Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1278
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: 27190
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:1199 original size:29 final size:29
Alignment explanation
Indices: 1159--2827 Score: 1467
Period size: 29 Copynumber: 58.9 Consensus size: 29
1149 ATGTTATCCC
* *
1159 TTTCAAAGCCCACAAATCCGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1188 TTTCAAAACCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1216 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1245 TTTCAAAG-CCACAAGTCAGTGGAACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * * *
1273 TTTCAAAGCCTATAAATAAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1301 TTTCAAAG----CTAGTCAGTGGCAC-C-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1324 CTTCAAAGCCCACAAGTCAGTGGCACTC-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1352 TTTCAAAGCCCA-AAATCAGTTGGCACTC-
1 TTTCAAAGCCCACAAGTCAG-TGGCACTCT
* *
1380 -TTCAAAGCCCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1407 TTTCAAAG-CCACCAAGTCAGTGGCA--CT
1 TTTCAAAGCCCA-CAAGTCAGTGGCACTCT
* *
1434 TTTCAAAGCCTA-AAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1462 TTTCAAAG-CCACGAGTTAGTGGC-C-CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1488 TTCCAAACGCCCACAAGT-AGTGGCACCCCT
1 TTTCAAA-GCCCACAAGTCAGTGGCA-CTCT
* *
1518 TTCCAAAGCCCACAAGTCAATGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1547 TTTCAAAGCCTACAA-TCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1575 TTTCAAAGCCCACAAGTCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
1604 TTTCAAAGCCCATTAAATTAG-GGCACTTT
1 TTTCAAAGCCCA-CAAGTCAGTGGCACTCT
* *
1633 TTTCAAAG-CCACGAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1660 TTTCAAAACCCACAAGTCCAGTGGCACTCT
1 TTTCAAAGCCCACAAGT-CAGTGGCACTCT
* * *
1690 TTTCAACGCCCATAAATTCAGTGGCACTC-
1 TTTCAAAGCCCA-CAAGTCAGTGGCACTCT
* *
1719 TTTCAAAGCCCACAAGTTAGTGACACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1748 TTTCAAATCCCACAAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
1777 TTCCAAAACCCACAAGTGAGTGGGCACTCT
1 TTTCAAAGCCCACAAGTCAGT-GGCACTCT
* *
1807 TTTCAAAGCCCACGAGTCAGTGGCACCCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1836 TTCCAAAGCCCACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
1865 TTTCAAAGCCCACAAATCAGTGCCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1894 TTTCAAAGCCCAC-AGTTAGTGGCA--CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1920 TTTCAAAGCCCACAAATCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
1949 TTT-AAAGCCCACAA-TCGGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
1976 TTTCAAAGCCCACTAAGTCAGTGGCACTC-
1 TTTCAAAGCCCAC-AAGTCAGTGGCACTCT
* * *
2005 TTTCAAAGCCCACGA-TGC-GTGACAC-CC
1 TTTCAAAGCCCACAAGT-CAGTGGCACTCT
*
2032 TTTCAAAGCCCAGAAGTCCAGTGGCA-TCCT
1 TTTCAAAGCCCACAAGT-CAGTGGCACT-CT
* *
2062 TTCCAAAGCCCACAAGTTAGTGGCA--C-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2088 TTTCAAAGCCCACAAATCA-TGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
2116 TTTCAAAGGCCCAC-AGTCCA-TGGCACTCT
1 TTTCAAA-GCCCACAAGT-CAGTGGCACTCT
* * **
2145 TTTC-AAGCCTATAGGAGTTGGTGGCACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGCACTCT
* *
2175 TTCCAAAGCTCACAAGTCAGTTGGCACTCT
1 TTTCAAAGCCCACAAGTCAG-TGGCACTCT
* *
2205 TTTCAAAAGCTCACAAGTCAGTGGGCACCCT
1 TTTC-AAAGCCCACAAGTCAGT-GGCACTCT
**
2236 TAAC-AAGCCCACAAGTCA-TGGCA--CT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
2261 TTTCAAAGCCCAC-AGTCAGTGGCAC-C-
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
2287 CTTCAAAAGGACCATGCAAGTTAGTGGCAC-C-
1 TTTC-AAA-GCCCA--CAAGTCAGTGGCACTCT
*
2318 CTTC-AAGCCCACCAA-TCAGTGGCACTC-
1 TTTCAAAGCCCA-CAAGTCAGTGGCACTCT
*
2345 TTTCAAAGCCCACAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2373 TTTCAAAGCCAACAA-TTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2401 TTTCACAGCCCCACAACGT-AGTGG--CTCC
1 TTTCAAAG-CCCACAA-GTCAGTGGCACTCT
*
2429 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* *
2457 TTTC-AAGCCCATAAGTCAGTGGCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
** *
2484 TTTCAAAGCCCATGTAGTCAGTTGGCAC-CC
1 TTTCAAAGCCCA-CAAGTCAG-TGGCACTCT
* * * *
2514 TTTCAACGCTCATAAATCAGTGGC-CTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
2542 TTTCAAAAACCCACAAGTCAATGGCACTTT
1 TTTC-AAAGCCCACAAGTCAGTGGCACTCT
* * * *
2572 TTTCGAAGCCCAAAAGTTAGTGGCA-TCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * * *
2600 TTTCAATGCCCACACGTTAGTGGCCAC-CC
1 TTTCAAAGCCCACAAGTCAGTGG-CACTCT
**
2629 TTTCAAAGCCCACGTAAGTTGGTGGCACTC-
1 TTTCAAAGCCCAC--AAGTCAGTGGCACTCT
* * *
2659 TTTCAAAACCCCCAAGTTAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
2688 TTTC-AAGCCCATAAGTC-GTGGCACCCC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2715 TTTC-AAGCCCACAAGTCAGTGG-AC-CC
1 TTTCAAAGCCCACAAGTCAGTGGCACTCT
*
2741 TTTCAAAGCCCATAAGGT-AGTGGCACTC-
1 TTTCAAAGCCCACAA-GTCAGTGGCACTCT
**
2769 TTTC-AAGCCCACACGAGTTGGTGGCAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGGC-ACTCT
*
2800 TTTCAAAGCCCACACAAGTTAGTGGCAC
1 TTTCAAAG-CC-CACAAGTCAGTGGCAC
2828 CATTTTTTTT
Statistics
Matches: 1363, Mismatches: 176, Indels: 200
0.78 0.10 0.12
Matches are distributed among these distances:
23 7 0.01
24 11 0.01
25 14 0.01
26 85 0.06
27 233 0.17
28 368 0.27
29 392 0.29
30 169 0.12
31 66 0.05
32 12 0.01
33 2 0.00
34 4 0.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (29 bp):
TTTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:1246 original size:57 final size:57
Alignment explanation
Indices: 1158--2827 Score: 1470
Period size: 57 Copynumber: 29.5 Consensus size: 57
1148 AATGTTATCC
* * *
1158 CTTTCAAAGCCCACAAATCCGTGGCACTCTTTTCAAAACCCACAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1215 CTTTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAG-CCACAAGTCAGTGGAACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * *
1271 CTTTTCAAAGCCTATAAATAAGTGGCAC-CCTTTCAAAG----CTAGTCAGTGGCAC-
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1323 CCTTCAAAGCCCACAAGTCAGTGGCACTC-TTTCAAAGCCCA-AAATCAGTTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAG-TGGCACT
* *
1379 C-TTCAAAGCCCACGAGTCAGTGGCAC-CCTTTCAAAG-CCACCAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA-CAAGTCAGTGGCACT
* * * *
1434 -TTTCAAAGCCTA-AAGTTAGTGGCACTCTTTTCAAAG-CCACGAGTTAGTGGC-C-
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * *
1486 CTTTCCAAACGCCCACAAGT-AGTGGCACCCCTTTCCAAAGCCCACAAGTCAATGGCACT
1 CTTT-CAAA-GCCCACAAGTCAGTGGCA-CTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1545 CTTTTCAAAGCCTACAA-TCAGTGGCACTCTTTTCAAAGCCCACAAGTCGGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * * * *
1602 CTTTTCAAAGCCCATTAAATTAG-GGCACTTTTTTCAAAG-CCACGAGTCAGTGGCACC
1 C-TTTCAAAGCCCA-CAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1659 CTTTCAAAACCCACAAGTCCAGTGGCACTCTTTTCAACGCCCATAAATTCAGTGGCACT
1 CTTTCAAAGCCCACAAGT-CAGTGGCACTCTTTTCAAAGCCCA-CAAGTCAGTGGCACT
* * * *
1718 CTTTCAAAGCCCACAAGTTAGTGACACTCTTTTCAAATCCCACAAGTCAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
1775 CTTTCCAAAACCCACAAGTGAGTGGGCACTCTTTTCAAAGCCCACGAGTCAGTGGCACC
1 CTTT-CAAAGCCCACAAGTCAGT-GGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1834 CTTTCCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGCCACT
1 CTTT-CAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1892 CTTTTCAAAGCCCAC-AGTTAGTGGCA--CTTTTCAAAGCCCACAAATCAGTGGCACT
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
1947 CTTTTAAAGCCCACAA-TCGGTGGCACTCTTTTCAAAGCCCACTAAGTCAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCAC-AAGTCAGTGGCACT
* * * *
2004 CTTTCAAAGCCCACGA-TGC-GTGACAC-CCTTTCAAAGCCCAGAAGTCCAGTGGCA-T
1 CTTTCAAAGCCCACAAGT-CAGTGGCACTCTTTTCAAAGCCCACAAGT-CAGTGGCACT
* *
2059 CCTTTCCAAAGCCCACAAGTTAGTGGCA--C-TTTCAAAGCCCACAAATCA-TGGCACT
1 -CTTT-CAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * **
2114 CTTTTCAAAGGCCCAC-AGTCCA-TGGCACTCTTTTC-AAGCCTATAGGAGTTGGTGGCACT
1 C-TTTCAAA-GCCCACAAGT-CAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGCACT
* *
2173 CTTTCCAAAGCTCACAAGTCAGTTGGCACTCTTTTCAAAAGCTCACAAGTCAGTGGGCAC-
1 CTTT-CAAAGCCCACAAGTCAG-TGGCACTCTTTTC-AAAGCCCACAAGTCAGT-GGCACT
* *
2233 CCTTAACAAGCCCACAAGTCA-TGGCA--CTTTTCAAAGCCCAC-AGTCAGTGGCAC-
1 CTTTCA-AAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
2286 CCTTCAAAAGGACCATGCAAGTTAGTGGCAC-C-CTTC-AAGCCCACCAA-TCAGTGGCACT
1 CTTTC-AAA-GCCCA--CAAGTCAGTGGCACTCTTTTCAAAGCCCA-CAAGTCAGTGGCACT
* * *
2344 CTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCAACAA-TTAGTGGCACT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* *
2399 CTTTTCACAGCCCCACAACGT-AGTGG--CTCCTTTCAAAGCCCACAAGTCAGTGGCA-T
1 C-TTTCAAAG-CCCACAA-GTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * ** *
2455 CCTTTC-AAGCCCATAAGTCAGTGGCAC-CCTTTCAAAGCCCATGTAGTCAGTTGGCACC
1 -CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCA-CAAGTCAG-TGGCACT
* * * * * *
2513 CTTTCAACGCTCATAAATCAGTGGC-CTCTTTTCAAAAACCCACAAGTCAATGGCACTT
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTC-AAAGCCCACAAGTCAGTGGCAC-T
* * * * * * * * *
2571 TTTTCGAAGCCCAAAAGTTAGTGGCA-TCCTTTCAATGCCCACACGTTAGTGGCCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGG-CACT
** * * *
2628 CTTTCAAAGCCCACGTAAGTTGGTGGCACTC-TTTCAAAACCCCCAAGTTAGTGGCACT
1 CTTTCAAAGCCCAC--AAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* * * *
2686 CTTTTC-AAGCCCATAAGTC-GTGGCACCCCTTTC-AAGCCCACAAGTCAGTGG-ACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
* **
2740 CTTTCAAAGCCCATAAGGT-AGTGGCACTC-TTTC-AAGCCCACACGAGTTGGTGGCAACT
1 CTTTCAAAGCCCACAA-GTCAGTGGCACTCTTTTCAAAGCCCACA--AGTCAGTGGC-ACT
*
2798 CTTTTCAAAGCCCACACAAGTTAGTGGCAC
1 C-TTTCAAAG-CC-CACAAGTCAGTGGCAC
2828 CATTTTTTTT
Statistics
Matches: 1343, Mismatches: 165, Indels: 206
0.78 0.10 0.12
Matches are distributed among these distances:
51 29 0.02
52 2 0.00
53 33 0.02
54 134 0.10
55 204 0.15
56 203 0.15
57 303 0.23
58 212 0.16
59 157 0.12
60 43 0.03
61 17 0.01
62 6 0.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (57 bp):
CTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACT
Found at i:1323 original size:24 final size:24
Alignment explanation
Indices: 1200--1470 Score: 98
Period size: 28 Copynumber: 10.0 Consensus size: 24
1190 TCAAAACCCA
*
1200 CAAGTCAGTGGCACTCTTTCAAAG
1 CAAGTCAGTGGCACCCTTTCAAAG
* *
1224 CCCACAAATCAGTGGCACTCTTTTCAAAG
1 ----CAAGTCAGTGGCAC-CCTTTCAAAG
* *
1253 CCACAAGTCAGTGGAACTCTTTTCAAAG
1 ---CAAGTCAGTGGCAC-CCTTTCAAAG
* *
1281 CCTATAAATAAGTGGCACCCTTTCAAAG
1 -C---AAGTCAGTGGCACCCTTTCAAAG
*
1309 CTAGTCAGTGGCACCC-TTCAAAG
1 CAAGTCAGTGGCACCCTTTCAAAG
*
1332 CCCACAAGTCAGTGGCACTCTTTCAAAG
1 ----CAAGTCAGTGGCACCCTTTCAAAG
* *
1360 CCCAAAATCAGTTGGCACTC-TTCAAAG
1 --C-AAGTCAG-TGGCACCCTTTCAAAG
1387 CCCACGAGTCAGTGGCACCCTTTCAAAG
1 --CA--AGTCAGTGGCACCCTTTCAAAG
*
1415 CCACCAAGTCAGTGGCA-CTTTTCAAAG
1 ----CAAGTCAGTGGCACCCTTTCAAAG
* *
1442 CCTAAAGTTAGTGGCACTCTTTTCAAAG
1 -C--AAGTCAGTGGCAC-CCTTTCAAAG
1470 C
1 C
1471 CACGAGTTAG
Statistics
Matches: 201, Mismatches: 22, Indels: 41
0.76 0.08 0.16
Matches are distributed among these distances:
23 7 0.03
24 14 0.07
26 15 0.07
27 48 0.24
28 96 0.48
29 18 0.09
30 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.18, T:0.24
Consensus pattern (24 bp):
CAAGTCAGTGGCACCCTTTCAAAG
Found at i:2811 original size:32 final size:30
Alignment explanation
Indices: 2303--2826 Score: 165
Period size: 28 Copynumber: 18.4 Consensus size: 30
2293 AAGGACCATG
*
2303 CAAGTTAGTGGC-AC-CCTTCAAGCCCAC-
1 CAAGTTAGTGGCAACTCTTTCAAGCCCACA
*
2330 CAA-TCAGTGGC-ACTCTTTCAAAG-CC-CA
1 CAAGTTAGTGGCAACTCTTTC-AAGCCCACA
* *
2357 CAAGTCAGTGGC-ACCCTTTCAAAG-CCA-A
1 CAAGTTAGTGGCAACTCTTTC-AAGCCCACA
2385 CAA-TTAGTGGC-ACTCTTTTCACAGCCC-CA
1 CAAGTTAGTGGCAACTC-TTTCA-AGCCCACA
*
2414 CAACG-TAGTGGC-TC-CTTTCAAAG-CC-CA
1 CAA-GTTAGTGGCAACTCTTTC-AAGCCCACA
* *
2441 CAAGTCAGTGGCATC-CTTTCAAG-CC-CA
1 CAAGTTAGTGGCAACTCTTTCAAGCCCACA
* * * *
2468 TAAGTCAGTGGC-ACCCTTTCAAAGCCCA-T
1 CAAGTTAGTGGCAACTCTTTC-AAGCCCACA
** * * * *
2497 GTAGTCAGTTGGC-ACCCTTTCAACGCTCATA
1 CAAGTTAG-TGGCAACTCTTTCAA-GCCCACA
* **
2528 -AA-TCAGTGGC--CTCTTTTCAAAAACC-CA
1 CAAGTTAGTGGCAACTC-TTTC-AAGCCCACA
* * *
2555 CAAGTCAATGGC-ACTTTTTTCGAAGCCCA-A
1 CAAGTTAGTGGCAAC-TCTTTC-AAGCCCACA
*
2585 -AAGTTAGTGGCATC-CTTTCAATGCCCACA
1 CAAGTTAGTGGCAACTCTTTCAA-GCCCACA
* * *
2614 C--GTTAGTGGCCACCCTTTCAAAGCCCACG
1 CAAGTTAGTGGCAACTCTTTC-AAGCCCACA
* * *
2643 TAAGTTGGTGGC-ACTCTTTCAAAACCC-C-
1 CAAGTTAGTGGCAACTCTTTC-AAGCCCACA
2671 CAAGTTAGTGGC-ACTCTTTTCAAG-CC-CA
1 CAAGTTAGTGGCAACTC-TTTCAAGCCCACA
* * * *
2699 TAAG-TCGTGGCACCCCTTTCAAG-CC-CA
1 CAAGTTAGTGGCAACTCTTTCAAGCCCACA
* *
2726 CAAGTCAGTGG--ACCCTTTCAAAG-CC-CA
1 CAAGTTAGTGGCAACTCTTTC-AAGCCCACA
* *
2753 TAAGGTAGTGGC-ACTCTTTCAAGCCCACA
1 CAAGTTAGTGGCAACTCTTTCAAGCCCACA
* *
2782 CGAGTTGGTGGCAACTCTTTTCAAAGCCCACA
1 CAAGTTAGTGGCAACTC-TTTC-AAGCCCACA
2814 CAAGTTAGTGGCA
1 CAAGTTAGTGGCA
2827 CCATTTTTTT
Statistics
Matches: 393, Mismatches: 57, Indels: 89
0.73 0.11 0.17
Matches are distributed among these distances:
26 19 0.05
27 105 0.27
28 114 0.29
29 67 0.17
30 55 0.14
31 13 0.03
32 20 0.05
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (30 bp):
CAAGTTAGTGGCAACTCTTTCAAGCCCACA
Found at i:4455 original size:23 final size:21
Alignment explanation
Indices: 4403--4456 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
4393 ATATGTCCAA
*
4403 ATTTCTCATTGCATGTTATCC
1 ATTTTTCATTGCATGTTATCC
* *
4424 ATTAGTTCATTGTATGATTATCAC
1 ATT-TTTCATTGCATG-TTATC-C
4448 ATTTTTCAT
1 ATTTTTCAT
4457 GTCAAGATGC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 3 0.12
22 9 0.35
23 10 0.38
24 4 0.15
ACGTcount: A:0.24, C:0.17, G:0.09, T:0.50
Consensus pattern (21 bp):
ATTTTTCATTGCATGTTATCC
Found at i:9992 original size:209 final size:209
Alignment explanation
Indices: 9624--10010 Score: 598
Period size: 209 Copynumber: 1.9 Consensus size: 209
9614 ATTACTAACC
*
9624 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGTTTTCTTATCGTAACCTGGAAAGTAT
1 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCTGGAAAGTAT
9689 TGAATTTCATTTTTGGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCAC
66 TGAATTTCATTTTTGGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCAC
*
9754 ATCCACTTTAAATCTTATGAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAA
131 ATCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAA
9819 TGATTGGATTGTCT
196 TGATTGGATTGTCT
* * **
9833 TGGCTGTTGATTGTATGGACAGATTGCAATACTATTATGGTTTCTTATCGTAACCTAAGTATTGT
1 TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCT--GGAAAGT
* ** * *
9898 GTTTCATTTCATTTTT-GGGAGTTGGAGCTTTATT-CTTAACCCAAAAGAATAGACCATAATTTC
64 ATTGAATTTCATTTTTGGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTC
* * * * *
9961 ACTTCCACTTTGAATCTTATCCGAGTAAACAACTAAGCAAATTGTTTATG
129 ACATCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATG
10011 AGCATTTATA
Statistics
Matches: 160, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
209 127 0.79
210 16 0.10
211 17 0.11
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (209 bp):
TGGCTGTTGATTGTATGGACAGATTGCAATACCATTATGGTTTCTTATCGTAACCTGGAAAGTAT
TGAATTTCATTTTTGGGGACTTGGAGCTTCATTCCTTAACCCAAAAGAATAGACCATAATTTCAC
ATCCACTTTAAATCTTATCAGAATAAACAACTAAACAAATTGTTTATGTTCTAAAGATGTCTTAA
TGATTGGATTGTCT
Found at i:11036 original size:17 final size:18
Alignment explanation
Indices: 11008--11043 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
10998 AATTTCTTAT
11008 TCATGCATTTTTCCCCTC
1 TCATGCATTTTTCCCCTC
11026 TCATGCA-TTTTCCCCTC
1 TCATGCATTTTTCCCCTC
11043 T
1 T
11044 TTTGCGTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.11, C:0.39, G:0.06, T:0.44
Consensus pattern (18 bp):
TCATGCATTTTTCCCCTC
Found at i:13570 original size:23 final size:22
Alignment explanation
Indices: 13544--13589 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
13534 AATAAGAATT
13544 TCATATCAAAATATTTTAATATA
1 TCATATCAAAAT-TTTTAATATA
* *
13567 TCATATTATAATTTTTAATATA
1 TCATATCAAAATTTTTAATATA
13589 T
1 T
13590 TAAATTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TCATATCAAAATTTTTAATATA
Found at i:15385 original size:6 final size:6
Alignment explanation
Indices: 15374--15428 Score: 53
Period size: 6 Copynumber: 9.2 Consensus size: 6
15364 TTATGATTAC
*
15374 TAATTT TAATTT TAATTT T-CTTT TAATTT TGAATTTTT TAATTT T-ATTT
1 TAATTT TAATTT TAATTT TAATTT TAATTT T-AA--TTT TAATTT TAATTT
15423 T-ATTT T
1 TAATTT T
15429 TTACTAGTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
5 14 0.33
6 21 0.49
7 2 0.05
8 2 0.05
9 4 0.09
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (6 bp):
TAATTT
Found at i:15399 original size:17 final size:18
Alignment explanation
Indices: 15377--15410 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
15367 TGATTACTAA
15377 TTTTAATTTT-AATTTTC
1 TTTTAATTTTGAATTTTC
15394 TTTTAATTTTGAATTTT
1 TTTTAATTTTGAATTTT
15411 TTAATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTGAATTTTC
Found at i:15980 original size:20 final size:21
Alignment explanation
Indices: 15948--15986 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
15938 TAGATGTTAT
15948 ATTTAATTTTTCTTAATAATA
1 ATTTAATTTTTCTTAATAATA
*
15969 ATTTAA-TTTTCTTCATAA
1 ATTTAATTTTTCTTAATAA
15987 AAATATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTAATTTTTCTTAATAATA
Found at i:18999 original size:15 final size:15
Alignment explanation
Indices: 18979--19029 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
18969 CTTGAAATTT
18979 AAATGATTTAAACTA
1 AAATGATTTAAACTA
*
18994 AAATGATATGAAACTA
1 AAATGAT-TTAAACTA
*
19010 AAATAATTTAAACTTA
1 AAATGATTTAAAC-TA
19026 AAAT
1 AAAT
19030 TTTAAAAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.39
16 19 0.61
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (15 bp):
AAATGATTTAAACTA
Found at i:19009 original size:16 final size:15
Alignment explanation
Indices: 18960--19029 Score: 59
Period size: 16 Copynumber: 4.5 Consensus size: 15
18950 TTATCTAAAC
*
18960 CTAAAATGTCTTGAAA
1 CTAAAATG-ATTGAAA
* * *
18976 TTTAAATGATTTAAA
1 CTAAAATGATTGAAA
18991 CTAAAATGATATGAAA
1 CTAAAATGAT-TGAAA
* *
19007 CTAAAATAATTTAAA
1 CTAAAATGATTGAAA
19022 CTTAAAAT
1 C-TAAAAT
19030 TTTAAAAATC
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
15 18 0.42
16 25 0.58
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
CTAAAATGATTGAAA
Found at i:22170 original size:3 final size:3
Alignment explanation
Indices: 22162--22191 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
22152 TTTTGCTGTT
22162 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
22192 AAAAACACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:22749 original size:19 final size:19
Alignment explanation
Indices: 22708--22784 Score: 147
Period size: 19 Copynumber: 4.1 Consensus size: 19
22698 ATTAATTAAG
22708 ATATAATATAATATTAT-A
1 ATATAATATAATATTATAA
22726 ATATAATATAATATTATAA
1 ATATAATATAATATTATAA
22745 ATATAATATAATATTATAA
1 ATATAATATAATATTATAA
22764 ATATAATATAATATTATAA
1 ATATAATATAATATTATAA
22783 AT
1 AT
22785 TATATTAATA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
18 17 0.29
19 41 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATAATATAATATTATAA
Found at i:22791 original size:5 final size:5
Alignment explanation
Indices: 22708--22777 Score: 94
Period size: 5 Copynumber: 14.8 Consensus size: 5
22698 ATTAATTAAG
*
22708 ATATA ATATA ATAT- -TATA ATATA ATATA ATATT ATA-A ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
*
22755 ATATT ATA-A ATATA ATATA ATAT
1 ATATA ATATA ATATA ATATA ATAT
22778 TATAAATTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 48 0.84
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:22876 original size:18 final size:17
Alignment explanation
Indices: 22834--22876 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
22824 ATATATCAAA
*
22834 ATTTATGTAATAAAATT
1 ATTTATATAATAAAATT
* *
22851 ATTAATATATTAAAATTT
1 ATTTATATAATAAAA-TT
22869 ATTTATAT
1 ATTTATAT
22877 TATATTAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTATATAATAAAATT
Found at i:22877 original size:16 final size:16
Alignment explanation
Indices: 22825--22878 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
22815 AATAATTAAA
* *
22825 TATATCAAAATTTATG
1 TATATTAAAATTTATT
22841 TA-A-TAAAA-TTATT
1 TATATTAAAATTTATT
22854 AATATATTAAAATTTATT
1 --TATATTAAAATTTATT
22872 TATATTA
1 TATATTA
22879 TATTAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
13 4 0.13
14 4 0.13
15 3 0.10
16 10 0.32
17 5 0.16
18 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
TATATTAAAATTTATT
Found at i:23410 original size:26 final size:25
Alignment explanation
Indices: 23381--23442 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 25
23371 AAAGATATTA
23381 AATTAAAATATGTATATATAA-TAAAT
1 AATTAAAATAT-TATAT-TAATTAAAT
23407 AATTAAAA-ATTATATTAATGTTAAAT
1 AATTAAAATATTATATTAA--TTAAAT
23433 AA-TAAAATAT
1 AATTAAAATAT
23443 ATGTTAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
23 3 0.09
24 5 0.16
25 7 0.22
26 17 0.53
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (25 bp):
AATTAAAATATTATATTAATTAAAT
Found at i:23495 original size:38 final size:36
Alignment explanation
Indices: 23403--23499 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 36
23393 TATATATAAT
*
23403 AAATAATTAAAAATTATA-TTAATGTTAAATAATAAA
1 AAATAATT-AAAATTATATTTAATGTTAAATAAAAAA
* * *
23439 ATATATGTTAAAATTATATTTTATGTTAAATAAAAATGA
1 AAATA-ATTAAAATTATATTTAATGTTAAATAAAAA--A
*
23478 AAATAATTAAAGTTATATTTAA
1 AAATAATTAAAATTATATTTAA
23500 ATTAAAAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
36 13 0.27
37 17 0.35
38 14 0.29
39 5 0.10
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (36 bp):
AAATAATTAAAATTATATTTAATGTTAAATAAAAAA
Found at i:23665 original size:23 final size:21
Alignment explanation
Indices: 23614--23687 Score: 58
Period size: 22 Copynumber: 3.2 Consensus size: 21
23604 AAATATATTT
*
23614 TTATTAATTTATTATATAATAAA
1 TTATTAATTT-TTAAATAA-AAA
*
23637 CTTTATTAATTATATTAAATAAAAG
1 --TTATTAATT-T-TTAAATAAAAA
*
23662 TTATTTCATTTTTAAATAAAAA
1 TTA-TTAATTTTTAAATAAAAA
23684 TTAT
1 TTAT
23688 AATAAAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 1 0.02
22 13 0.30
23 4 0.09
24 5 0.12
25 11 0.26
26 9 0.21
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (21 bp):
TTATTAATTTTTAAATAAAAA
Found at i:23932 original size:2 final size:2
Alignment explanation
Indices: 23925--23956 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
23915 TTAAAAGTTC
23925 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23957 CACACACACA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24419 original size:32 final size:32
Alignment explanation
Indices: 24378--24441 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
24368 TAATAATTTT
* *
24378 CAAACTTAAGACCACGCACTTTGTTAAGTTAA
1 CAAACTTAAGACCACGCACTTTGCTAAATTAA
*
24410 CAAACTTAAGACCACGCGCTTTGCTAAATTAA
1 CAAACTTAAGACCACGCACTTTGCTAAATTAA
24442 AATCTAAGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (32 bp):
CAAACTTAAGACCACGCACTTTGCTAAATTAA
Found at i:24924 original size:18 final size:18
Alignment explanation
Indices: 24898--24939 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
24888 TCAAAAAATC
24898 TTTAATTTTATTT-ATTAT
1 TTTAATTTTATTTGATT-T
*
24916 TTTACTTTTATTTGATTT
1 TTTAATTTTATTTGATTT
24934 TTTAAT
1 TTTAAT
24940 AATTTTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTAATTTTATTTGATTT
Found at i:25455 original size:23 final size:22
Alignment explanation
Indices: 25412--25457 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
25402 AATACTCTAT
* **
25412 ATTTTTAAAAAATAATTAATAA
1 ATTTTTAAAAAAAAAAAAATAA
25434 ATTTTTAAAAATAAAAAAAATAA
1 ATTTTTAAAAA-AAAAAAAATAA
25457 A
1 A
25458 ATAATTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
ATTTTTAAAAAAAAAAAAATAA
Found at i:26452 original size:13 final size:13
Alignment explanation
Indices: 26434--26536 Score: 89
Period size: 13 Copynumber: 7.0 Consensus size: 13
26424 TTTAGCGATT
26434 TGTATCGATACAA
1 TGTATCGATACAA
26447 TGTATCGATACAA
1 TGTATCGATACAA
26460 TGTATCGATACATAAGTGA
1 TGTATCGATAC---A---A
26479 TGTATCGATACAA
1 TGTATCGATACAA
26492 TGTATCGATACATAAGTGA
1 TGTATCGATAC---A---A
26511 TGTATCGATACAA
1 TGTATCGATACAA
*
26524 TGTATCGCTACAA
1 TGTATCGATACAA
26537 AGCTACTGCC
Statistics
Matches: 77, Mismatches: 1, Indels: 24
0.75 0.01 0.24
Matches are distributed among these distances:
13 49 0.64
16 4 0.05
19 24 0.31
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:26483 original size:19 final size:19
Alignment explanation
Indices: 26459--26522 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
26449 TATCGATACA
26459 ATGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
26478 ATGTATCGATAC---A---
1 ATGTATCGATACATAAGTG
26491 ATGTATCGATACATAAGTG
1 ATGTATCGATACATAAGTG
26510 ATGTATCGATACA
1 ATGTATCGATACA
26523 ATGTATCGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 12 0.31
16 2 0.05
19 25 0.64
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (19 bp):
ATGTATCGATACATAAGTG
Found at i:26487 original size:32 final size:32
Alignment explanation
Indices: 26446--26535 Score: 171
Period size: 32 Copynumber: 2.8 Consensus size: 32
26436 TATCGATACA
26446 ATGTATCGATACAATGTATCGATACATAAGTG
1 ATGTATCGATACAATGTATCGATACATAAGTG
26478 ATGTATCGATACAATGTATCGATACATAAGTG
1 ATGTATCGATACAATGTATCGATACATAAGTG
*
26510 ATGTATCGATACAATGTATCGCTACA
1 ATGTATCGATACAATGTATCGATACA
26536 AAGCTACTGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (32 bp):
ATGTATCGATACAATGTATCGATACATAAGTG
Done.