
105 18 0.03
ACGTcount: A:0.29, C:0.13, G:0.37, T:0.21
Consensus pattern (98 bp):
CACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGAAGAAGGTGCC
ACGGAGTTGTGGGCTTTGAAAAAAGAAGAGTGC
Found at i:1304228 original size:27 final size:27
Alignment explanation
Indices: 1304159--1304248 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 27
1304149 TGGAAAGAAG
1304159 AAGG-TGCCACGGAGTTGTGGGCTTTAAAA
1 AAGGATGCCACGGAGTTGTGGGC-TT--AA
*
1304188 AAGAAGGTGCCACGGAGTTGTGGGCTTAA
1 AAG--GATGCCACGGAGTTGTGGGCTTAA
*
1304217 AAGGATGCCACGGAGTTGTGGGCTTAG
1 AAGGATGCCACGGAGTTGTGGGCTTAA
1304244 AAGGA
1 AAGGA
1304249 AAAAGAGTGC
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
27 27 0.48
29 8 0.14
31 3 0.05
32 18 0.32
ACGTcount: A:0.28, C:0.13, G:0.38, T:0.21
Consensus pattern (27 bp):
AAGGATGCCACGGAGTTGTGGGCTTAA
Found at i:1304427 original size:27 final size:27
Alignment explanation
Indices: 1304389--1304440 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
1304379 ACAGAAAAAG
*
1304389 GTGCCACGGAGTTGTGGGCTTTGAAGA
1 GTGCCACGGAGTCGTGGGCTTTGAAGA
1304416 GTGCCACGGAGTCGTGGGCTTTGAA
1 GTGCCACGGAGTCGTGGGCTTTGAA
1304441 AAGAGAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.40, T:0.25
Consensus pattern (27 bp):
GTGCCACGGAGTCGTGGGCTTTGAAGA
Found at i:1305537 original size:16 final size:16
Alignment explanation
Indices: 1305513--1305544 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1305503 TTTTCCTCTC
*
1305513 TTTTTTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
1305529 TTTTGTTTCTTTTTTG
1 TTTTGTTTCTTTTTTG
1305545 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (16 bp):
TTTTGTTTCTTTTTTG
Found at i:1305870 original size:1 final size:1
Alignment explanation
Indices: 1305785--1305856 Score: 72
Period size: 1 Copynumber: 72.0 Consensus size: 1
1305775 TTGCACTTTC
* * * * * * * *
1305785 TTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTGTGTGTTTTTTTTGTTTGTTTGTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1305850 TTTTTTT
1 TTTTTTT
1305857 CCATCACCTT
Statistics
Matches: 55, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (1 bp):
T
Found at i:1312813 original size:52 final size:52
Alignment explanation
Indices: 1312743--1312863 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1312733 GAAAATTTAT
*
1312743 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1312795 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1312847 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1312864 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1312876 original size:52 final size:51
Alignment explanation
Indices: 1312743--1312883 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1312733 GAAAATTTAT
1312743 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1312795 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1312847 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1312884 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1312890 original size:13 final size:13
Alignment explanation
Indices: 1312872--1312896 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312862 CAAAGATCAG
1312872 TGTATCGATACAA
1 TGTATCGATACAA
1312885 TGTATCGATACA
1 TGTATCGATACA
1312897 TGTGAGTAAT
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:1312985 original size:13 final size:13
Alignment explanation
Indices: 1312967--1312991 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1312957 CAAAAAAATA
1312967 TGTATCGATACAT
1 TGTATCGATACAT
1312980 TGTATCGATACA
1 TGTATCGATACA
1312992 ACATTTTGTG
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:1316808 original size:13 final size:13
Alignment explanation
Indices: 1316768--1316816 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1316758 TTGTTACAAG
1316768 CAATGTATCGATA
1 CAATGTATCGATA
1316781 CAA--T-TC-AT-
1 CAATGTATCGATA
1316789 C-ATGTATCGATA
1 CAATGTATCGATA
1316801 CAATGTATCGATA
1 CAATGTATCGATA
1316814 CAA
1 CAA
1316817 ACAGTGGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.13
11 3 0.10
12 1 0.03
13 17 0.57
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1316889 original size:19 final size:20
Alignment explanation
Indices: 1316845--1316898 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1316835 CTGCCAGTTT
**
1316845 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
1316865 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1316884 CATGTATCGATACAA
1 CATGTATCGATACAA
1316899 AGCATAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1316910 original size:20 final size:19
Alignment explanation
Indices: 1316845--1316915 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
1316835 CTGCCAGTTT
* **
1316845 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-AGAA
*
1316865 CATGTATCGATACAATGAA
1 CATGTATCGATACAAAGAA
1316884 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAAAG-A-A
1316905 -ATGTATCGATA
1 CATGTATCGATA
1316916 TATCTGGGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 18 0.39
20 27 0.59
21 1 0.02
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:1318143 original size:29 final size:29
Alignment explanation
Indices: 1318101--1318157 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1318091 TATCATGGAA
1318101 CAAAGTAACCATTGCCCTTTGATAAATTT
1 CAAAGTAACCATTGCCCTTTGATAAATTT
1318130 CAAAGTAACCATTGCCCTTTGATAAATT
1 CAAAGTAACCATTGCCCTTTGATAAATT
1318158 GCTCTAACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (29 bp):
CAAAGTAACCATTGCCCTTTGATAAATTT
Found at i:1324674 original size:51 final size:50
Alignment explanation
Indices: 1324582--1324750 Score: 221
Period size: 51 Copynumber: 3.3 Consensus size: 50
1324572 ATTTAACTAG
* * *
1324582 ATGTATCGATACATTTGGATAAAAAACCCAGAATGTATCGATATGATGAAGA
1 ATGTATCAATACATTTGGAT-CAAAACCCAAAATGTATCGATATGAT-AAGA
*
1324634 ATGTATCAATACATTTGGATCAAAACCCAAAATGTATCGATAGGATAAAGA
1 ATGTATCAATACATTTGGATCAAAACCCAAAATGTATCGATATGAT-AAGA
* * * *
1324685 GTGTATCAATAAATTTGGATCAAAACCCAAAATGTATCGATATAATAAAA
1 ATGTATCAATACATTTGGATCAAAACCCAAAATGTATCGATATGATAAGA
* *
1324735 ATGTATCGATATATTT
1 ATGTATCAATACATTT
1324751 TCTTTCCATA
Statistics
Matches: 104, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 16 0.15
51 69 0.66
52 19 0.18
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (50 bp):
ATGTATCAATACATTTGGATCAAAACCCAAAATGTATCGATATGATAAGA
Found at i:1324835 original size:21 final size:20
Alignment explanation
Indices: 1324788--1324839 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
1324778 ACAAGGTCCA
*
1324788 GTATCGATACATTCACTTAT
1 GTATCAATACATTCACTTAT
*
1324808 ATATCAATACATTCACTCGT-T
1 GTATCAATACATTCACT--TAT
1324829 GTATCAATACA
1 GTATCAATACA
1324840 AATCATAGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 15 0.56
21 11 0.41
22 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
GTATCAATACATTCACTTAT
Found at i:1331003 original size:30 final size:30
Alignment explanation
Indices: 1330967--1331037 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
1330957 GATCTAAACA
*
1330967 ATCTAAAGTACTTAAAAGGTATTAAAATGC
1 ATCTAAAATACTTAAAAGGTATTAAAATGC
*
1330997 ATCTAAAATACTTAAAAGGTATTAAAATGG
1 ATCTAAAATACTTAAAAGGTATTAAAATGC
1331027 ATCTAAAATAC
1 ATCTAAAATAC
1331038 ATGAAACATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (30 bp):
ATCTAAAATACTTAAAAGGTATTAAAATGC
Found at i:1334097 original size:16 final size:16
Alignment explanation
Indices: 1334076--1334108 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1334066 TCTTGAAATA
*
1334076 TCTCACACTTTGCTAT
1 TCTCACACTCTGCTAT
1334092 TCTCACACTCTGCTAT
1 TCTCACACTCTGCTAT
1334108 T
1 T
1334109 ACTATTAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.33, G:0.06, T:0.42
Consensus pattern (16 bp):
TCTCACACTCTGCTAT
Found at i:1342029 original size:69 final size:69
Alignment explanation
Indices: 1341892--1342030 Score: 174
Period size: 69 Copynumber: 2.0 Consensus size: 69
1341882 CTTAAAAATC
* * * *
1341892 ACTTCCTTATATACTTAAGTCAGCCTTTAAATACTCAAAAAGAGAAACTTTGAATTTCCTAAGGT
1 ACTTCCTTATATACTTAAGTCAGCCTTTAAATACTCAAAAAGAAAAACTCTAAATTTCCTAAGAT
1341957 ACTA
66 ACTA
* * * *
1341961 ACTTCCTTATAT-GTCTAAGTCAGTCTTTAAATACTTAAAAAGAAAAACTCTAAA-TTCTTTAAG
1 ACTTCCTTATATACT-TAAGTCAGCCTTTAAATACTCAAAAAGAAAAACTCTAAATTTC-CTAAG
1342024 ATACTA
64 ATACTA
1342030 A
1 A
1342031 AGCTAAAGAG
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 4 0.07
69 56 0.93
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.35
Consensus pattern (69 bp):
ACTTCCTTATATACTTAAGTCAGCCTTTAAATACTCAAAAAGAAAAACTCTAAATTTCCTAAGAT
ACTA
Found at i:1343428 original size:33 final size:33
Alignment explanation
Indices: 1343377--1343450 Score: 132
Period size: 33 Copynumber: 2.3 Consensus size: 33
1343367 ATTATGAATA
*
1343377 GTATCGAT-ACATCACTGTTCATCACTATTCAT
1 GTATCGATAAAATCACTGTTCATCACTATTCAT
1343409 GTATCGATAAAATCACTGTTCATCACTATTCAT
1 GTATCGATAAAATCACTGTTCATCACTATTCAT
1343442 GTATCGATA
1 GTATCGATA
1343451 CAGTGTATCG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 8 0.20
33 32 0.80
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (33 bp):
GTATCGATAAAATCACTGTTCATCACTATTCAT
Found at i:1343459 original size:13 final size:13
Alignment explanation
Indices: 1343441--1343465 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1343431 TCACTATTCA
1343441 TGTATCGATACAG
1 TGTATCGATACAG
1343454 TGTATCGATACA
1 TGTATCGATACA
1343466 TTATAAATAG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1343478 original size:98 final size:94
Alignment explanation
Indices: 1343326--1343502 Score: 275
Period size: 98 Copynumber: 1.8 Consensus size: 94
1343316 ATCTCATTTT
* *
1343326 TCACTGTTCATCACTATTCATTACTGTTCATGCATCGATACATTATGAATAGTATCGATACATCA
1 TCACTGTTCATCACTATTCATTACTGTACATGCATCGATACATTATAAATAGTATCGATACATCA
1343391 CTGTTCATCACTATTCATGTATCGATAAAA
66 CTGTTCA-CACTATTCATGTATCGATAAAA
*
1343421 TCACTGTTCATCACTATTCATGTA-TCGATACAGTGTATCGATACATTATAAATAGTATCGATAC
1 TCACTGTTCATCACTATTCAT-TACT-G-TACA-TGCATCGATACATTATAAATAGTATCGATAC
1343485 ATCACTGTTCACACTATT
62 ATCACTGTTCACACTATT
1343503 TAATAAAAGC
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
95 22 0.29
96 3 0.04
97 10 0.13
98 40 0.53
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (94 bp):
TCACTGTTCATCACTATTCATTACTGTACATGCATCGATACATTATAAATAGTATCGATACATCA
CTGTTCACACTATTCATGTATCGATAAAA
Found at i:1343999 original size:34 final size:35
Alignment explanation
Indices: 1343936--1344002 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1343926 CTAAGTGATT
1343936 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1343972 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1344003 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1346008 original size:51 final size:51
Alignment explanation
Indices: 1345949--1346059 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
1345939 ACAGGATTAG
*
1345949 AGTATCCCCGATTGTGAAAAATCGATAATTTAG-AAATA-AGGCCGGGGTTGA
1 AGTATCCCCGATTGTGAAAAATCAAT-ATTTAGTAAATACA-GCCGGGGTTGA
* * * *
1346000 AGTATCCCCGATTGTGAGAAATCAATATTTTGTAAATACAGTCGGGGTTGG
1 AGTATCCCCGATTGTGAAAAATCAATATTTAGTAAATACAGCCGGGGTTGA
1346051 AGTATCCCC
1 AGTATCCCC
1346060 TTGAAAATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
50 5 0.09
51 47 0.89
52 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (51 bp):
AGTATCCCCGATTGTGAAAAATCAATATTTAGTAAATACAGCCGGGGTTGA
Found at i:1346049 original size:130 final size:130
Alignment explanation
Indices: 1345888--1346230 Score: 330
Period size: 130 Copynumber: 2.6 Consensus size: 130
1345878 TGATTATAGA
* **
1345888 AAATCGATATTTTGAAAATAAAATCGAGGTTGGAGTATTTCCTCGAAAATAACAGGATTAGAGTA
1 AAATCAATATTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGATTAGAGTA
**
1345953 TCCCCGATTGTGAAAAATCGATAATTTAGAAATAAGGCCGGGGTTGAAGTATCCCCGATTGTGAG
66 TCCCCGATTGTGAAAAATCGATAATTTAGAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGAG
* * * * * ** * *
1346018 AAATCAATATTTTGTAAATACAGTCGGGGTTGGAGTATCCCCTTGAAAATAATGGGGTTGGAGTA
1 AAATCAATATTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGATTAGAGTA
* * * ** * * * *
1346083 TCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATCCCCGATTATG-G
66 TCCCCGATTGTGAAAAATCGATAATTTAGAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGAG
* * * * * * * * * * *
1346147 AAAATTAGTGTTTTAGAAAAAAAAACCGGGGTTGGAGTATCCTCTC-AGAAATGACGGGGTTGGA
1 -AAATCAATATTTT-GAAAATAAAATCGAGGTTGGAGTATCCCCTCGA-AAATAACAGGATTAGA
*
1346211 GTATCCCCAATTGTGAAAAA
63 GTATCCCCGATTGTGAAAAA
1346231 CTGATGTTTT
Statistics
Matches: 173, Mismatches: 37, Indels: 5
0.80 0.17 0.02
Matches are distributed among these distances:
129 1 0.01
130 116 0.67
131 56 0.32
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (130 bp):
AAATCAATATTTTGAAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGATTAGAGTA
TCCCCGATTGTGAAAAATCGATAATTTAGAAATAAAACCGGGGTTGAAGTATCCCCGATTGTGAG
Found at i:1346124 original size:79 final size:79
Alignment explanation
Indices: 1345992--1346138 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 79
1345982 AAATAAGGCC
* * * *
1345992 GGGGTTGAAGTATCCCCGATTGTGAGAAATCAATATTTTGTAAATACAGTCGGGGTTGGAGTATC
1 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAATCGGGGTTGGAGTATC
1346057 CCCTTGAAAATAAT
66 CCCTTGAAAATAAT
* * *** *
1346071 GGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAATCGGGGTTGGAGTATC
1346136 CCC
66 CCC
1346139 GATTATGGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 58 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (79 bp):
GGGGTTGAAGTATCCCCGATTGTGAAAAATCAATATTTTGGAAATAAAATCGGGGTTGGAGTATC
CCCTTGAAAATAAT
Found at i:1346142 original size:51 final size:52
Alignment explanation
Indices: 1346071--1346188 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 52
1346061 TGAAAATAAT
* * * * * *
1346071 GGGGTTGGAGTATCCTCGATTGTGAAAAATTGGTGTTTT-GGAAATAAAATC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAAAAAAAACC
*
1346122 GGGGTTGGAGTATCCCCGATTATGGAAAATTAGTGTTTTAGAAAAAAAAACC
1 GGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAAAAAAAACC
1346174 GGGGTTGGAGTATCC
1 GGGGTTGGAGTATCC
1346189 TCTCAGAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
51 35 0.59
52 24 0.41
ACGTcount: A:0.31, C:0.10, G:0.30, T:0.30
Consensus pattern (52 bp):
GGGGTTGGAGTATCCCCGATTATGAAAAATTAGTGTTTTAGAAAAAAAAACC
Done.